Daily Papers

Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models.

We study the fractal structure of language, aiming to provide a precise formalism for quantifying properties that may have been previously suspected but not formally shown. We establish that language is: (1) self-similar, exhibiting complexities at all levels of granularity, with no particular characteristic context length, and (2) long-range dependent (LRD), with a Hurst parameter of approximately H=0.70. Based on these findings, we argue that short-term patterns/dependencies in language, such as in paragraphs, mirror the patterns/dependencies over larger scopes, like entire documents. This may shed some light on how next-token prediction can lead to a comprehension of the structure of text at multiple levels of granularity, from words and clauses to broader contexts and intents. We also demonstrate that fractal parameters improve upon perplexity-based bits-per-byte (BPB) in predicting downstream performance. We hope these findings offer a fresh perspective on language and the mechanisms underlying the success of LLMs.

Code completion is an essential feature of IDEs, yet current autocompleters are restricted to either grammar-based or NLP-based single token completions. Both approaches have significant drawbacks: grammar-based autocompletion is restricted in dynamically-typed language environments, whereas NLP-based autocompleters struggle to understand the semantics of the programming language and the developer's code context. In this work, we present CodeFill, a language model for autocompletion that combines learned structure and naming information. Using a parallel Transformer architecture and multi-task learning, CodeFill consumes sequences of source code token names and their equivalent AST token types. Uniquely, CodeFill is trained both for single-token and multi-token (statement) prediction, which enables it to learn long-range dependencies among grammatical and naming elements. We train CodeFill on two datasets, consisting of 29M and 425M lines of code, respectively. To make the evaluation more realistic, we develop a method to automatically infer points in the source code at which completion matters. We compare CodeFill against four baselines and two state-of-the-art models, GPT-C and TravTrans+.CodeFill surpasses all baselines in single token prediction (MRR: 70.9% vs. 66.2% and 67.8%) and outperforms the state of the art for multi-token prediction (ROUGE-L: 63.7% vs. 52.4% and 59.2%, for n=4 tokens). We publicly release our source code and datasets.

Entity linking is a prominent thread of research focused on structured data creation by linking spans of text to an ontology or knowledge source. We revisit the use of structured prediction for entity linking which classifies each individual input token as an entity, and aggregates the token predictions. Our system, called SpEL (Structured prediction for Entity Linking) is a state-of-the-art entity linking system that uses some new ideas to apply structured prediction to the task of entity linking including: two refined fine-tuning steps; a context sensitive prediction aggregation strategy; reduction of the size of the model's output vocabulary, and; we address a common problem in entity-linking systems where there is a training vs. inference tokenization mismatch. Our experiments show that we can outperform the state-of-the-art on the commonly used AIDA benchmark dataset for entity linking to Wikipedia. Our method is also very compute efficient in terms of number of parameters and speed of inference.

Large Language Models (LLMs) for code are a family of high-parameter, transformer-based neural networks pre-trained on massive datasets of both natural and programming languages. These models are rapidly being employed in commercial AI-based developer tools, such as GitHub CoPilot. However, measuring and explaining their effectiveness on programming tasks is a challenging proposition, given their size and complexity. The methods for evaluating and explaining LLMs for code are inextricably linked. That is, in order to explain a model's predictions, they must be reliably mapped to fine-grained, understandable concepts. Once this mapping is achieved, new methods for detailed model evaluations are possible. However, most current explainability techniques and evaluation benchmarks focus on model robustness or individual task performance, as opposed to interpreting model predictions. To this end, this paper introduces ASTxplainer, an explainability method specific to LLMs for code that enables both new methods for LLM evaluation and visualizations of LLM predictions that aid end-users in understanding model predictions. At its core, ASTxplainer provides an automated method for aligning token predictions with AST nodes, by extracting and aggregating normalized model logits within AST structures. To demonstrate the practical benefit of ASTxplainer, we illustrate the insights that our framework can provide by performing an empirical evaluation on 12 popular LLMs for code using a curated dataset of the most popular GitHub projects. Additionally, we perform a user study examining the usefulness of an ASTxplainer-derived visualization of model predictions aimed at enabling model users to explain predictions. The results of these studies illustrate the potential for ASTxplainer to provide insights into LLM effectiveness, and aid end-users in understanding predictions.

Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but lack the structural knowledge essential for many biological applications. To address this, we integrate structural insights from pre-trained protein graph neural networks (pGNNs) into pLMs through a latent-level contrastive learning task. This task aligns residue representations from pLMs with those from pGNNs across multiple proteins, enriching pLMs with inter-protein structural knowledge. Additionally, we incorporate a physical-level task that infuses intra-protein structural knowledge by optimizing pLMs to predict structural tokens. The proposed dual-task framework effectively incorporates both inter-protein and intra-protein structural knowledge into pLMs. Given the variability in the quality of protein structures in PDB, we further introduce a residue loss selection module, which uses a small model trained on high-quality structures to select reliable yet challenging residue losses for the pLM to learn. Applying our structure alignment method to the state-of-the-art ESM2 and AMPLIFY results in notable performance gains across a wide range of tasks, including a 12.7% increase in ESM2 contact prediction. The data, code, and resulting SaESM2 and SaAMPLIFY models will be released on Hugging Face.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

We introduce TreeMeshGPT, an autoregressive Transformer designed to generate high-quality artistic meshes aligned with input point clouds. Instead of the conventional next-token prediction in autoregressive Transformer, we propose a novel Autoregressive Tree Sequencing where the next input token is retrieved from a dynamically growing tree structure that is built upon the triangle adjacency of faces within the mesh. Our sequencing enables the mesh to extend locally from the last generated triangular face at each step, and therefore reduces training difficulty and improves mesh quality. Our approach represents each triangular face with two tokens, achieving a compression rate of approximately 22% compared to the naive face tokenization. This efficient tokenization enables our model to generate highly detailed artistic meshes with strong point cloud conditioning, surpassing previous methods in both capacity and fidelity. Furthermore, our method generates mesh with strong normal orientation constraints, minimizing flipped normals commonly encountered in previous methods. Our experiments show that TreeMeshGPT enhances the mesh generation quality with refined details and normal orientation consistency.

Self-supervised pre-training based on next-token prediction has enabled large language models to capture the underlying structure of text, and has led to unprecedented performance on a large array of tasks when applied at scale. Similarly, autonomous driving generates vast amounts of spatiotemporal data, alluding to the possibility of harnessing scale to learn the underlying geometric and semantic structure of the environment and its evolution over time. In this direction, we propose a geometric and semantic self-supervised pre-training method, GASP, that learns a unified representation by predicting, at any queried future point in spacetime, (1) general occupancy, capturing the evolving structure of the 3D scene; (2) ego occupancy, modeling the ego vehicle path through the environment; and (3) distilled high-level features from a vision foundation model. By modeling geometric and semantic 4D occupancy fields instead of raw sensor measurements, the model learns a structured, generalizable representation of the environment and its evolution through time. We validate GASP on multiple autonomous driving benchmarks, demonstrating significant improvements in semantic occupancy forecasting, online mapping, and ego trajectory prediction. Our results demonstrate that continuous 4D geometric and semantic occupancy prediction provides a scalable and effective pre-training paradigm for autonomous driving. For code and additional visualizations, see \href{https://research.zenseact.com/publications/gasp/.

We present Chain-of-Action (CoA), a novel visuo-motor policy paradigm built upon Trajectory Autoregressive Modeling. Unlike conventional approaches that predict next step action(s) forward, CoA generates an entire trajectory by explicit backward reasoning with task-specific goals through an action-level Chain-of-Thought (CoT) process. This process is unified within a single autoregressive structure: (1) the first token corresponds to a stable keyframe action that encodes the task-specific goals; and (2) subsequent action tokens are generated autoregressively, conditioned on the initial keyframe and previously predicted actions. This backward action reasoning enforces a global-to-local structure, allowing each local action to be tightly constrained by the final goal. To further realize the action reasoning structure, CoA incorporates four complementary designs: continuous action token representation; dynamic stopping for variable-length trajectory generation; reverse temporal ensemble; and multi-token prediction to balance action chunk modeling with global structure. As a result, CoA gives strong spatial generalization capabilities while preserving the flexibility and simplicity of a visuo-motor policy. Empirically, we observe CoA achieves the state-of-the-art performance across 60 RLBench tasks and 8 real-world manipulation tasks.

