Daily Papers

Medical benchmarks are indispensable for evaluating the capabilities of language models in healthcare for non-English-speaking communities,therefore help ensuring the quality of real-life applications. However, not every community has sufficient resources and standardized methods to effectively build and design such benchmark, and available non-English medical data is normally fragmented and difficult to verify. We developed an approach to tackle this problem and applied it to create the first Vietnamese medical question benchmark, featuring 14,000 multiple-choice questions across 34 medical specialties. Our benchmark was constructed using various verifiable sources, including carefully curated medical exams and clinical records, and eventually annotated by medical experts. The benchmark includes four difficulty levels, ranging from foundational biological knowledge commonly found in textbooks to typical clinical case studies that require advanced reasoning. This design enables assessment of both the breadth and depth of language models' medical understanding in the target language thanks to its extensive coverage and in-depth subject-specific expertise. We release the benchmark in three parts: a sample public set (4k questions), a full public set (10k questions), and a private set (2k questions) used for leaderboard evaluation. Each set contains all medical subfields and difficulty levels. Our approach is scalable to other languages, and we open-source our data construction pipeline to support the development of future multilingual benchmarks in the medical domain.

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data, and model organisms from both spaceborne and ground-analog studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally autonomous, light, agile, and intelligent to expedite knowledge discovery. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning, and modeling applications which offer key solutions toward these space biology challenges. In the next decade, the synthesis of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modeling and analytics, support maximally autonomous and reproducible experiments, and efficiently manage spaceborne data and metadata, all with the goal to enable life to thrive in deep space.

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

Dictionary learning (DL) has emerged as a powerful interpretability tool for large language models. By extracting known concepts (e.g., Golden-Gate Bridge) from human-interpretable data (e.g., text), sparse DL can elucidate a model's inner workings. In this work, we ask if DL can also be used to discover unknown concepts from less human-interpretable scientific data (e.g., cell images), ultimately enabling modern approaches to scientific discovery. As a first step, we use DL algorithms to study microscopy foundation models trained on multi-cell image data, where little prior knowledge exists regarding which high-level concepts should arise. We show that sparse dictionaries indeed extract biologically-meaningful concepts such as cell type and genetic perturbation type. We also propose a new DL algorithm, Iterative Codebook Feature Learning~(ICFL), and combine it with a pre-processing step that uses PCA whitening from a control dataset. In our experiments, we demonstrate that both ICFL and PCA improve the selectivity of extracted features compared to TopK sparse autoencoders.

Foundation models encompass an extensive knowledge base and offer remarkable transferability. However, this knowledge becomes outdated or insufficient over time. The challenge lies in continuously updating foundation models to accommodate novel information while retaining their original capabilities. Leveraging the fact that foundation models have initial knowledge on various tasks and domains, we propose a novel approach that, instead of updating all parameters equally, localizes the updates to a sparse set of parameters relevant to the task being learned. We strike a balance between efficiency and new task performance, while maintaining the transferability and generalizability of foundation models. We extensively evaluate our method on foundational vision-language models with a diverse spectrum of continual learning tasks. Our method achieves improvements on the accuracy of the newly learned tasks up to 7% while preserving the pretraining knowledge with a negligible decrease of 0.9% on a representative control set accuracy.

The accelerating loss of biodiversity presents critical challenges for ecological research and conservation strategies. The preservation of biodiversity is paramount for maintaining ecological balance and ensuring the sustainability of ecosystems. However, biodiversity faces numerous threats, including habitat loss, climate change, and the proliferation of invasive species. Addressing these and other ecology-related challenges, both at local and global scales, requires comprehensive monitoring, predictive and conservation planning capabilities. Artificial Intelligence (AI) Foundation Models (FMs) have gained significant momentum in numerous scientific domains by leveraging vast datasets to learn general-purpose representations adaptable to various downstream tasks. This paradigm holds immense promise for biodiversity conservation. In response, we introduce BioAnalyst, the first Foundation Model tailored for biodiversity analysis and conservation planning. BioAnalyst employs a transformer-based architecture, pre-trained on extensive multi-modal datasets encompassing species occurrence records, remote sensing indicators, climate and environmental variables. BioAnalyst is designed for adaptability, allowing for fine-tuning of a range of downstream tasks, such as species distribution modelling, habitat suitability assessments, invasive species detection, and population trend forecasting. We evaluate the model's performance on two downstream use cases, demonstrating its generalisability compared to existing methods, particularly in data-scarce scenarios for two distinct use-cases, establishing a new accuracy baseline for ecological forecasting. By openly releasing BioAnalyst and its fine-tuning workflows to the scientific community, we aim to foster collaborative efforts in biodiversity modelling and advance AI-driven solutions to pressing ecological challenges.

Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research - protein structure prediction and single cell RNA-sequencing - we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems.

Biometric capture devices have been utilised to estimate a person's alertness through near-infrared iris images, expanding their use beyond just biometric recognition. However, capturing a substantial number of corresponding images related to alcohol consumption, drug use, and sleep deprivation to create a dataset for training an AI model presents a significant challenge. Typically, a large quantity of images is required to effectively implement a deep learning approach. Currently, training downstream models with a huge number of images based on foundational models provides a real opportunity to enhance this area, thanks to the generalisation capabilities of self-supervised models. This work examines the application of deep learning and foundational models in predicting fitness for duty, which is defined as the subject condition related to determining the alertness for work.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

Unlocking deep, interpretable biological reasoning from complex genomic data is a major AI challenge hindering scientific discovery. Current DNA foundation models, despite strong sequence representation, struggle with multi-step reasoning and lack inherent transparent, biologically intuitive explanations. We introduce BioReason, a pioneering architecture that, for the first time, deeply integrates a DNA foundation model with a Large Language Model (LLM). This novel connection enables the LLM to directly process and reason with genomic information as a fundamental input, fostering a new form of multimodal biological understanding. BioReason's sophisticated multi-step reasoning is developed through supervised fine-tuning and targeted reinforcement learning, guiding the system to generate logical, biologically coherent deductions. On biological reasoning benchmarks including KEGG-based disease pathway prediction - where accuracy improves from 88% to 97% - and variant effect prediction, BioReason demonstrates an average 15% performance gain over strong single-modality baselines. BioReason reasons over unseen biological entities and articulates decision-making through interpretable, step-by-step biological traces, offering a transformative approach for AI in biology that enables deeper mechanistic insights and accelerates testable hypothesis generation from genomic data. Data, code, and checkpoints are publicly available at https://github.com/bowang-lab/BioReason

Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery. Our project is available at https://github.com/usail-hkust/Awesome-Foundation-Models-for-Scientific-Discovery.

Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation of biomedical FMs, we present BioBridge, a novel parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our empirical results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by around 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs.

This work investigates descriptive captions as an additional source of supervision for biological multimodal foundation models. Images and captions can be viewed as complementary samples from the latent morphospace of a species, each capturing certain biological traits. Incorporating captions during training encourages alignment with this shared latent structure, emphasizing potentially diagnostic characters while suppressing spurious correlations. The main challenge, however, lies in obtaining faithful, instance-specific captions at scale. This requirement has limited the utilization of natural language supervision in organismal biology compared with many other scientific domains. We complement this gap by generating synthetic captions with multimodal large language models (MLLMs), guided by Wikipedia-derived visual information and taxon-tailored format examples. These domain-specific contexts help reduce hallucination and yield accurate, instance-based descriptive captions. Using these captions, we train BIOCAP (i.e., BIOCLIP with Captions), a biological foundation model that captures rich semantics and achieves strong performance in species classification and text-image retrieval. These results demonstrate the value of descriptive captions beyond labels in bridging biological images with multimodal foundation models.

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

This position paper explores the rapid development of Foundation Models (FMs) in AI and their implications for intelligence and reasoning. It examines the characteristics of FMs, including their training on vast datasets and use of embedding spaces to capture semantic relationships. The paper discusses recent advancements in FMs' reasoning abilities which we argue cannot be attributed to increased model size but to novel training techniques which yield learning phenomena like grokking. It also addresses the challenges in benchmarking FMs and compares their structure to the human brain. We argue that while FMs show promising developments in reasoning and knowledge representation, understanding their inner workings remains a significant challenge, similar to ongoing efforts in neuroscience to comprehend human brain function. Despite having some similarities, fundamental differences between FMs and the structure of human brain warn us against making direct comparisons or expecting neuroscience to provide immediate insights into FM function.

Scientific knowledge creation is fundamentally transforming as humans and AI systems evolve beyond tool-user relationships into co-evolutionary epistemic partnerships. When AlphaFold revolutionized protein structure prediction, researchers described engaging with an epistemic partner that reshaped how they conceptualized fundamental relationships. This article introduces Cognitio Emergens (CE), a framework addressing critical limitations in existing models that focus on static roles or narrow metrics while failing to capture how scientific understanding emerges through recursive human-AI interaction over time. CE integrates three components addressing these limitations: Agency Configurations describing how authority distributes between humans and AI (Directed, Contributory, Partnership), with partnerships dynamically oscillating between configurations rather than following linear progression; Epistemic Dimensions capturing six specific capabilities emerging through collaboration across Discovery, Integration, and Projection axes, creating distinctive "capability signatures" that guide development; and Partnership Dynamics identifying forces shaping how these relationships evolve, particularly the risk of epistemic alienation where researchers lose interpretive control over knowledge they formally endorse. Drawing from autopoiesis theory, social systems theory, and organizational modularity, CE reveals how knowledge co-creation emerges through continuous negotiation of roles, values, and organizational structures. By reconceptualizing human-AI scientific collaboration as fundamentally co-evolutionary, CE offers a balanced perspective that neither uncritically celebrates nor unnecessarily fears AI's evolving role, instead providing conceptual tools for cultivating partnerships that maintain meaningful human participation while enabling transformative scientific breakthroughs.

