Daily Papers

We provide the first exploration of sentence embeddings from text-to-text transformers (T5). Sentence embeddings are broadly useful for language processing tasks. While T5 achieves impressive performance on language tasks cast as sequence-to-sequence mapping problems, it is unclear how to produce sentence embeddings from encoder-decoder models. We investigate three methods for extracting T5 sentence embeddings: two utilize only the T5 encoder and one uses the full T5 encoder-decoder model. To support our investigation, we establish a new sentence representation transfer benchmark, SentGLUE, which extends the SentEval toolkit to nine tasks from the GLUE benchmark. Our encoder-only models outperforms Sentence-BERT and SimCSE sentence embeddings on both SentEval and SentGLUE transfer tasks, including semantic textual similarity (STS). Scaling up T5 from millions to billions of parameters is found to produce consistent further improvements. Finally, our encoder-decoder method achieves a new state-of-the-art on STS when using sentence embeddings. Our models are released at https://tfhub.dev/google/collections/sentence-t5/1.

Attention is a key part of the transformer architecture. It is a sequence-to-sequence mapping that transforms each sequence element into a weighted sum of values. The weights are typically obtained as the softmax of dot products between keys and queries. Recent work has explored alternatives to softmax attention in transformers, such as ReLU and sigmoid activations. In this work, we revisit sigmoid attention and conduct an in-depth theoretical and empirical analysis. Theoretically, we prove that transformers with sigmoid attention are universal function approximators and benefit from improved regularity compared to softmax attention. Through detailed empirical analysis, we identify stabilization of large initial attention norms during the early stages of training as a crucial factor for the successful training of models with sigmoid attention, outperforming prior attempts. We also introduce FLASHSIGMOID, a hardware-aware and memory-efficient implementation of sigmoid attention yielding a 17% inference kernel speed-up over FLASHATTENTION2 on H100 GPUs. Experiments across language, vision, and speech show that properly normalized sigmoid attention matches the strong performance of softmax attention on a wide range of domains and scales, which previous attempts at sigmoid attention were unable to fully achieve. Our work unifies prior art and establishes best practices for sigmoid attention as a drop-in softmax replacement in transformers.

In this note (work in progress towards a full-length paper) we show that a family of sequence models based on recurrent linear layers~(including S4, S5, and the LRU) interleaved with position-wise multi-layer perceptrons~(MLPs) can approximate arbitrarily well any sufficiently regular non-linear sequence-to-sequence map. The main idea behind our result is to see recurrent layers as compression algorithms that can faithfully store information about the input sequence into an inner state, before it is processed by the highly expressive MLP.

Deep learning employs multi-layer neural networks trained via the backpropagation algorithm. This approach has achieved success across many domains and relies on adaptive gradient methods such as the Adam optimizer. Sequence modeling evolved from recurrent neural networks to attention-based models, culminating in the Transformer architecture. Transformers have achieved state-of-the-art performance in natural language processing (for example, BERT and GPT-3) and have been applied in computer vision and computational biology. However, theoretical understanding of these models remains limited. In this paper, we examine the mathematical foundations of deep learning and Transformers and present a novel theoretical result. We review key concepts from linear algebra, probability, and optimization that underpin deep learning, and we analyze the multi-head self-attention mechanism and the backpropagation algorithm in detail. Our main contribution is a universal approximation theorem for Transformers: we prove that a single-layer Transformer, comprising one self-attention layer followed by a position-wise feed-forward network with ReLU activation, can approximate any continuous sequence-to-sequence mapping on a compact domain to arbitrary precision. We provide a formal statement and a complete proof. Finally, we present case studies that demonstrate the practical implications of this result. Our findings advance the theoretical understanding of Transformer models and help bridge the gap between theory and practice.

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

Neural sequence-to-sequence models provide a competitive approach to the task of mapping a question in natural language to an SQL query, also referred to as text-to-SQL generation. The Byte-Pair Encoding algorithm (BPE) has previously been used to improve machine translation (MT) between natural languages. In this work, we adapt BPE for text-to-SQL generation. As the datasets for this task are rather small compared to MT, we present a novel stopping criterion that prevents overfitting the BPE encoding to the training set. Additionally, we present AST BPE, which is a version of BPE that uses the Abstract Syntax Tree (AST) of the SQL statement to guide BPE merges and therefore produce BPE encodings that generalize better. We improved the accuracy of a strong attentive seq2seq baseline on five out of six English text-to-SQL tasks while reducing training time by more than 50% on four of them due to the shortened targets. Finally, on two of these tasks we exceeded previously reported accuracies.

In open-domain dialogue intelligent agents should exhibit the use of knowledge, however there are few convincing demonstrations of this to date. The most popular sequence to sequence models typically "generate and hope" generic utterances that can be memorized in the weights of the model when mapping from input utterance(s) to output, rather than employing recalled knowledge as context. Use of knowledge has so far proved difficult, in part because of the lack of a supervised learning benchmark task which exhibits knowledgeable open dialogue with clear grounding. To that end we collect and release a large dataset with conversations directly grounded with knowledge retrieved from Wikipedia. We then design architectures capable of retrieving knowledge, reading and conditioning on it, and finally generating natural responses. Our best performing dialogue models are able to conduct knowledgeable discussions on open-domain topics as evaluated by automatic metrics and human evaluations, while our new benchmark allows for measuring further improvements in this important research direction.

Visual Speech Recognition (VSR) differs from the common perception tasks as it requires deeper reasoning over the video sequence, even by human experts. Despite the recent advances in VSR, current approaches rely on labeled data to fully train or finetune their models predicting the target speech. This hinders their ability to generalize well beyond the training set and leads to performance degeneration under out-of-distribution challenging scenarios. Unlike previous works that involve auxiliary losses or complex training procedures and architectures, we propose a simple approach, named Lip2Vec that is based on learning a prior model. Given a robust visual speech encoder, this network maps the encoded latent representations of the lip sequence to their corresponding latents from the audio pair, which are sufficiently invariant for effective text decoding. The generated audio representation is then decoded to text using an off-the-shelf Audio Speech Recognition (ASR) model. The proposed model compares favorably with fully-supervised learning methods on the LRS3 dataset achieving 26 WER. Unlike SoTA approaches, our model keeps a reasonable performance on the VoxCeleb test set. We believe that reprogramming the VSR as an ASR task narrows the performance gap between the two and paves the way for more flexible formulations of lip reading.

Visual signals in a video can be divided into content and motion. While content specifies which objects are in the video, motion describes their dynamics. Based on this prior, we propose the Motion and Content decomposed Generative Adversarial Network (MoCoGAN) framework for video generation. The proposed framework generates a video by mapping a sequence of random vectors to a sequence of video frames. Each random vector consists of a content part and a motion part. While the content part is kept fixed, the motion part is realized as a stochastic process. To learn motion and content decomposition in an unsupervised manner, we introduce a novel adversarial learning scheme utilizing both image and video discriminators. Extensive experimental results on several challenging datasets with qualitative and quantitative comparison to the state-of-the-art approaches, verify effectiveness of the proposed framework. In addition, we show that MoCoGAN allows one to generate videos with same content but different motion as well as videos with different content and same motion.

The reward model has become increasingly important in alignment, assessment, and data construction for large language models (LLMs). Most existing researchers focus on enhancing reward models through data improvements, following the conventional training framework for reward models that directly optimizes the predicted rewards. In this paper, we propose a hybrid alignment framework HaF-RM for reward model training by introducing an additional constraint on token-level policy probabilities in addition to the reward score. It can simultaneously supervise the internal preference model at the token level and optimize the mapping layer of the reward model at the sequence level. Theoretical justifications and experiment results on five datasets show the validity and effectiveness of our proposed hybrid framework for training a high-quality reward model. By decoupling the reward modeling procedure and incorporating hybrid supervision, our HaF-RM framework offers a principled and effective approach to enhancing the performance and alignment of reward models, a critical component in the responsible development of powerful language models. We release our code at https://haf-rm.github.io.

Mixture of Experts (MoE) models enhance neural network scalability by dynamically selecting relevant experts per input token, enabling larger model sizes while maintaining manageable computation costs. However, efficient training of large-scale MoE models across thousands of GPUs presents significant challenges due to limitations in existing parallelism strategies. We introduce an end-to-end training framework for large-scale MoE models that utilizes five-dimensional hybrid parallelism: Tensor Parallelism, Expert Parallelism, Context Parallelism, Data Parallelism, and Pipeline Parallelism. Central to our approach is MoE Parallel Folding, a novel strategy that decouples the parallelization of attention and MoE layers in Transformer models, allowing each layer type to adopt optimal parallel configurations. Additionally, we develop a flexible token-level dispatcher that supports both token-dropping and token-dropless MoE training across all five dimensions of parallelism. This dispatcher accommodates dynamic tensor shapes and coordinates different parallelism schemes for Attention and MoE layers, facilitating complex parallelism implementations. Our experiments demonstrate significant improvements in training efficiency and scalability. We achieve up to 49.3% Model Flops Utilization (MFU) for the Mixtral 8x22B model and 39.0% MFU for the Qwen2-57B-A14B model on H100 GPUs, outperforming existing methods. The framework scales efficiently up to 1,024 GPUs and maintains high performance with sequence lengths up to 128K tokens, validating its effectiveness for large-scale MoE model training. The code is available in Megatron-Core.

In recent years, text-driven image editing has made significant progress. However, due to the inherent ambiguity and discreteness of natural language, color editing still faces challenges such as insufficient precision and difficulty in achieving continuous control. Although linearly interpolating the embedding vectors of different textual descriptions can guide the model to generate a sequence of images with varying colors, this approach lacks precise control over the range of color changes in the output images. Moreover, the relationship between the interpolation coefficient and the resulting image color is unknown and uncontrollable. To address these issues, we introduce a color mapping module that explicitly models the correspondence between the text embedding space and image RGB values. This module predicts the corresponding embedding vector based on a given RGB value, enabling precise color control of the generated images while maintaining semantic consistency. Users can specify a target RGB range to generate images with continuous color variations within the desired range, thereby achieving finer-grained, continuous, and controllable color editing. Experimental results demonstrate that our method performs well in terms of color continuity and controllability.

We propose a methodology for planting watermarks in text from an autoregressive language model that are robust to perturbations without changing the distribution over text up to a certain maximum generation budget. We generate watermarked text by mapping a sequence of random numbers -- which we compute using a randomized watermark key -- to a sample from the language model. To detect watermarked text, any party who knows the key can align the text to the random number sequence. We instantiate our watermark methodology with two sampling schemes: inverse transform sampling and exponential minimum sampling. We apply these watermarks to three language models -- OPT-1.3B, LLaMA-7B and Alpaca-7B -- to experimentally validate their statistical power and robustness to various paraphrasing attacks. Notably, for both the OPT-1.3B and LLaMA-7B models, we find we can reliably detect watermarked text (p leq 0.01) from 35 tokens even after corrupting between 40-50\% of the tokens via random edits (i.e., substitutions, insertions or deletions). For the Alpaca-7B model, we conduct a case study on the feasibility of watermarking responses to typical user instructions. Due to the lower entropy of the responses, detection is more difficult: around 25% of the responses -- whose median length is around 100 tokens -- are detectable with p leq 0.01, and the watermark is also less robust to certain automated paraphrasing attacks we implement.

In this paper, we develop a new method to automatically convert 2D line drawings from three orthographic views into 3D CAD models. Existing methods for this problem reconstruct 3D models by back-projecting the 2D observations into 3D space while maintaining explicit correspondence between the input and output. Such methods are sensitive to errors and noises in the input, thus often fail in practice where the input drawings created by human designers are imperfect. To overcome this difficulty, we leverage the attention mechanism in a Transformer-based sequence generation model to learn flexible mappings between the input and output. Further, we design shape programs which are suitable for generating the objects of interest to boost the reconstruction accuracy and facilitate CAD modeling applications. Experiments on a new benchmark dataset show that our method significantly outperforms existing ones when the inputs are noisy or incomplete.

