Daily Papers

Large language models lack persistent, structured memory for long-term interaction and context-sensitive retrieval. Expanding context windows does not solve this: recent evidence shows that context length alone degrades reasoning by up to 85% - even with perfect retrieval. We propose a bio-inspired memory framework grounded in complementary learning systems theory, cognitive behavioral therapy's belief hierarchy, dual-process cognition, and fuzzy-trace theory, organized around three principles: (1) Memory has valence, not just content - pre-computed emotional-associative summaries (valence vectors) organized in an emergent belief hierarchy inspired by Beck's cognitive model enable instant orientation before deliberation; (2) Retrieval defaults to System 1 with System 2 escalation - automatic spreading activation and passive priming as default, with deliberate retrieval only when needed, and graded epistemic states that address hallucination structurally; and (3) Encoding is active, present, and feedback-dependent - a thalamic gateway tags and routes information between stores, while the executive forms gists through curiosity-driven investigation, not passive exposure. Seven functional properties specify what any implementation must satisfy. Over time, the system converges toward System 1 processing - the computational analog of clinical expertise - producing interactions that become cheaper, not more expensive, with experience.

Activation-based steering can personalize large language models at inference time, but its effects in educational settings remain unclear. We study persona vectors for seven character traits in short-answer generation and automated scoring on the ASAP-SAS benchmark across three models spanning two architectures. Persona steering lowers answer quality overall, with much larger effects on open-ended English Language Arts (ELA) prompts than on factual science prompts; interpretive and argumentative tasks are up to 11x more sensitive. On the scoring side, we observe predictable valence-aligned calibration shifts: evil and impolite scorers grade more harshly, while good and optimistic scorers grade more leniently. ELA tasks are 2.5-3x more susceptible to scorer personalization than science tasks, and the Mixture-of-Experts model shows roughly 6x larger calibration shifts than the dense models. To our knowledge, this is the first study to systematically examine the effects of activation-steered persona traits in educational generation and scoring, and the results highlight the need for task-aware and architecture-aware calibration when deploying steered models in educational settings.

This paper develops small vision language models to understand visual art, which, given an art work, aims to identify its emotion category and explain this prediction with natural language. While small models are computationally efficient, their capacity is much limited compared with large models. To break this trade-off, this paper builds a small emotional vision language model (SEVLM) by emotion modeling and input-output feature alignment. On the one hand, based on valence-arousal-dominance (VAD) knowledge annotated by psychology experts, we introduce and fuse emotional features derived through VAD dictionary and a VAD head to align VAD vectors of predicted emotion explanation and the ground truth. This allows the vision language model to better understand and generate emotional texts, compared with using traditional text embeddings alone. On the other hand, we design a contrastive head to pull close embeddings of the image, its emotion class, and explanation, which aligns model outputs and inputs. On two public affective explanation datasets, we show that the proposed techniques consistently improve the visual art understanding performance of baseline SEVLMs. Importantly, the proposed model can be trained and evaluated on a single RTX 2080 Ti while exhibiting very strong performance: it not only outperforms the state-of-the-art small models but is also competitive compared with LLaVA 7B after fine-tuning and GPT4(V). The code is available at https://github.com/BetterZH/SEVLM-code.

The tradeoff between precision and performance in molecular simulations can nowadays be addressed by machine-learned force fields (MLFF), which combine ab initio accuracy with force field numerical efficiency. Different from conventional force fields however, incorporating relevant electronic degrees of freedom into MLFFs becomes important. Here, we implement an equivariant transformer that embeds molecular net charge and spin state without additional neural network parameters. The model trained on a singlet/triplet non-correlated CH2 dataset can identify different spin states and shows state-of-the-art extrapolation capability. Therein, self-attention sensibly captures non-local effects, which, as we show, can be finely tuned over the network hyper-parameters. We indeed found that Softmax activation functions utilised in the self-attention mechanism of graph networks outperformed ReLU-like functions in prediction accuracy. Increasing the attention temperature from τ= d to 2d further improved the extrapolation capability, indicating a weighty role of nonlocality. Additionally, a weight initialisation method was purposed that sensibly accelerated the training process.

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular structures presents significant challenges. Two primary obstacles emerge: (1) the difficulty in designing a 3D line notation that ensures SE(3)-invariant atomic coordinates, and (2) the non-trivial task of tokenizing continuous coordinates for use in LMs, which inherently require discrete inputs. To address these challenges, we propose Mol-StrucTok, a novel method for tokenizing 3D molecular structures. Our approach comprises two key innovations: (1) We design a line notation for 3D molecules by extracting local atomic coordinates in a spherical coordinate system. This notation builds upon existing 2D line notations and remains agnostic to their specific forms, ensuring compatibility with various molecular representation schemes. (2) We employ a Vector Quantized Variational Autoencoder (VQ-VAE) to tokenize these coordinates, treating them as generation descriptors. To further enhance the representation, we incorporate neighborhood bond lengths and bond angles as understanding descriptors. Leveraging this tokenization framework, we train a GPT-2 style model for 3D molecular generation tasks. Results demonstrate strong performance with significantly faster generation speeds and competitive chemical stability compared to previous methods. Further, by integrating our learned discrete representations into Graphormer model for property prediction on QM9 dataset, Mol-StrucTok reveals consistent improvements across various molecular properties, underscoring the versatility and robustness of our approach.

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

The development of efficient machine learning models for molecular systems representation is becoming crucial in scientific research. We introduce TensorNet, an innovative O(3)-equivariant message-passing neural network architecture that leverages Cartesian tensor representations. By using Cartesian tensor atomic embeddings, feature mixing is simplified through matrix product operations. Furthermore, the cost-effective decomposition of these tensors into rotation group irreducible representations allows for the separate processing of scalars, vectors, and tensors when necessary. Compared to higher-rank spherical tensor models, TensorNet demonstrates state-of-the-art performance with significantly fewer parameters. For small molecule potential energies, this can be achieved even with a single interaction layer. As a result of all these properties, the model's computational cost is substantially decreased. Moreover, the accurate prediction of vector and tensor molecular quantities on top of potential energies and forces is possible. In summary, TensorNet's framework opens up a new space for the design of state-of-the-art equivariant models.

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

Molecule generation is advancing rapidly in chemical discovery and drug design. Flow matching methods have recently set the state of the art (SOTA) in unconditional molecule generation, surpassing score-based diffusion models. However, diffusion models still lead in property-guided generation. In this work, we introduce PropMolFlow, a novel approach for property-guided molecule generation based on geometry-complete SE(3)-equivariant flow matching. Integrating five different property embedding methods with a Gaussian expansion of scalar properties, PropMolFlow outperforms previous SOTA diffusion models in conditional molecule generation across various properties while preserving the stability and validity of the generated molecules, consistent with its unconditional counterpart. Additionally, it enables faster inference with significantly fewer time steps compared to baseline models. We highlight the importance of validating the properties of generated molecules through DFT calculations performed at the same level of theory as the training data. Specifically, our analysis identifies properties that require DFT validation and others where a pretrained SE(3) geometric vector perceptron regressors provide sufficiently accurate predictions on generated molecules. Furthermore, we introduce a new property metric designed to assess the model's ability to propose molecules with underrepresented property values, assessing its capacity for out-of-distribution generalization. Our findings reveal shortcomings in existing structural metrics, which mistakenly validate open-shell molecules or molecules with invalid valence-charge configurations, underscoring the need for improved evaluation frameworks. Overall, this work paves the way for developing targeted property-guided generation methods, enhancing the design of molecular generative models for diverse applications.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

3D molecule generation is crucial for drug discovery and material science, requiring models to process complex multi-modalities, including atom types, chemical bonds, and 3D coordinates. A key challenge is integrating these modalities of different shapes while maintaining SE(3) equivariance for 3D coordinates. To achieve this, existing approaches typically maintain separate latent spaces for invariant and equivariant modalities, reducing efficiency in both training and sampling. In this work, we propose Unified Variational Auto-Encoder for 3D Molecular Latent Diffusion Modeling (UAE-3D), a multi-modal VAE that compresses 3D molecules into latent sequences from a unified latent space, while maintaining near-zero reconstruction error. This unified latent space eliminates the complexities of handling multi-modality and equivariance when performing latent diffusion modeling. We demonstrate this by employing the Diffusion Transformer--a general-purpose diffusion model without any molecular inductive bias--for latent generation. Extensive experiments on GEOM-Drugs and QM9 datasets demonstrate that our method significantly establishes new benchmarks in both de novo and conditional 3D molecule generation, achieving leading efficiency and quality.

Recently, text-guided scalable vector graphics (SVG) synthesis has demonstrated significant potential in domains such as iconography and sketching. However, SVGs generated from existing Text-to-SVG methods often lack editability and exhibit deficiencies in visual quality and diversity. In this paper, we propose a novel text-guided vector graphics synthesis method to address these limitations. To enhance the editability of output SVGs, we introduce a Hierarchical Image VEctorization (HIVE) framework that operates at the semantic object level and supervises the optimization of components within the vector object. This approach facilitates the decoupling of vector graphics into distinct objects and component levels. Our proposed HIVE algorithm, informed by image segmentation priors, not only ensures a more precise representation of vector graphics but also enables fine-grained editing capabilities within vector objects. To improve the diversity of output SVGs, we present a Vectorized Particle-based Score Distillation (VPSD) approach. VPSD addresses over-saturation issues in existing methods and enhances sample diversity. A pre-trained reward model is incorporated to re-weight vector particles, improving aesthetic appeal and enabling faster convergence. Additionally, we design a novel adaptive vector primitives control strategy, which allows for the dynamic adjustment of the number of primitives, thereby enhancing the presentation of graphic details. Extensive experiments validate the effectiveness of the proposed method, demonstrating its superiority over baseline methods in terms of editability, visual quality, and diversity. We also show that our new method supports up to six distinct vector styles, capable of generating high-quality vector assets suitable for stylized vector design and poster design. Code and demo will be released at: http://ximinng.github.io/SVGDreamerV2Project/

Vector graphics are widely used in digital art and highly favored by designers due to their scalability and layer-wise properties. However, the process of creating and editing vector graphics requires creativity and design expertise, making it a time-consuming task. Recent advancements in text-to-vector (T2V) generation have aimed to make this process more accessible. However, existing T2V methods directly optimize control points of vector graphics paths, often resulting in intersecting or jagged paths due to the lack of geometry constraints. To overcome these limitations, we propose a novel neural path representation by designing a dual-branch Variational Autoencoder (VAE) that learns the path latent space from both sequence and image modalities. By optimizing the combination of neural paths, we can incorporate geometric constraints while preserving expressivity in generated SVGs. Furthermore, we introduce a two-stage path optimization method to improve the visual and topological quality of generated SVGs. In the first stage, a pre-trained text-to-image diffusion model guides the initial generation of complex vector graphics through the Variational Score Distillation (VSD) process. In the second stage, we refine the graphics using a layer-wise image vectorization strategy to achieve clearer elements and structure. We demonstrate the effectiveness of our method through extensive experiments and showcase various applications. The project page is https://intchous.github.io/T2V-NPR.