We tackle the task of long-form music generation--particularly the challenging lyrics-to-song problem--by introducing YuE, a family of open foundation models based on the LLaMA2 architecture. Specifically, YuE scales to trillions of tokens and generates up to five minutes of music while maintaining lyrical alignment, coherent musical structure, and engaging vocal melodies with appropriate accompaniment. It achieves this through (1) track-decoupled next-token prediction to overcome dense mixture signals, (2) structural progressive conditioning for long-context lyrical alignment, and (3) a multitask, multiphase pre-training recipe to converge and generalize. In addition, we redesign the in-context learning technique for music generation, enabling versatile style transfer (e.g., converting Japanese city pop into an English rap while preserving the original accompaniment) and bidirectional generation. Through extensive evaluation, we demonstrate that YuE matches or even surpasses some of the proprietary systems in musicality and vocal agility. In addition, fine-tuning YuE enables additional controls and enhanced support for tail languages. Furthermore, beyond generation, we show that YuE's learned representations can perform well on music understanding tasks, where the results of YuE match or exceed state-of-the-art methods on the MARBLE benchmark. Keywords: lyrics2song, song generation, long-form, foundation model, music generation

Autoregressive (AR) modeling has achieved remarkable success in natural language processing by enabling models to generate text with coherence and contextual understanding through next token prediction. Recently, in image generation, VAR proposes scale-wise autoregressive modeling, which extends the next token prediction to the next scale prediction, preserving the 2D structure of images. However, VAR encounters two primary challenges: (1) its complex and rigid scale design limits generalization in next scale prediction, and (2) the generator's dependence on a discrete tokenizer with the same complex scale structure restricts modularity and flexibility in updating the tokenizer. To address these limitations, we introduce FlowAR, a general next scale prediction method featuring a streamlined scale design, where each subsequent scale is simply double the previous one. This eliminates the need for VAR's intricate multi-scale residual tokenizer and enables the use of any off-the-shelf Variational AutoEncoder (VAE). Our simplified design enhances generalization in next scale prediction and facilitates the integration of Flow Matching for high-quality image synthesis. We validate the effectiveness of FlowAR on the challenging ImageNet-256 benchmark, demonstrating superior generation performance compared to previous methods. Codes will be available at https://github.com/OliverRensu/FlowAR.

Both graph structures and textual information play a critical role in Knowledge Graph Completion (KGC). With the success of Pre-trained Language Models (PLMs) such as BERT, they have been applied for text encoding for KGC. However, the current methods mostly prefer to fine-tune PLMs, leading to huge training costs and limited scalability to larger PLMs. In contrast, we propose to utilize prompts and perform KGC on a frozen PLM with only the prompts trained. Accordingly, we propose a new KGC method named PDKGC with two prompts -- a hard task prompt which is to adapt the KGC task to the PLM pre-training task of token prediction, and a disentangled structure prompt which learns disentangled graph representation so as to enable the PLM to combine more relevant structure knowledge with the text information. With the two prompts, PDKGC builds a textual predictor and a structural predictor, respectively, and their combination leads to more comprehensive entity prediction. Solid evaluation on two widely used KGC datasets has shown that PDKGC often outperforms the baselines including the state-of-the-art, and its components are all effective. Our codes and data are available at https://github.com/genggengcss/PDKGC.

Uncertainty quantification (UQ) for open-ended language generation remains a critical yet underexplored challenge, especially under black-box constraints where internal model signals are inaccessible. In this paper, we introduce Token-Entropy Conformal Prediction (TECP), a novel framework that leverages token-level entropy as a logit-free, reference-free uncertainty measure and integrates it into a split conformal prediction (CP) pipeline to construct prediction sets with formal coverage guarantees. Unlike existing approaches that rely on semantic consistency heuristics or white-box features, TECP directly estimates epistemic uncertainty from the token entropy structure of sampled generations and calibrates uncertainty thresholds via CP quantiles to ensure provable error control. Empirical evaluations across six large language models and two benchmarks (CoQA and TriviaQA) demonstrate that TECP consistently achieves reliable coverage and compact prediction sets, outperforming prior self-consistency-based UQ methods. Our method provides a principled and efficient solution for trustworthy generation in black-box LLM settings.