Large language models (LLMs) have significantly impacted many aspects of our lives. However, assessing and ensuring their chronological knowledge remains challenging. Existing approaches fall short in addressing the accumulative nature of knowledge, often relying on a single time stamp. To overcome this, we introduce ChroKnowBench, a benchmark dataset designed to evaluate chronologically accumulated knowledge across three key aspects: multiple domains, time dependency, temporal state. Our benchmark distinguishes between knowledge that evolves (e.g., scientific discoveries, amended laws) and knowledge that remain constant (e.g., mathematical truths, commonsense facts). Building on this benchmark, we present ChroKnowledge (Chronological Categorization of Knowledge), a novel sampling-based framework for evaluating and updating LLMs' non-parametric chronological knowledge. Our evaluation shows: (1) The ability of eliciting temporal knowledge varies depending on the data format that model was trained on. (2) LLMs partially recall knowledge or show a cut-off at temporal boundaries rather than recalling all aspects of knowledge correctly. Thus, we apply our ChroKnowPrompt, an in-depth prompting to elicit chronological knowledge by traversing step-by-step through the surrounding time spans. We observe that our framework successfully updates the overall knowledge across the entire timeline in both the biomedical domain (+11.9%) and the general domain (+2.8%), demonstrating its effectiveness in refining temporal knowledge. This non-parametric approach also enables knowledge updates not only in open-source models but also in proprietary LLMs, ensuring comprehensive applicability across model types. We perform a comprehensive analysis based on temporal characteristics of ChroKnowPrompt and validate the potential of various models to elicit intrinsic temporal knowledge through our method.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Foundation models are premised on the idea that sequence prediction can uncover deeper domain understanding, much like how Kepler's predictions of planetary motion later led to the discovery of Newtonian mechanics. However, evaluating whether these models truly capture deeper structure remains a challenge. We develop a technique for evaluating foundation models that examines how they adapt to synthetic datasets generated from some postulated world model. Our technique measures whether the foundation model's inductive bias aligns with the world model, and so we refer to it as an inductive bias probe. Across multiple domains, we find that foundation models can excel at their training tasks yet fail to develop inductive biases towards the underlying world model when adapted to new tasks. We particularly find that foundation models trained on orbital trajectories consistently fail to apply Newtonian mechanics when adapted to new physics tasks. Further analysis reveals that these models behave as if they develop task-specific heuristics that fail to generalize.

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

A multi-decade exploration into the theoretical foundations of artificial and natural general intelligence, which has been expressed in a series of books and papers and used to guide a series of practical and research-prototype software systems, is reviewed at a moderate level of detail. The review covers underlying philosophies (patternist philosophy of mind, foundational phenomenological and logical ontology), formalizations of the concept of intelligence, and a proposed high level architecture for AGI systems partly driven by these formalizations and philosophies. The implementation of specific cognitive processes such as logical reasoning, program learning, clustering and attention allocation in the context and language of this high level architecture is considered, as is the importance of a common (e.g. typed metagraph based) knowledge representation for enabling "cognitive synergy" between the various processes. The specifics of human-like cognitive architecture are presented as manifestations of these general principles, and key aspects of machine consciousness and machine ethics are also treated in this context. Lessons for practical implementation of advanced AGI in frameworks such as OpenCog Hyperon are briefly considered.

Foundational mapping remains a challenge in many parts of the world, particularly in dynamic scenarios such as natural disasters when timely updates are critical. Updating maps is currently a highly manual process requiring a large number of human labelers to either create features or rigorously validate automated outputs. We propose that the frequent revisits of earth imaging satellite constellations may accelerate existing efforts to quickly update foundational maps when combined with advanced machine learning techniques. Accordingly, the SpaceNet partners (CosmiQ Works, Radiant Solutions, and NVIDIA), released a large corpus of labeled satellite imagery on Amazon Web Services (AWS) called SpaceNet. The SpaceNet partners also launched a series of public prize competitions to encourage improvement of remote sensing machine learning algorithms. The first two of these competitions focused on automated building footprint extraction, and the most recent challenge focused on road network extraction. In this paper we discuss the SpaceNet imagery, labels, evaluation metrics, prize challenge results to date, and future plans for the SpaceNet challenge series.

In this work, we evaluate the capacity for foundation models to retrieve encyclopedic knowledge across a wide range of languages, topics, and contexts. To support this effort, we 1) produce a new dataset containing 303k factual associations in 20 different languages, 2) formulate a new counterfactual knowledge assessment, Polyglot or Not, and 3) benchmark 5 foundation models in a multilingual setting and a diverse set of 20 models in an English-only setting. We observed significant accuracy differences in models of interest, with Meta's LLaMA topping both the multilingual and English-only assessments. Error analysis reveals a significant deficiency in LLaMA's ability to retrieve facts in languages written in the Cyrillic script and gaps in its understanding of facts based on the location and gender of entailed subjects. Ultimately, we argue that the promise of utilizing foundation language models as bonafide polyglots is greatly diminished when they are tasked with retrieving information in languages other than English. Supporting code (https://github.com/daniel-furman/Polyglot-or-Not) and dataset (https://huggingface.co/datasets/Polyglot-or-Not/Fact-Completion) are openly released.

Over the past few decades, Artificial Intelligence(AI) has progressed from the initial machine learning stage to the deep learning stage, and now to the stage of foundational models. Foundational models have the characteristics of pre-training, transfer learning, and self-supervised learning, and pre-trained models can be fine-tuned and applied to various downstream tasks. Under the framework of foundational models, models such as Bidirectional Encoder Representations from Transformers(BERT) and Generative Pre-trained Transformer(GPT) have greatly advanced the development of natural language processing(NLP), especially the emergence of many models based on BERT. BERT broke through the limitation of only using one-way methods for language modeling in pre-training by using a masked language model. It can capture bidirectional context information to predict the masked words in the sequence, this can improve the feature extraction ability of the model. This makes the model very useful for downstream tasks, especially for specialized applications. The model using the bidirectional encoder can better understand the domain knowledge and be better applied to these downstream tasks. So we hope to help understand how this technology has evolved and improved model performance in various natural language processing tasks under the background of foundational models and reveal its importance in capturing context information and improving the model's performance on downstream tasks. This article analyzes one-way and bidirectional models based on GPT and BERT and compares their differences based on the purpose of the model. It also briefly analyzes BERT and the improvements of some models based on BERT. The model's performance on the Stanford Question Answering Dataset(SQuAD) and General Language Understanding Evaluation(GLUE) was compared.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

In this position paper, we argue that human baselines in foundation model evaluations must be more rigorous and more transparent to enable meaningful comparisons of human vs. AI performance, and we provide recommendations and a reporting checklist towards this end. Human performance baselines are vital for the machine learning community, downstream users, and policymakers to interpret AI evaluations. Models are often claimed to achieve "super-human" performance, but existing baselining methods are neither sufficiently rigorous nor sufficiently well-documented to robustly measure and assess performance differences. Based on a meta-review of the measurement theory and AI evaluation literatures, we derive a framework with recommendations for designing, executing, and reporting human baselines. We synthesize our recommendations into a checklist that we use to systematically review 115 human baselines (studies) in foundation model evaluations and thus identify shortcomings in existing baselining methods; our checklist can also assist researchers in conducting human baselines and reporting results. We hope our work can advance more rigorous AI evaluation practices that can better serve both the research community and policymakers. Data is available at: https://github.com/kevinlwei/human-baselines

We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy, it is biology at work. Biology in the physical world is too complex to manipulate and always expensive and risky to tamper with. In this perspective, we layout an engineering viable approach to address this challenge by constructing an AI-Driven Digital Organism (AIDO), a system of integrated multiscale foundation models, in a modular, connectable, and holistic fashion to reflect biological scales, connectedness, and complexities. An AIDO opens up a safe, affordable and high-throughput alternative platform for predicting, simulating and programming biology at all levels from molecules to cells to individuals. We envision that an AIDO is poised to trigger a new wave of better-guided wet-lab experimentation and better-informed first-principle reasoning, which can eventually help us better decode and improve life.

Following its success for vision and text, the "foundation model" (FM) paradigm -- pretraining large models on massive data, then fine-tuning on target tasks -- has rapidly expanded to domains in the sciences, engineering, healthcare, and beyond. Has this achieved what the original FMs accomplished, i.e. the supplanting of traditional supervised learning in their domains? To answer we look at three modalities -- genomics, satellite imaging, and time series -- with multiple recent FMs and compare them to a standard supervised learning workflow: model development, hyperparameter tuning, and training, all using only data from the target task. Across these three specialized domains, we find that it is consistently possible to train simple supervised models -- no more complicated than a lightly modified wide ResNet or UNet -- that match or even outperform the latest foundation models. Our work demonstrates that the benefits of large-scale pretraining have yet to be realized in many specialized areas, reinforces the need to compare new FMs to strong, well-tuned baselines, and introduces two new, easy-to-use, open-source, and automated workflows for doing so.

Vision systems to see and reason about the compositional nature of visual scenes are fundamental to understanding our world. The complex relations between objects and their locations, ambiguities, and variations in the real-world environment can be better described in human language, naturally governed by grammatical rules and other modalities such as audio and depth. The models learned to bridge the gap between such modalities coupled with large-scale training data facilitate contextual reasoning, generalization, and prompt capabilities at test time. These models are referred to as foundational models. The output of such models can be modified through human-provided prompts without retraining, e.g., segmenting a particular object by providing a bounding box, having interactive dialogues by asking questions about an image or video scene or manipulating the robot's behavior through language instructions. In this survey, we provide a comprehensive review of such emerging foundational models, including typical architecture designs to combine different modalities (vision, text, audio, etc), training objectives (contrastive, generative), pre-training datasets, fine-tuning mechanisms, and the common prompting patterns; textual, visual, and heterogeneous. We discuss the open challenges and research directions for foundational models in computer vision, including difficulties in their evaluations and benchmarking, gaps in their real-world understanding, limitations of their contextual understanding, biases, vulnerability to adversarial attacks, and interpretability issues. We review recent developments in this field, covering a wide range of applications of foundation models systematically and comprehensively. A comprehensive list of foundational models studied in this work is available at https://github.com/awaisrauf/Awesome-CV-Foundational-Models.

Knowledge-grounded dialogue is a task of generating an informative response based on both the dialogue history and external knowledge source. In general, there are two forms of knowledge: manually annotated knowledge graphs and knowledge text from website. From various evaluation viewpoints, each type of knowledge has advantages and downsides. To further distinguish the principles and determinants from the intricate factors, we conduct a thorough experiment and study on the task to answer three essential questions. The questions involve the choice of appropriate knowledge form, the degree of mutual effects between knowledge and the model selection, and the few-shot performance of knowledge. Supported by statistical shreds of evidence, we offer conclusive solutions and sensible suggestions for directions and standards of future research.