Transformer components such as non-linear activations and normalization are inherently non-injective, suggesting that different inputs could map to the same output and prevent exact recovery of the input from a model's representations. In this paper, we challenge this view. First, we prove mathematically that transformer language models mapping discrete input sequences to their corresponding sequence of continuous representations are injective and therefore lossless, a property established at initialization and preserved during training. Second, we confirm this result empirically through billions of collision tests on six state-of-the-art language models, and observe no collisions. Third, we operationalize injectivity: we introduce SipIt, the first algorithm that provably and efficiently reconstructs the exact input text from hidden activations, establishing linear-time guarantees and demonstrating exact invertibility in practice. Overall, our work establishes injectivity as a fundamental and exploitable property of language models, with direct implications for transparency, interpretability, and safe deployment.

Directly learning to model 4D content, including shape, color and motion, is challenging. Existing methods depend on skeleton-based motion control and offer limited continuity in detail. To address this, we propose a novel framework that generates coherent 4D sequences with animation of 3D shapes under given conditions with dynamic evolution of shape and color over time through integrative latent mapping. We first employ an integrative latent unified representation to encode shape and color information of each detailed 3D geometry frame. The proposed skeleton-free latent 4D sequence joint representation allows us to leverage diffusion models in a low-dimensional space to control the generation of 4D sequences. Finally, temporally coherent 4D sequences are generated conforming well to the input images and text prompts. Extensive experiments on the ShapeNet, 3DBiCar and DeformingThings4D datasets for several tasks demonstrate that our method effectively learns to generate quality 3D shapes with color and 4D mesh animations, improving over the current state-of-the-art. Source code will be released.

Extraction of building footprint polygons from remotely sensed data is essential for several urban understanding tasks such as reconstruction, navigation, and mapping. Despite significant progress in the area, extracting accurate polygonal building footprints remains an open problem. In this paper, we introduce Pix2Poly, an attention-based end-to-end trainable and differentiable deep neural network capable of directly generating explicit high-quality building footprints in a ring graph format. Pix2Poly employs a generative encoder-decoder transformer to produce a sequence of graph vertex tokens whose connectivity information is learned by an optimal matching network. Compared to previous graph learning methods, ours is a truly end-to-end trainable approach that extracts high-quality building footprints and road networks without requiring complicated, computationally intensive raster loss functions and intricate training pipelines. Upon evaluating Pix2Poly on several complex and challenging datasets, we report that Pix2Poly outperforms state-of-the-art methods in several vector shape quality metrics while being an entirely explicit method. Our code is available at https://github.com/yeshwanth95/Pix2Poly.

We consider the challenging task of training models for image-to-video deblurring, which aims to recover a sequence of sharp images corresponding to a given blurry image input. A critical issue disturbing the training of an image-to-video model is the ambiguity of the frame ordering since both the forward and backward sequences are plausible solutions. This paper proposes an effective self-supervised ordering scheme that allows training high-quality image-to-video deblurring models. Unlike previous methods that rely on order-invariant losses, we assign an explicit order for each video sequence, thus avoiding the order-ambiguity issue. Specifically, we map each video sequence to a vector in a latent high-dimensional space so that there exists a hyperplane such that for every video sequence, the vectors extracted from it and its reversed sequence are on different sides of the hyperplane. The side of the vectors will be used to define the order of the corresponding sequence. Last but not least, we propose a real-image dataset for the image-to-video deblurring problem that covers a variety of popular domains, including face, hand, and street. Extensive experimental results confirm the effectiveness of our method. Code and data are available at https://github.com/VinAIResearch/HyperCUT.git

Focusing on the task of point-to-point navigation for an autonomous driving vehicle, we propose a novel deep learning model trained with end-to-end and multi-task learning manners to perform both perception and control tasks simultaneously. The model is used to drive the ego vehicle safely by following a sequence of routes defined by the global planner. The perception part of the model is used to encode high-dimensional observation data provided by an RGBD camera while performing semantic segmentation, semantic depth cloud (SDC) mapping, and traffic light state and stop sign prediction. Then, the control part decodes the encoded features along with additional information provided by GPS and speedometer to predict waypoints that come with a latent feature space. Furthermore, two agents are employed to process these outputs and make a control policy that determines the level of steering, throttle, and brake as the final action. The model is evaluated on CARLA simulator with various scenarios made of normal-adversarial situations and different weathers to mimic real-world conditions. In addition, we do a comparative study with some recent models to justify the performance in multiple aspects of driving. Moreover, we also conduct an ablation study on SDC mapping and multi-agent to understand their roles and behavior. As a result, our model achieves the highest driving score even with fewer parameters and computation load. To support future studies, we share our codes at https://github.com/oskarnatan/end-to-end-driving.

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

We demonstrate that the inference operations of several open-weight large language models (LLMs) can be mapped to an exactly equivalent linear system for an input sequence without modifying the model weights or altering output predictions. Extending techniques from image diffusion models that exhibit local or piecewise linearity, we strategically alter the gradient computation with respect to a given input sequence for a next-token prediction such that the Jacobian of the model nearly exactly reproduces the forward prediction with a linear system. We demonstrate this approach across models (Llama 3, Gemma 3, Qwen 3, Phi 4, Mistral Ministral and OLMo 2, up to Llama 3.3 70B Q4) and show through the singular value decomposition of the detached Jacobian that these LLMs operate in extremely low-dimensional subspaces where many of the largest singular vectors decode to concepts related to the most-likely output token. This approach also allows us to examine the operation of each successive layer (and its attention and MLP components) as nearly-exact linear systems and observe the emergence of semantic concepts. Despite their expressive power and global nonlinearity, modern LLMs can be interpreted through nearly-exact locally linear decompositions that provide insights into their internal representations and reveal interpretable semantic structures in the next-token prediction process.

Autonomous driving promises transformative improvements to transportation, but building systems capable of safely navigating the unstructured complexity of real-world scenarios remains challenging. A critical problem lies in effectively predicting the various potential outcomes that may emerge in response to the vehicle's actions as the world evolves. To address this challenge, we introduce GAIA-1 ('Generative AI for Autonomy'), a generative world model that leverages video, text, and action inputs to generate realistic driving scenarios while offering fine-grained control over ego-vehicle behavior and scene features. Our approach casts world modeling as an unsupervised sequence modeling problem by mapping the inputs to discrete tokens, and predicting the next token in the sequence. Emerging properties from our model include learning high-level structures and scene dynamics, contextual awareness, generalization, and understanding of geometry. The power of GAIA-1's learned representation that captures expectations of future events, combined with its ability to generate realistic samples, provides new possibilities for innovation in the field of autonomy, enabling enhanced and accelerated training of autonomous driving technology.

Despite the ubiquity of mobile and wearable text messaging applications, the problem of keyboard text decoding is not tackled sufficiently in the light of the enormous success of the deep learning Recurrent Neural Network (RNN) and Convolutional Neural Networks (CNN) for natural language understanding. In particular, considering that the keyboard decoders should operate on devices with memory and processor resource constraints, makes it challenging to deploy industrial scale deep neural network (DNN) models. This paper proposes a sequence-to-sequence neural attention network system for automatic text correction and completion. Given an erroneous sequence, our model encodes character level hidden representations and then decodes the revised sequence thus enabling auto-correction and completion. We achieve this by a combination of character level CNN and gated recurrent unit (GRU) encoder along with and a word level gated recurrent unit (GRU) attention decoder. Unlike traditional language models that learn from billions of words, our corpus size is only 12 million words; an order of magnitude smaller. The memory footprint of our learnt model for inference and prediction is also an order of magnitude smaller than the conventional language model based text decoders. We report baseline performance for neural keyboard decoders in such limited domain. Our models achieve a word level accuracy of 90% and a character error rate CER of 2.4% over the Twitter typo dataset. We present a novel dataset of noisy to corrected mappings by inducing the noise distribution from the Twitter data over the OpenSubtitles 2009 dataset; on which our model predicts with a word level accuracy of 98% and sequence accuracy of 68.9%. In our user study, our model achieved an average CER of 2.6% with the state-of-the-art non-neural touch-screen keyboard decoder at CER of 1.6%.

Transformer based language models exhibit intelligent behaviors such as understanding natural language, recognizing patterns, acquiring knowledge, reasoning, planning, reflecting and using tools. This paper explores how their underlying mechanics give rise to intelligent behaviors. Towards that end, we propose framing Transformer dynamics as movement through embedding space. Examining Transformers through this perspective reveals key insights, establishing a Theory of Transformers: 1) Intelligent behaviours map to paths in Embedding Space which, the Transformer random-walks through during inferencing. 2) LM training learns a probability distribution over all possible paths. `Intelligence' is learnt by assigning higher probabilities to paths representing intelligent behaviors. No learning can take place in-context; context only narrows the subset of paths sampled during decoding. 5) The Transformer is a self-mapping composition function, folding a context sequence into a context-vector such that it's proximity to a token-vector reflects its co-occurrence and conditioned probability. Thus, the physical arrangement of vectors in Embedding Space determines path probabilities. 6) Context vectors are composed by aggregating features of the sequence's tokens via a process we call the encoding walk. Attention contributes a - potentially redundant - association-bias to this process. 7) This process is comprised of two principal operation types: filtering (data independent) and aggregation (data dependent). This generalization unifies Transformers with other sequence models. Building upon this foundation, we formalize a popular semantic interpretation of embeddings into a ``concept-space theory'' and find some evidence of it's validity.

Contents generated by recent advanced Text-to-Image (T2I) diffusion models are sometimes too imaginative for existing off-the-shelf dense predictors to estimate due to the immitigable domain gap. We introduce DMP, a pipeline utilizing pre-trained T2I models as a prior for dense prediction tasks. To address the misalignment between deterministic prediction tasks and stochastic T2I models, we reformulate the diffusion process through a sequence of interpolations, establishing a deterministic mapping between input RGB images and output prediction distributions. To preserve generalizability, we use low-rank adaptation to fine-tune pre-trained models. Extensive experiments across five tasks, including 3D property estimation, semantic segmentation, and intrinsic image decomposition, showcase the efficacy of the proposed method. Despite limited-domain training data, the approach yields faithful estimations for arbitrary images, surpassing existing state-of-the-art algorithms.

There has been a growing interest in developing multimodal machine translation (MMT) systems that enhance neural machine translation (NMT) with visual knowledge. This problem setup involves using images as auxiliary information during training, and more recently, eliminating their use during inference. Towards this end, previous works face a challenge in training powerful MMT models from scratch due to the scarcity of annotated multilingual vision-language data, especially for low-resource languages. Simultaneously, there has been an influx of multilingual pre-trained models for NMT and multimodal pre-trained models for vision-language tasks, primarily in English, which have shown exceptional generalisation ability. However, these are not directly applicable to MMT since they do not provide aligned multimodal multilingual features for generative tasks. To alleviate this issue, instead of designing complex modules for MMT, we propose CLIPTrans, which simply adapts the independently pre-trained multimodal M-CLIP and the multilingual mBART. In order to align their embedding spaces, mBART is conditioned on the M-CLIP features by a prefix sequence generated through a lightweight mapping network. We train this in a two-stage pipeline which warms up the model with image captioning before the actual translation task. Through experiments, we demonstrate the merits of this framework and consequently push forward the state-of-the-art across standard benchmarks by an average of +2.67 BLEU. The code can be found at www.github.com/devaansh100/CLIPTrans.

Pre-trained models for programming languages have recently demonstrated great success on code intelligence. To support both code-related understanding and generation tasks, recent works attempt to pre-train unified encoder-decoder models. However, such encoder-decoder framework is sub-optimal for auto-regressive tasks, especially code completion that requires a decoder-only manner for efficient inference. In this paper, we present UniXcoder, a unified cross-modal pre-trained model for programming language. The model utilizes mask attention matrices with prefix adapters to control the behavior of the model and leverages cross-modal contents like AST and code comment to enhance code representation. To encode AST that is represented as a tree in parallel, we propose a one-to-one mapping method to transform AST in a sequence structure that retains all structural information from the tree. Furthermore, we propose to utilize multi-modal contents to learn representation of code fragment with contrastive learning, and then align representations among programming languages using a cross-modal generation task. We evaluate UniXcoder on five code-related tasks over nine datasets. To further evaluate the performance of code fragment representation, we also construct a dataset for a new task, called zero-shot code-to-code search. Results show that our model achieves state-of-the-art performance on most tasks and analysis reveals that comment and AST can both enhance UniXcoder.