We introduce Clifford Group Equivariant Simplicial Message Passing Networks, a method for steerable E(n)-equivariant message passing on simplicial complexes. Our method integrates the expressivity of Clifford group-equivariant layers with simplicial message passing, which is topologically more intricate than regular graph message passing. Clifford algebras include higher-order objects such as bivectors and trivectors, which express geometric features (e.g., areas, volumes) derived from vectors. Using this knowledge, we represent simplex features through geometric products of their vertices. To achieve efficient simplicial message passing, we share the parameters of the message network across different dimensions. Additionally, we restrict the final message to an aggregation of the incoming messages from different dimensions, leading to what we term shared simplicial message passing. Experimental results show that our method is able to outperform both equivariant and simplicial graph neural networks on a variety of geometric tasks.

Vector graphic documents present visual elements in a resolution free, compact format and are often seen in creative applications. In this work, we attempt to learn a generative model of vector graphic documents. We define vector graphic documents by a multi-modal set of attributes associated to a canvas and a sequence of visual elements such as shapes, images, or texts, and train variational auto-encoders to learn the representation of the documents. We collect a new dataset of design templates from an online service that features complete document structure including occluded elements. In experiments, we show that our model, named CanvasVAE, constitutes a strong baseline for generative modeling of vector graphic documents.

Recently, text-guided scalable vector graphics (SVGs) synthesis has shown promise in domains such as iconography and sketch. However, existing text-to-SVG generation methods lack editability and struggle with visual quality and result diversity. To address these limitations, we propose a novel text-guided vector graphics synthesis method called SVGDreamer. SVGDreamer incorporates a semantic-driven image vectorization (SIVE) process that enables the decomposition of synthesis into foreground objects and background, thereby enhancing editability. Specifically, the SIVE process introduce attention-based primitive control and an attention-mask loss function for effective control and manipulation of individual elements. Additionally, we propose a Vectorized Particle-based Score Distillation (VPSD) approach to tackle the challenges of color over-saturation, vector primitives over-smoothing, and limited result diversity in existing text-to-SVG generation methods. Furthermore, on the basis of VPSD, we introduce Reward Feedback Learning (ReFL) to accelerate VPSD convergence and improve aesthetic appeal. Extensive experiments have been conducted to validate the effectiveness of SVGDreamer, demonstrating its superiority over baseline methods in terms of editability, visual quality, and diversity.

We propose a simple auto-encoder framework for molecule generation. The molecular graph is first encoded into a continuous latent representation z, which is then decoded back to a molecule. The encoding process is easy, but the decoding process remains challenging. In this work, we introduce a simple two-step decoding process. In a first step, a fully connected neural network uses the latent vector z to produce a molecular formula, for example CO_2 (one carbon and two oxygen atoms). In a second step, a graph convolutional neural network uses the same latent vector z to place bonds between the atoms that were produced in the first step (for example a double bond will be placed between the carbon and each of the oxygens). This two-step process, in which a bag of atoms is first generated, and then assembled, provides a simple framework that allows us to develop an efficient molecule auto-encoder. Numerical experiments on basic tasks such as novelty, uniqueness, validity and optimized chemical property for the 250k ZINC molecules demonstrate the performances of the proposed system. Particularly, we achieve the highest reconstruction rate of 90.5\%, improving the previous rate of 76.7\%. We also report the best property improvement results when optimization is constrained by the molecular distance between the original and generated molecules.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

In this paper, we propose Multiresolution Equivariant Graph Variational Autoencoders (MGVAE), the first hierarchical generative model to learn and generate graphs in a multiresolution and equivariant manner. At each resolution level, MGVAE employs higher order message passing to encode the graph while learning to partition it into mutually exclusive clusters and coarsening into a lower resolution that eventually creates a hierarchy of latent distributions. MGVAE then constructs a hierarchical generative model to variationally decode into a hierarchy of coarsened graphs. Importantly, our proposed framework is end-to-end permutation equivariant with respect to node ordering. MGVAE achieves competitive results with several generative tasks including general graph generation, molecular generation, unsupervised molecular representation learning to predict molecular properties, link prediction on citation graphs, and graph-based image generation.

The study demonstrates the capabilities of a vector-based approach for calculating stoichiometric coefficients in chemical equations, using black powder as an illustrative example. A method is proposed for selecting and constraining intermediate interactions between reactants, as well as for identifying final products. It is shown that even a small number of components can lead to a large number of final and intermediate products. Through concrete calculations, a correlation is established between the number of possible chemical equations and the number of reactants. A methodology is proposed for computing all possible chemical equations within a reaction system for arbitrary component ratios, enabling the derivation of all feasible chemical reactions. Additionally, a method is developed for calculating the chemical composition for a fixed set of reactants, allowing for the evaluation of the set of products resulting from all possible chemical interactions given a specified initial composition.

Accurate and scalable machine-learned inter-atomic potentials (MLIPs) are essential for molecular simulations ranging from drug discovery to new material design. Current state-of-the-art models enforce roto-translational symmetries through equivariant neural network architectures, a hard-wired inductive bias that can often lead to reduced flexibility, computational efficiency, and scalability. In this work, we introduce TransIP: Transformer-based Inter-Atomic Potentials, a novel training paradigm for interatomic potentials achieving symmetry compliance without explicit architectural constraints. Our approach guides a generic non-equivariant Transformer-based model to learn SO(3)-equivariance by optimizing its representations in the embedding space. Trained on the recent Open Molecules (OMol25) collection, a large and diverse molecular dataset built specifically for MLIPs and covering different types of molecules (including small organics, biomolecular fragments, and electrolyte-like species), TransIP attains comparable performance in machine-learning force fields versus state-of-the-art equivariant baselines. Further, compared to a data augmentation baseline, TransIP achieves 40% to 60% improvement in performance across varying OMol25 dataset sizes. More broadly, our work shows that learned equivariance can be a powerful and efficient alternative to equivariant or augmentation-based MLIP models.

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

Molecules are frequently represented as graphs, but the underlying 3D molecular geometry (the locations of the atoms) ultimately determines most molecular properties. However, most molecules are not static and at room temperature adopt a wide variety of geometries or conformations. The resulting distribution on geometries p(x) is known as the Boltzmann distribution, and many molecular properties are expectations computed under this distribution. Generating accurate samples from the Boltzmann distribution is therefore essential for computing these expectations accurately. Traditional sampling-based methods are computationally expensive, and most recent machine learning-based methods have focused on identifying modes in this distribution rather than generating true samples. Generating such samples requires capturing conformational variability, and it has been widely recognized that the majority of conformational variability in molecules arises from rotatable bonds. In this work, we present VonMisesNet, a new graph neural network that captures conformational variability via a variational approximation of rotatable bond torsion angles as a mixture of von Mises distributions. We demonstrate that VonMisesNet can generate conformations for arbitrary molecules in a way that is both physically accurate with respect to the Boltzmann distribution and orders of magnitude faster than existing sampling methods.

Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of multi-modalities -- continuous 3D positions and discrete 2D topologies -- which jointly determine molecular geometries. By establishing the fact that noise schedules decide the Variational Lower Bound (VLB) for the twisted probability path, we propose VLB-Optimal Scheduling (VOS) strategy in this under-explored area, which optimizes VLB as a path integral for SBDD. Our model effectively enhances molecular geometries and interaction modeling, achieving state-of-the-art PoseBusters passing rate of 95.9% on CrossDock, more than 10% improvement upon strong baselines, while maintaining high affinities and robust intramolecular validity evaluated on held-out test set. Code is available at https://github.com/AlgoMole/MolCRAFT.

Deep generative models have shown significant promise in generating valid 3D molecular structures, with the GEOM-Drugs dataset serving as a key benchmark. However, current evaluation protocols suffer from critical flaws, including incorrect valency definitions, bugs in bond order calculations, and reliance on force fields inconsistent with the reference data. In this work, we revisit GEOM-Drugs and propose a corrected evaluation framework: we identify and fix issues in data preprocessing, construct chemically accurate valency tables, and introduce a GFN2-xTB-based geometry and energy benchmark. We retrain and re-evaluate several leading models under this framework, providing updated performance metrics and practical recommendations for future benchmarking. Our results underscore the need for chemically rigorous evaluation practices in 3D molecular generation. Our recommended evaluation methods and GEOM-Drugs processing scripts are available at https://github.com/isayevlab/geom-drugs-3dgen-evaluation.

Generative models have recently shown great promise for accelerating the design and discovery of new functional materials. Conditional generation enhances this capacity by allowing inverse design, where specific desired properties can be requested during the generation process. However, conditioning of transformer-based approaches, in particular, is constrained by discrete tokenisation schemes and the risk of catastrophic forgetting during fine-tuning. This work introduces CrystaLLM-π (property injection), a conditional autoregressive framework that integrates continuous property representations directly into the transformer's attention mechanism. Two architectures, Property-Key-Value (PKV) Prefix attention and PKV Residual attention, are presented. These methods bypass inefficient sequence-level tokenisation and preserve foundational knowledge from unsupervised pre-training on Crystallographic Information Files (CIFs) as textual input. We establish the efficacy of these mechanisms through systematic robustness studies and evaluate the framework's versatility across two distinct tasks. First, for structure recovery, the model processes high-dimensional, heterogeneous X-ray diffraction patterns, achieving structural accuracy competitive with specialised models and demonstrating applications to experimental structure recovery and polymorph differentiation. Second, for materials discovery, the model is fine-tuned on a specialised photovoltaic dataset to generate novel, stable candidates validated by Density Functional Theory (DFT). It implicitly learns to target optimal band gap regions for high photovoltaic efficiency, demonstrating a capability to map complex structure-property relationships. CrystaLLM-π provides a unified, flexible, and computationally efficient framework for inverse materials design.