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Generative artificial intelligence (AI) systems based on large-scale pretrained foundation models (PFMs) such as vision-language models, large language models (LLMs), diffusion models and vision-language-action (VLA) models have demonstrated the ability to solve complex and truly non-trivial AI problems in a wide variety of domains and contexts. Multimodal large language models (MLLMs), in particular, learn from vast and diverse data sources, allowing rich and nuanced representations of the world and, thereby, providing extensive capabilities, including the ability to reason, engage in meaningful dialog; collaborate with humans and other agents to jointly solve complex problems; and understand social and emotional aspects of humans. Despite this impressive feat, the cognitive abilities of state-of-the-art LLMs trained on large-scale datasets are still superficial and brittle. Consequently, generic LLMs are severely limited in their generalist capabilities. A number of foundational problems -- embodiment, symbol grounding, causality and memory -- are required to be addressed for LLMs to attain human-level general intelligence. These concepts are more aligned with human cognition and provide LLMs with inherent human-like cognitive properties that support the realization of physically-plausible, semantically meaningful, flexible and more generalizable knowledge and intelligence. In this work, we discuss the aforementioned foundational issues and survey state-of-the art approaches for implementing these concepts in LLMs. Specifically, we discuss how the principles of embodiment, symbol grounding, causality and memory can be leveraged toward the attainment of artificial general intelligence (AGI) in an organic manner.

Biomedical knowledge is uniquely complex and structured, requiring distinct reasoning strategies compared to other scientific disciplines like physics or chemistry. Biomedical scientists do not rely on a single approach to reasoning; instead, they use various strategies, including rule-based, prototype-based, and case-based reasoning. This diversity calls for flexible approaches that accommodate multiple reasoning strategies while leveraging in-domain knowledge. We introduce KGARevion, a knowledge graph (KG) based agent designed to address the complexity of knowledge-intensive medical queries. Upon receiving a query, KGARevion generates relevant triplets by using the knowledge base of the LLM. These triplets are then verified against a grounded KG to filter out erroneous information and ensure that only accurate, relevant data contribute to the final answer. Unlike RAG-based models, this multi-step process ensures robustness in reasoning while adapting to different models of medical reasoning. Evaluations on four gold-standard medical QA datasets show that KGARevion improves accuracy by over 5.2%, outperforming 15 models in handling complex medical questions. To test its capabilities, we curated three new medical QA datasets with varying levels of semantic complexity, where KGARevion achieved a 10.4% improvement in accuracy.

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount significance in facilitating biomedical research. However, existing multimodal molecular foundation models exhibit limitations in capturing intricate connections between molecular structures and texts, and more importantly, none of them attempt to leverage a wealth of molecular expertise derived from knowledge graphs. In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs. We propose cross-modal attention between atoms of molecular structures, neighbors of molecule entities and semantically related texts to facilitate cross-modal comprehension. We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule, as well as molecules sharing similar structures or functions. MolFM achieves state-of-the-art performance on various downstream tasks. On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively. Furthermore, qualitative analysis showcases MolFM's implicit ability to provide grounding from molecular substructures and knowledge graphs. Code and models are available on https://github.com/BioFM/OpenBioMed.

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly for applications in drug discovery, remains a challenge due to the complexity of RNA structures and interactions. While foundational models in biology have demonstrated success in modeling several biomolecules, especially proteins, achieving similar breakthroughs for RNA has proven more difficult. Current RNA models have yet to match the performance observed in the protein domain, leaving an important gap in computational biology. In this work, we present ChaRNABERT, a suite of sample and parameter-efficient RNA foundational models, that through a learnable tokenization process, are able to reach state-of-the-art performance on several tasks in established benchmarks. We extend its testing in relevant downstream tasks such as RNA-protein and aptamer-protein interaction prediction. Weights and inference code for ChaRNABERT-8M will be provided for academic research use. The other models will be available upon request.

This document serves as a position paper that outlines the authors' vision for a potential pathway towards generalist robots. The purpose of this document is to share the excitement of the authors with the community and highlight a promising research direction in robotics and AI. The authors believe the proposed paradigm is a feasible path towards accomplishing the long-standing goal of robotics research: deploying robots, or embodied AI agents more broadly, in various non-factory real-world settings to perform diverse tasks. This document presents a specific idea for mining knowledge in the latest large-scale foundation models for robotics research. Instead of directly using or adapting these models to produce low-level policies and actions, it advocates for a fully automated generative pipeline (termed as generative simulation), which uses these models to generate diversified tasks, scenes and training supervisions at scale, thereby scaling up low-level skill learning and ultimately leading to a foundation model for robotics that empowers generalist robots. The authors are actively pursuing this direction, but in the meantime, they recognize that the ambitious goal of building generalist robots with large-scale policy training demands significant resources such as computing power and hardware, and research groups in academia alone may face severe resource constraints in implementing the entire vision. Therefore, the authors believe sharing their thoughts at this early stage could foster discussions, attract interest towards the proposed pathway and related topics from industry groups, and potentially spur significant technical advancements in the field.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

This open access book provides a comprehensive overview of the state of the art in research and applications of Foundation Models and is intended for readers familiar with basic Natural Language Processing (NLP) concepts. Over the recent years, a revolutionary new paradigm has been developed for training models for NLP. These models are first pre-trained on large collections of text documents to acquire general syntactic knowledge and semantic information. Then, they are fine-tuned for specific tasks, which they can often solve with superhuman accuracy. When the models are large enough, they can be instructed by prompts to solve new tasks without any fine-tuning. Moreover, they can be applied to a wide range of different media and problem domains, ranging from image and video processing to robot control learning. Because they provide a blueprint for solving many tasks in artificial intelligence, they have been called Foundation Models. After a brief introduction to basic NLP models the main pre-trained language models BERT, GPT and sequence-to-sequence transformer are described, as well as the concepts of self-attention and context-sensitive embedding. Then, different approaches to improving these models are discussed, such as expanding the pre-training criteria, increasing the length of input texts, or including extra knowledge. An overview of the best-performing models for about twenty application areas is then presented, e.g., question answering, translation, story generation, dialog systems, generating images from text, etc. For each application area, the strengths and weaknesses of current models are discussed, and an outlook on further developments is given. In addition, links are provided to freely available program code. A concluding chapter summarizes the economic opportunities, mitigation of risks, and potential developments of AI.

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

Traditional foundation models are pre-trained on broad datasets to reduce the training resources (e.g., time, energy, labeled samples) needed for fine-tuning a wide range of downstream tasks. However, traditional foundation models struggle with out-of-distribution prediction and can produce outputs that are unrealistic and physically infeasible. We propose the notation of physics-guided foundation models (PGFM), that is, foundation models integrated with broad or general domain (e.g., scientific) physical knowledge applicable to a wide range of downstream tasks.

Large Language Models (LLMs) assist in specialized tasks but struggle to align with evolving domain knowledge without costly fine-tuning. Domain knowledge consists of: Knowledge: Immutable facts (e.g., 'A stone is solid') and generally accepted principles (e.g., ethical standards); Refined Memory: Evolving insights shaped by business needs and real-world changes. However, a significant gap often exists between a domain expert's deep, nuanced understanding and the system's domain knowledge, which can hinder accurate information retrieval and application. Our Memory-Augmented Refinement of Knowledge (MARK) framework enables LLMs to continuously learn without retraining by leveraging structured refined memory, inspired by the Society of Mind. MARK operates through specialized agents, each serving a distinct role: Residual Refined Memory Agent: Stores and retrieves domain-specific insights to maintain context over time; User Question Refined Memory Agent: Captures user-provided facts, abbreviations, and terminology for better comprehension; LLM Response Refined Memory Agent: Extracts key elements from responses for refinement and personalization. These agents analyse stored refined memory, detect patterns, resolve contradictions, and improve response accuracy. Temporal factors like recency and frequency prioritize relevant information while discarding outdated insights. MARK enhances LLMs in multiple ways: Ground Truth Strategy: Reduces hallucinations by establishing a structured reference; Domain-Specific Adaptation: Essential for fields like healthcare, law, and manufacturing, where proprietary insights are absent from public datasets; Personalized AI Assistants: Improves virtual assistants by remembering user preferences, ensuring coherent responses over time.

Wearable devices record physiological and behavioral signals that can improve health predictions. While foundation models are increasingly used for such predictions, they have been primarily applied to low-level sensor data, despite behavioral data often being more informative due to their alignment with physiologically relevant timescales and quantities. We develop foundation models of such behavioral signals using over 2.5B hours of wearable data from 162K individuals, systematically optimizing architectures and tokenization strategies for this unique dataset. Evaluated on 57 health-related tasks, our model shows strong performance across diverse real-world applications including individual-level classification and time-varying health state prediction. The model excels in behavior-driven tasks like sleep prediction, and improves further when combined with representations of raw sensor data. These results underscore the importance of tailoring foundation model design to wearables and demonstrate the potential to enable new health applications.

Inductive reasoning is a core component of human intelligence. In the past research of inductive reasoning within computer science, formal language is used as representations of knowledge (facts and rules, more specifically). However, formal language can cause systematic problems for inductive reasoning such as disability of handling raw input such as natural language, sensitiveness to mislabeled data, and incapacity to handle ambiguous input. To this end, we propose a new paradigm (task) for inductive reasoning, which is to induce natural language rules from natural language facts, and create a dataset termed DEER containing 1.2k rule-fact pairs for the task, where rules and facts are written in natural language. New automatic metrics are also proposed and analysed for the evaluation of this task. With DEER, we investigate a modern approach for inductive reasoning where we use natural language as representation for knowledge instead of formal language and use pretrained language models as ''reasoners''. Moreover, we provide the first and comprehensive analysis of how well pretrained language models can induce natural language rules from natural language facts. We also propose a new framework drawing insights from philosophy literature for this task, which we show in the experiment section that surpasses baselines in both automatic and human evaluations. We discuss about our future perspectives for inductive reasoning in Section 7. Dataset and code are available at https://github.com/ZonglinY/Inductive_Reasoning.