Synthesizing human's movements such as dancing is a flourishing research field which has several applications in computer graphics. Recent studies have demonstrated the advantages of deep neural networks (DNNs) for achieving remarkable performance in motion and music tasks with little effort for feature pre-processing. However, applying DNNs for generating dance to a piece of music is nevertheless challenging, because of 1) DNNs need to generate large sequences while mapping the music input, 2) the DNN needs to constraint the motion beat to the music, and 3) DNNs require a considerable amount of hand-crafted data. In this study, we propose a weakly supervised deep recurrent method for real-time basic dance generation with audio power spectrum as input. The proposed model employs convolutional layers and a multilayered Long Short-Term memory (LSTM) to process the audio input. Then, another deep LSTM layer decodes the target dance sequence. Notably, this end-to-end approach has 1) an auto-conditioned decode configuration that reduces accumulation of feedback error of large dance sequence, 2) uses a contrastive cost function to regulate the mapping between the music and motion beat, and 3) trains with weak labels generated from the motion beat, reducing the amount of hand-crafted data. We evaluate the proposed network based on i) the similarities between generated and the baseline dancer motion with a cross entropy measure for large dance sequences, and ii) accurate timing between the music and motion beat with an F-measure. Experimental results revealed that, after training using a small dataset, the model generates basic dance steps with low cross entropy and maintains an F-measure score similar to that of a baseline dancer.

We present a novel approach for synthesizing 3D talking heads with controllable emotion, featuring enhanced lip synchronization and rendering quality. Despite significant progress in the field, prior methods still suffer from multi-view consistency and a lack of emotional expressiveness. To address these issues, we collect EmoTalk3D dataset with calibrated multi-view videos, emotional annotations, and per-frame 3D geometry. By training on the EmoTalk3D dataset, we propose a `Speech-to-Geometry-to-Appearance' mapping framework that first predicts faithful 3D geometry sequence from the audio features, then the appearance of a 3D talking head represented by 4D Gaussians is synthesized from the predicted geometry. The appearance is further disentangled into canonical and dynamic Gaussians, learned from multi-view videos, and fused to render free-view talking head animation. Moreover, our model enables controllable emotion in the generated talking heads and can be rendered in wide-range views. Our method exhibits improved rendering quality and stability in lip motion generation while capturing dynamic facial details such as wrinkles and subtle expressions. Experiments demonstrate the effectiveness of our approach in generating high-fidelity and emotion-controllable 3D talking heads. The code and EmoTalk3D dataset are released at https://nju-3dv.github.io/projects/EmoTalk3D.

Generating human motion from text has been dominated by denoising motion models either through diffusion or generative masking process. However, these models face great limitations in usability by requiring prior knowledge of the motion length. Conversely, autoregressive motion models address this limitation by adaptively predicting motion endpoints, at the cost of degraded generation quality and editing capabilities. To address these challenges, we propose Bidirectional Autoregressive Motion Model (BAMM), a novel text-to-motion generation framework. BAMM consists of two key components: (1) a motion tokenizer that transforms 3D human motion into discrete tokens in latent space, and (2) a masked self-attention transformer that autoregressively predicts randomly masked tokens via a hybrid attention masking strategy. By unifying generative masked modeling and autoregressive modeling, BAMM captures rich and bidirectional dependencies among motion tokens, while learning the probabilistic mapping from textual inputs to motion outputs with dynamically-adjusted motion sequence length. This feature enables BAMM to simultaneously achieving high-quality motion generation with enhanced usability and built-in motion editability. Extensive experiments on HumanML3D and KIT-ML datasets demonstrate that BAMM surpasses current state-of-the-art methods in both qualitative and quantitative measures. Our project page is available at https://exitudio.github.io/BAMM-page

Humans generally use natural language to communicate task requirements to each other. Ideally, natural language should also be usable for communicating goals to autonomous machines (e.g., robots) to minimize friction in task specification. However, understanding and mapping natural language goals to sequences of states and actions is challenging. Specifically, existing work along these lines has encountered difficulty in generalizing learned policies to new natural language goals and environments. In this paper, we propose a novel adversarial inverse reinforcement learning algorithm to learn a language-conditioned policy and reward function. To improve generalization of the learned policy and reward function, we use a variational goal generator to relabel trajectories and sample diverse goals during training. Our algorithm outperforms multiple baselines by a large margin on a vision-based natural language instruction following dataset (Room-2-Room), demonstrating a promising advance in enabling the use of natural language instructions in specifying agent goals.

Skeleton-based multi-entity action recognition is a challenging task aiming to identify interactive actions or group activities involving multiple diverse entities. Existing models for individuals often fall short in this task due to the inherent distribution discrepancies among entity skeletons, leading to suboptimal backbone optimization. To this end, we introduce a Convex Hull Adaptive Shift based multi-Entity action recognition method (CHASE), which mitigates inter-entity distribution gaps and unbiases subsequent backbones. Specifically, CHASE comprises a learnable parameterized network and an auxiliary objective. The parameterized network achieves plausible, sample-adaptive repositioning of skeleton sequences through two key components. First, the Implicit Convex Hull Constrained Adaptive Shift ensures that the new origin of the coordinate system is within the skeleton convex hull. Second, the Coefficient Learning Block provides a lightweight parameterization of the mapping from skeleton sequences to their specific coefficients in convex combinations. Moreover, to guide the optimization of this network for discrepancy minimization, we propose the Mini-batch Pair-wise Maximum Mean Discrepancy as the additional objective. CHASE operates as a sample-adaptive normalization method to mitigate inter-entity distribution discrepancies, thereby reducing data bias and improving the subsequent classifier's multi-entity action recognition performance. Extensive experiments on six datasets, including NTU Mutual 11/26, H2O, Assembly101, Collective Activity and Volleyball, consistently verify our approach by seamlessly adapting to single-entity backbones and boosting their performance in multi-entity scenarios. Our code is publicly available at https://github.com/Necolizer/CHASE .

We present ALFRED (Action Learning From Realistic Environments and Directives), a benchmark for learning a mapping from natural language instructions and egocentric vision to sequences of actions for household tasks. ALFRED includes long, compositional tasks with non-reversible state changes to shrink the gap between research benchmarks and real-world applications. ALFRED consists of expert demonstrations in interactive visual environments for 25k natural language directives. These directives contain both high-level goals like "Rinse off a mug and place it in the coffee maker." and low-level language instructions like "Walk to the coffee maker on the right." ALFRED tasks are more complex in terms of sequence length, action space, and language than existing vision-and-language task datasets. We show that a baseline model based on recent embodied vision-and-language tasks performs poorly on ALFRED, suggesting that there is significant room for developing innovative grounded visual language understanding models with this benchmark.

A central goal of sequence modeling is designing a single principled model that can address sequence data across a range of modalities and tasks, particularly on long-range dependencies. Although conventional models including RNNs, CNNs, and Transformers have specialized variants for capturing long dependencies, they still struggle to scale to very long sequences of 10000 or more steps. A promising recent approach proposed modeling sequences by simulating the fundamental state space model (SSM) \( x'(t) = Ax(t) + Bu(t), y(t) = Cx(t) + Du(t) \), and showed that for appropriate choices of the state matrix \( A \), this system could handle long-range dependencies mathematically and empirically. However, this method has prohibitive computation and memory requirements, rendering it infeasible as a general sequence modeling solution. We propose the Structured State Space sequence model (S4) based on a new parameterization for the SSM, and show that it can be computed much more efficiently than prior approaches while preserving their theoretical strengths. Our technique involves conditioning \( A \) with a low-rank correction, allowing it to be diagonalized stably and reducing the SSM to the well-studied computation of a Cauchy kernel. S4 achieves strong empirical results across a diverse range of established benchmarks, including (i) 91\% accuracy on sequential CIFAR-10 with no data augmentation or auxiliary losses, on par with a larger 2-D ResNet, (ii) substantially closing the gap to Transformers on image and language modeling tasks, while performing generation 60times faster (iii) SoTA on every task from the Long Range Arena benchmark, including solving the challenging Path-X task of length 16k that all prior work fails on, while being as efficient as all competitors.

Many machine learning tasks can be expressed as the transformation---or transduction---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to represent both the input and output sequences in a way that is invariant to sequential distortions such as shrinking, stretching and translating. Recurrent neural networks (RNNs) are a powerful sequence learning architecture that has proven capable of learning such representations. However RNNs traditionally require a pre-defined alignment between the input and output sequences to perform transduction. This is a severe limitation since finding the alignment is the most difficult aspect of many sequence transduction problems. Indeed, even determining the length of the output sequence is often challenging. This paper introduces an end-to-end, probabilistic sequence transduction system, based entirely on RNNs, that is in principle able to transform any input sequence into any finite, discrete output sequence. Experimental results for phoneme recognition are provided on the TIMIT speech corpus.

We introduce Delayed Streams Modeling (DSM), a flexible formulation for streaming, multimodal sequence-to-sequence learning. Sequence-to-sequence generation is often cast in an offline manner, where the model consumes the complete input sequence before generating the first output timestep. Alternatively, streaming sequence-to-sequence rely on learning a policy for choosing when to advance on the input stream, or write to the output stream. DSM instead models already time-aligned streams with a decoder-only language model. By moving the alignment to a pre-processing step,and introducing appropriate delays between streams, DSM provides streaming inference of arbitrary output sequences, from any input combination, making it applicable to many sequence-to-sequence problems. In particular, given text and audio streams, automatic speech recognition (ASR) corresponds to the text stream being delayed, while the opposite gives a text-to-speech (TTS) model. We perform extensive experiments for these two major sequence-to-sequence tasks, showing that DSM provides state-of-the-art performance and latency while supporting arbitrary long sequences, being even competitive with offline baselines. Code, samples and demos are available at https://github.com/kyutai-labs/delayed-streams-modeling

Mapping sequences of discrete data to a point in a continuous space makes it difficult to retrieve those sequences via random sampling. Mapping the input to a volume would make it easier to retrieve at test time, and that's the strategy followed by the family of approaches based on Variational Autoencoder. However the fact that they are at the same time optimizing for prediction and for smoothness of representation, forces them to trade-off between the two. We improve on the performance of some of the standard methods in deep learning to generate sentences by uniformly sampling a continuous space. We do it by proposing AriEL, that constructs volumes in a continuous space, without the need of encouraging the creation of volumes through the loss function. We first benchmark on a toy grammar, that allows to automatically evaluate the language learned and generated by the models. Then, we benchmark on a real dataset of human dialogues. Our results indicate that the random access to the stored information is dramatically improved, and our method AriEL is able to generate a wider variety of correct language by randomly sampling the latent space. VAE follows in performance for the toy dataset while, AE and Transformer follow for the real dataset. This partially supports to the hypothesis that encoding information into volumes instead of into points, can lead to improved retrieval of learned information with random sampling. This can lead to better generators and we also discuss potential disadvantages.

Music is used to convey emotions, and thus generating emotional music is important in automatic music generation. Previous work on emotional music generation directly uses annotated emotion labels as control signals, which suffers from subjective bias: different people may annotate different emotions on the same music, and one person may feel different emotions under different situations. Therefore, directly mapping emotion labels to music sequences in an end-to-end way would confuse the learning process and hinder the model from generating music with general emotions. In this paper, we propose EmoGen, an emotional music generation system that leverages a set of emotion-related music attributes as the bridge between emotion and music, and divides the generation into two stages: emotion-to-attribute mapping with supervised clustering, and attribute-to-music generation with self-supervised learning. Both stages are beneficial: in the first stage, the attribute values around the clustering center represent the general emotions of these samples, which help eliminate the impacts of the subjective bias of emotion labels; in the second stage, the generation is completely disentangled from emotion labels and thus free from the subjective bias. Both subjective and objective evaluations show that EmoGen outperforms previous methods on emotion control accuracy and music quality respectively, which demonstrate our superiority in generating emotional music. Music samples generated by EmoGen are available via this link:https://ai-muzic.github.io/emogen/, and the code is available at this link:https://github.com/microsoft/muzic/.