While large multimodal models excel in broad vision-language benchmarks, they often struggle with tasks requiring precise perception of low-level visual details, such as comparing line lengths or solving simple mazes. In particular, this failure mode persists in question-answering tasks about vector graphics -- images composed purely of 2D objects and shapes. To address this challenge, we propose the Visually Descriptive Language Model (VDLM), which performs text-based reasoning about vector graphics. VDLM leverages Scalable Vector Graphics (SVG) for a more precise visual description and first uses an off-the-shelf raster-to-SVG algorithm for encoding. Since existing language models cannot understand raw SVGs in a zero-shot setting, VDLM then bridges SVG with pretrained language models through a newly introduced intermediate symbolic representation, Primal Visual Description (PVD), comprising primitive attributes (e.g., shape, position, measurement) with their corresponding predicted values. PVD is task-agnostic and represents visual primitives that are universal across all vector graphics. It can be learned with procedurally generated (SVG, PVD) pairs and also enables the direct use of LLMs for generalization to complex reasoning tasks. By casting an image to a text-based representation, we can leverage the power of language models to learn alignment from SVG to visual primitives and generalize to unseen question-answering tasks. Empirical results show that VDLM achieves stronger zero-shot performance compared to state-of-the-art LMMs, such as GPT-4V, in various low-level multimodal perception and reasoning tasks on vector graphics. We additionally present extensive analyses on VDLM's performance, demonstrating that our framework offers better interpretability due to its disentangled perception and reasoning processes. Project page: https://mikewangwzhl.github.io/VDLM/

We aim to learn wavefunctions simulated by time-dependent density functional theory (TDDFT), which can be efficiently represented as linear combination coefficients of atomic orbitals. In real-time TDDFT, the electronic wavefunctions of a molecule evolve over time in response to an external excitation, enabling first-principles predictions of physical properties such as optical absorption, electron dynamics, and high-order response. However, conventional real-time TDDFT relies on time-consuming propagation of all occupied states with fine time steps. In this work, we propose OrbEvo, which is based on an equivariant graph transformer architecture and learns to evolve the full electronic wavefunction coefficients across time steps. First, to account for external field, we design an equivariant conditioning to encode both strength and direction of external electric field and break the symmetry from SO(3) to SO(2). Furthermore, we design two OrbEvo models, OrbEvo-WF and OrbEvo-DM, using wavefunction pooling and density matrix as interaction method, respectively. Motivated by the central role of the density functional in TDDFT, OrbEvo-DM encodes the density matrix aggregated from all occupied electronic states into feature vectors via tensor contraction, providing a more intuitive approach to learn the time evolution operator. We adopt a training strategy specifically tailored to limit the error accumulation of time-dependent wavefunctions over autoregressive rollout. To evaluate our approach, we generate TDDFT datasets consisting of 5,000 different molecules in the QM9 dataset and 1,500 molecular configurations of the malonaldehyde molecule in the MD17 dataset. Results show that our OrbEvo model accurately captures quantum dynamics of excited states under external field, including time-dependent wavefunctions, time-dependent dipole moment, and optical absorption spectra.

Self-supervised learning holds promise to revolutionize molecule property prediction - a central task to drug discovery and many more industries - by enabling data efficient learning from scarce experimental data. Despite significant progress, non-pretrained methods can be still competitive in certain settings. We reason that architecture might be a key bottleneck. In particular, enriching the backbone architecture with domain-specific inductive biases has been key for the success of self-supervised learning in other domains. In this spirit, we methodologically explore the design space of the self-attention mechanism tailored to molecular data. We identify a novel variant of self-attention adapted to processing molecules, inspired by the relative self-attention layer, which involves fusing embedded graph and distance relationships between atoms. Our main contribution is Relative Molecule Attention Transformer (R-MAT): a novel Transformer-based model based on the developed self-attention layer that achieves state-of-the-art or very competitive results across a~wide range of molecule property prediction tasks.

Molecular dynamics (MD) simulations are essential tools for unraveling atomistic insights into the structure and dynamics of condensed-phase systems. However, the universal and accurate prediction of macroscopic properties from ab initio calculations remains a significant challenge, often hindered by the trade-off between computational cost and simulation accuracy. Here, we present ByteFF-Pol, a graph neural network (GNN)-parameterized polarizable force field, trained exclusively on high-level quantum mechanics (QM) data. Leveraging physically-motivated force field forms and training strategies, ByteFF-Pol exhibits exceptional performance in predicting thermodynamic and transport properties for a wide range of small-molecule liquids and electrolytes, outperforming state-of-the-art (SOTA) classical and machine learning force fields. The zero-shot prediction capability of ByteFF-Pol bridges the gap between microscopic QM calculations and macroscopic liquid properties, enabling the exploration of previously intractable chemical spaces. This advancement holds transformative potential for applications such as electrolyte design and custom-tailored solvent, representing a pivotal step toward data-driven materials discovery.

Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation learning. However, relying on straightforward alignment strategies that treat each modality separately, these methods fail to exploit the intrinsic correlation between 2D and 3D representations that reflect the underlying structural characteristics of molecules, and only perform coarse-grained molecule-level alignment. To derive fine-grained alignment and promote structural molecule understanding, we introduce an atomic-relation level "blend-then-predict" self-supervised learning approach, MoleBLEND, which first blends atom relations represented by different modalities into one unified relation matrix for joint encoding, then recovers modality-specific information for 2D and 3D structures individually. By treating atom relationships as anchors, MoleBLEND organically aligns and integrates visually dissimilar 2D and 3D modalities of the same molecule at fine-grained atomic level, painting a more comprehensive depiction of each molecule. Extensive experiments show that MoleBLEND achieves state-of-the-art performance across major 2D/3D molecular benchmarks. We further provide theoretical insights from the perspective of mutual-information maximization, demonstrating that our method unifies contrastive, generative (cross-modality prediction) and mask-then-predict (single-modality prediction) objectives into one single cohesive framework.

Graph Neural Networks (GNNs) are the dominant architecture for molecular machine learning, particularly for molecular property prediction and machine learning interatomic potentials (MLIPs). GNNs perform message passing on predefined graphs often induced by a fixed radius cutoff or k-nearest neighbor scheme. While this design aligns with the locality present in many molecular tasks, a hard-coded graph can limit expressivity due to the fixed receptive field and slows down inference with sparse graph operations. In this work, we investigate whether pure, unmodified Transformers trained directly on Cartesian coordinatesx2013without predefined graphs or physical priorsx2013can approximate molecular energies and forces. As a starting point for our analysis, we demonstrate how to train a Transformer to competitive energy and force mean absolute errors under a matched training compute budget, relative to a state-of-the-art equivariant GNN on the OMol25 dataset. We discover that the Transformer learns physically consistent patternsx2013such as attention weights that decay inversely with interatomic distancex2013and flexibly adapts them across different molecular environments due to the absence of hard-coded biases. The use of a standard Transformer also unlocks predictable improvements with respect to scaling training resources, consistent with empirical scaling laws observed in other domains. Our results demonstrate that many favorable properties of GNNs can emerge adaptively in Transformers, challenging the necessity of hard-coded graph inductive biases and pointing toward standardized, scalable architectures for molecular modeling.

Generating VectorArt from text prompts is a challenging vision task, requiring diverse yet realistic depictions of the seen as well as unseen entities. However, existing research has been mostly limited to the generation of single objects, rather than comprehensive scenes comprising multiple elements. In response, this work introduces SVGCraft, a novel end-to-end framework for the creation of vector graphics depicting entire scenes from textual descriptions. Utilizing a pre-trained LLM for layout generation from text prompts, this framework introduces a technique for producing masked latents in specified bounding boxes for accurate object placement. It introduces a fusion mechanism for integrating attention maps and employs a diffusion U-Net for coherent composition, speeding up the drawing process. The resulting SVG is optimized using a pre-trained encoder and LPIPS loss with opacity modulation to maximize similarity. Additionally, this work explores the potential of primitive shapes in facilitating canvas completion in constrained environments. Through both qualitative and quantitative assessments, SVGCraft is demonstrated to surpass prior works in abstraction, recognizability, and detail, as evidenced by its performance metrics (CLIP-T: 0.4563, Cosine Similarity: 0.6342, Confusion: 0.66, Aesthetic: 6.7832). The code will be available at https://github.com/ayanban011/SVGCraft.

Spherical equivariant graph neural networks (EGNNs) provide a principled framework for learning on three-dimensional molecular and biomolecular systems, where predictions must respect the rotational symmetries inherent in physics. These models extend traditional message-passing GNNs and Transformers by representing node and edge features as spherical tensors that transform under irreducible representations of the rotation group SO(3), ensuring that predictions change in physically meaningful ways under rotations of the input. This guide develops a complete, intuitive foundation for spherical equivariant modeling - from group representations and spherical harmonics, to tensor products, Clebsch-Gordan decomposition, and the construction of SO(3)-equivariant kernels. Building on this foundation, we construct the Tensor Field Network and SE(3)-Transformer architectures and explain how they perform equivariant message-passing and attention on geometric graphs. Through clear mathematical derivations and annotated code excerpts, this guide serves as a self-contained introduction for researchers and learners seeking to understand or implement spherical EGNNs for applications in chemistry, molecular property prediction, protein structure modeling, and generative modeling.

Vector graphics are essential in design, providing artists with a versatile medium for creating resolution-independent and highly editable visual content. Recent advancements in vision-language and diffusion models have fueled interest in text-to-vector graphics generation. However, existing approaches often suffer from over-parameterized outputs or treat the layered structure - a core feature of vector graphics - as a secondary goal, diminishing their practical use. Recognizing the importance of layered SVG representations, we propose NeuralSVG, an implicit neural representation for generating vector graphics from text prompts. Inspired by Neural Radiance Fields (NeRFs), NeuralSVG encodes the entire scene into the weights of a small MLP network, optimized using Score Distillation Sampling (SDS). To encourage a layered structure in the generated SVG, we introduce a dropout-based regularization technique that strengthens the standalone meaning of each shape. We additionally demonstrate that utilizing a neural representation provides an added benefit of inference-time control, enabling users to dynamically adapt the generated SVG based on user-provided inputs, all with a single learned representation. Through extensive qualitative and quantitative evaluations, we demonstrate that NeuralSVG outperforms existing methods in generating structured and flexible SVG.

This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly operates on both continuous (atom coordinates) and categorical features (atom types). In addition, we provide a probabilistic analysis which admits likelihood computation of molecules using our model. Experimentally, the proposed method significantly outperforms previous 3D molecular generative methods regarding the quality of generated samples and efficiency at training time.