As AI foundation models grow in capability, a deeper question emerges: What shapes their internal cognitive identity -- beyond fluency and output? Benchmarks measure behavior, but the soul of a model resides in its latent geometry. In this work, we propose Neural DNA (nDNA) as a semantic-genotypic representation that captures this latent identity through the intrinsic geometry of belief. At its core, nDNA is synthesized from three principled and indispensable dimensions of latent geometry: spectral curvature, which reveals the curvature of conceptual flow across layers; thermodynamic length, which quantifies the semantic effort required to traverse representational transitions through layers; and belief vector field, which delineates the semantic torsion fields that guide a model's belief directional orientations. Like biological DNA, it encodes ancestry, mutation, and semantic inheritance, found in finetuning and alignment scars, cultural imprints, and architectural drift. In naming it, we open a new field: Neural Genomics, where models are not just tools, but digital semantic organisms with traceable inner cognition. Modeling statement. We read AI foundation models as semantic fluid dynamics: meaning is transported through layers like fluid in a shaped conduit; nDNA is the physics-grade readout of that flow -- a geometry-first measure of how meaning is bent, paid for, and pushed -- yielding a stable, coordinate-free neural DNA fingerprint tied to on-input behavior; with this fingerprint we cross into biology: tracing lineages across pretraining, fine-tuning, alignment, pruning, distillation, and merges; measuring inheritance between checkpoints; detecting drift as traits shift under new data or objectives; and, ultimately, studying the evolution of artificial cognition to compare models, diagnose risks, and govern change over time.

Understanding emotions is fundamental to human interaction and experience. Humans easily infer emotions from situations or facial expressions, situations from emotions, and do a variety of other affective cognition. How adept is modern AI at these inferences? We introduce an evaluation framework for testing affective cognition in foundation models. Starting from psychological theory, we generate 1,280 diverse scenarios exploring relationships between appraisals, emotions, expressions, and outcomes. We evaluate the abilities of foundation models (GPT-4, Claude-3, Gemini-1.5-Pro) and humans (N = 567) across carefully selected conditions. Our results show foundation models tend to agree with human intuitions, matching or exceeding interparticipant agreement. In some conditions, models are ``superhuman'' -- they better predict modal human judgements than the average human. All models benefit from chain-of-thought reasoning. This suggests foundation models have acquired a human-like understanding of emotions and their influence on beliefs and behavior.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

We introduce the Structured Knowledge Accumulation (SKA) framework, which reinterprets entropy as a dynamic, layer-wise measure of knowledge alignment in neural networks. Instead of relying on traditional gradient-based optimization, SKA defines entropy in terms of knowledge vectors and their influence on decision probabilities across multiple layers. This formulation naturally leads to the emergence of activation functions such as the sigmoid as a consequence of entropy minimization. Unlike conventional backpropagation, SKA allows each layer to optimize independently by aligning its knowledge representation with changes in decision probabilities. As a result, total network entropy decreases in a hierarchical manner, allowing knowledge structures to evolve progressively. This approach provides a scalable, biologically plausible alternative to gradient-based learning, bridging information theory and artificial intelligence while offering promising applications in resource-constrained and parallel computing environments.

The transcriptional response to genetic perturbation reveals fundamental insights into complex cellular systems. While current approaches have made progress in predicting genetic perturbation responses, they provide limited biological understanding and cannot systematically refine existing knowledge. Overcoming these limitations requires an end-to-end integration of data-driven learning and existing knowledge. However, this integration is challenging due to inconsistencies between data and knowledge bases, such as noise, misannotation, and incompleteness. To address this challenge, we propose ALIGNED (Adaptive aLignment for Inconsistent Genetic kNowledgE and Data), a neuro-symbolic framework based on the Abductive Learning (ABL) paradigm. This end-to-end framework aligns neural and symbolic components and performs systematic knowledge refinement. We introduce a balanced consistency metric to evaluate the predictions' consistency against both data and knowledge. Our results show that ALIGNED outperforms state-of-the-art methods by achieving the highest balanced consistency, while also re-discovering biologically meaningful knowledge. Our work advances beyond existing methods to enable both the transparency and the evolution of mechanistic biological understanding.

We introduce PHYSICS, a comprehensive benchmark for university-level physics problem solving. It contains 1297 expert-annotated problems covering six core areas: classical mechanics, quantum mechanics, thermodynamics and statistical mechanics, electromagnetism, atomic physics, and optics. Each problem requires advanced physics knowledge and mathematical reasoning. We develop a robust automated evaluation system for precise and reliable validation. Our evaluation of leading foundation models reveals substantial limitations. Even the most advanced model, o3-mini, achieves only 59.9% accuracy, highlighting significant challenges in solving high-level scientific problems. Through comprehensive error analysis, exploration of diverse prompting strategies, and Retrieval-Augmented Generation (RAG)-based knowledge augmentation, we identify key areas for improvement, laying the foundation for future advancements.

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

Reasoning, a crucial ability for complex problem-solving, plays a pivotal role in various real-world settings such as negotiation, medical diagnosis, and criminal investigation. It serves as a fundamental methodology in the field of Artificial General Intelligence (AGI). With the ongoing development of foundation models, e.g., Large Language Models (LLMs), there is a growing interest in exploring their abilities in reasoning tasks. In this paper, we introduce seminal foundation models proposed or adaptable for reasoning, highlighting the latest advancements in various reasoning tasks, methods, and benchmarks. We then delve into the potential future directions behind the emergence of reasoning abilities within foundation models. We also discuss the relevance of multimodal learning, autonomous agents, and super alignment in the context of reasoning. By discussing these future research directions, we hope to inspire researchers in their exploration of this field, stimulate further advancements in reasoning with foundation models, and contribute to the development of AGI.

In recent years, there has been a proliferation of spatiotemporal foundation models in different scientific disciplines. While promising, these models are often domain-specific and are only assessed within the particular applications for which they are designed. Given that many tasks can be represented as video modeling problems, video foundation models (ViFMs) hold considerable promise as general-purpose domain-agnostic approaches. However, it is not known whether the knowledge acquired on large-scale but potentially out-of-domain data can be effectively transferred across diverse scientific disciplines, and if a single, pretrained ViFM can be competitive with domain-specific baselines. To address this, we introduce SciVid, a comprehensive benchmark comprising five *Sci*entific *Vid*eo tasks, across medical computer vision, animal behavior, and weather forecasting. We adapt six leading ViFMs to SciVid using simple trainable readout modules, establishing strong baselines and demonstrating the potential for effective transfer learning. Specifically, we show that state-of-the-art results can be obtained in several applications by leveraging the general-purpose representations from ViFM backbones. Furthermore, our results reveal the limitations of existing ViFMs, and highlight opportunities for the development of generalizable models for high-impact scientific applications. We release our code at https://github.com/google-deepmind/scivid to facilitate further research in the development of ViFMs.

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a new high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g. the rbs locus and pykF) and species (e.g. Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide mathematical intuition and justification for exploration of biological networks in higher dimensions.

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.

Recent advances in AI weather forecasting have led to the emergence of so-called "foundation models", typically defined by expensive pretraining and minimal fine-tuning for downstream tasks. However, in the natural sciences, a desirable foundation model should also encode meaningful statistical relationships between the underlying physical variables. This study evaluates the performance of the state-of-the-art Aurora foundation model in predicting hydrological variables, which were not considered during pretraining. We introduce a lightweight approach using shallow decoders trained on the latent representations of the pretrained model to predict these new variables. As a baseline, we compare this to fine-tuning the full model, which allows further optimization of the latent space while incorporating new variables into both inputs and outputs. The decoder-based approach requires 50% less training time and 35% less memory, while achieving strong accuracy across various hydrological variables and preserving desirable properties of the foundation model, such as autoregressive stability. Notably, decoder accuracy depends on the physical correlation between the new variables and those used during pretraining, indicating that Aurora's latent space captures meaningful physical relationships. In this sense, we argue that an important quality metric for foundation models in Earth sciences is their ability to be extended to new variables without a full fine-tuning. This provides a new perspective for making foundation models more accessible to communities with limited computational resources, while supporting broader adoption in Earth sciences.

AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.

Despite their success in numerous fields, the potential of foundation models for modeling and understanding human behavior remains largely unexplored. We introduce Be.FM, one of the first open foundation models designed for human behavior modeling. Built upon open-source large language models and fine-tuned on a diverse range of behavioral data, Be.FM can be used to understand and predict human decision-making. We construct a comprehensive set of benchmark tasks for testing the capabilities of behavioral foundation models. Our results demonstrate that Be.FM can predict behaviors, infer characteristics of individuals and populations, generate insights about contexts, and apply behavioral science knowledge.

The burgeoning utilization of Large Language Models (LLMs) in scientific research necessitates advanced benchmarks capable of evaluating their understanding and application of scientific knowledge comprehensively. To address this need, we introduce the SciKnowEval benchmark, a novel framework that systematically evaluates LLMs across five progressive levels of scientific knowledge: studying extensively, inquiring earnestly, thinking profoundly, discerning clearly, and practicing assiduously. These levels aim to assess the breadth and depth of scientific knowledge in LLMs, including knowledge coverage, inquiry and exploration capabilities, reflection and reasoning abilities, ethic and safety considerations, as well as practice proficiency. Specifically, we take biology and chemistry as the two instances of SciKnowEval and construct a dataset encompassing 50K multi-level scientific problems and solutions. By leveraging this dataset, we benchmark 20 leading open-source and proprietary LLMs using zero-shot and few-shot prompting strategies. The results reveal that despite achieving state-of-the-art performance, the proprietary LLMs still have considerable room for improvement, particularly in addressing scientific computations and applications. We anticipate that SciKnowEval will establish a comprehensive standard for benchmarking LLMs in science research and discovery, and promote the development of LLMs that integrate scientific knowledge with strong safety awareness. The dataset and code are publicly available at https://github.com/hicai-zju/sciknoweval .

Inevitable domain and task discrepancies in real-world scenarios can impair the generalization performance of the pre-trained deep models for medical data. Therefore, we audaciously propose that we should build a general-purpose medical AI system that can be seamlessly adapted to downstream domains/tasks. Since the domain/task adaption procedures usually involve additional labeling work for the target data, designing a data-efficient adaption algorithm is desired to save the cost of transferring the learned knowledge. Our recent work found that vision-language models (VLMs) are efficient learners with extraordinary cross-domain ability. Therefore, in this work, we further explore the possibility of leveraging pre-trained VLMs as medical foundation models for building general-purpose medical AI, where we thoroughly investigate three machine-learning paradigms, i.e., domain/task-specialized learning, joint learning, and continual learning, for training the VLMs and evaluate their generalization performance on cross-domain and cross-task test sets. To alleviate the catastrophic forgetting during sequential training, we employ rehearsal learning and receive a sharp boost in terms of generalization capability. In a nutshell, our empirical evidence suggests that continual learning may be a practical and efficient learning paradigm for the medical foundation model. And we hope researchers can use our empirical evidence as basement to further explore the path toward medical foundation model.