Inspired by the impressive capabilities of GPT-4o, there is growing interest in enabling speech language models (SLMs) to engage in natural, fluid spoken interactions with humans. Recent advancements have led to the development of several SLMs that demonstrate promising results in this area. However, current approaches have yet to fully exploit dual-channel speech data, which inherently captures the structure and dynamics of human conversation. In this work, we systematically explore the use of dual-channel speech data in the context of modern large language models, and introduce a novel generative modeling paradigm, Next-Token-Pair Prediction (NTPP), to enable speaker-independent dual-channel spoken dialogue learning using decoder-only architectures for the first time. We evaluate our approach on standard benchmarks, and empirical results show that our proposed method, NTPP, significantly improves the conversational abilities of SLMs in terms of turn-taking prediction, response coherence, and naturalness. Moreover, compared to existing methods, NTPP achieves substantially lower inference latency, highlighting its practical efficiency for real-time applications.

Tokenization methods like Byte-Pair Encoding (BPE) enhance computational efficiency in large language models (LLMs) but often obscure internal character structures within tokens. This limitation hinders LLMs' ability to predict precise character positions, which is crucial in tasks like Chinese Spelling Correction (CSC) where identifying the positions of misspelled characters accelerates correction processes. We propose Token Internal Position Awareness (TIPA), a method that significantly improves models' ability to capture character positions within tokens by training them on reverse character prediction tasks using the tokenizer's vocabulary. Experiments demonstrate that TIPA enhances position prediction accuracy in LLMs, enabling more precise identification of target characters in original text. Furthermore, when applied to downstream tasks that do not require exact position prediction, TIPA still boosts performance in tasks needing character-level information, validating its versatility and effectiveness.

This paper presents DetailFlow, a coarse-to-fine 1D autoregressive (AR) image generation method that models images through a novel next-detail prediction strategy. By learning a resolution-aware token sequence supervised with progressively degraded images, DetailFlow enables the generation process to start from the global structure and incrementally refine details. This coarse-to-fine 1D token sequence aligns well with the autoregressive inference mechanism, providing a more natural and efficient way for the AR model to generate complex visual content. Our compact 1D AR model achieves high-quality image synthesis with significantly fewer tokens than previous approaches, i.e. VAR/VQGAN. We further propose a parallel inference mechanism with self-correction that accelerates generation speed by approximately 8x while reducing accumulation sampling error inherent in teacher-forcing supervision. On the ImageNet 256x256 benchmark, our method achieves 2.96 gFID with 128 tokens, outperforming VAR (3.3 FID) and FlexVAR (3.05 FID), which both require 680 tokens in their AR models. Moreover, due to the significantly reduced token count and parallel inference mechanism, our method runs nearly 2x faster inference speed compared to VAR and FlexVAR. Extensive experimental results demonstrate DetailFlow's superior generation quality and efficiency compared to existing state-of-the-art methods.

We present Probabilistic Structure Integration (PSI), a system for learning richly controllable and flexibly promptable world models from data. PSI consists of a three-step cycle. The first step, Probabilistic prediction, involves building a probabilistic graphical model Psi of the data, in the form of a random-access autoregressive sequence model. Psi supports a complete set of learned conditional distributions describing the dependence of any variables in the data on any other set of variables. In step 2, Structure extraction, we show how to extract underlying low-dimensional properties in the data, corresponding to a diverse set of meaningful "intermediate structures", in a zero-shot fashion via causal inference on Psi. Step 3, Integration, completes the cycle by converting these structures into new token types that are then continually mixed back into the training diet as conditioning signals and prediction targets. Each such cycle augments the capabilities of Psi, both allowing it to model the underlying data better, and creating new control handles -- akin to an LLM-like universal prompting language. We train an instance of Psi on 1.4 trillion tokens of internet video data; we use it to perform a variety of useful video prediction and understanding inferences; we extract state-of-the-art optical flow, self-supervised depth and object segmentation; and we use these structures to support a full cycle of predictive improvements.