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our representation satisfies all structural, geometric, efficiency, and generalizability constraints. Afterward, we provide a general algorithm to encode any atomistic system. Finally, we report performance comparable to state-of-the-art methods on numerous tasks. We open-source all code and datasets. The code and data are available at https://github.com/rahulkhorana/PolyatomicComplexes.

We consider the task of predicting Hamiltonian matrices to accelerate electronic structure calculations, which plays an important role in physics, chemistry, and materials science. Motivated by the inherent relationship between the off-diagonal blocks of the Hamiltonian matrix and the SO(2) local frame, we propose a novel and efficient network, called QHNetV2, that achieves global SO(3) equivariance without the costly SO(3) Clebsch-Gordan tensor products. This is achieved by introducing a set of new efficient and powerful SO(2)-equivariant operations and performing all off-diagonal feature updates and message passing within SO(2) local frames, thereby eliminating the need of SO(3) tensor products. Moreover, a continuous SO(2) tensor product is performed within the SO(2) local frame at each node to fuse node features, mimicking the symmetric contraction operation. Extensive experiments on the large QH9 and MD17 datasets demonstrate that our model achieves superior performance across a wide range of molecular structures and trajectories, highlighting its strong generalization capability. The proposed SO(2) operations on SO(2) local frames offer a promising direction for scalable and symmetry-aware learning of electronic structures. Our code will be released as part of the AIRS library https://github.com/divelab/AIRS.

Graph neural networks have recently achieved great successes in predicting quantum mechanical properties of molecules. These models represent a molecule as a graph using only the distance between atoms (nodes). They do not, however, consider the spatial direction from one atom to another, despite directional information playing a central role in empirical potentials for molecules, e.g. in angular potentials. To alleviate this limitation we propose directional message passing, in which we embed the messages passed between atoms instead of the atoms themselves. Each message is associated with a direction in coordinate space. These directional message embeddings are rotationally equivariant since the associated directions rotate with the molecule. We propose a message passing scheme analogous to belief propagation, which uses the directional information by transforming messages based on the angle between them. Additionally, we use spherical Bessel functions and spherical harmonics to construct theoretically well-founded, orthogonal representations that achieve better performance than the currently prevalent Gaussian radial basis representations while using fewer than 1/4 of the parameters. We leverage these innovations to construct the directional message passing neural network (DimeNet). DimeNet outperforms previous GNNs on average by 76% on MD17 and by 31% on QM9. Our implementation is available online.

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

Large-scale molecular representation methods have revolutionized applications in material science, such as drug discovery, chemical modeling, and material design. With the rise of transformers, models now learn representations directly from molecular structures. In this study, we develop an encoder-decoder model based on BART that is capable of leaning molecular representations and generate new molecules. Trained on SELFIES, a robust molecular string representation, our model outperforms existing baselines in downstream tasks, demonstrating its potential in efficient and effective molecular data analysis and manipulation.

Machine Learning Force Fields (MLFFs) are a promising alternative to expensive ab initio quantum mechanical molecular simulations. Given the diversity of chemical spaces that are of interest and the cost of generating new data, it is important to understand how MLFFs generalize beyond their training distributions. In order to characterize and better understand distribution shifts in MLFFs, we conduct diagnostic experiments on chemical datasets, revealing common shifts that pose significant challenges, even for large foundation models trained on extensive data. Based on these observations, we hypothesize that current supervised training methods inadequately regularize MLFFs, resulting in overfitting and learning poor representations of out-of-distribution systems. We then propose two new methods as initial steps for mitigating distribution shifts for MLFFs. Our methods focus on test-time refinement strategies that incur minimal computational cost and do not use expensive ab initio reference labels. The first strategy, based on spectral graph theory, modifies the edges of test graphs to align with graph structures seen during training. Our second strategy improves representations for out-of-distribution systems at test-time by taking gradient steps using an auxiliary objective, such as a cheap physical prior. Our test-time refinement strategies significantly reduce errors on out-of-distribution systems, suggesting that MLFFs are capable of and can move towards modeling diverse chemical spaces, but are not being effectively trained to do so. Our experiments establish clear benchmarks for evaluating the generalization capabilities of the next generation of MLFFs. Our code is available at https://tkreiman.github.io/projects/mlff_distribution_shifts/.

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community.

Recent advances in fast sampling methods for diffusion models have demonstrated significant potential to accelerate generation on image modalities. We apply these methods to 3-dimensional molecular conformations by building on the recently introduced GeoLDM equivariant latent diffusion model (Xu et al., 2023). We evaluate trade-offs between speed gains and quality loss, as measured by molecular conformation structural stability. We introduce Equivariant Latent Progressive Distillation, a fast sampling algorithm that preserves geometric equivariance and accelerates generation from latent diffusion models. Our experiments demonstrate up to 7.5x gains in sampling speed with limited degradation in molecular stability. These results suggest this accelerated sampling method has strong potential for high-throughput in silico molecular conformations screening in computational biochemistry, drug discovery, and life sciences applications.

We present Symphony, an E(3)-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments. Existing autoregressive models such as G-SchNet and G-SphereNet for molecules utilize rotationally invariant features to respect the 3D symmetries of molecules. In contrast, Symphony uses message-passing with higher-degree E(3)-equivariant features. This allows a novel representation of probability distributions via spherical harmonic signals to efficiently model the 3D geometry of molecules. We show that Symphony is able to accurately generate small molecules from the QM9 dataset, outperforming existing autoregressive models and approaching the performance of diffusion models.

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions R^3, position and orientations R^3 {times} S^2, and the group SE(3) itself. Among these, R^3 {times} S^2 is an optimal choice due to the ability to represent directional information, which R^3 methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full SE(3) group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.

We introduce Suiren-1.0, a family of molecular foundation models for the accurate modeling of diverse organic systems. Suiren-1.0 comprising three specialized variants (Suiren-Base, Suiren-Dimer, and Suiren-ConfAvg) is integrated within an algorithmic framework that bridges the gap between 3D conformational geometry and 2D statistical ensemble spaces. We first pre-train Suiren-Base (1.8B parameters) on a 70M-sample Density Functional Theory dataset using spatial self-supervision and SE(3)-equivariant architectures, achieving robust performance in quantum property prediction. Suiren-Dimer extends this capability through continued pre-training on 13.5M intermolecular interaction samples. To enable efficient downstream application, we propose Conformation Compression Distillation (CCD), a diffusion-based framework that distills complex 3D structural representations into 2D conformation-averaged representations. This yields the lightweight Suiren-ConfAvg, which generates high-fidelity representations from SMILES or molecular graphs. Our extensive evaluations demonstrate that Suiren-1.0 establishes state-of-the-art results across a range of tasks. All models and benchmarks are open-sourced.

Diffusion models have shown impressive results in text-to-image synthesis. Using massive datasets of captioned images, diffusion models learn to generate raster images of highly diverse objects and scenes. However, designers frequently use vector representations of images like Scalable Vector Graphics (SVGs) for digital icons or art. Vector graphics can be scaled to any size, and are compact. We show that a text-conditioned diffusion model trained on pixel representations of images can be used to generate SVG-exportable vector graphics. We do so without access to large datasets of captioned SVGs. By optimizing a differentiable vector graphics rasterizer, our method, VectorFusion, distills abstract semantic knowledge out of a pretrained diffusion model. Inspired by recent text-to-3D work, we learn an SVG consistent with a caption using Score Distillation Sampling. To accelerate generation and improve fidelity, VectorFusion also initializes from an image sample. Experiments show greater quality than prior work, and demonstrate a range of styles including pixel art and sketches. See our project webpage at https://ajayj.com/vectorfusion .

SO(3)-equivariant networks are the dominant models for machine learning interatomic potentials (MLIPs). The key operation of such networks is the Clebsch-Gordan (CG) tensor product, which is computationally expensive. To accelerate the computation, we develop tensor decomposition networks (TDNs) as a class of approximately equivariant networks in which CG tensor products are replaced by low-rank tensor decompositions, such as the CANDECOMP/PARAFAC (CP) decomposition. With the CP decomposition, we prove (i) a uniform bound on the induced error of SO(3)-equivariance, and (ii) the universality of approximating any equivariant bilinear map. To further reduce the number of parameters, we propose path-weight sharing that ties all multiplicity-space weights across the O(L^3) CG paths into a single shared parameter set without compromising equivariance, where L is the maximum angular degree. The resulting layer acts as a plug-and-play replacement for tensor products in existing networks, and the computational complexity of tensor products is reduced from O(L^6) to O(L^4). We evaluate TDNs on PubChemQCR, a newly curated molecular relaxation dataset containing 105 million DFT-calculated snapshots. We also use existing datasets, including OC20, and OC22. Results show that TDNs achieve competitive performance with dramatic speedup in computations. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS/tree/main/OpenMol/TDN{https://github.com/divelab/AIRS/}).

Despite the widespread applications of machine learning force field (MLFF) on solids and small molecules, there is a notable gap in applying MLFF to complex liquid electrolytes. In this work, we introduce BAMBOO (ByteDance AI Molecular Simulation Booster), a novel framework for molecular dynamics (MD) simulations, with a demonstration of its capabilities in the context of liquid electrolytes for lithium batteries. We design a physics-inspired graph equivariant transformer architecture as the backbone of BAMBOO to learn from quantum mechanical simulations. Additionally, we pioneer an ensemble knowledge distillation approach and apply it on MLFFs to improve the stability of MD simulations. Finally, we propose the density alignment algorithm to align BAMBOO with experimental measurements. BAMBOO demonstrates state-of-the-art accuracy in predicting key electrolyte properties such as density, viscosity, and ionic conductivity across various solvents and salt combinations. Our current model, trained on more than 15 chemical species, achieves the average density error of 0.01 g/cm^3 on various compositions compared with experimental data. Moreover, our model demonstrates transferability to molecules not included in the quantum mechanical dataset. We envision this work as paving the way to a "universal MLFF" capable of simulating properties of common organic liquids.