Understanding the creation, evolution, and dissemination of scientific knowledge is crucial for bridging diverse subject areas and addressing complex global challenges such as pandemics, climate change, and ethical AI. Scientometrics, the quantitative and qualitative study of scientific literature, provides valuable insights into these processes. We introduce Scito2M, a longitudinal scientometric dataset with over two million academic publications, providing comprehensive contents information and citation graphs to support cross-disciplinary analyses. Using Scito2M, we conduct a temporal study spanning over 30 years to explore key questions in scientometrics: the evolution of academic terminology, citation patterns, and interdisciplinary knowledge exchange. Our findings reveal critical insights, such as disparities in epistemic cultures, knowledge production modes, and citation practices. For example, rapidly developing, application-driven fields like LLMs exhibit significantly shorter citation age (2.48 years) compared to traditional theoretical disciplines like oral history (9.71 years).

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pretraining on publicly available biomedical corpora. These works typically claim that such domain-adaptive pretraining (DAPT) improves performance on downstream medical tasks, such as answering medical licensing exam questions. In this paper, we compare seven public "medical" LLMs and two VLMs against their corresponding base models, arriving at a different conclusion: all medical VLMs and nearly all medical LLMs fail to consistently improve over their base models in the zero-/few-shot prompting regime for medical question-answering (QA) tasks. For instance, across the tasks and model pairs we consider in the 3-shot setting, medical LLMs only outperform their base models in 12.1% of cases, reach a (statistical) tie in 49.8% of cases, and are significantly worse than their base models in the remaining 38.2% of cases. Our conclusions are based on (i) comparing each medical model head-to-head, directly against the corresponding base model; (ii) optimizing the prompts for each model separately; and (iii) accounting for statistical uncertainty in comparisons. While these basic practices are not consistently adopted in the literature, our ablations show that they substantially impact conclusions. Our findings suggest that state-of-the-art general-domain models may already exhibit strong medical knowledge and reasoning capabilities, and offer recommendations to strengthen the conclusions of future studies.

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

Understanding the origin(s) of life (OoL) is a fundamental challenge for science in the 21st century. Research on OoL spans many disciplines, including chemistry, physics, biology, planetary sciences, computer science, mathematics and philosophy. The sheer number of different scientific perspectives relevant to the problem has resulted in the coexistence of diverse tools, techniques, data, and software in OoL studies. This has made communication between the disciplines relevant to the OoL extremely difficult because the interpretation of data, analyses, or standards of evidence can vary dramatically. Here, we hope to bridge this wide field of study by providing common ground via the consolidation of tools and techniques rather than positing a unifying view on how life emerges. We review the common tools and techniques that have been used significantly in OoL studies in recent years. In particular, we aim to identify which information is most relevant for comparing and integrating the results of experimental analyses into mathematical and computational models. This review aims to provide a baseline expectation and understanding of technical aspects of origins research, rather than being a primer on any particular topic. As such, it spans broadly -- from analytical chemistry to mathematical models -- and highlights areas of future work that will benefit from a multidisciplinary approach to tackling the mystery of life's origin. Ultimately, we hope to empower a new generation of OoL scientists by reviewing how they can investigate life's origin, rather than dictating how to think about the problem.

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and reasoning on textbook-style science questions, but few if any benchmarks are designed to evaluate language model performance on practical tasks required for scientific research, such as literature search, protocol planning, and data analysis. As a step toward building such benchmarks, we introduce the Language Agent Biology Benchmark (LAB-Bench), a broad dataset of over 2,400 multiple choice questions for evaluating AI systems on a range of practical biology research capabilities, including recall and reasoning over literature, interpretation of figures, access and navigation of databases, and comprehension and manipulation of DNA and protein sequences. Importantly, in contrast to previous scientific benchmarks, we expect that an AI system that can achieve consistently high scores on the more difficult LAB-Bench tasks would serve as a useful assistant for researchers in areas such as literature search and molecular cloning. As an initial assessment of the emergent scientific task capabilities of frontier language models, we measure performance of several against our benchmark and report results compared to human expert biology researchers. We will continue to update and expand LAB-Bench over time, and expect it to serve as a useful tool in the development of automated research systems going forward. A public subset of LAB-Bench is available for use at the following URL: https://huggingface.co/datasets/futurehouse/lab-bench

We present a design framework called Conversational Learning with Analytical Step-by-Step Strategies (CLASS) for developing high-performance Intelligent Tutoring Systems (ITS). The CLASS framework aims to empower ITS with with two critical capabilities: imparting tutor-like step-by-step guidance and enabling tutor-like conversations in natural language to effectively engage learners. To empower ITS with the aforementioned capabilities, the CLASS framework employs two carefully curated synthetic datasets. The first scaffolding dataset encompasses a variety of elements, including problems, their corresponding subproblems, hints, incorrect solutions, and tailored feedback. This dataset provides ITS with essential problem-solving strategies necessary for guiding students through each step of the conversation. The second conversational dataset contains simulated student-tutor conversations that involve the application of problem-solving strategies learned from the first dataset. In the second dataset, the tutoring system adheres to a pre-defined response template, which helps to maintain consistency and structure in ITS's responses during its interactions. This structured methodology facilitates seamless integration of user feedback and yields valuable insights into ITS's internal decision-making process, allowing for continuous refinement and improvement of the system. We also present a proof-of-concept ITS, referred to as SPOCK, trained using the CLASS framework with a focus on college level introductory biology content. A carefully constructed protocol was developed for SPOCK's preliminary evaluation, examining aspects such as the factual accuracy and relevance of its responses. Experts in the field of biology offered favorable remarks, particularly highlighting SPOCK's capability to break down questions into manageable subproblems and provide step-by-step guidance to students.

Foundation model-enabled generative artificial intelligence facilitates the development and implementation of agents, which can leverage distinguished reasoning and language processing capabilities to takes a proactive, autonomous role to pursue users' goals. Nevertheless, there is a lack of systematic knowledge to guide practitioners in designing the agents considering challenges of goal-seeking (including generating instrumental goals and plans), such as hallucinations inherent in foundation models, explainability of reasoning process, complex accountability, etc. To address this issue, we have performed a systematic literature review to understand the state-of-the-art foundation model-based agents and the broader ecosystem. In this paper, we present a pattern catalogue consisting of 18 architectural patterns with analyses of the context, forces, and trade-offs as the outcomes from the previous literature review. We propose a decision model for selecting the patterns. The proposed catalogue can provide holistic guidance for the effective use of patterns, and support the architecture design of foundation model-based agents by facilitating goal-seeking and plan generation.

Large language models (LLMs) have majorly advanced NLP and AI, and next to their ability to perform a wide range of procedural tasks, a major success factor is their internalized factual knowledge. Since Petroni et al. (2019), analyzing this knowledge has gained attention. However, most approaches investigate one question at a time via modest-sized pre-defined samples, introducing an ``availability bias'' (Tversky&Kahnemann, 1973) that prevents the analysis of knowledge (or beliefs) of LLMs beyond the experimenter's predisposition. To address this challenge, we propose a novel methodology to comprehensively materialize an LLM's factual knowledge through recursive querying and result consolidation. Our approach is a milestone for LLM research, for the first time providing constructive insights into the scope and structure of LLM knowledge (or beliefs). As a prototype, we build GPTKB, a knowledge base (KB) comprising 101 million relational triples for over 2.9 million entities from GPT-4o-mini. We use GPTKB to exemplarily analyze GPT-4o-mini's factual knowledge in terms of scale, accuracy, bias, cutoff and consistency, at the same time. GPTKB is accessible at https://gptkb.org

Aquaculture plays a vital role in global food security and coastal economies by providing sustainable protein sources. As the industry expands to meet rising demand, it faces growing challenges such as disease outbreaks, inefficient feeding practices, rising labor costs, logistical inefficiencies, and critical hatchery issues, including high mortality rates and poor water quality control. Although artificial intelligence has made significant progress, existing machine learning methods fall short of addressing the domain-specific complexities of aquaculture. To bridge this gap, we introduce AQUA, the first large language model (LLM) tailored for aquaculture, designed to support farmers, researchers, and industry practitioners. Central to this effort is AQUADAPT (Data Acquisition, Processing and Tuning), an Agentic Framework for generating and refining high-quality synthetic data using a combination of expert knowledge, largescale language models, and automated evaluation techniques. Our work lays the foundation for LLM-driven innovations in aquaculture research, advisory systems, and decision-making tools.

Human sciences have traditionally relied on human reasoning and intelligence to infer knowledge from a wide range of sources, such as oral and written narrations, reports, and traditions. Here we develop an extension of classical social network analysis approaches to incorporate the concept of meaning in each actor, as a mean to quantify and infer further knowledge from the original source of the network. This extension is based on a new affinity function, the semantic affinity, that establishes fuzzy-like relationships between the different actors in the network, using combinations of affinity functions. We also propose a new heuristic algorithm based on the shortest capacity problem to compute this affinity function. We use these concept of meaning and semantic affinity to analyze and compare the gods and heroes from three different classical mythologies: Greek, Celtic and Nordic. We study the relationships of each individual mythology and those of common structure that is formed when we fuse the three of them. We show a strong connection between the Celtic and Nordic gods and that Greeks put more emphasis on heroic characters rather than deities. Our approach provides a technique to highlight and quantify important relationships in the original domain of the network not deducible from its structural properties.

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach to decoding the genome. As GFMs scale up and reshape the landscape of AI-driven genomics, the field faces an urgent need for rigorous and reproducible evaluation. We present OmniGenBench, a modular benchmarking platform designed to unify the data, model, benchmarking, and interpretability layers across GFMs. OmniGenBench enables standardized, one-command evaluation of any GFM across five benchmark suites, with seamless integration of over 31 open-source models. Through automated pipelines and community-extensible features, the platform addresses critical reproducibility challenges, including data transparency, model interoperability, benchmark fragmentation, and black-box interpretability. OmniGenBench aims to serve as foundational infrastructure for reproducible genomic AI research, accelerating trustworthy discovery and collaborative innovation in the era of genome-scale modeling.