In text-to-SQL task, seq-to-seq models often lead to sub-optimal performance due to limitations in their architecture. In this paper, we present a simple yet effective approach that adapts transformer-based seq-to-seq model to robust text-to-SQL generation. Instead of inducing constraint to decoder or reformat the task as slot-filling, we propose to train seq-to-seq model with Schema aware Denoising (SeaD), which consists of two denoising objectives that train model to either recover input or predict output from two novel erosion and shuffle noises. These denoising objectives acts as the auxiliary tasks for better modeling the structural data in S2S generation. In addition, we improve and propose a clause-sensitive execution guided (EG) decoding strategy to overcome the limitation of EG decoding for generative model. The experiments show that the proposed method improves the performance of seq-to-seq model in both schema linking and grammar correctness and establishes new state-of-the-art on WikiSQL benchmark. The results indicate that the capacity of vanilla seq-to-seq architecture for text-to-SQL may have been under-estimated.

Graph Neural Networks (GNNs) have empowered the advance in graph-structured data analysis. Recently, the rise of Large Language Models (LLMs) like GPT-4 has heralded a new era in deep learning. However, their application to graph data poses distinct challenges due to the inherent difficulty of translating graph structures to language. To this end, we introduce the Large Language and Graph Assistant (LLaGA), an innovative model that effectively integrates LLM capabilities to handle the complexities of graph-structured data. LLaGA retains the general-purpose nature of LLMs while adapting graph data into a format compatible with LLM input. LLaGA achieves this by reorganizing graph nodes to structure-aware sequences and then mapping these into the token embedding space through a versatile projector. LLaGA excels in versatility, generalizability and interpretability, allowing it to perform consistently well across different datasets and tasks, extend its ability to unseen datasets or tasks, and provide explanations for graphs. Our extensive experiments across popular graph benchmarks show that LLaGA delivers outstanding performance across four datasets and three tasks using one single model, surpassing state-of-the-art graph models in both supervised and zero-shot scenarios. Our code is available at https://github.com/VITA-Group/LLaGA.

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

Sequence modeling is a crucial area across various domains, including Natural Language Processing (NLP), speech recognition, time series forecasting, music generation, and bioinformatics. Recurrent Neural Networks (RNNs) and Long Short Term Memory Networks (LSTMs) have historically dominated sequence modeling tasks like Machine Translation, Named Entity Recognition (NER), etc. However, the advancement of transformers has led to a shift in this paradigm, given their superior performance. Yet, transformers suffer from O(N^2) attention complexity and challenges in handling inductive bias. Several variations have been proposed to address these issues which use spectral networks or convolutions and have performed well on a range of tasks. However, they still have difficulty in dealing with long sequences. State Space Models(SSMs) have emerged as promising alternatives for sequence modeling paradigms in this context, especially with the advent of S4 and its variants, such as S4nd, Hippo, Hyena, Diagnol State Spaces (DSS), Gated State Spaces (GSS), Linear Recurrent Unit (LRU), Liquid-S4, Mamba, etc. In this survey, we categorize the foundational SSMs based on three paradigms namely, Gating architectures, Structural architectures, and Recurrent architectures. This survey also highlights diverse applications of SSMs across domains such as vision, video, audio, speech, language (especially long sequence modeling), medical (including genomics), chemical (like drug design), recommendation systems, and time series analysis, including tabular data. Moreover, we consolidate the performance of SSMs on benchmark datasets like Long Range Arena (LRA), WikiText, Glue, Pile, ImageNet, Kinetics-400, sstv2, as well as video datasets such as Breakfast, COIN, LVU, and various time series datasets. The project page for Mamba-360 work is available on this webpage.https://github.com/badripatro/mamba360.

The sequence-to-sequence (seq2seq) task aims at generating the target sequence based on the given input source sequence. Traditionally, most of the seq2seq task is resolved by the Encoder-Decoder framework which requires an encoder to encode the source sequence and a decoder to generate the target text. Recently, a bunch of new approaches have emerged that apply decoder-only language models directly to the seq2seq task. Despite the significant advancements in applying language models to the seq2seq task, there is still a lack of thorough analysis on the effectiveness of the decoder-only language model architecture. This paper aims to address this gap by conducting a detailed comparison between the encoder-decoder architecture and the decoder-only language model framework through the analysis of a regularized encoder-decoder structure. This structure is designed to replicate all behaviors in the classical decoder-only language model but has an encoder and a decoder making it easier to be compared with the classical encoder-decoder structure. Based on the analysis, we unveil the attention degeneration problem in the language model, namely, as the generation step number grows, less and less attention is focused on the source sequence. To give a quantitative understanding of this problem, we conduct a theoretical sensitivity analysis of the attention output with respect to the source input. Grounded on our analysis, we propose a novel partial attention language model to solve the attention degeneration problem. Experimental results on machine translation, summarization, and data-to-text generation tasks support our analysis and demonstrate the effectiveness of our proposed model.

Sequence-to-sequence models are commonly trained via maximum likelihood estimation (MLE). However, standard MLE training considers a word-level objective, predicting the next word given the previous ground-truth partial sentence. This procedure focuses on modeling local syntactic patterns, and may fail to capture long-range semantic structure. We present a novel solution to alleviate these issues. Our approach imposes global sequence-level guidance via new supervision based on optimal transport, enabling the overall characterization and preservation of semantic features. We further show that this method can be understood as a Wasserstein gradient flow trying to match our model to the ground truth sequence distribution. Extensive experiments are conducted to validate the utility of the proposed approach, showing consistent improvements over a wide variety of NLP tasks, including machine translation, abstractive text summarization, and image captioning.

Encoder-decoder models have become an effective approach for sequence learning tasks like machine translation, image captioning and speech recognition, but have yet to show competitive results for handwritten text recognition. To this end, we propose an attention-based sequence-to-sequence model. It combines a convolutional neural network as a generic feature extractor with a recurrent neural network to encode both the visual information, as well as the temporal context between characters in the input image, and uses a separate recurrent neural network to decode the actual character sequence. We make experimental comparisons between various attention mechanisms and positional encodings, in order to find an appropriate alignment between the input and output sequence. The model can be trained end-to-end and the optional integration of a hybrid loss allows the encoder to retain an interpretable and usable output, if desired. We achieve competitive results on the IAM and ICFHR2016 READ data sets compared to the state-of-the-art without the use of a language model, and we significantly improve over any recent sequence-to-sequence approaches.

Positional embeddings (PE) play a crucial role in Vision Transformers (ViTs) by providing spatial information otherwise lost due to the permutation invariant nature of self attention. While absolute positional embeddings (APE) have shown theoretical advantages over relative positional embeddings (RPE), particularly due to the ability of sinusoidal functions to preserve spatial inductive biases like monotonicity and shift invariance, a fundamental challenge arises when mapping a 2D grid to a 1D sequence. Existing methods have mostly overlooked or never explored the impact of patch ordering in positional embeddings. To address this, we propose LOOPE, a learnable patch-ordering method that optimizes spatial representation for a given set of frequencies, providing a principled approach to patch order optimization. Empirical results show that our PE significantly improves classification accuracy across various ViT architectures. To rigorously evaluate the effectiveness of positional embeddings, we introduce the "Three Cell Experiment", a novel benchmarking framework that assesses the ability of PEs to retain relative and absolute positional information across different ViT architectures. Unlike standard evaluations, which typically report a performance gap of 4 to 6% between models with and without PE, our method reveals a striking 30 to 35% difference, offering a more sensitive diagnostic tool to measure the efficacy of PEs. Our experimental analysis confirms that the proposed LOOPE demonstrates enhanced effectiveness in retaining both relative and absolute positional information.

Synthesizing SQL queries from natural language is a long-standing open problem and has been attracting considerable interest recently. Toward solving the problem, the de facto approach is to employ a sequence-to-sequence-style model. Such an approach will necessarily require the SQL queries to be serialized. Since the same SQL query may have multiple equivalent serializations, training a sequence-to-sequence-style model is sensitive to the choice from one of them. This phenomenon is documented as the "order-matters" problem. Existing state-of-the-art approaches rely on reinforcement learning to reward the decoder when it generates any of the equivalent serializations. However, we observe that the improvement from reinforcement learning is limited. In this paper, we propose a novel approach, i.e., SQLNet, to fundamentally solve this problem by avoiding the sequence-to-sequence structure when the order does not matter. In particular, we employ a sketch-based approach where the sketch contains a dependency graph so that one prediction can be done by taking into consideration only the previous predictions that it depends on. In addition, we propose a sequence-to-set model as well as the column attention mechanism to synthesize the query based on the sketch. By combining all these novel techniques, we show that SQLNet can outperform the prior art by 9% to 13% on the WikiSQL task.

Sequence-to-sequence (Seq2Seq) models with attention have excelled at tasks which involve generating natural language sentences such as machine translation, image captioning and speech recognition. Performance has further been improved by leveraging unlabeled data, often in the form of a language model. In this work, we present the Cold Fusion method, which leverages a pre-trained language model during training, and show its effectiveness on the speech recognition task. We show that Seq2Seq models with Cold Fusion are able to better utilize language information enjoying i) faster convergence and better generalization, and ii) almost complete transfer to a new domain while using less than 10% of the labeled training data.

We present a new problem: grounding natural language instructions to mobile user interface actions, and create three new datasets for it. For full task evaluation, we create PIXELHELP, a corpus that pairs English instructions with actions performed by people on a mobile UI emulator. To scale training, we decouple the language and action data by (a) annotating action phrase spans in HowTo instructions and (b) synthesizing grounded descriptions of actions for mobile user interfaces. We use a Transformer to extract action phrase tuples from long-range natural language instructions. A grounding Transformer then contextually represents UI objects using both their content and screen position and connects them to object descriptions. Given a starting screen and instruction, our model achieves 70.59% accuracy on predicting complete ground-truth action sequences in PIXELHELP.

A wide array of sequence models are built on a framework modeled after Transformers, comprising alternating sequence mixer and channel mixer layers. This paper studies a unifying matrix mixer view of sequence mixers that can be conceptualized as a linear map on the input sequence. This framework encompasses a broad range of well-known sequence models, including the self-attention of Transformers as well as recent strong alternatives such as structured state space models (SSMs), and allows understanding downstream characteristics such as efficiency and expressivity through properties of their structured matrix class. We identify a key axis of matrix parameterizations termed sequence alignment, which increases the flexibility and performance of matrix mixers, providing insights into the strong performance of Transformers and recent SSMs such as Mamba. Furthermore, the matrix mixer framework offers a systematic approach to developing sequence mixers with desired properties, allowing us to develop several new sub-quadratic sequence models. In particular, we propose a natural bidirectional extension of the Mamba model (Hydra), parameterized as a quasiseparable matrix mixer, which demonstrates superior performance over other sequence models including Transformers on non-causal tasks. As a drop-in replacement for attention layers, Hydra outperforms BERT by 0.8 points on the GLUE benchmark and ViT by 2% Top-1 accuracy on ImageNet.

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families. To address this, we propose Protein Evolutionary Transformer (PoET), an autoregressive generative model of whole protein families that learns to generate sets of related proteins as sequences-of-sequences across tens of millions of natural protein sequence clusters. PoET can be used as a retrieval-augmented language model to generate and score arbitrary modifications conditioned on any protein family of interest, and can extrapolate from short context lengths to generalize well even for small families. This is enabled by a unique Transformer layer; we model tokens sequentially within sequences while attending between sequences order invariantly, allowing PoET to scale to context lengths beyond those used during training. In extensive experiments on deep mutational scanning datasets, we show that PoET outperforms existing protein language models and evolutionary sequence models for variant function prediction across proteins of all MSA depths. We also demonstrate PoET's ability to controllably generate new protein sequences.