Cancer is the second leading cause of death, with chemotherapy as one of the primary forms of treatment. As a result, researchers are turning to drug combination therapy to decrease drug resistance and increase efficacy. Current methods of drug combination screening, such as in vivo and in vitro, are inefficient due to stark time and monetary costs. In silico methods have become increasingly important for screening drugs, but current methods are inaccurate and generalize poorly to unseen anticancer drugs. In this paper, I employ a geometric deep-learning model utilizing a graph attention network that is equivariant to 3D rotations, translations, and reflections with structural motifs. Additionally, the gene expression of cancer cell lines is utilized to classify synergistic drug combinations specific to each cell line. I compared the proposed geometric deep learning framework to current state-of-the-art (SOTA) methods, and the proposed model architecture achieved greater performance on all 12 benchmark tasks performed on the DrugComb dataset. Specifically, the proposed framework outperformed other SOTA methods by an accuracy difference greater than 28%. Based on these results, I believe that the equivariant graph attention network's capability of learning geometric data accounts for the large performance improvements. The model's ability to generalize to foreign drugs is thought to be due to the structural motifs providing a better representation of the molecule. Overall, I believe that the proposed equivariant geometric deep learning framework serves as an effective tool for virtually screening anticancer drug combinations for further validation in a wet lab environment. The code for this work is made available online at: https://github.com/WeToTheMoon/EGAT_DrugSynergy.

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.

Processing information on 3D objects requires methods stable to rigid-body transformations, in particular rotations, of the input data. In image processing tasks, convolutional neural networks achieve this property using rotation-equivariant operations. However, contrary to images, graphs generally have irregular topology. This makes it challenging to define a rotation-equivariant convolution operation on these structures. In this work, we propose Spherical Graph Convolutional Network (S-GCN) that processes 3D models of proteins represented as molecular graphs. In a protein molecule, individual amino acids have common topological elements. This allows us to unambiguously associate each amino acid with a local coordinate system and construct rotation-equivariant spherical filters that operate on angular information between graph nodes. Within the framework of the protein model quality assessment problem, we demonstrate that the proposed spherical convolution method significantly improves the quality of model assessment compared to the standard message-passing approach. It is also comparable to state-of-the-art methods, as we demonstrate on Critical Assessment of Structure Prediction (CASP) benchmarks. The proposed technique operates only on geometric features of protein 3D models. This makes it universal and applicable to any other geometric-learning task where the graph structure allows constructing local coordinate systems.

Machine learning force fields (MLFFs) have revolutionized molecular simulations by providing quantum mechanical accuracy at the speed of molecular mechanical computations. However, a fundamental reliance of these models on fixed-cutoff architectures limits their applicability to macromolecular systems where long-range interactions dominate. We demonstrate that this locality constraint causes force prediction errors to scale monotonically with system size, revealing a critical architectural bottleneck. To overcome this, we establish the systematically designed MolLR25 ({Mol}ecules with {L}ong-{R}ange effect) benchmark up to 1200 atoms, generated using high-fidelity DFT, and introduce E2Former-LSR, an equivariant transformer that explicitly integrates long-range attention blocks. E2Former-LSR exhibits stable error scaling, achieves superior fidelity in capturing non-covalent decay, and maintains precision on complex protein conformations. Crucially, its efficient design provides up to 30% speedup compared to purely local models. This work validates the necessity of non-local architectures for generalizable MLFFs, enabling high-fidelity molecular dynamics for large-scale chemical and biological systems.

Scalable Vector Graphics (SVG) offer a powerful format for representing visual designs as interpretable code. Recent advances in vision-language models (VLMs) have enabled high-quality SVG generation by framing the problem as a code generation task and leveraging large-scale pretraining. VLMs are particularly suitable for this task as they capture both global semantics and fine-grained visual patterns, while transferring knowledge across vision, natural language, and code domains. However, existing VLM approaches often struggle to produce faithful and efficient SVGs because they never observe the rendered images during training. Although differentiable rendering for autoregressive SVG code generation remains unavailable, rendered outputs can still be compared to original inputs, enabling evaluative feedback suitable for reinforcement learning (RL). We introduce RLRF(Reinforcement Learning from Rendering Feedback), an RL method that enhances SVG generation in autoregressive VLMs by leveraging feedback from rendered SVG outputs. Given an input image, the model generates SVG roll-outs that are rendered and compared to the original image to compute a reward. This visual fidelity feedback guides the model toward producing more accurate, efficient, and semantically coherent SVGs. RLRF significantly outperforms supervised fine-tuning, addressing common failure modes and enabling precise, high-quality SVG generation with strong structural understanding and generalization.

Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using drug-like molecule datasets, which teaches A-GFNs about inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further implement a goal-conditioned finetuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on a subset of ZINC dataset, and by employing robust evaluation metrics we show the effectiveness of our approach when compared to other relevant baseline methods for a wide range of drug design tasks. The code is accessible at https://github.com/diamondspark/AGFN.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utilizing graph neural network (GNN) parametrizations, with rotational symmetries baked in via E(3) invariant layers. We prove that such models must necessarily disregard chirality, a geometric property of the molecules that cannot be superimposed on their mirror image by rotation and translation. Chirality plays a key role in determining drug safety and potency. To address this glaring issue, we introduce a novel field-based representation, proposing reference rotations that replace rotational symmetry constraints. The proposed model captures all molecular geometries including chirality, while still achieving highly competitive performance with E(3)-based methods across standard benchmarking metrics.

Unlike bitmap images, scalable vector graphics (SVG) maintain quality when scaled, frequently employed in computer vision and artistic design in the representation of SVG code. In this era of proliferating AI-powered systems, enabling AI to understand and generate SVG has become increasingly urgent. However, AI-driven SVG understanding and generation (U&G) remain significant challenges. SVG code, equivalent to a set of curves and lines controlled by floating-point parameters, demands high precision in SVG U&G. Besides, SVG generation operates under diverse conditional constraints, including textual prompts and visual references, which requires powerful multi-modal processing for condition-to-SVG transformation. Recently, the rapid growth of Multi-modal Large Language Models (MLLMs) have demonstrated capabilities to process multi-modal inputs and generate complex vector controlling parameters, suggesting the potential to address SVG U&G tasks within a unified model. To unlock MLLM's capabilities in the SVG area, we propose an SVG-centric dataset called UniSVG, comprising 525k data items, tailored for MLLM training and evaluation. To our best knowledge, it is the first comprehensive dataset designed for unified SVG generation (from textual prompts and images) and SVG understanding (color, category, usage, etc.). As expected, learning on the proposed dataset boosts open-source MLLMs' performance on various SVG U&G tasks, surpassing SOTA close-source MLLMs like GPT-4V. We release dataset, benchmark, weights, codes and experiment details on https://ryanlijinke.github.io/.

A creative idea is often born from transforming, combining, and modifying ideas from existing visual examples capturing various concepts. However, one cannot simply copy the concept as a whole, and inspiration is achieved by examining certain aspects of the concept. Hence, it is often necessary to separate a concept into different aspects to provide new perspectives. In this paper, we propose a method to decompose a visual concept, represented as a set of images, into different visual aspects encoded in a hierarchical tree structure. We utilize large vision-language models and their rich latent space for concept decomposition and generation. Each node in the tree represents a sub-concept using a learned vector embedding injected into the latent space of a pretrained text-to-image model. We use a set of regularizations to guide the optimization of the embedding vectors encoded in the nodes to follow the hierarchical structure of the tree. Our method allows to explore and discover new concepts derived from the original one. The tree provides the possibility of endless visual sampling at each node, allowing the user to explore the hidden sub-concepts of the object of interest. The learned aspects in each node can be combined within and across trees to create new visual ideas, and can be used in natural language sentences to apply such aspects to new designs.

As SE(3)-equivariant graph neural networks mature as a core tool for 3D atomistic modeling, improving their efficiency, expressivity, and physical consistency has become a central challenge for large-scale applications. In this work, we introduce EquiformerV3, the third generation of the SE(3)-equivariant graph attention Transformer, designed to advance all three dimensions: efficiency, expressivity, and generality. Building on EquiformerV2, we have the following three key advances. First, we optimize the software implementation, achieving 1.75times speedup. Second, we introduce simple and effective modifications to EquiformerV2, including equivariant merged layer normalization, improved feedforward network hyper-parameters, and attention with smooth radius cutoff. Third, we propose SwiGLU-S^2 activations to incorporate many-body interactions for better theoretical expressivity and to preserve strict equivariance while reducing the complexity of sampling S^2 grids. Together, SwiGLU-S^2 activations and smooth-cutoff attention enable accurate modeling of smoothly varying potential energy surfaces (PES), generalizing EquiformerV3 to tasks requiring energy-conserving simulations and higher-order derivatives of PES. With these improvements, EquiformerV3 trained with the auxiliary task of denoising non-equilibrium structures (DeNS) achieves state-of-the-art results on OC20, OMat24, and Matbench Discovery.

Recently, sophisticated deep learning-based approaches have been developed for generating efficient initial guesses to accelerate the convergence of density functional theory (DFT) calculations. While the actual initial guesses are often density matrices (DM), quantities that can convert into density matrices also qualify as alternative forms of initial guesses. Hence, existing works mostly rely on the prediction of the Hamiltonian matrix for obtaining high-quality initial guesses. However, the Hamiltonian matrix is both numerically difficult to predict and intrinsically non-transferable, hindering the application of such models in real scenarios. In light of this, we propose a method that constructs DFT initial guesses by predicting the electron density in a compact auxiliary basis representation using E(3)-equivariant neural networks. Trained on small molecules with up to 20 atoms, our model is able to achieve an average 33.3% self-consistent field (SCF) step reduction on systems up to 60 atoms, substantially outperforming Hamiltonian-centric and DM-centric models. Critically, this acceleration remains nearly constant with increasing system sizes and exhibits strong transferring behaviors across orbital basis sets and exchange-correlation (XC) functionals. To the best of our knowledge, this work represents the first and robust candidate for a universally transferable DFT acceleration method. We are also releasing the SCFbench dataset and its accompanying code to facilitate future research in this promising direction.

Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) Non-uniqueness: there are many different eigendecompositions of the same Laplacian, and (2) Instability: small perturbations to the Laplacian could result in completely different eigenspaces, leading to unpredictable changes in positional encoding. Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures. We identify the cause of instability to be a "hard partition" of eigenspaces. Hence, we introduce Stable and Expressive Positional Encodings (SPE), an architecture for processing eigenvectors that uses eigenvalues to "softly partition" eigenspaces. SPE is the first architecture that is (1) provably stable, and (2) universally expressive for basis invariant functions whilst respecting all symmetries of eigenvectors. Besides guaranteed stability, we prove that SPE is at least as expressive as existing methods, and highly capable of counting graph structures. Finally, we evaluate the effectiveness of our method on molecular property prediction, and out-of-distribution generalization tasks, finding improved generalization compared to existing positional encoding methods.