Predicting drug-target interaction (DTI) is critical in the drug discovery process. Despite remarkable advances in recent DTI models through the integration of representations from diverse drug and target encoders, such models often struggle to capture the fine-grained interactions between drugs and protein, i.e. the binding of specific drug atoms (or substructures) and key amino acids of proteins, which is crucial for understanding the binding mechanisms and optimising drug design. To address this issue, this paper introduces a novel model, called FusionDTI, which uses a token-level Fusion module to effectively learn fine-grained information for Drug-Target Interaction. In particular, our FusionDTI model uses the SELFIES representation of drugs to mitigate sequence fragment invalidation and incorporates the structure-aware (SA) vocabulary of target proteins to address the limitation of amino acid sequences in structural information, additionally leveraging pre-trained language models extensively trained on large-scale biomedical datasets as encoders to capture the complex information of drugs and targets. Experiments on three well-known benchmark datasets show that our proposed FusionDTI model achieves the best performance in DTI prediction compared with seven existing state-of-the-art baselines. Furthermore, our case study indicates that FusionDTI could highlight the potential binding sites, enhancing the explainability of the DTI prediction.

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

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Large language models (LLMs) have achieved notable progress. Despite their success, next-token prediction (NTP), the dominant method for LLM training and inference, is constrained in both contextual coverage and inference efficiency due to its inherently sequential process. To overcome these challenges, we propose leap multi-token prediction~(L-MTP), an innovative token prediction method that extends the capabilities of multi-token prediction (MTP) by introducing a leap-based mechanism. Unlike conventional MTP, which generates multiple tokens at adjacent positions, L-MTP strategically skips over intermediate tokens, predicting non-sequential ones in a single forward pass. This structured leap not only enhances the model's ability to capture long-range dependencies but also enables a decoding strategy specially optimized for non-sequential leap token generation, effectively accelerating inference. We theoretically demonstrate the benefit of L-MTP in improving inference efficiency. Experiments across diverse benchmarks validate its merit in boosting both LLM performance and inference speed. The source code is available at https://github.com/Xiaohao-Liu/L-MTP.

Visual Planning for Assistance (VPA) aims to predict a sequence of user actions required to achieve a specified goal based on a video showing the user's progress. Although recent advances in multimodal large language models (MLLMs) have shown promising results in video understanding, long-horizon visual planning remains a challenging problem. We identify two challenges in training large MLLMs for video-based planning tasks: (1) scarcity of procedural annotations, limiting the model's ability to learn procedural task dynamics effectively, and (2) inefficiency of next-token prediction objective to explicitly capture the structured action space for visual planning when compared to free-form, natural language. To tackle data scarcity, we introduce Auxiliary Task Augmentation. We design and train our model on auxiliary tasks relevant to long-horizon video-based planning (e.g., goal prediction) to augment the model's planning ability. To more explicitly model the structured action space unique to visual planning tasks, we leverage Multi-token Prediction, extending traditional next-token prediction by using multiple heads to predict multiple future tokens during training. Our approach, VideoPlan, achieves state-of-the-art VPA performance on the COIN and CrossTask datasets, surpassing prior methods by 7.3% and 3.4%, respectively, when predicting 3 future actions. We further extend our method to the challenging Ego4D Long-term Action Anticipation task, and show that it is on par with the state-of-the-art approaches despite not using specialized egocentric features. Code will be made available.