Relation linking is essential to enable question answering over knowledge bases. Although there are various efforts to improve relation linking performance, the current state-of-the-art methods do not achieve optimal results, therefore, negatively impacting the overall end-to-end question answering performance. In this work, we propose a novel approach for relation linking framing it as a generative problem facilitating the use of pre-trained sequence-to-sequence models. We extend such sequence-to-sequence models with the idea of infusing structured data from the target knowledge base, primarily to enable these models to handle the nuances of the knowledge base. Moreover, we train the model with the aim to generate a structured output consisting of a list of argument-relation pairs, enabling a knowledge validation step. We compared our method against the existing relation linking systems on four different datasets derived from DBpedia and Wikidata. Our method reports large improvements over the state-of-the-art while using a much simpler model that can be easily adapted to different knowledge bases.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Semantic parsing models with applications in task oriented dialog systems require efficient sequence to sequence (seq2seq) architectures to be run on-device. To this end, we propose a projection based encoder-decoder model referred to as pQRNN-MAtt. Studies based on projection methods were restricted to encoder-only models, and we believe this is the first study extending it to seq2seq architectures. The resulting quantized models are less than 3.5MB in size and are well suited for on-device latency critical applications. We show that on MTOP, a challenging multilingual semantic parsing dataset, the average model performance surpasses LSTM based seq2seq model that uses pre-trained embeddings despite being 85x smaller. Furthermore, the model can be an effective student for distilling large pre-trained models such as T5/BERT.

Scaling multi-dimensional transformers to long sequences is indispensable across various domains. However, the challenges of large memory requirements and slow speeds of such sequences necessitate sequence parallelism. All existing approaches fall under the category of embedded sequence parallelism, which are limited to shard along a single sequence dimension, thereby introducing significant communication overhead. However, the nature of multi-dimensional transformers involves independent calculations across multiple sequence dimensions. To this end, we propose Dynamic Sequence Parallelism (DSP) as a novel abstraction of sequence parallelism. DSP dynamically switches the parallel dimension among all sequences according to the computation stage with efficient resharding strategy. DSP offers significant reductions in communication costs, adaptability across modules, and ease of implementation with minimal constraints. Experimental evaluations demonstrate DSP's superiority over state-of-the-art embedded sequence parallelism methods by remarkable throughput improvements ranging from 32.2% to 10x, with less than 25% communication volume.

Vectorized high-definition map online construction has garnered considerable attention in the field of autonomous driving research. Most existing approaches model changeable map elements using a fixed number of points, or predict local maps in a two-stage autoregressive manner, which may miss essential details and lead to error accumulation. Towards precise map element learning, we propose a simple yet effective architecture named PivotNet, which adopts unified pivot-based map representations and is formulated as a direct set prediction paradigm. Concretely, we first propose a novel point-to-line mask module to encode both the subordinate and geometrical point-line priors in the network. Then, a well-designed pivot dynamic matching module is proposed to model the topology in dynamic point sequences by introducing the concept of sequence matching. Furthermore, to supervise the position and topology of the vectorized point predictions, we propose a dynamic vectorized sequence loss. Extensive experiments and ablations show that PivotNet is remarkably superior to other SOTAs by 5.9 mAP at least. The code will be available soon.

Translating natural language queries into SQLs in a seq2seq manner has attracted much attention recently. However, compared with abstract-syntactic-tree-based SQL generation, seq2seq semantic parsers face much more challenges, including poor quality on schematical information prediction and poor semantic coherence between natural language queries and SQLs. This paper analyses the above difficulties and proposes a seq2seq-oriented decoding strategy called SR, which includes a new intermediate representation SSQL and a reranking method with score re-estimator to solve the above obstacles respectively. Experimental results demonstrate the effectiveness of our proposed techniques and T5-SR-3b achieves new state-of-the-art results on the Spider dataset.

We build upon vec2vec, a procedure designed to align text embedding spaces without parallel data. vec2vec finds a near-perfect alignment, but it is expensive and unstable. We present mini-vec2vec, a simple and efficient alternative that requires substantially lower computational cost and is highly robust. Moreover, the learned mapping is a linear transformation. Our method consists of three main stages: a tentative matching of pseudo-parallel embedding vectors, transformation fitting, and iterative refinement. Our linear alternative exceeds the original instantiation of vec2vec by orders of magnitude in efficiency, while matching or exceeding their results. The method's stability and interpretable algorithmic steps facilitate scaling and unlock new opportunities for adoption in new domains and fields.

This work proposes a novel adaptation of a pretrained sequence-to-sequence model to the task of document ranking. Our approach is fundamentally different from a commonly-adopted classification-based formulation of ranking, based on encoder-only pretrained transformer architectures such as BERT. We show how a sequence-to-sequence model can be trained to generate relevance labels as "target words", and how the underlying logits of these target words can be interpreted as relevance probabilities for ranking. On the popular MS MARCO passage ranking task, experimental results show that our approach is at least on par with previous classification-based models and can surpass them with larger, more-recent models. On the test collection from the TREC 2004 Robust Track, we demonstrate a zero-shot transfer-based approach that outperforms previous state-of-the-art models requiring in-dataset cross-validation. Furthermore, we find that our approach significantly outperforms an encoder-only model in a data-poor regime (i.e., with few training examples). We investigate this observation further by varying target words to probe the model's use of latent knowledge.

Dynamic human rendering from video sequences has achieved remarkable progress by formulating the rendering as a mapping from static poses to human images. However, existing methods focus on the human appearance reconstruction of every single frame while the temporal motion relations are not fully explored. In this paper, we propose a new 4D motion modeling paradigm, SurMo, that jointly models the temporal dynamics and human appearances in a unified framework with three key designs: 1) Surface-based motion encoding that models 4D human motions with an efficient compact surface-based triplane. It encodes both spatial and temporal motion relations on the dense surface manifold of a statistical body template, which inherits body topology priors for generalizable novel view synthesis with sparse training observations. 2) Physical motion decoding that is designed to encourage physical motion learning by decoding the motion triplane features at timestep t to predict both spatial derivatives and temporal derivatives at the next timestep t+1 in the training stage. 3) 4D appearance decoding that renders the motion triplanes into images by an efficient volumetric surface-conditioned renderer that focuses on the rendering of body surfaces with motion learning conditioning. Extensive experiments validate the state-of-the-art performance of our new paradigm and illustrate the expressiveness of surface-based motion triplanes for rendering high-fidelity view-consistent humans with fast motions and even motion-dependent shadows. Our project page is at: https://taohuumd.github.io/projects/SurMo/

Deep Neural Networks (DNNs) are powerful models that have achieved excellent performance on difficult learning tasks. Although DNNs work well whenever large labeled training sets are available, they cannot be used to map sequences to sequences. In this paper, we present a general end-to-end approach to sequence learning that makes minimal assumptions on the sequence structure. Our method uses a multilayered Long Short-Term Memory (LSTM) to map the input sequence to a vector of a fixed dimensionality, and then another deep LSTM to decode the target sequence from the vector. Our main result is that on an English to French translation task from the WMT'14 dataset, the translations produced by the LSTM achieve a BLEU score of 34.8 on the entire test set, where the LSTM's BLEU score was penalized on out-of-vocabulary words. Additionally, the LSTM did not have difficulty on long sentences. For comparison, a phrase-based SMT system achieves a BLEU score of 33.3 on the same dataset. When we used the LSTM to rerank the 1000 hypotheses produced by the aforementioned SMT system, its BLEU score increases to 36.5, which is close to the previous best result on this task. The LSTM also learned sensible phrase and sentence representations that are sensitive to word order and are relatively invariant to the active and the passive voice. Finally, we found that reversing the order of the words in all source sentences (but not target sentences) improved the LSTM's performance markedly, because doing so introduced many short term dependencies between the source and the target sentence which made the optimization problem easier.

Every act of language generation compresses a rich internal state into a single token sequence. We call this process intention collapse: a many-to-one projection from a high dimensional intention space I into an external language space L. We formalize intention collapse for contemporary language models, define three simple, model agnostic intention metrics (intention entropy Hint, effective dimensionality dimeff, and latent knowledge recoverability Recov), and propose an empirical agenda for studying how inference time computation shapes internal intentions before they are verbalized. We also report a first small scale experiment. Using a 4 bit Mistral 7B model on 200 GSM8K problems, we compare a direct answer baseline, a chain of thought (CoT) regime, and a babble control. CoT raises accuracy from 5.5 percent to 53 percent, sharply reduces pre collapse intention entropy (from 1.42 to 0.37 bits), and shows higher global effective dimensionality than the other regimes despite producing fewer tokens than babble. At the same time, Hint has little item level predictive power, and a linear probe on I achieves AUROC 0.65 in the CoT regime but only about chance in the baseline regime, where it collapses to the majority class. These preliminary results indicate that intention level metrics can distinguish inference regimes and expose latent information that is partly lost during collapse, while also revealing important limitations of our current proxies

Existing datasets for autonomous driving (AD) often lack diversity and long-range capabilities, focusing instead on 360{\deg} perception and temporal reasoning. To address this gap, we introduce Zenseact Open Dataset (ZOD), a large-scale and diverse multimodal dataset collected over two years in various European countries, covering an area 9x that of existing datasets. ZOD boasts the highest range and resolution sensors among comparable datasets, coupled with detailed keyframe annotations for 2D and 3D objects (up to 245m), road instance/semantic segmentation, traffic sign recognition, and road classification. We believe that this unique combination will facilitate breakthroughs in long-range perception and multi-task learning. The dataset is composed of Frames, Sequences, and Drives, designed to encompass both data diversity and support for spatio-temporal learning, sensor fusion, localization, and mapping. Frames consist of 100k curated camera images with two seconds of other supporting sensor data, while the 1473 Sequences and 29 Drives include the entire sensor suite for 20 seconds and a few minutes, respectively. ZOD is the only large-scale AD dataset released under a permissive license, allowing for both research and commercial use. The dataset is accompanied by an extensive development kit. Data and more information are available online (https://zod.zenseact.com).

LiDAR-based SLAM is a core technology for autonomous vehicles and robots. One key contribution of this work to 3D LiDAR SLAM and localization is a fierce defense of view-based maps (pose graphs with time-stamped sensor readings) as the fundamental representation of maps. As will be shown, they allow for the greatest flexibility, enabling the posterior generation of arbitrary metric maps optimized for particular tasks, e.g. obstacle avoidance, real-time localization. Moreover, this work introduces a new framework in which mapping pipelines can be defined without coding, defining the connections of a network of reusable blocks much like deep-learning networks are designed by connecting layers of standardized elements. We also introduce tightly-coupled estimation of linear and angular velocity vectors within the Iterative Closest Point (ICP)-like optimizer, leading to superior robustness against aggressive motion profiles without the need for an IMU. Extensive experimental validation reveals that the proposal compares well to, or improves, former state-of-the-art (SOTA) LiDAR odometry systems, while also successfully mapping some hard sequences where others diverge. A proposed self-adaptive configuration has been used, without parameter changes, for all 3D LiDAR datasets with sensors between 16 and 128 rings, and has been extensively tested on 83 sequences over more than 250~km of automotive, hand-held, airborne, and quadruped LiDAR datasets, both indoors and outdoors. The system flexibility is demonstrated with additional configurations for 2D LiDARs and for building 3D NDT-like maps. The framework is open-sourced online: https://github.com/MOLAorg/mola

Recently, state space models have exhibited strong global modeling capabilities and linear computational complexity in contrast to transformers. This research focuses on applying such architecture to more efficiently and effectively model point cloud data globally with linear computational complexity. In particular, for the first time, we demonstrate that Mamba-based point cloud methods can outperform previous methods based on transformer or multi-layer perceptrons (MLPs). To enable Mamba to process 3-D point cloud data more effectively, we propose a novel Consistent Traverse Serialization method to convert point clouds into 1-D point sequences while ensuring that neighboring points in the sequence are also spatially adjacent. Consistent Traverse Serialization yields six variants by permuting the order of x, y, and z coordinates, and the synergistic use of these variants aids Mamba in comprehensively observing point cloud data. Furthermore, to assist Mamba in handling point sequences with different orders more effectively, we introduce point prompts to inform Mamba of the sequence's arrangement rules. Finally, we propose positional encoding based on spatial coordinate mapping to inject positional information into point cloud sequences more effectively. Point Cloud Mamba surpasses the state-of-the-art (SOTA) point-based method PointNeXt and achieves new SOTA performance on the ScanObjectNN, ModelNet40, ShapeNetPart, and S3DIS datasets. It is worth mentioning that when using a more powerful local feature extraction module, our PCM achieves 79.6 mIoU on S3DIS, significantly surpassing the previous SOTA models, DeLA and PTv3, by 5.5 mIoU and 4.9 mIoU, respectively.