Scientific discovery has long been constrained by human limitations in expertise, physical capability, and sleep cycles. The recent rise of AI scientists and automated laboratories has accelerated both the cognitive and operational aspects of research. However, key limitations persist: AI systems are often confined to virtual environments, while automated laboratories lack the flexibility and autonomy to adaptively test new hypotheses in the physical world. Recent advances in embodied AI, such as generalist robot foundation models, diffusion-based action policies, fine-grained manipulation learning, and sim-to-real transfer, highlight the promise of integrating cognitive and embodied intelligence. This convergence opens the door to closed-loop systems that support iterative, autonomous experimentation and the possibility of serendipitous discovery. In this position paper, we propose the paradigm of Intelligent Science Laboratories (ISLs): a multi-layered, closed-loop framework that deeply integrates cognitive and embodied intelligence. ISLs unify foundation models for scientific reasoning, agent-based workflow orchestration, and embodied agents for robust physical experimentation. We argue that such systems are essential for overcoming the current limitations of scientific discovery and for realizing the full transformative potential of AI-driven science.

Large Language Models (LLMs) have reshaped our world with significant advancements in science, engineering, and society through applications ranging from scientific discoveries and medical diagnostics to Chatbots. Despite their ubiquity and utility, the underlying mechanisms of LLM remain concealed within billions of parameters and complex structures, making their inner architecture and cognitive processes challenging to comprehend. We address this gap by adopting approaches to understanding emerging cognition in biology and developing a network-based framework that links cognitive skills, LLM architectures, and datasets, ushering in a paradigm shift in foundation model analysis. The skill distribution in the module communities demonstrates that while LLMs do not strictly parallel the focalized specialization observed in specific biological systems, they exhibit unique communities of modules whose emergent skill patterns partially mirror the distributed yet interconnected cognitive organization seen in avian and small mammalian brains. Our numerical results highlight a key divergence from biological systems to LLMs, where skill acquisition benefits substantially from dynamic, cross-regional interactions and neural plasticity. By integrating cognitive science principles with machine learning, our framework provides new insights into LLM interpretability and suggests that effective fine-tuning strategies should leverage distributed learning dynamics rather than rigid modular interventions.

Artificial Intelligence (AI) has made incredible progress recently. On the one hand, advanced foundation models like ChatGPT can offer powerful conversation, in-context learning and code generation abilities on a broad range of open-domain tasks. They can also generate high-level solution outlines for domain-specific tasks based on the common sense knowledge they have acquired. However, they still face difficulties with some specialized tasks because they lack enough domain-specific data during pre-training or they often have errors in their neural network computations on those tasks that need accurate executions. On the other hand, there are also many existing models and systems (symbolic-based or neural-based) that can do some domain-specific tasks very well. However, due to the different implementation or working mechanisms, they are not easily accessible or compatible with foundation models. Therefore, there is a clear and pressing need for a mechanism that can leverage foundation models to propose task solution outlines and then automatically match some of the sub-tasks in the outlines to the off-the-shelf models and systems with special functionalities to complete them. Inspired by this, we introduce TaskMatrix.AI as a new AI ecosystem that connects foundation models with millions of APIs for task completion. Unlike most previous work that aimed to improve a single AI model, TaskMatrix.AI focuses more on using existing foundation models (as a brain-like central system) and APIs of other AI models and systems (as sub-task solvers) to achieve diversified tasks in both digital and physical domains. As a position paper, we will present our vision of how to build such an ecosystem, explain each key component, and use study cases to illustrate both the feasibility of this vision and the main challenges we need to address next.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Human intelligence, the most evident and accessible form of source of reasoning, hosted by biological hardware, has evolved and been refined over thousands of years, positioning itself today to create new artificial forms and preparing to self--design their evolutionary path forward. Beginning with the advent of foundation models, the rate at which human and artificial intelligence interact with each other has surpassed any anticipated quantitative figures. The close engagement led to both bits of intelligence to be impacted in various ways, which naturally resulted in complex confluences that warrant close scrutiny. In the sequel, we shall explore the interplay between human and machine intelligence, focusing on the crucial role humans play in developing ethical, responsible, and robust intelligent systems. We slightly delve into interesting aspects of implementation inspired by the mechanisms underlying neuroscience and human cognition. Additionally, we propose future perspectives, capitalizing on the advantages of symbiotic designs to suggest a human-centered direction for next-generation AI development. We finalize this evolving document with a few thoughts and open questions yet to be addressed by the broader community.

Artificial Intelligence (AI) Foundation models (FMs), pre-trained on massive unlabelled datasets, have the potential to drastically change AI applications in ocean science, where labelled data are often sparse and expensive to collect. In this work, we describe a new foundation model using the Prithvi-EO Vision Transformer architecture which has been pre-trained to reconstruct data from the Sentinel-3 Ocean and Land Colour Instrument (OLCI). We evaluate the model by fine-tuning on two downstream marine earth observation tasks. We first assess model performance compared to current baseline models used to quantify chlorophyll concentration. We then evaluate the FMs ability to refine remote sensing-based estimates of ocean primary production. Our results demonstrate the utility of self-trained FMs for marine monitoring, in particular for making use of small amounts of high quality labelled data and in capturing detailed spatial patterns of ocean colour whilst matching point observations. We conclude that this new generation of geospatial AI models has the potential to provide more robust, data-driven insights into ocean ecosystems and their role in global climate processes.

Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades, these knowledge graphs have been developed via expert curation; however, this method can no longer keep up with today's AI development, and a transition to algorithmically generated BioMedKGs is necessary. In this work, we introduce the Biomedical Informatics Ontology System (BIOS), the first large-scale publicly available BioMedKG generated completely by machine learning algorithms. BIOS currently contains 4.1 million concepts, 7.4 million terms in two languages, and 7.3 million relation triplets. We present the methodology for developing BIOS, including the curation of raw biomedical terms, computational identification of synonymous terms and aggregation of these terms to create concept nodes, semantic type classification of the concepts, relation identification, and biomedical machine translation. We provide statistics on the current BIOS content and perform preliminary assessments of term quality, synonym grouping, and relation extraction. The results suggest that machine learning-based BioMedKG development is a viable alternative to traditional expert curation.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

In this paper, we present a new theoretical approach for enabling domain knowledge acquisition by intelligent systems. We introduce a hybrid model that starts with minimal input knowledge in the form of an upper ontology of concepts, stores and reasons over this knowledge through a knowledge graph database and learns new information through a Logic Neural Network. We study the behavior of this architecture when handling new data and show that the final system is capable of enriching its current knowledge as well as extending it to new domains.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Gait patterns play a critical role in human identification and healthcare analytics, yet current progress remains constrained by small, narrowly designed models that fail to scale or generalize. Building a unified gait foundation model requires addressing two longstanding barriers: (a) Scalability. Why have gait models historically failed to follow scaling laws? (b) Generalization. Can one model serve the diverse gait tasks that have traditionally been studied in isolation? We introduce FoundationGait, the first scalable, self-supervised pretraining framework for gait understanding. Its largest version has nearly 0.13 billion parameters and is pretrained on 12 public gait datasets comprising over 2 million walking sequences. Extensive experiments demonstrate that FoundationGait, with or without fine-tuning, performs robustly across a wide spectrum of gait datasets, conditions, tasks (e.g., human identification, scoliosis screening, depression prediction, and attribute estimation), and even input modality. Notably, it achieves 48.0% zero-shot rank-1 accuracy on the challenging in-the-wild Gait3D dataset (1,000 test subjects) and 64.5% on the largest in-the-lab OU-MVLP dataset (5,000+ test subjects), setting a new milestone in robust gait recognition. Coming code and model: https://github.com/ShiqiYu/OpenGait.

Artificial intelligence (AI) has undergone a renaissance recently, making major progress in key domains such as vision, language, control, and decision-making. This has been due, in part, to cheap data and cheap compute resources, which have fit the natural strengths of deep learning. However, many defining characteristics of human intelligence, which developed under much different pressures, remain out of reach for current approaches. In particular, generalizing beyond one's experiences--a hallmark of human intelligence from infancy--remains a formidable challenge for modern AI. The following is part position paper, part review, and part unification. We argue that combinatorial generalization must be a top priority for AI to achieve human-like abilities, and that structured representations and computations are key to realizing this objective. Just as biology uses nature and nurture cooperatively, we reject the false choice between "hand-engineering" and "end-to-end" learning, and instead advocate for an approach which benefits from their complementary strengths. We explore how using relational inductive biases within deep learning architectures can facilitate learning about entities, relations, and rules for composing them. We present a new building block for the AI toolkit with a strong relational inductive bias--the graph network--which generalizes and extends various approaches for neural networks that operate on graphs, and provides a straightforward interface for manipulating structured knowledge and producing structured behaviors. We discuss how graph networks can support relational reasoning and combinatorial generalization, laying the foundation for more sophisticated, interpretable, and flexible patterns of reasoning. As a companion to this paper, we have released an open-source software library for building graph networks, with demonstrations of how to use them in practice.

The rapid advancements of AI agents have ignited the long-held ambition of leveraging them to accelerate scientific discovery. Achieving this goal requires a deep understanding of the frontiers of human knowledge. As such, Humanity's Last Exam (HLE) provides an exceptionally challenging touchstone for evaluating scientific AI agents. In this work, we aim to construct the foundational architecture for general-purpose agents and validate the capabilities through leading performance on HLE. To achieve this, we introduce X-Master, a tool-augmented reasoning agent designed to emulate human researchers by interacting flexibly with external tools during its reasoning process. This agent, guided by the conceptualization of code as an interaction language, can flexibly leverage built-in Python libraries and our customized tools to augment the reasoning. We further scale its capabilities through X-Masters, a scattered-and-stacked agentic workflow that systematically enhances breadth and depth of reasoning. Our open-source solution, X-Masters, sets a new state-of-the-art record on HLE with a score of 32.1%, surpassing OpenAI's and Google's Deep Research (26.6% and 26.9%) and becoming the first to exceed the 30% threshold. This work allows us to gain a deeper understanding of complex task-solving and accumulates valuable experience that can inform future advancements, guiding subsequent model training.