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making them well-suited for modeling complex molecular systems. In this work, we introduce EquiHGNN, an Equivariant HyperGraph Neural Network framework that integrates symmetry-aware representations to improve molecular modeling. By enforcing the equivariance under relevant transformation groups, our approach preserves geometric and topological properties, leading to more robust and physically meaningful representations. We examine a range of equivariant architectures and demonstrate that integrating symmetry constraints leads to notable performance gains on large-scale molecular datasets. Experiments on both small and large molecules show that high-order interactions offer limited benefits for small molecules but consistently outperform 2D graphs on larger ones. Adding geometric features to these high-order structures further improves the performance, emphasizing the value of spatial information in molecular learning. Our source code is available at https://github.com/HySonLab/EquiHGNN/

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

With the popularity of multimodal techniques, it receives growing interests to acquire useful information in visual forms. In this work, we formally define an emerging IR paradigm called Visualized Information Retrieval, or Vis-IR, where multimodal information, such as texts, images, tables and charts, is jointly represented by a unified visual format called Screenshots, for various retrieval applications. We further make three key contributions for Vis-IR. First, we create VIRA (Vis-IR Aggregation), a large-scale dataset comprising a vast collection of screenshots from diverse sources, carefully curated into captioned and question-answer formats. Second, we develop UniSE (Universal Screenshot Embeddings), a family of retrieval models that enable screenshots to query or be queried across arbitrary data modalities. Finally, we construct MVRB (Massive Visualized IR Benchmark), a comprehensive benchmark covering a variety of task forms and application scenarios. Through extensive evaluations on MVRB, we highlight the deficiency from existing multimodal retrievers and the substantial improvements made by UniSE. Our work will be shared with the community, laying a solid foundation for this emerging field.

We present VecFusion, a new neural architecture that can generate vector fonts with varying topological structures and precise control point positions. Our approach is a cascaded diffusion model which consists of a raster diffusion model followed by a vector diffusion model. The raster model generates low-resolution, rasterized fonts with auxiliary control point information, capturing the global style and shape of the font, while the vector model synthesizes vector fonts conditioned on the low-resolution raster fonts from the first stage. To synthesize long and complex curves, our vector diffusion model uses a transformer architecture and a novel vector representation that enables the modeling of diverse vector geometry and the precise prediction of control points. Our experiments show that, in contrast to previous generative models for vector graphics, our new cascaded vector diffusion model generates higher quality vector fonts, with complex structures and diverse styles.

Machine learning techniques are essential tools to compute efficient, yet accurate, force fields for atomistic simulations. This approach has recently been extended to incorporate quantum computational methods, making use of variational quantum learning models to predict potential energy surfaces and atomic forces from ab initio training data. However, the trainability and scalability of such models are still limited, due to both theoretical and practical barriers. Inspired by recent developments in geometric classical and quantum machine learning, here we design quantum neural networks that explicitly incorporate, as a data-inspired prior, an extensive set of physically relevant symmetries. We find that our invariant quantum learning models outperform their more generic counterparts on individual molecules of growing complexity. Furthermore, we study a water dimer as a minimal example of a system with multiple components, showcasing the versatility of our proposed approach and opening the way towards larger simulations. Our results suggest that molecular force fields generation can significantly profit from leveraging the framework of geometric quantum machine learning, and that chemical systems represent, in fact, an interesting and rich playground for the development and application of advanced quantum machine learning tools.

Real-valued functions on geometric data -- such as node attributes on a graph -- can be optimized using descriptors from persistent homology, allowing the user to incorporate topological terms in the loss function. When optimizing a single real-valued function (the one-parameter setting), there is a canonical choice of descriptor for persistent homology: the barcode. The operation mapping a real-valued function to its barcode is differentiable almost everywhere, and the convergence of gradient descent for losses using barcodes is relatively well understood. When optimizing a vector-valued function (the multiparameter setting), there is no unique choice of descriptor for multiparameter persistent homology, and many distinct descriptors have been proposed. This calls for the development of a general framework for differentiability and optimization that applies to a wide range of multiparameter homological descriptors. In this article, we develop such a framework and show that it encompasses well-known descriptors of different flavors, such as signed barcodes and the multiparameter persistence landscape. We complement the theory with numerical experiments supporting the idea that optimizing multiparameter homological descriptors can lead to improved performances compared to optimizing one-parameter descriptors, even when using the simplest and most efficiently computable multiparameter descriptors.

Graph neural networks that model 3D data, such as point clouds or atoms, are typically desired to be SO(3) equivariant, i.e., equivariant to 3D rotations. Unfortunately equivariant convolutions, which are a fundamental operation for equivariant networks, increase significantly in computational complexity as higher-order tensors are used. In this paper, we address this issue by reducing the SO(3) convolutions or tensor products to mathematically equivalent convolutions in SO(2) . This is accomplished by aligning the node embeddings' primary axis with the edge vectors, which sparsifies the tensor product and reduces the computational complexity from O(L^6) to O(L^3), where L is the degree of the representation. We demonstrate the potential implications of this improvement by proposing the Equivariant Spherical Channel Network (eSCN), a graph neural network utilizing our novel approach to equivariant convolutions, which achieves state-of-the-art results on the large-scale OC-20 and OC-22 datasets.

Liquid electrolytes are critical components of next-generation energy storage systems, enabling fast ion transport, minimizing interfacial resistance, and ensuring electrochemical stability for long-term battery performance. However, measuring electrolyte properties and designing formulations remain experimentally and computationally expensive. In this work, we present a unified framework for designing liquid electrolyte formulation, integrating a forward predictive model with an inverse generative approach. Leveraging both computational and experimental data collected from literature and extensive molecular simulations, we train a predictive model capable of accurately estimating electrolyte properties from ionic conductivity to solvation structure. Our physics-informed architecture preserves permutation invariance and incorporates empirical dependencies on temperature and salt concentration, making it broadly applicable to property prediction tasks across molecular mixtures. Furthermore, we introduce -- to the best of our knowledge -- the first generative machine learning framework for molecular mixture design, demonstrated on electrolyte systems. This framework supports multi-condition-constrained generation, addressing the inherently multi-objective nature of materials design. As a proof of concept, we experimentally identified three liquid electrolytes with both high ionic conductivity and anion-concentrated solvation structure. This unified framework advances data-driven electrolyte design and can be readily extended to other complex chemical systems beyond electrolytes.

Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to efficiently navigate chemical space. Scientific foundation models trained on large unlabeled datasets offer a path toward exploring chemical space across diverse application domains. Here we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenization scheme that comprehensively captures nuclear, electronic, and geometric information, MIST learns from a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure -- property relationships and match or exceed state-of-the-art performance across benchmarks spanning physiology, electrochemistry, and quantum chemistry. We demonstrate the ability of these models to solve real-world problems across chemical space, including multiobjective electrolyte solvent screening, olfactory perception mapping, isotope half-life prediction, stereochemical reasoning for chiral organometallic compounds, and binary and multi-component mixture property prediction. Probing MIST models using mechanistic interpretability methods reveals identifiable patterns and trends not explicitly present in the training data, suggesting that the models learn generalizable scientific concepts. We formulate hyperparameter-penalized Bayesian neural scaling laws and use them to reduce the computational cost of model development by an order of magnitude. The methods and findings presented here represent a significant step toward accelerating materials discovery, design, and optimization using foundation models and provide valuable guidance for training compute-optimal scientific foundation models.

Predicting physical properties of materials from their crystal structures is a fundamental problem in materials science. In peripheral areas such as the prediction of molecular properties, fully connected attention networks have been shown to be successful. However, unlike these finite atom arrangements, crystal structures are infinitely repeating, periodic arrangements of atoms, whose fully connected attention results in infinitely connected attention. In this work, we show that this infinitely connected attention can lead to a computationally tractable formulation, interpreted as neural potential summation, that performs infinite interatomic potential summations in a deeply learned feature space. We then propose a simple yet effective Transformer-based encoder architecture for crystal structures called Crystalformer. Compared to an existing Transformer-based model, the proposed model requires only 29.4% of the number of parameters, with minimal modifications to the original Transformer architecture. Despite the architectural simplicity, the proposed method outperforms state-of-the-art methods for various property regression tasks on the Materials Project and JARVIS-DFT datasets.

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost--driven by high-order tensor product (TP) operations--restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network, that incorporates adaptive SParsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70%. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact. Our code can be found at https://github.com/microsoft/SPHNet.

Generative machine learning models can potentially provide direct access to novel and relevant portions of the full chemical space, overcoming the cost of systematic sampling. However, the training of these models generally requires a large amount of data, often precluding the use of expensive high-level ab initio simulations for this task. The generation of coordination compounds of Dy with large magnetic anisotropy represents a topical example, where multireference simulations of large molecules are necessary to perform reliable predictions. Here, we show that a semi-supervised chemically-inspired training-by-proxy of generative variational autoencoders can reduce the cost associated with building a training set from multireference simulations by two orders of magnitude. We illustrate the power of this approach by generating 100s of new organic ligands for Dy(III) pentagonal bipyramidal complexes exhibiting record values of magnetic anisotropy, while starting from datasets as small as 1k multireference calculations. This work thus paves the way to the computational generation of molecules as complex coordination compounds with target electronic and magnetic properties.

High-quality molecular representations are essential for property prediction and molecular design, yet large labeled datasets remain scarce. While self-supervised pretraining on molecular graphs has shown promise, many existing approaches either depend on hand-crafted augmentations or complex generative objectives, and often rely solely on 2D topology, leaving valuable 3D structural information underutilized. To address this gap, we introduce C-FREE (Contrast-Free Representation learning on Ego-nets), a simple framework that integrates 2D graphs with ensembles of 3D conformers. C-FREE learns molecular representations by predicting subgraph embeddings from their complementary neighborhoods in the latent space, using fixed-radius ego-nets as modeling units across different conformers. This design allows us to integrate both geometric and topological information within a hybrid Graph Neural Network (GNN)-Transformer backbone, without negatives, positional encodings, or expensive pre-processing. Pretraining on the GEOM dataset, which provides rich 3D conformational diversity, C-FREE achieves state-of-the-art results on MoleculeNet, surpassing contrastive, generative, and other multimodal self-supervised methods. Fine-tuning across datasets with diverse sizes and molecule types further demonstrates that pretraining transfers effectively to new chemical domains, highlighting the importance of 3D-informed molecular representations.