Research on question answering with knowledge base has recently seen an increasing use of deep architectures. In this extended abstract, we study the application of the neural machine translation paradigm for question parsing. We employ a sequence-to-sequence model to learn graph patterns in the SPARQL graph query language and their compositions. Instead of inducing the programs through question-answer pairs, we expect a semi-supervised approach, where alignments between questions and queries are built through templates. We argue that the coverage of language utterances can be expanded using late notable works in natural language generation.

Efficient computation or approximation of Levenshtein distance, a widely-used metric for evaluating sequence similarity, has attracted significant attention with the emergence of DNA storage and other biological applications. Sequence embedding, which maps Levenshtein distance to a conventional distance between embedding vectors, has emerged as a promising solution. In this paper, a novel neural network-based sequence embedding technique using Poisson regression is proposed. We first provide a theoretical analysis of the impact of embedding dimension on model performance and present a criterion for selecting an appropriate embedding dimension. Under this embedding dimension, the Poisson regression is introduced by assuming the Levenshtein distance between sequences of fixed length following a Poisson distribution, which naturally aligns with the definition of Levenshtein distance. Moreover, from the perspective of the distribution of embedding distances, Poisson regression approximates the negative log likelihood of the chi-squared distribution and offers advancements in removing the skewness. Through comprehensive experiments on real DNA storage data, we demonstrate the superior performance of the proposed method compared to state-of-the-art approaches.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

In many domains, autoregressive models can attain high likelihood on the task of predicting the next observation. However, this maximum-likelihood (MLE) objective does not necessarily match a downstream use-case of autoregressively generating high-quality sequences. The MLE objective weights sequences proportionally to their frequency under the data distribution, with no guidance for the model's behaviour out of distribution (OOD): leading to compounding error during autoregressive generation. In order to address this compounding error problem, we formulate sequence generation as an imitation learning (IL) problem. This allows us to minimize a variety of divergences between the distribution of sequences generated by an autoregressive model and sequences from a dataset, including divergences with weight on OOD generated sequences. The IL framework also allows us to incorporate backtracking by introducing a backspace action into the generation process. This further mitigates the compounding error problem by allowing the model to revert a sampled token if it takes the sequence OOD. Our resulting method, SequenceMatch, can be implemented without adversarial training or major architectural changes. We identify the SequenceMatch-chi^2 divergence as a more suitable training objective for autoregressive models which are used for generation. We show that empirically, SequenceMatch training leads to improvements over MLE on text generation with language models.

Sequence-to-sequence models excel at handling natural language variation, but have been shown to struggle with out-of-distribution compositional generalization. This has motivated new specialized architectures with stronger compositional biases, but most of these approaches have only been evaluated on synthetically-generated datasets, which are not representative of natural language variation. In this work we ask: can we develop a semantic parsing approach that handles both natural language variation and compositional generalization? To better assess this capability, we propose new train and test splits of non-synthetic datasets. We demonstrate that strong existing approaches do not perform well across a broad set of evaluations. We also propose NQG-T5, a hybrid model that combines a high-precision grammar-based approach with a pre-trained sequence-to-sequence model. It outperforms existing approaches across several compositional generalization challenges on non-synthetic data, while also being competitive with the state-of-the-art on standard evaluations. While still far from solving this problem, our study highlights the importance of diverse evaluations and the open challenge of handling both compositional generalization and natural language variation in semantic parsing.

Extending the context length (i.e., the maximum supported sequence length) of LLMs is of paramount significance. To facilitate long context training of LLMs, sequence parallelism has emerged as an essential technique, which scatters each input sequence across multiple devices and necessitates communication to process the sequence. In essence, existing sequence parallelism methods assume homogeneous sequence lengths (i.e., all input sequences are equal in length) and therefore leverages a single, static scattering strategy for all input sequences. However, in reality, the sequence lengths in LLM training corpora exhibit substantial variability, often following a long-tail distribution, which leads to workload heterogeneity. In this paper, we show that employing a single, static strategy results in inefficiency and resource under-utilization, highlighting the need for adaptive approaches to handle the heterogeneous workloads across sequences. To address this, we propose a heterogeneity-adaptive sequence parallelism method. For each training step, our approach captures the variability in sequence lengths and assigns the optimal combination of scattering strategies based on workload characteristics. We model this problem as a linear programming optimization and design an efficient and effective solver to find the optimal solution. Furthermore, we implement our method in a high-performance system that supports adaptive parallelization in distributed LLM training. Experimental results demonstrate that our system outperforms state-of-the-art training frameworks by up to 1.98x.

A central challenge in sequence modeling is efficiently handling tasks with extended contexts. While recent state-space models (SSMs) have made significant progress in this area, they often lack input-dependent filtering or require substantial increases in model complexity to handle input variability. We address this gap by introducing S7, a simplified yet powerful SSM that can handle input dependence while incorporating stable reparameterization and specific design choices to dynamically adjust state transitions based on input content, maintaining efficiency and performance. We prove that this reparameterization ensures stability in long-sequence modeling by keeping state transitions well-behaved over time. Additionally, it controls the gradient norm, enabling efficient training and preventing issues like exploding or vanishing gradients. S7 significantly outperforms baselines across various sequence modeling tasks, including neuromorphic event-based datasets, Long Range Arena benchmarks, and various physical and biological time series. Overall, S7 offers a more straightforward approach to sequence modeling without relying on complex, domain-specific inductive biases, achieving significant improvements across key benchmarks.

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

Recent sequence modeling approaches using selective state space sequence models, referred to as Mamba models, have seen a surge of interest. These models allow efficient processing of long sequences in linear time and are rapidly being adopted in a wide range of applications such as language modeling, demonstrating promising performance. To foster their reliable use in real-world scenarios, it is crucial to augment their transparency. Our work bridges this critical gap by bringing explainability, particularly Layer-wise Relevance Propagation (LRP), to the Mamba architecture. Guided by the axiom of relevance conservation, we identify specific components in the Mamba architecture, which cause unfaithful explanations. To remedy this issue, we propose MambaLRP, a novel algorithm within the LRP framework, which ensures a more stable and reliable relevance propagation through these components. Our proposed method is theoretically sound and excels in achieving state-of-the-art explanation performance across a diverse range of models and datasets. Moreover, MambaLRP facilitates a deeper inspection of Mamba architectures, uncovering various biases and evaluating their significance. It also enables the analysis of previous speculations regarding the long-range capabilities of Mamba models.

This paper presents Okapi, a new dataset for Natural Language to executable web Application Programming Interfaces (NL2API). This dataset is in English and contains 22,508 questions and 9,019 unique API calls, covering three domains. We define new compositional generalization tasks for NL2API which explore the models' ability to extrapolate from simple API calls in the training set to new and more complex API calls in the inference phase. Also, the models are required to generate API calls that execute correctly as opposed to the existing approaches which evaluate queries with placeholder values. Our dataset is different than most of the existing compositional semantic parsing datasets because it is a non-synthetic dataset studying the compositional generalization in a low-resource setting. Okapi is a step towards creating realistic datasets and benchmarks for studying compositional generalization alongside the existing datasets and tasks. We report the generalization capabilities of sequence-to-sequence baseline models trained on a variety of the SCAN and Okapi datasets tasks. The best model achieves 15\% exact match accuracy when generalizing from simple API calls to more complex API calls. This highlights some challenges for future research. Okapi dataset and tasks are publicly available at https://aka.ms/nl2api/data.

Training monolingual language models for low and mid-resource languages is made challenging by limited and often inadequate pretraining data. In this study, we propose a novel model conversion strategy to address this issue, adapting high-resources monolingual language models to a new target language. By generalizing over a word translation dictionary encompassing both the source and target languages, we map tokens from the target tokenizer to semantically similar tokens from the source language tokenizer. This one-to-many token mapping improves tremendously the initialization of the embedding table for the target language. We conduct experiments to convert high-resource models to mid- and low-resource languages, namely Dutch and Frisian. These converted models achieve a new state-of-the-art performance on these languages across all sorts of downstream tasks. By reducing significantly the amount of data and time required for training state-of-the-art models, our novel model conversion strategy has the potential to benefit many languages worldwide.

Since self-attention layers in Transformers are permutation invariant by design, positional encodings must be explicitly incorporated to enable spatial understanding. However, fixed-size lookup tables used in traditional learnable position embeddings (PEs) limit extrapolation capabilities beyond pre-trained sequence lengths. Expert-designed methods such as ALiBi and RoPE, mitigate this limitation but demand extensive modifications for adapting to new modalities, underscoring fundamental challenges in adaptability and scalability. In this work, we present SeqPE, a unified and fully learnable position encoding framework that represents each n-dimensional position index as a symbolic sequence and employs a lightweight sequential position encoder to learn their embeddings in an end-to-end manner. To regularize SeqPE's embedding space, we introduce two complementary objectives: a contrastive objective that aligns embedding distances with a predefined position-distance function, and a knowledge distillation loss that anchors out-of-distribution position embeddings to in-distribution teacher representations, further enhancing extrapolation performance. Experiments across language modeling, long-context question answering, and 2D image classification demonstrate that SeqPE not only surpasses strong baselines in perplexity, exact match (EM), and accuracy--particularly under context length extrapolation--but also enables seamless generalization to multi-dimensional inputs without requiring manual architectural redesign. We release our code, data, and checkpoints at https://github.com/ghrua/seqpe.

Linear Recurrence has proven to be a powerful tool for modeling long sequences efficiently. In this work, we show that existing models fail to take full advantage of its potential. Motivated by this finding, we develop GateLoop, a foundational sequence model that generalizes linear recurrent models such as S4, S5, LRU and RetNet, by employing data-controlled state transitions. Utilizing this theoretical advance, GateLoop empirically outperforms existing models for auto-regressive language modeling. Our method comes with a low-cost O(l) recurrent mode and an efficient O(l log_{2} l) parallel mode making use of highly optimized associative scan implementations. Furthermore, we derive an O(l^2) surrogate attention mode, revealing remarkable implications for Transformer and recently proposed architectures. Specifically, we prove that our approach can be interpreted as providing data-controlled relative-positional information to Attention. While many existing models solely rely on data-controlled cumulative sums for context aggregation, our findings suggest that incorporating data-controlled complex cumulative products may be a crucial step towards more powerful sequence models.

This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible completions and evaluating these completions based on model confidence. By considering various paths in the search tree and scoring them according to the model's confidence in each completion, we can generate diverse and high-quality sequences. This research explores the implementation of this paradigm by using confidence as a proxy for response quality akin to beam search vijayakumar2016diverse. The primary goal of this paper is to outline the paradigm and demonstrate its potential, rather than focusing on achieving perfect results. The paper will outline the reasons why we believe this paradigm has the potential to improve LLMs in the following manners: 1) increase output quality, 2) decrease errors, 3) eliminate or reduce the compound error problems, 4) generate diverse and creative completions, 5) allow for iterative problem-solving, and 6) self-training. We expect this approach to yield a set of diverse and coherent sequences, offering insights into balancing exploration and exploitation in sequence generation. Potential applications include creative text generation tasks, such as storytelling and content creation, as well as other natural language processing domains, like machine translation and automated summarization. The goal is that the model will be far more effective as it will be able to consider many possible variations allowing it to find the ideal completion. This research aims to contribute to the understanding of effective search strategies in sequence generation and their impact on generating high-quality, varied textual outputs.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

We present significant extensions to diffusion-based sequence generation models, blurring the line with autoregressive language models. We introduce hyperschedules, which assign distinct noise schedules to individual token positions, generalizing both autoregressive models (e.g., GPT) and conventional diffusion models (e.g., SEDD, MDLM) as special cases. Second, we propose two hybrid token-wise noising processes that interpolate between absorbing and uniform processes, enabling the model to fix past mistakes, and we introduce a novel inference algorithm that leverages this new feature in a simplified context inspired from MDLM. To support efficient training and inference, we design attention masks compatible with KV-caching. Our methods achieve state-of-the-art perplexity and generate diverse, high-quality sequences across standard benchmarks, suggesting a promising path for autoregressive diffusion-based sequence generation.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

For most deep learning practitioners, sequence modeling is synonymous with recurrent networks. Yet recent results indicate that convolutional architectures can outperform recurrent networks on tasks such as audio synthesis and machine translation. Given a new sequence modeling task or dataset, which architecture should one use? We conduct a systematic evaluation of generic convolutional and recurrent architectures for sequence modeling. The models are evaluated across a broad range of standard tasks that are commonly used to benchmark recurrent networks. Our results indicate that a simple convolutional architecture outperforms canonical recurrent networks such as LSTMs across a diverse range of tasks and datasets, while demonstrating longer effective memory. We conclude that the common association between sequence modeling and recurrent networks should be reconsidered, and convolutional networks should be regarded as a natural starting point for sequence modeling tasks. To assist related work, we have made code available at http://github.com/locuslab/TCN .