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

While Multimodal Large Language Models (MLLMs) demonstrate impressive abilities over high level perception and reasoning, their robustness in the wild still lags behind humans and exhibits diminished efficacy on simple tasks that are intuitive for humans. We examine the hypothesis that these deficiencies stem from the absence of core knowledge, rudimentary cognitive abilities innate to humans from early childhood. To probe core knowledge representation in MLLMs, we draw from developmental cognitive sciences and develop a large-scale benchmark, CoreCognition dataset, encompassing 12 core cognitive concepts. We evaluate 219 models with 10 different prompts, leading to a total of 2409 data points for analysis. Our findings reveal core knowledge deficits in early developed core abilities while models demonstrate human comparable performance in high level cognition. Moreover, we find that low level abilities show little to no scaling, in stark contrast to high level abilities. Finally, we introduce an evaluation technique, Concept Hacking, through which we demonstrate that MLLMs do not genuinely advance toward core knowledge but instead rely on illusory understanding and shortcut learning as they scale. Website with this https://growing-ai-like-a-child.github.io/{link}.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

In precision agriculture, the detection and recognition of insects play an essential role in the ability of crops to grow healthy and produce a high-quality yield. The current machine vision model requires a large volume of data to achieve high performance. However, there are approximately 5.5 million different insect species in the world. None of the existing insect datasets can cover even a fraction of them due to varying geographic locations and acquisition costs. In this paper, we introduce a novel ``Insect-1M'' dataset, a game-changing resource poised to revolutionize insect-related foundation model training. Covering a vast spectrum of insect species, our dataset, including 1 million images with dense identification labels of taxonomy hierarchy and insect descriptions, offers a panoramic view of entomology, enabling foundation models to comprehend visual and semantic information about insects like never before. Then, to efficiently establish an Insect Foundation Model, we develop a micro-feature self-supervised learning method with a Patch-wise Relevant Attention mechanism capable of discerning the subtle differences among insect images. In addition, we introduce Description Consistency loss to improve micro-feature modeling via insect descriptions. Through our experiments, we illustrate the effectiveness of our proposed approach in insect modeling and achieve State-of-the-Art performance on standard benchmarks of insect-related tasks. Our Insect Foundation Model and Dataset promise to empower the next generation of insect-related vision models, bringing them closer to the ultimate goal of precision agriculture.

Conceptual knowledge is fundamental to human cognition and knowledge bases. However, existing knowledge probing works only focus on evaluating factual knowledge of pre-trained language models (PLMs) and ignore conceptual knowledge. Since conceptual knowledge often appears as implicit commonsense behind texts, designing probes for conceptual knowledge is hard. Inspired by knowledge representation schemata, we comprehensively evaluate conceptual knowledge of PLMs by designing three tasks to probe whether PLMs organize entities by conceptual similarities, learn conceptual properties, and conceptualize entities in contexts, respectively. For the tasks, we collect and annotate 24k data instances covering 393 concepts, which is COPEN, a COnceptual knowledge Probing bENchmark. Extensive experiments on different sizes and types of PLMs show that existing PLMs systematically lack conceptual knowledge and suffer from various spurious correlations. We believe this is a critical bottleneck for realizing human-like cognition in PLMs. COPEN and our codes are publicly released at https://github.com/THU-KEG/COPEN.

Artificial General Intelligence (AGI) is often envisioned as inherently embodied. With recent advances in robotics and foundational AI models, we stand at the threshold of a new era-one marked by increasingly generalized embodied AI systems. This paper contributes to the discourse by introducing a systematic taxonomy of Embodied AGI spanning five levels (L1-L5). We review existing research and challenges at the foundational stages (L1-L2) and outline the key components required to achieve higher-level capabilities (L3-L5). Building on these insights and existing technologies, we propose a conceptual framework for an L3+ robotic brain, offering both a technical outlook and a foundation for future exploration.

Foundation models (FMs), i.e., models trained on a vast amount of typically unlabeled data, have become popular and available recently for the domain of histopathology. The key idea is to extract semantically rich vectors from any input patch, allowing for the use of simple subsequent classification networks potentially reducing the required amounts of labeled data, and increasing domain robustness. In this work, we investigate to which degree this also holds for mitotic figure classification. Utilizing two popular public mitotic figure datasets, we compared linear probing of five publicly available FMs against models trained on ImageNet and a simple ResNet50 end-to-end-trained baseline. We found that the end-to-end-trained baseline outperformed all FM-based classifiers, regardless of the amount of data provided. Additionally, we did not observe the FM-based classifiers to be more robust against domain shifts, rendering both of the above assumptions incorrect.

Histopathology plays a central role in clinical medicine and biomedical research. While artificial intelligence shows promising results on many pathological tasks, generalization and dealing with rare diseases, where training data is scarce, remains a challenge. Distilling knowledge from unlabeled data into a foundation model before learning from, potentially limited, labeled data provides a viable path to address these challenges. In this work, we extend the state of the art of foundation models for digital pathology whole slide images by semi-automated data curation and incorporating pathologist domain knowledge. Specifically, we combine computational and pathologist domain knowledge (1) to curate a diverse dataset of 103k slides corresponding to 750 million image patches covering data from different fixation, staining, and scanning protocols as well as data from different indications and labs across the EU and US, (2) for grouping semantically similar slides and tissue patches, and (3) to augment the input images during training. We evaluate the resulting model on a set of public and internal benchmarks and show that although our foundation model is trained with an order of magnitude less slides, it performs on par or better than competing models. We expect that scaling our approach to more data and larger models will further increase its performance and capacity to deal with increasingly complex real world tasks in diagnostics and biomedical research.

The rapid expansion of medical literature presents growing challenges for structuring and integrating domain knowledge at scale. Knowledge Graphs (KGs) offer a promising solution by enabling efficient retrieval, automated reasoning, and knowledge discovery. However, current KG construction methods often rely on supervised pipelines with limited generalizability or naively aggregate outputs from Large Language Models (LLMs), treating biomedical corpora as static and ignoring the temporal dynamics and contextual uncertainty of evolving knowledge. To address these limitations, we introduce MedKGent, a LLM agent framework for constructing temporally evolving medical KGs. Leveraging over 10 million PubMed abstracts published between 1975 and 2023, we simulate the emergence of biomedical knowledge via a fine-grained daily time series. MedKGent incrementally builds the KG in a day-by-day manner using two specialized agents powered by the Qwen2.5-32B-Instruct model. The Extractor Agent identifies knowledge triples and assigns confidence scores via sampling-based estimation, which are used to filter low-confidence extractions and inform downstream processing. The Constructor Agent incrementally integrates the retained triples into a temporally evolving graph, guided by confidence scores and timestamps to reinforce recurring knowledge and resolve conflicts. The resulting KG contains 156,275 entities and 2,971,384 relational triples. Quality assessments by two SOTA LLMs and three domain experts demonstrate an accuracy approaching 90%, with strong inter-rater agreement. To evaluate downstream utility, we conduct RAG across seven medical question answering benchmarks using five leading LLMs, consistently observing significant improvements over non-augmented baselines. Case studies further demonstrate the KG's value in literature-based drug repurposing via confidence-aware causal inference.

Knowledge-grounded conversation (KGC) shows excellent potential to deliver an engaging and informative response. However, existing approaches emphasize selecting one golden knowledge given a particular dialogue context, overlooking the one-to-many phenomenon in dialogue. As a result, the existing paradigm limits the diversity of knowledge selection and generation. To this end, we establish a multi-reference KGC dataset and propose a series of metrics to systematically assess the one-to-many efficacy of existing KGC models. Furthermore, to extend the hypothesis space of knowledge selection to enhance the mapping relationship between multiple knowledge and multiple responses, we devise a span-based variational model and optimize the model in a wake-sleep style with an ameliorated evidence lower bound objective to learn the one-to-many generalization. Both automatic and human evaluations demonstrate the efficacy of our approach.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

We explore local vs. global evolution of knowledge systems through the framework of socio-epistemic networks (SEN), applying two complementary methods to a corpus of scientific texts. The framework comprises three interconnected layers-social, semiotic (material), and semantic-proposing a multilayered approach to understanding structural developments of knowledge. To analyse diachronic changes on the semantic layer, we first use information-theoretic measures based on relative entropy to detect semantic shifts, assess their significance, and identify key driving features. Second, variations in document embedding densities reveal changes in semantic neighbourhoods, tracking how concentration of similar documents increase, remain stable, or disperse. This enables us to trace document trajectories based on content (topics) or metadata (authorship, institution). Case studies of Joseph Silk and Hans-J\"urgen Treder illustrate how individual scholar's work aligns with broader disciplinary shifts in general relativity and gravitation research, demonstrating the applications, limitations, and further potential of this approach.

We investigate how to teach large language models (LLMs) to perform scientific reasoning by leveraging expert discussions as a learning signal. Focusing on the genomics domain, we develop an automated pipeline to extract trainable data and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learning-friendly multiple-choice questions format, supported by 3000+ high-quality question-answer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. We fine-tune an LLM using RL with a rule-based reward signal derived from the synthetic MCQ dataset to enhance domain-specific reasoning. Our results show that reinforcement learning from scientific discussions improves model performance by over 15% compared to the base model on Genome-Bench, narrowing the gap between open-source LLMs and expert-level reasoning. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology.

Recent advancements in large foundation models have remarkably enhanced our understanding of sensory information in open-world environments. In leveraging the power of foundation models, it is crucial for AI research to pivot away from excessive reductionism and toward an emphasis on systems that function as cohesive wholes. Specifically, we emphasize developing Agent AI -- an embodied system that integrates large foundation models into agent actions. The emerging field of Agent AI spans a wide range of existing embodied and agent-based multimodal interactions, including robotics, gaming, and healthcare systems, etc. In this paper, we propose a novel large action model to achieve embodied intelligent behavior, the Agent Foundation Model. On top of this idea, we discuss how agent AI exhibits remarkable capabilities across a variety of domains and tasks, challenging our understanding of learning and cognition. Furthermore, we discuss the potential of Agent AI from an interdisciplinary perspective, underscoring AI cognition and consciousness within scientific discourse. We believe that those discussions serve as a basis for future research directions and encourage broader societal engagement.

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

We investigated the evolution and transformation of scientific knowledge in the early modern period, analyzing more than 350 different editions of textbooks used for teaching astronomy in European universities from the late fifteenth century to mid-seventeenth century. These historical sources constitute the Sphaera Corpus. By examining different semantic relations among individual parts of each edition on record, we built a multiplex network consisting of six layers, as well as the aggregated network built from the superposition of all the layers. The network analysis reveals the emergence of five different communities. The contribution of each layer in shaping the communities and the properties of each community are studied. The most influential books in the corpus are found by calculating the average age of all the out-going and in-coming links for each book. A small group of editions is identified as a transmitter of knowledge as they bridge past knowledge to the future through a long temporal interval. Our analysis, moreover, identifies the most disruptive books. These books introduce new knowledge that is then adopted by almost all the books published afterwards until the end of the whole period of study. The historical research on the content of the identified books, as an empirical test, finally corroborates the results of all our analyses.