Equivariant Transformers such as Equiformer have demonstrated the efficacy of applying Transformers to the domain of 3D atomistic systems. However, they are still limited to small degrees of equivariant representations due to their computational complexity. In this paper, we investigate whether these architectures can scale well to higher degrees. Starting from Equiformer, we first replace SO(3) convolutions with eSCN convolutions to efficiently incorporate higher-degree tensors. Then, to better leverage the power of higher degrees, we propose three architectural improvements -- attention re-normalization, separable S^2 activation and separable layer normalization. Putting this all together, we propose EquiformerV2, which outperforms previous state-of-the-art methods on the large-scale OC20 dataset by up to 12% on forces, 4% on energies, offers better speed-accuracy trade-offs, and 2times reduction in DFT calculations needed for computing adsorption energies.

Scalable Vector Graphics (SVG) are central to digital design due to their inherent scalability and editability. Despite significant advancements in content generation enabled by Visual Language Models (VLMs), existing text-to-SVG generation methods are limited by a core challenge: the autoregressive training process does not incorporate visual perception of the final rendered image, which fundamentally constrains generation quality. To address this limitation, we propose an Introspective SVG Generation Framework (IntroSVG). At its core, the framework instantiates a unified VLM that operates in a closed loop, assuming dual roles of both generator and critic. Specifically, through Supervised Fine-Tuning (SFT), the model learns to draft SVGs and to provide feedback on their rendered outputs; moreover, we systematically convert early-stage failures into high-quality error-correction training data, thereby enhancing model robustness. Subsequently, we leverage a high-capacity teacher VLM to construct a preference dataset and further align the generator's policy through Direct Preference Optimization (DPO). During inference, the optimized generator and critic operate collaboratively in an iterative "generate-review-refine" cycle, starting from imperfect intermediate drafts to autonomously improve output quality. Experimental results demonstrate that our method achieves state-of-the-art performance across several key evaluation metrics, generating SVGs with more complex structures, stronger semantic alignment, and greater editability. These results corroborate the effectiveness of incorporating explicit visual feedback into the generation loop.

Creating fast and accurate force fields is a long-standing challenge in computational chemistry and materials science. Recently, several equivariant message passing neural networks (MPNNs) have been shown to outperform models built using other approaches in terms of accuracy. However, most MPNNs suffer from high computational cost and poor scalability. We propose that these limitations arise because MPNNs only pass two-body messages leading to a direct relationship between the number of layers and the expressivity of the network. In this work, we introduce MACE, a new equivariant MPNN model that uses higher body order messages. In particular, we show that using four-body messages reduces the required number of message passing iterations to just two, resulting in a fast and highly parallelizable model, reaching or exceeding state-of-the-art accuracy on the rMD17, 3BPA, and AcAc benchmark tasks. We also demonstrate that using higher order messages leads to an improved steepness of the learning curves.

We introduce VIRES, a video instance repainting method with sketch and text guidance, enabling video instance repainting, replacement, generation, and removal. Existing approaches struggle with temporal consistency and accurate alignment with the provided sketch sequence. VIRES leverages the generative priors of text-to-video models to maintain temporal consistency and produce visually pleasing results. We propose the Sequential ControlNet with the standardized self-scaling, which effectively extracts structure layouts and adaptively captures high-contrast sketch details. We further augment the diffusion transformer backbone with the sketch attention to interpret and inject fine-grained sketch semantics. A sketch-aware encoder ensures that repainted results are aligned with the provided sketch sequence. Additionally, we contribute the VireSet, a dataset with detailed annotations tailored for training and evaluating video instance editing methods. Experimental results demonstrate the effectiveness of VIRES, which outperforms state-of-the-art methods in visual quality, temporal consistency, condition alignment, and human ratings. Project page:https://suimuc.github.io/suimu.github.io/projects/VIRES/

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on conformer ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D molecular representation learning models, along with two strategies that explicitly incorporate conformer ensembles into 3D MRL models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.

The generation of Scalable Vector Graphics (SVG) assets from textual data remains a significant challenge, largely due to the scarcity of high-quality vector datasets and the limitations in scalable vector representations required for modeling intricate graphic distributions. This work introduces SVGFusion, a Text-to-SVG model capable of scaling to real-world SVG data without reliance on a text-based discrete language model or prolonged SDS optimization. The essence of SVGFusion is to learn a continuous latent space for vector graphics with a popular Text-to-Image framework. Specifically, SVGFusion consists of two modules: a Vector-Pixel Fusion Variational Autoencoder (VP-VAE) and a Vector Space Diffusion Transformer (VS-DiT). VP-VAE takes both the SVGs and corresponding rasterizations as inputs and learns a continuous latent space, whereas VS-DiT learns to generate a latent code within this space based on the text prompt. Based on VP-VAE, a novel rendering sequence modeling strategy is proposed to enable the latent space to embed the knowledge of construction logics in SVGs. This empowers the model to achieve human-like design capabilities in vector graphics, while systematically preventing occlusion in complex graphic compositions. Moreover, our SVGFusion's ability can be continuously improved by leveraging the scalability of the VS-DiT by adding more VS-DiT blocks. A large-scale SVG dataset is collected to evaluate the effectiveness of our proposed method. Extensive experimentation has confirmed the superiority of our SVGFusion over existing SVG generation methods, achieving enhanced quality and generalizability, thereby establishing a novel framework for SVG content creation. Code, model, and data will be released at: https://ximinng.github.io/SVGFusionProject/{https://ximinng.github.io/SVGFusionProject/}

Topological Neural Networks (TNNs) incorporate higher-order relational information beyond pairwise interactions, enabling richer representations than Graph Neural Networks (GNNs). Concurrently, topological descriptors based on persistent homology (PH) are being increasingly employed to augment the GNNs. We investigate the benefits of integrating these two paradigms. Specifically, we introduce TopNets as a broad framework that subsumes and unifies various methods in the intersection of GNNs/TNNs and PH such as (generalizations of) RePHINE and TOGL. TopNets can also be readily adapted to handle (symmetries in) geometric complexes, extending the scope of TNNs and PH to spatial settings. Theoretically, we show that PH descriptors can provably enhance the expressivity of simplicial message-passing networks. Empirically, (continuous and E(n)-equivariant extensions of) TopNets achieve strong performance across diverse tasks, including antibody design, molecular dynamics simulation, and drug property prediction.

The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the observation of their conformational changes in real time. The innovative liquid-phase electron microscopy (liquid-phase EM) technique allows molecules to be placed in the native liquid environment, providing a unique opportunity to observe their dynamics. In this paper, we propose TEMPOR, a Temporal Electron MicroscoPy Object Reconstruction algorithm for liquid-phase EM that leverages an implicit neural representation (INR) and a dynamical variational auto-encoder (DVAE) to recover time series of molecular structures. We demonstrate its advantages in recovering different motion dynamics from two simulated datasets, 7bcq and Cas9. To our knowledge, our work is the first attempt to directly recover 3D structures of a temporally-varying particle from liquid-phase EM movies. It provides a promising new approach for studying molecules' 3D dynamics in structural biology.

We report an accurate study of interactions between Benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory (DFT) using different van der Waals (vdW) functionals. In our QMC calculations, we use accurate correlated trial wave functions including three-body Jastrow factors, and backflow transformations. We consider two benzene molecules in the parallel displaced (PD) geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the CCSD(T)/CBS limit is -2.65(2) kcal/mol [E. Miliordos et al, J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their widespread adoption in the biomolecular domain has been limited by a lack of either systematic performance benchmarks or a unified toolkit for interacting with molecular data. To address this, we present ATOM3D, a collection of both novel and existing benchmark datasets spanning several key classes of biomolecules. We implement several classes of three-dimensional molecular learning methods for each of these tasks and show that they consistently improve performance relative to methods based on one- and two-dimensional representations. The specific choice of architecture proves to be critical for performance, with three-dimensional convolutional networks excelling at tasks involving complex geometries, graph networks performing well on systems requiring detailed positional information, and the more recently developed equivariant networks showing significant promise. Our results indicate that many molecular problems stand to gain from three-dimensional molecular learning, and that there is potential for improvement on many tasks which remain underexplored. To lower the barrier to entry and facilitate further developments in the field, we also provide a comprehensive suite of tools for dataset processing, model training, and evaluation in our open-source atom3d Python package. All datasets are available for download from https://www.atom3d.ai .

Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design. Inspired by the recent huge success of Stable (latent) Diffusion models, we propose a novel and principled method for 3D molecule generation named Geometric Latent Diffusion Models (GeoLDM). GeoLDM is the first latent DM model for the molecular geometry domain, composed of autoencoders encoding structures into continuous latent codes and DMs operating in the latent space. Our key innovation is that for modeling the 3D molecular geometries, we capture its critical roto-translational equivariance constraints by building a point-structured latent space with both invariant scalars and equivariant tensors. Extensive experiments demonstrate that GeoLDM can consistently achieve better performance on multiple molecule generation benchmarks, with up to 7\% improvement for the valid percentage of large biomolecules. Results also demonstrate GeoLDM's higher capacity for controllable generation thanks to the latent modeling. Code is provided at https://github.com/MinkaiXu/GeoLDM.

Equivariant Graph Neural Networks (EGNNs) have become a widely used approach for modeling 3D atomistic systems. However, mainstream architectures face critical scalability bottlenecks due to the explicit construction of geometric features or dense tensor products on every edge. To overcome this, we introduce E2Former-V2, a scalable architecture that integrates algebraic sparsity with hardware-aware execution. We first propose Equivariant Axis-Aligned Sparsification (EAAS). EAAS builds on Wigner-6j convolution by exploiting an SO(3) rightarrow SO(2) change of basis to transform computationally expensive dense tensor contractions into efficient, sparse parity re-indexing operations. Building on this representation, we introduce On-the-Fly Equivariant Attention, a fully node-centric mechanism implemented via a custom fused Triton kernel. By eliminating materialized edge tensors and maximizing SRAM utilization, our kernel achieves a 20times improvement in TFLOPS compared to standard implementations. Extensive experiments on the SPICE and OMol25 datasets demonstrate that E2Former-V2 maintains comparable predictive performance while notably accelerating inference. This work demonstrates that large equivariant transformers can be trained efficiently using widely accessible GPU platforms. The code is avalible at https://github.com/IQuestLab/UBio-MolFM/tree/e2formerv2.