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding nine-species benchmark of de novo peptide sequencing show that our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Code is available at https://github.com/BEAM-Labs/denovo.

State of the art sequence-to-sequence models for large scale tasks perform a fixed number of computations for each input sequence regardless of whether it is easy or hard to process. In this paper, we train Transformer models which can make output predictions at different stages of the network and we investigate different ways to predict how much computation is required for a particular sequence. Unlike dynamic computation in Universal Transformers, which applies the same set of layers iteratively, we apply different layers at every step to adjust both the amount of computation as well as the model capacity. On IWSLT German-English translation our approach matches the accuracy of a well tuned baseline Transformer while using less than a quarter of the decoder layers.

Recent advancements in sequence modeling have led to the emergence of Structured State Space Models (SSMs) as an efficient alternative to Recurrent Neural Networks (RNNs) and Transformers, addressing challenges in long-range dependency modeling and computational efficiency. While RNNs suffer from vanishing gradients and sequential inefficiencies, and Transformers face quadratic complexity, SSMs leverage structured recurrence and state-space representations to achieve superior long-sequence processing with linear or near-linear complexity. This survey provides a comprehensive review of SSMs, tracing their evolution from the foundational S4 model to its successors like Mamba, Simplified Structured State Space Sequence Model (S5), and Jamba, highlighting their improvements in computational efficiency, memory optimization, and inference speed. By comparing SSMs with traditional sequence models across domains such as natural language processing (NLP), speech recognition, vision, and time-series forecasting, we demonstrate their advantages in handling long-range dependencies while reducing computational overhead. Despite their potential, challenges remain in areas such as training optimization, hybrid modeling, and interpretability. This survey serves as a structured guide for researchers and practitioners, detailing the advancements, trade-offs, and future directions of SSM-based architectures in AI and deep learning.

Sequence models such as transformers require inputs to be represented as one-dimensional sequences. In vision, this typically involves flattening images using a fixed row-major (raster-scan) order. While full self-attention is permutation-equivariant, modern long-sequence transformers increasingly rely on architectural approximations that break this invariance and introduce sensitivity to patch ordering. We show that patch order significantly affects model performance in such settings, with simple alternatives like column-major or Hilbert curves yielding notable accuracy shifts. Motivated by this, we propose REOrder, a two-stage framework for discovering task-optimal patch orderings. First, we derive an information-theoretic prior by evaluating the compressibility of various patch sequences. Then, we learn a policy over permutations by optimizing a Plackett-Luce policy using REINFORCE. This approach enables efficient learning in a combinatorial permutation space. REOrder improves top-1 accuracy over row-major ordering on ImageNet-1K by up to 3.01% and Functional Map of the World by 13.35%.

Keyphrase Generation (KPG) is a longstanding task in NLP with widespread applications. The advent of sequence-to-sequence (seq2seq) pre-trained language models (PLMs) has ushered in a transformative era for KPG, yielding promising performance improvements. However, many design decisions remain unexplored and are often made arbitrarily. This paper undertakes a systematic analysis of the influence of model selection and decoding strategies on PLM-based KPG. We begin by elucidating why seq2seq PLMs are apt for KPG, anchored by an attention-driven hypothesis. We then establish that conventional wisdom for selecting seq2seq PLMs lacks depth: (1) merely increasing model size or performing task-specific adaptation is not parameter-efficient; (2) although combining in-domain pre-training with task adaptation benefits KPG, it does partially hinder generalization. Regarding decoding, we demonstrate that while greedy search achieves strong F1 scores, it lags in recall compared with sampling-based methods. Based on these insights, we propose DeSel, a likelihood-based decode-select algorithm for seq2seq PLMs. DeSel improves greedy search by an average of 4.7% semantic F1 across five datasets. Our collective findings pave the way for deeper future investigations into PLM-based KPG.

A booming amount of information is continuously added to the Internet as structured and unstructured data, feeding knowledge bases such as DBpedia and Wikidata with billions of statements describing millions of entities. The aim of Question Answering systems is to allow lay users to access such data using natural language without needing to write formal queries. However, users often submit questions that are complex and require a certain level of abstraction and reasoning to decompose them into basic graph patterns. In this short paper, we explore the use of architectures based on Neural Machine Translation called Neural SPARQL Machines to learn pattern compositions. We show that sequence-to-sequence models are a viable and promising option to transform long utterances into complex SPARQL queries.

Aligning large language models (LLMs) with human preferences is essential for their applications. Recently, decoding-time alignment has emerged as an effective plug-and-play technique that avoids fine-tuning model parameters. This approach retains the general utility of pretrained LLMs but often suffers from significant inefficiencies during decoding, primarily due to wasted token generation and excessive reward evaluations. To address these challenges, we introduce Cascade Reward Sampling (CARDS) to resolve both efficiency bottlenecks in decoding-time alignment. Specifically, we develop a segment-level rejection sampling algorithm that minimizes redundant computations of both LLMs and reward models (RMs). Central to CARDS is an uncertainty-based segmentation mechanism, which ensures the accuracy of RMs evaluations on incomplete segments. Furthermore, we provide a detailed analysis of reward scores on segments to elucidate the improved alignment performance. Experimental results demonstrate that CARDS significantly improves decoding efficiency, alignment quality, and general utility compared to existing decoding-time alignment methods, achieving approximately a 70% reduction in decoding time and over 90% win-ties in utility and safety benchmarks.

Several recent works have suggested to represent semantic relations with questions and answers, decomposing textual information into separate interrogative natural language statements. In this paper, we consider three QA-based semantic tasks - namely, QA-SRL, QANom and QADiscourse, each targeting a certain type of predication - and propose to regard them as jointly providing a comprehensive representation of textual information. To promote this goal, we investigate how to best utilize the power of sequence-to-sequence (seq2seq) pre-trained language models, within the unique setup of semi-structured outputs, consisting of an unordered set of question-answer pairs. We examine different input and output linearization strategies, and assess the effect of multitask learning and of simple data augmentation techniques in the setting of imbalanced training data. Consequently, we release the first unified QASem parsing tool, practical for downstream applications who can benefit from an explicit, QA-based account of information units in a text.

Neural text generation models are typically trained by maximizing log-likelihood with the sequence cross entropy (CE) loss, which encourages an exact token-by-token match between a target sequence with a generated sequence. Such training objective is sub-optimal when the target sequence is not perfect, e.g., when the target sequence is corrupted with noises, or when only weak sequence supervision is available. To address the challenge, we propose a novel Edit-Invariant Sequence Loss (EISL), which computes the matching loss of a target n-gram with all n-grams in the generated sequence. EISL is designed to be robust to various noises and edits in the target sequences. Moreover, the EISL computation is essentially an approximate convolution operation with target n-grams as kernels, which is easy to implement and efficient to compute with existing libraries. To demonstrate the effectiveness of EISL, we conduct experiments on a wide range of tasks, including machine translation with noisy target sequences, unsupervised text style transfer with only weak training signals, and non-autoregressive generation with non-predefined generation order. Experimental results show our method significantly outperforms the common CE loss and other strong baselines on all the tasks. EISL has a simple API that can be used as a drop-in replacement of the CE loss: https://github.com/guangyliu/EISL.

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

Neural sequence-to-sequence models are currently the dominant approach in several natural language processing tasks, but require large parallel corpora. We present a sequence-to-sequence-to-sequence autoencoder (SEQ^3), consisting of two chained encoder-decoder pairs, with words used as a sequence of discrete latent variables. We apply the proposed model to unsupervised abstractive sentence compression, where the first and last sequences are the input and reconstructed sentences, respectively, while the middle sequence is the compressed sentence. Constraining the length of the latent word sequences forces the model to distill important information from the input. A pretrained language model, acting as a prior over the latent sequences, encourages the compressed sentences to be human-readable. Continuous relaxations enable us to sample from categorical distributions, allowing gradient-based optimization, unlike alternatives that rely on reinforcement learning. The proposed model does not require parallel text-summary pairs, achieving promising results in unsupervised sentence compression on benchmark datasets.

Dynamic sequences with varying lengths have been widely used in the training of Transformer-based large language models (LLMs). However, current training frameworks adopt a pre-defined static parallel strategy for these sequences, causing neither communication-parallelization cancellation on short sequences nor out-of-memory on long sequences. To mitigate these issues, we propose ParaDySe, a novel adaptive Parallel strategy switching framework for Dynamic Sequences. ParaDySe enables on-the-fly optimal strategy adoption according to the immediate input sequence. It first implements the modular function libraries for parallel strategies with unified tensor layout specifications, and then builds sequence-aware memory and time cost models with hybrid methods. Guided by cost models, ParaDySe selects optimal layer-wise strategies for dynamic sequences via an efficient heuristic algorithm. By integrating these techniques together, ParaDySe achieves seamless hot-switching of optimal strategies through its well-designed function libraries. We compare ParaDySe with baselines on representative LLMs under datasets with sequence lengths up to 624K. Experimental results indicate that ParaDySe addresses OOM and CPC bottlenecks in LLM training by systematically integrating long-sequence optimizations with existing frameworks.

Recently, simultaneous translation has gathered a lot of attention since it enables compelling applications such as subtitle translation for a live event or real-time video-call translation. Some of these translation applications allow editing of partial translation giving rise to re-translation approaches. The current re-translation approaches are based on autoregressive sequence generation models (ReTA), which generate tar-get tokens in the (partial) translation sequentially. The multiple re-translations with sequential generation inReTAmodelslead to an increased inference time gap between the incoming source input and the corresponding target output as the source input grows. Besides, due to the large number of inference operations involved, the ReTA models are not favorable for resource-constrained devices. In this work, we propose a faster re-translation system based on a non-autoregressive sequence generation model (FReTNA) to overcome the aforementioned limitations. We evaluate the proposed model on multiple translation tasks and our model reduces the inference times by several orders and achieves a competitive BLEUscore compared to the ReTA and streaming (Wait-k) models.The proposed model reduces the average computation time by a factor of 20 when compared to the ReTA model by incurring a small drop in the translation quality. It also outperforms the streaming-based Wait-k model both in terms of computation time (1.5 times lower) and translation quality.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

We present a neural transducer model with visual attention that learns to generate LaTeX markup of a real-world math formula given its image. Applying sequence modeling and transduction techniques that have been very successful across modalities such as natural language, image, handwriting, speech and audio; we construct an image-to-markup model that learns to produce syntactically and semantically correct LaTeX markup code over 150 words long and achieves a BLEU score of 89%; improving upon the previous state-of-art for the Im2Latex problem. We also demonstrate with heat-map visualization how attention helps in interpreting the model and can pinpoint (detect and localize) symbols on the image accurately despite having been trained without any bounding box data.

Conditional language models are predominantly trained with maximum likelihood estimation (MLE), giving probability mass to sparsely observed target sequences. While MLE trained models assign high probability to plausible sequences given the context, the model probabilities often do not accurately rank-order generated sequences by quality. This has been empirically observed in beam search decoding as output quality degrading with large beam sizes, and decoding strategies benefiting from heuristics such as length normalization and repetition-blocking. In this work, we introduce sequence likelihood calibration (SLiC) where the likelihood of model generated sequences are calibrated to better align with reference sequences in the model's latent space. With SLiC, decoding heuristics become unnecessary and decoding candidates' quality significantly improves regardless of the decoding method. Furthermore, SLiC shows no sign of diminishing returns with model scale, and presents alternative ways to improve quality with limited training and inference budgets. With SLiC, we exceed or match SOTA results on a wide range of generation tasks spanning abstractive summarization, question generation, abstractive question answering and data-to-text generation, even with modest-sized models.