Foundation Models (FMs) have demonstrated unprecedented capabilities including zero-shot learning, high fidelity data synthesis, and out of domain generalization. However, as we show in this paper, FMs still have poor out-of-the-box performance on expert tasks (e.g. retrieval of car manuals technical illustrations from language queries), data for which is either unseen or belonging to a long-tail part of the data distribution of the huge datasets used for FM pre-training. This underlines the necessity to explicitly evaluate and finetune FMs on such expert tasks, arguably ones that appear the most in practical real-world applications. In this paper, we propose a first of its kind FETA benchmark built around the task of teaching FMs to understand technical documentation, via learning to match their graphical illustrations to corresponding language descriptions. Our FETA benchmark focuses on text-to-image and image-to-text retrieval in public car manuals and sales catalogue brochures. FETA is equipped with a procedure for completely automatic annotation extraction (code would be released upon acceptance), allowing easy extension of FETA to more documentation types and application domains in the future. Our automatic annotation leads to an automated performance metric shown to be consistent with metrics computed on human-curated annotations (also released). We provide multiple baselines and analysis of popular FMs on FETA leading to several interesting findings that we believe would be very valuable to the FM community, paving the way towards real-world application of FMs for practical expert tasks currently 'overlooked' by standard benchmarks focusing on common objects.

A large language model (LLM) with knowledge in both scientific and general tasks is the foundation of science general intelligence. However, directly continued pretraining an LLM using science data usually leads to catastrophic forgetting, which indicates severe degradation in general ability. In this report, we present Innovator, which solves this problem by upcycling a pre-trained dense LLM into a fine-grained Mixtures-of-Experts model during continued pretraining, where different experts are expected to learn science knowledge in different disciplines, and a shared expert is utilized for general tasks. Innovator introduces a four-stage upcycle training paradigm: (1) Scientific Expert Induction on discipline-specific data, (2) Fine-grained Expert Splitting via FFN dimension decomposition, (3) Science-Aware Routing warmup, and (4) Generalist-Scientist Integration training on hybrid datasets. Such a paradigm enables knowledge in the general domain, and different scientific disciplines can be decoupled, avoiding the negative influence among knowledge in different domains. With 53.3B total parameters and 13.3B activated, Innovator extends Qwen2.5-7B using a shared general expert and 64 specialized scientific experts with 8 activated. Trained on 300B tokens with tri-level quality-controlled data, Innovator achieves 25% average improvement across 30 scientific tasks with a win rate as 70%, while retaining 99% performance in general tasks. Furthermore, Innovator-Reason, which is post-trained from Innovator for reasoning boosting, exhibits excellent reasoning performance in solving complex scientific problems with improvements over 30%.

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

Foundation models pretrained on large-scale datasets are revolutionizing the field of computational pathology (CPath). The generalization ability of foundation models is crucial for the success in various downstream clinical tasks. However, current foundation models have only been evaluated on a limited type and number of tasks, leaving their generalization ability and overall performance unclear. To address this gap, we established a most comprehensive benchmark to evaluate the performance of off-the-shelf foundation models across six distinct clinical task types, encompassing a total of 39 specific tasks. Our findings reveal that existing foundation models excel at certain task types but struggle to effectively handle the full breadth of clinical tasks. To improve the generalization of pathology foundation models, we propose a unified knowledge distillation framework consisting of both expert and self knowledge distillation, where the former allows the model to learn from the knowledge of multiple expert models, while the latter leverages self-distillation to enable image representation learning via local-global alignment. Based on this framework, a Generalizable Pathology Foundation Model (GPFM) is pretrained on a large-scale dataset consisting of 190 million images from around 86,000 public H&E whole slides across 34 major tissue types. Evaluated on the established benchmark, GPFM achieves an impressive average rank of 1.36, with 29 tasks ranked 1st, while the the second-best model, UNI, attains an average rank of 2.96, with only 4 tasks ranked 1st. The superior generalization of GPFM demonstrates its exceptional modeling capabilities across a wide range of clinical tasks, positioning it as a new cornerstone for feature representation in CPath.

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

Decision making demands intricate interplay between perception, memory, and reasoning to discern optimal policies. Conventional approaches to decision making face challenges related to low sample efficiency and poor generalization. In contrast, foundation models in language and vision have showcased rapid adaptation to diverse new tasks. Therefore, we advocate for the construction of foundation agents as a transformative shift in the learning paradigm of agents. This proposal is underpinned by the formulation of foundation agents with their fundamental characteristics and challenges motivated by the success of large language models (LLMs). Moreover, we specify the roadmap of foundation agents from large interactive data collection or generation, to self-supervised pretraining and adaptation, and knowledge and value alignment with LLMs. Lastly, we pinpoint critical research questions derived from the formulation and delineate trends for foundation agents supported by real-world use cases, addressing both technical and theoretical aspects to propel the field towards a more comprehensive and impactful future.

Clinicians spend a significant amount of time reviewing medical images and transcribing their findings regarding patient diagnosis, referral and treatment in text form. Vision-language models (VLMs), which automatically interpret images and summarize their findings as text, have enormous potential to alleviate clinical workloads and increase patient access to high-quality medical care. While foundational models have stirred considerable interest in the medical community, it is unclear whether their general capabilities translate to real-world clinical utility. In this work, we show that foundation VLMs markedly underperform compared to practicing ophthalmologists on specialist tasks crucial to the care of patients with age-related macular degeneration (AMD). To address this, we initially identified the essential capabilities required for image-based clinical decision-making, and then developed a curriculum to selectively train VLMs in these skills. The resulting model, RetinaVLM, can be instructed to write reports that significantly outperform those written by leading foundation medical VLMs in disease staging (F1 score of 0.63 vs. 0.11) and patient referral (0.67 vs. 0.39), and approaches the diagnostic performance of junior ophthalmologists (who achieve 0.77 and 0.78 on the respective tasks). Furthermore, in a reader study involving two senior ophthalmologists with up to 32 years of experience, RetinaVLM's reports were found to be similarly correct (78.6% vs. 82.1%) and complete (both 78.6%) as reports written by junior ophthalmologists with up to 10 years of experience. These results demonstrate that our curriculum-based approach provides a blueprint for specializing generalist foundation medical VLMs to handle real-world clinical tasks.

As LLMs grow more powerful, their most profound achievement may be recognising when to say "I don't know". Existing studies on LLM self-knowledge have been largely constrained by human-defined notions of feasibility, often neglecting the reasons behind unanswerability by LLMs and failing to study deficient types of self-knowledge. This study aims to obtain intrinsic insights into different types of LLM self-knowledge with a novel methodology: allowing them the flexibility to set their own feasibility boundaries and then analysing the consistency of these limits. We find that even frontier models like GPT-4o and Mistral Large are not sure of their own capabilities more than 80% of the time, highlighting a significant lack of trustworthiness in responses. Our analysis of confidence balance in LLMs indicates that models swing between overconfidence and conservatism in feasibility boundaries depending on task categories and that the most significant self-knowledge weaknesses lie in temporal awareness and contextual understanding. These difficulties in contextual comprehension additionally lead models to question their operational boundaries, resulting in considerable confusion within the self-knowledge of LLMs. We make our code and results available publicly at https://github.com/knowledge-verse-ai/LLM-Self_Knowledge_Eval

We introduce MIRAGE, a new benchmark for multimodal expert-level reasoning and decision-making in consultative interaction settings. Designed for the agriculture domain, MIRAGE captures the full complexity of expert consultations by combining natural user queries, expert-authored responses, and image-based context, offering a high-fidelity benchmark for evaluating models on grounded reasoning, clarification strategies, and long-form generation in a real-world, knowledge-intensive domain. Grounded in over 35,000 real user-expert interactions and curated through a carefully designed multi-step pipeline, MIRAGE spans diverse crop health, pest diagnosis, and crop management scenarios. The benchmark includes more than 7,000 unique biological entities, covering plant species, pests, and diseases, making it one of the most taxonomically diverse benchmarks available for vision-language models, grounded in the real world. Unlike existing benchmarks that rely on well-specified user inputs and closed-set taxonomies, MIRAGE features underspecified, context-rich scenarios with open-world settings, requiring models to infer latent knowledge gaps, handle rare entities, and either proactively guide the interaction or respond. Project Page: https://mirage-benchmark.github.io

The ability to research and synthesize knowledge is central to human expertise and progress. An emerging class of systems promises these exciting capabilities through generative research synthesis, performing retrieval over the live web and synthesizing discovered sources into long-form, cited summaries. However, evaluating such systems remains an open challenge: existing question-answering benchmarks focus on short-form factual responses, while expert-curated datasets risk staleness and data contamination. Both fail to capture the complexity and evolving nature of real research synthesis tasks. In this work, we introduce DeepScholar-bench, a live benchmark and holistic, automated evaluation framework designed to evaluate generative research synthesis. DeepScholar-bench draws queries from recent, high-quality ArXiv papers and focuses on a real research synthesis task: generating the related work sections of a paper by retrieving, synthesizing, and citing prior research. Our evaluation framework holistically assesses performance across three key dimensions, knowledge synthesis, retrieval quality, and verifiability. We also develop DeepScholar-base, a reference pipeline implemented efficiently using the LOTUS API. Using the DeepScholar-bench framework, we perform a systematic evaluation of prior open-source systems, search AI's, OpenAI's DeepResearch, and DeepScholar-base. We find that DeepScholar-base establishes a strong baseline, attaining competitive or higher performance than each other method. We also find that DeepScholar-bench remains far from saturated, with no system exceeding a score of 19% across all metrics. These results underscore the difficulty of DeepScholar-bench, as well as its importance for progress towards AI systems capable of generative research synthesis. We make our code available at https://github.com/guestrin-lab/deepscholar-bench.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

In this study, we introduce FEET, a standardized protocol designed to guide the development and benchmarking of foundation models. While numerous benchmark datasets exist for evaluating these models, we propose a structured evaluation protocol across three distinct scenarios to gain a comprehensive understanding of their practical performance. We define three primary use cases: frozen embeddings, few-shot embeddings, and fully fine-tuned embeddings. Each scenario is detailed and illustrated through two case studies: one in sentiment analysis and another in the medical domain, demonstrating how these evaluations provide a thorough assessment of foundation models' effectiveness in research applications. We recommend this protocol as a standard for future research aimed at advancing representation learning models.