Generative AI has matured to a point where large-scale models can generate text that seems indistinguishable from human-written text and remarkably photorealistic images. Automatically measuring how close the distribution of generated data is to the target real data distribution is a key step in diagnosing existing models and developing better models. We present MAUVE, a family of comparison measures between pairs of distributions such as those encountered in the generative modeling of text or images. These scores are statistical summaries of divergence frontiers capturing two types of errors in generative modeling. We explore four approaches to statistically estimate these scores: vector quantization, non-parametric estimation, classifier-based estimation, and parametric Gaussian approximations. We provide statistical bounds for the vector quantization approach. Empirically, we find that the proposed scores paired with a range of f-divergences and statistical estimation methods can quantify the gaps between the distributions of human-written text and those of modern neural language models by correlating with human judgments and identifying known properties of the generated texts. We conclude the paper by demonstrating its applications to other AI domains and discussing practical recommendations.

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

Existing visual parsers for molecule diagrams translate pixel-based raster images such as PNGs to chemical structure representations (e.g., SMILES). However, PDFs created by word processors including LaTeX and Word provide explicit locations and shapes for characters, lines, and polygons. We extract symbols from born-digital PDF molecule images and then apply simple graph transformations to capture both visual and chemical structure in editable ChemDraw files (CDXML). Our fast ( PDF rightarrow visual graph rightarrow chemical graph ) pipeline does not require GPUs, Optical Character Recognition (OCR) or vectorization. We evaluate on standard benchmarks using SMILES strings, along with a novel evaluation that provides graph-based metrics and error compilation using LgEval. The geometric information in born-digital PDFs produces a highly accurate parser, motivating generating training data for visual parsers that recognize from raster images, with extracted graphics, visual structure, and chemical structure as annotations. To do this we render SMILES strings in Indigo, parse molecule structure, and then validate recognized structure to select correct files.

GNNs and chemical fingerprints are the predominant approaches to representing molecules for property prediction. However, in NLP, transformers have become the de-facto standard for representation learning thanks to their strong downstream task transfer. In parallel, the software ecosystem around transformers is maturing rapidly, with libraries like HuggingFace and BertViz enabling streamlined training and introspection. In this work, we make one of the first attempts to systematically evaluate transformers on molecular property prediction tasks via our ChemBERTa model. ChemBERTa scales well with pretraining dataset size, offering competitive downstream performance on MoleculeNet and useful attention-based visualization modalities. Our results suggest that transformers offer a promising avenue of future work for molecular representation learning and property prediction. To facilitate these efforts, we release a curated dataset of 77M SMILES from PubChem suitable for large-scale self-supervised pretraining.

Recent neural network-based wave functions have achieved state-of-the-art accuracies in modeling ab-initio ground-state potential energy surface. However, these networks can only solve different spatial arrangements of the same set of atoms. To overcome this limitation, we present Graph-learned orbital embeddings (Globe), a neural network-based reparametrization method that can adapt neural wave functions to different molecules. Globe learns representations of local electronic structures that generalize across molecules via spatial message passing by connecting molecular orbitals to covalent bonds. Further, we propose a size-consistent wave function Ansatz, the Molecular orbital network (Moon), tailored to jointly solve Schr\"odinger equations of different molecules. In our experiments, we find Moon converging in 4.5 times fewer steps to similar accuracy as previous methods or to lower energies given the same time. Further, our analysis shows that Moon's energy estimate scales additively with increased system sizes, unlike previous work where we observe divergence. In both computational chemistry and machine learning, we are the first to demonstrate that a single wave function can solve the Schr\"odinger equation of molecules with different atoms jointly.

Training native 3D texture generative models remains a fundamental yet challenging problem, largely due to the limited availability of large-scale, high-quality 3D texture datasets. This scarcity hinders generalization to real-world scenarios. To address this, most existing methods finetune foundation image generative models to exploit their learned visual priors. However, these approaches typically generate only multi-view images and rely on post-processing to produce UV texture maps -- an essential representation in modern graphics pipelines. Such two-stage pipelines often suffer from error accumulation and spatial inconsistencies across the 3D surface. In this paper, we introduce SeqTex, a novel end-to-end framework that leverages the visual knowledge encoded in pretrained video foundation models to directly generate complete UV texture maps. Unlike previous methods that model the distribution of UV textures in isolation, SeqTex reformulates the task as a sequence generation problem, enabling the model to learn the joint distribution of multi-view renderings and UV textures. This design effectively transfers the consistent image-space priors from video foundation models into the UV domain. To further enhance performance, we propose several architectural innovations: a decoupled multi-view and UV branch design, geometry-informed attention to guide cross-domain feature alignment, and adaptive token resolution to preserve fine texture details while maintaining computational efficiency. Together, these components allow SeqTex to fully utilize pretrained video priors and synthesize high-fidelity UV texture maps without the need for post-processing. Extensive experiments show that SeqTex achieves state-of-the-art performance on both image-conditioned and text-conditioned 3D texture generation tasks, with superior 3D consistency, texture-geometry alignment, and real-world generalization.

In the realm of vision models, the primary mode of representation is using pixels to rasterize the visual world. Yet this is not always the best or unique way to represent visual content, especially for designers and artists who depict the world using geometry primitives such as polygons. Vector graphics (VG), on the other hand, offer a textual representation of visual content, which can be more concise and powerful for content like cartoons or sketches. Recent studies have shown promising results on processing vector graphics with capable Large Language Models (LLMs). However, such works focus solely on qualitative results, understanding, or a specific type of vector graphics. We propose VGBench, a comprehensive benchmark for LLMs on handling vector graphics through diverse aspects, including (a) both visual understanding and generation, (b) evaluation of various vector graphics formats, (c) diverse question types, (d) wide range of prompting techniques, (e) under multiple LLMs. Evaluating on our collected 4279 understanding and 5845 generation samples, we find that LLMs show strong capability on both aspects while exhibiting less desirable performance on low-level formats (SVG). Both data and evaluation pipeline will be open-sourced at https://vgbench.github.io.

Machine learning potentials (MLPs) trained on accurate quantum chemical data can retain the high accuracy, while inflicting little computational demands. On the downside, they need to be trained for each individual system. In recent years, a vast number of MLPs has been trained from scratch because learning additional data typically requires to train again on all data to not forget previously acquired knowledge. Additionally, most common structural descriptors of MLPs cannot represent efficiently a large number of different chemical elements. In this work, we tackle these problems by introducing element-embracing atom-centered symmetry functions (eeACSFs) which combine structural properties and element information from the periodic table. These eeACSFs are a key for our development of a lifelong machine learning potential (lMLP). Uncertainty quantification can be exploited to transgress a fixed, pre-trained MLP to arrive at a continuously adapting lMLP, because a predefined level of accuracy can be ensured. To extend the applicability of an lMLP to new systems, we apply continual learning strategies to enable autonomous and on-the-fly training on a continuous stream of new data. For the training of deep neural networks, we propose the continual resilient (CoRe) optimizer and incremental learning strategies relying on rehearsal of data, regularization of parameters, and the architecture of the model.

Accurate prediction of bond dissociation energies (BDEs) underpins mechanistic insight and the rational design of molecules and materials. We present a systematic, reproducible benchmark comparing quantum and classical machine learning models for BDE prediction using a chemically curated feature set encompassing atomic properties (atomic numbers, hybridization), bond characteristics (bond order, type), and local environmental descriptors. Our quantum framework, implemented in Qiskit Aer on six qubits, employs ZZFeatureMap encodings with variational ansatz (RealAmplitudes) across multiple architectures Variational Quantum Regressors (VQR), Quantum Support Vector Regressors (QSVR), Quantum Neural Networks (QNN), Quantum Convolutional Neural Networks (QCNN), and Quantum Random Forests (QRF). These are rigorously benchmarked against strong classical baselines, including Support Vector Regression (SVR), Random Forests (RF), and Multi-Layer Perceptrons (MLP). Comprehensive evaluation spanning absolute and relative error metrics, threshold accuracies, and error distributions shows that top-performing quantum models (QCNN, QRF) match the predictive accuracy and robustness of classical ensembles and deep networks, particularly within the chemically prevalent mid-range BDE regime. These findings establish a transparent baseline for quantum-enhanced molecular property prediction and outline a practical foundation for advancing quantum computational chemistry toward near chemical accuracy.

We consider the prediction of the Hamiltonian matrix, which finds use in quantum chemistry and condensed matter physics. Efficiency and equivariance are two important, but conflicting factors. In this work, we propose a SE(3)-equivariant network, named QHNet, that achieves efficiency and equivariance. Our key advance lies at the innovative design of QHNet architecture, which not only obeys the underlying symmetries, but also enables the reduction of number of tensor products by 92\%. In addition, QHNet prevents the exponential growth of channel dimension when more atom types are involved. We perform experiments on MD17 datasets, including four molecular systems. Experimental results show that our QHNet can achieve comparable performance to the state of the art methods at a significantly faster speed. Besides, our QHNet consumes 50\% less memory due to its streamlined architecture. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Group equivariant neural networks are used as building blocks of group invariant neural networks, which have been shown to improve generalisation performance and data efficiency through principled parameter sharing. Such works have mostly focused on group equivariant convolutions, building on the result that group equivariant linear maps are necessarily convolutions. In this work, we extend the scope of the literature to self-attention, that is emerging as a prominent building block of deep learning models. We propose the LieTransformer, an architecture composed of LieSelfAttention layers that are equivariant to arbitrary Lie groups and their discrete subgroups. We demonstrate the generality of our approach by showing experimental results that are competitive to baseline methods on a wide range of tasks: shape counting on point clouds, molecular property regression and modelling particle trajectories under Hamiltonian dynamics.

Vector Symbolic Architectures (VSAs) give a way to represent a complex object as a single fixed-length vector, so that similar objects have similar vector representations. These vector representations then become easy to use for machine learning or nearest-neighbor search. We review a previously proposed VSA method, MBAT (Matrix Binding of Additive Terms), which uses multiplication by random matrices for binding related terms. However, multiplying by such matrices introduces instabilities which can harm performance. Making the random matrices be orthogonal matrices provably fixes this problem. With respect to larger scale applications, we see how to apply MBAT vector representations for any data expressed in JSON. JSON is used in numerous programming languages to express complex data, but its native format appears highly unsuited for machine learning. Expressing JSON as a fixed-length vector makes it readily usable for machine learning and nearest-neighbor search. Creating such JSON vectors also shows that a VSA needs to employ binding operations that are non-commutative. VSAs are now ready to try with full-scale practical applications, including healthcare, pharmaceuticals, and genomics. Keywords: MBAT (Matrix Binding of Additive Terms), VSA (Vector Symbolic Architecture), HDC (Hyperdimensional Computing), Distributed Representations, Binding, Orthogonal Matrices, Recurrent Connections, Machine Learning, Search, JSON, VSA Applications

Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.