Deep autoregressive sequence-to-sequence models have demonstrated impressive performance across a wide variety of tasks in recent years. While common architecture classes such as recurrent, convolutional, and self-attention networks make different trade-offs between the amount of computation needed per layer and the length of the critical path at training time, generation still remains an inherently sequential process. To overcome this limitation, we propose a novel blockwise parallel decoding scheme in which we make predictions for multiple time steps in parallel then back off to the longest prefix validated by a scoring model. This allows for substantial theoretical improvements in generation speed when applied to architectures that can process output sequences in parallel. We verify our approach empirically through a series of experiments using state-of-the-art self-attention models for machine translation and image super-resolution, achieving iteration reductions of up to 2x over a baseline greedy decoder with no loss in quality, or up to 7x in exchange for a slight decrease in performance. In terms of wall-clock time, our fastest models exhibit real-time speedups of up to 4x over standard greedy decoding.

Autoregressive modeling has been a huge success in the field of natural language processing (NLP). Recently, autoregressive models have emerged as a significant area of focus in computer vision, where they excel in producing high-quality visual content. Autoregressive models in NLP typically operate on subword tokens. However, the representation strategy in computer vision can vary in different levels, i.e., pixel-level, token-level, or scale-level, reflecting the diverse and hierarchical nature of visual data compared to the sequential structure of language. This survey comprehensively examines the literature on autoregressive models applied to vision. To improve readability for researchers from diverse research backgrounds, we start with preliminary sequence representation and modeling in vision. Next, we divide the fundamental frameworks of visual autoregressive models into three general sub-categories, including pixel-based, token-based, and scale-based models based on the strategy of representation. We then explore the interconnections between autoregressive models and other generative models. Furthermore, we present a multi-faceted categorization of autoregressive models in computer vision, including image generation, video generation, 3D generation, and multi-modal generation. We also elaborate on their applications in diverse domains, including emerging domains such as embodied AI and 3D medical AI, with about 250 related references. Finally, we highlight the current challenges to autoregressive models in vision with suggestions about potential research directions. We have also set up a Github repository to organize the papers included in this survey at: https://github.com/ChaofanTao/Autoregressive-Models-in-Vision-Survey.

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

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

The most fundamental capability of modern AI methods such as Large Language Models (LLMs) is the ability to predict the next token in a long sequence of tokens, known as ``sequence modeling." Although the Transformers model is the current dominant approach to sequence modeling, its quadratic computational cost with respect to sequence length is a significant drawback. State-space models (SSMs) offer a promising alternative due to their linear decoding efficiency and high parallelizability during training. However, existing SSMs often rely on seemingly ad hoc linear recurrence designs. In this work, we explore SSM design through the lens of online learning, conceptualizing SSMs as meta-modules for specific online learning problems. This approach links SSM design to formulating precise online learning objectives, with state transition rules derived from optimizing these objectives. Based on this insight, we introduce a novel deep SSM architecture based on the implicit update for optimizing an online regression objective. Our experimental results show that our models outperform state-of-the-art SSMs, including the Mamba model, on standard sequence modeling benchmarks and language modeling tasks.

Recently, substantial progress has been made in text ranking based on pretrained language models such as BERT. However, there are limited studies on how to leverage more powerful sequence-to-sequence models such as T5. Existing attempts usually formulate text ranking as classification and rely on postprocessing to obtain a ranked list. In this paper, we propose RankT5 and study two T5-based ranking model structures, an encoder-decoder and an encoder-only one, so that they not only can directly output ranking scores for each query-document pair, but also can be fine-tuned with "pairwise" or "listwise" ranking losses to optimize ranking performances. Our experiments show that the proposed models with ranking losses can achieve substantial ranking performance gains on different public text ranking data sets. Moreover, when fine-tuned with listwise ranking losses, the ranking model appears to have better zero-shot ranking performance on out-of-domain data sets compared to the model fine-tuned with classification losses.

Sequential dependencies present a fundamental bottleneck in deploying large-scale autoregressive models, particularly for real-time applications. While traditional optimization approaches like pruning and quantization often compromise model quality, recent advances in generation-refinement frameworks demonstrate that this trade-off can be significantly mitigated. This survey presents a comprehensive taxonomy of generation-refinement frameworks, analyzing methods across autoregressive sequence tasks. We categorize methods based on their generation strategies (from simple n-gram prediction to sophisticated draft models) and refinement mechanisms (including single-pass verification and iterative approaches). Through systematic analysis of both algorithmic innovations and system-level implementations, we examine deployment strategies across computing environments and explore applications spanning text, images, and speech generation. This systematic examination of both theoretical frameworks and practical implementations provides a foundation for future research in efficient autoregressive decoding.

Sequence-to-sequence models have been used to transform erroneous programs into correct ones when trained with a large enough dataset. Some recent studies also demonstrated strong empirical evidence that code review could improve the program repair further. Large language models, trained with Natural Language (NL) and Programming Language (PL), can contain inherent knowledge of both. In this study, we investigate if this inherent knowledge of PL and NL can be utilized to improve automated program repair. We applied PLBART and CodeT5, two state-of-the-art language models that are pre-trained with both PL and NL, on two such natural language-based program repair datasets and found that the pre-trained language models fine-tuned with datasets containing both code review and subsequent code changes notably outperformed each of the previous models. With the advent of code generative models like Codex and GPT-3.5-Turbo, we also performed zero-shot and few-shots learning-based prompt engineering to assess their performance on these datasets. However, the practical application of using LLMs in the context of automated program repair is still a long way off based on our manual analysis of the generated repaired codes by the learning models.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

In the last years, the Linked Data Cloud has achieved a size of more than 100 billion facts pertaining to a multitude of domains. However, accessing this information has been significantly challenging for lay users. Approaches to problems such as Question Answering on Linked Data and Link Discovery have notably played a role in increasing information access. These approaches are often based on handcrafted and/or statistical models derived from data observation. Recently, Deep Learning architectures based on Neural Networks called seq2seq have shown to achieve state-of-the-art results at translating sequences into sequences. In this direction, we propose Neural SPARQL Machines, end-to-end deep architectures to translate any natural language expression into sentences encoding SPARQL queries. Our preliminary results, restricted on selected DBpedia classes, show that Neural SPARQL Machines are a promising approach for Question Answering on Linked Data, as they can deal with known problems such as vocabulary mismatch and perform graph pattern composition.

In this paper we propose a Sequential Representation Quantization AutoEncoder (SeqRQ-AE) to learn from primarily unpaired audio data and produce sequences of representations very close to phoneme sequences of speech utterances. This is achieved by proper temporal segmentation to make the representations phoneme-synchronized, and proper phonetic clustering to have total number of distinct representations close to the number of phonemes. Mapping between the distinct representations and phonemes is learned from a small amount of annotated paired data. Preliminary experiments on LJSpeech demonstrated the learned representations for vowels have relative locations in latent space in good parallel to that shown in the IPA vowel chart defined by linguistics experts. With less than 20 minutes of annotated speech, our method outperformed existing methods on phoneme recognition and is able to synthesize intelligible speech that beats our baseline model.

Autoregressive models (ARMs), which predict subsequent tokens one-by-one ``from left to right,'' have achieved significant success across a wide range of sequence generation tasks. However, they struggle to accurately represent sequences that require satisfying sophisticated constraints or whose sequential dependencies are better addressed by out-of-order generation. Masked Diffusion Models (MDMs) address some of these limitations, but the process of unmasking multiple tokens simultaneously in MDMs can introduce incoherences, and MDMs cannot handle arbitrary infilling constraints when the number of tokens to be filled in is not known in advance. In this work, we introduce Insertion Language Models (ILMs), which learn to insert tokens at arbitrary positions in a sequence -- that is, they select jointly both the position and the vocabulary element to be inserted. By inserting tokens one at a time, ILMs can represent strong dependencies between tokens, and their ability to generate sequences in arbitrary order allows them to accurately model sequences where token dependencies do not follow a left-to-right sequential structure. To train ILMs, we propose a tailored network parameterization and use a simple denoising objective. Our empirical evaluation demonstrates that ILMs outperform both ARMs and MDMs on common planning tasks. Furthermore, we show that ILMs outperform MDMs and perform on par with ARMs in an unconditional text generation task while offering greater flexibility than MDMs in arbitrary-length text infilling.

Training keyphrase generation (KPG) models require a large amount of annotated data, which can be prohibitively expensive and often limited to specific domains. In this study, we first demonstrate that large distribution shifts among different domains severely hinder the transferability of KPG models. We then propose a three-stage pipeline, which gradually guides KPG models' learning focus from general syntactical features to domain-related semantics, in a data-efficient manner. With Domain-general Phrase pre-training, we pre-train Sequence-to-Sequence models with generic phrase annotations that are widely available on the web, which enables the models to generate phrases in a wide range of domains. The resulting model is then applied in the Transfer Labeling stage to produce domain-specific pseudo keyphrases, which help adapt models to a new domain. Finally, we fine-tune the model with limited data with true labels to fully adapt it to the target domain. Our experiment results show that the proposed process can produce good-quality keyphrases in new domains and achieve consistent improvements after adaptation with limited in-domain annotated data. All code and datasets are available at https://github.com/memray/OpenNMT-kpg-release.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Modern recurrent architectures, such as xLSTM and Mamba, have recently challenged the Transformer in language modeling. However, their structure constrains their applicability to sequences only or requires processing multi-dimensional data structures, such as images or molecular graphs, in a pre-defined sequential order. In contrast, Multi-Dimensional RNNs (MDRNNs) are well suited for data with a higher level structure, like 2D grids, trees, and directed acyclic graphs (DAGs). In this work, we extend the notion of multi-dimensionality to linear RNNs. We introduce parallelizable Linear Source Transition Mark networks (pLSTMs) using Source, Transition, and Mark gates that act on the line graph of a general DAG. This enables parallelization in analogy to parallel associative scans and the chunkwise-recurrent form of sequential linear RNNs, but for DAGs. For regular grids (1D and 2D), like images, this scheme can be efficiently implemented using einsum operations, concatenations, and padding in logarithmic time. pLSTMs tackle the vanishing/exploding activation/gradient problem for long distances in DAGs via two distinct modes: a directed propagation mode (P-mode) and a diffusive distribution mode (D-mode). To showcase the long-range capabilities of pLSTM, we introduce arrow-pointing extrapolation as a synthetic computer vision task that contains long-distance directional information. We demonstrate that pLSTMs generalize well to larger image sizes, whereas Transformers struggle to extrapolate. On established molecular graph and computer vision benchmarks, pLSTMs also show strong performance. Code and Datasets are available at: https://github.com/ml-jku/plstm_experiments.

Large language models (LLMs) have emerged as a cornerstone in real-world applications with lengthy streaming inputs, such as LLM-driven agents. However, existing LLMs, pre-trained on sequences with restricted maximum length, cannot generalize to longer sequences due to the out-of-domain and distraction issues. To alleviate these issues, existing efforts employ sliding attention windows and discard distant tokens to achieve the processing of extremely long sequences. Unfortunately, these approaches inevitably fail to capture long-distance dependencies within sequences to deeply understand semantics. This paper introduces a training-free memory-based method, InfLLM, to unveil the intrinsic ability of LLMs to process streaming long sequences. Specifically, InfLLM stores distant contexts into additional memory units and employs an efficient mechanism to lookup token-relevant units for attention computation. Thereby, InfLLM allows LLMs to efficiently process long sequences while maintaining the ability to capture long-distance dependencies. Without any training, InfLLM enables LLMs pre-trained on sequences of a few thousand tokens to achieve superior performance than competitive baselines continually training these LLMs on long sequences. Even when the sequence length is scaled to 1,024K, InfLLM still effectively captures long-distance dependencies.