Scene synthesis and editing has emerged as a promising direction in computer graphics. Current trained approaches for 3D indoor scenes either oversimplify object semantics through one-hot class encodings (e.g., 'chair' or 'table'), require masked diffusion for editing, ignore room boundaries, or rely on floor plan renderings that fail to capture complex layouts. In contrast, LLM-based methods enable richer semantics via natural language (e.g., 'modern studio with light wood furniture') but do not support editing, remain limited to rectangular layouts or rely on weak spatial reasoning from implicit world models. We introduce ReSpace, a generative framework for text-driven 3D indoor scene synthesis and editing using autoregressive language models. Our approach features a compact structured scene representation with explicit room boundaries that frames scene editing as a next-token prediction task. We leverage a dual-stage training approach combining supervised fine-tuning and preference alignment, enabling a specially trained language model for object addition that accounts for user instructions, spatial geometry, object semantics, and scene-level composition. For scene editing, we employ a zero-shot LLM to handle object removal and prompts for addition. We further introduce a novel voxelization-based evaluation that captures fine-grained geometry beyond 3D bounding boxes. Experimental results surpass state-of-the-art on object addition while maintaining competitive results on full scene synthesis.

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.

Large Language Models (LLMs) excel at generating fluent text but struggle to enforce external constraints because they generate tokens sequentially without explicit control mechanisms. GenCP addresses this limitation by combining LLM predictions with Constraint Programming (CP) reasoning, formulating text generation as a Constraint Satisfaction Problem (CSP). In this paper, we improve GenCP by integrating Masked Language Models (MLMs) for domain generation, which allows bidirectional constraint propagation that leverages both past and future tokens. This integration bridges the gap between token-level prediction and structured constraint enforcement, leading to more reliable and constraint-aware text generation. Our evaluation on COLLIE benchmarks demonstrates that incorporating domain preview via MLM calls significantly improves GenCP's performance. Although this approach incurs additional MLM calls and, in some cases, increased backtracking, the overall effect is a more efficient use of LLM inferences and an enhanced ability to generate feasible and meaningful solutions, particularly in tasks with strict content constraints.

Cross Attention is a popular method for retrieving information from a set of context tokens for making predictions. At inference time, for each prediction, Cross Attention scans the full set of O(N) tokens. In practice, however, often only a small subset of tokens are required for good performance. Methods such as Perceiver IO are cheap at inference as they distill the information to a smaller-sized set of latent tokens L < N on which cross attention is then applied, resulting in only O(L) complexity. However, in practice, as the number of input tokens and the amount of information to distill increases, the number of latent tokens needed also increases significantly. In this work, we propose Tree Cross Attention (TCA) - a module based on Cross Attention that only retrieves information from a logarithmic O(log(N)) number of tokens for performing inference. TCA organizes the data in a tree structure and performs a tree search at inference time to retrieve the relevant tokens for prediction. Leveraging TCA, we introduce ReTreever, a flexible architecture for token-efficient inference. We show empirically that Tree Cross Attention (TCA) performs comparable to Cross Attention across various classification and uncertainty regression tasks while being significantly more token-efficient. Furthermore, we compare ReTreever against Perceiver IO, showing significant gains while using the same number of tokens for inference.

Autoregressive (AR) modeling, known for its next-token prediction paradigm, underpins state-of-the-art language and visual generative models. Traditionally, a ``token'' is treated as the smallest prediction unit, often a discrete symbol in language or a quantized patch in vision. However, the optimal token definition for 2D image structures remains an open question. Moreover, AR models suffer from exposure bias, where teacher forcing during training leads to error accumulation at inference. In this paper, we propose xAR, a generalized AR framework that extends the notion of a token to an entity X, which can represent an individual patch token, a cell (a ktimes k grouping of neighboring patches), a subsample (a non-local grouping of distant patches), a scale (coarse-to-fine resolution), or even a whole image. Additionally, we reformulate discrete token classification as continuous entity regression, leveraging flow-matching methods at each AR step. This approach conditions training on noisy entities instead of ground truth tokens, leading to Noisy Context Learning, which effectively alleviates exposure bias. As a result, xAR offers two key advantages: (1) it enables flexible prediction units that capture different contextual granularity and spatial structures, and (2) it mitigates exposure bias by avoiding reliance on teacher forcing. On ImageNet-256 generation benchmark, our base model, xAR-B (172M), outperforms DiT-XL/SiT-XL (675M) while achieving 20times faster inference. Meanwhile, xAR-H sets a new state-of-the-art with an FID of 1.24, running 2.2times faster than the previous best-performing model without relying on vision foundation modules (\eg, DINOv2) or advanced guidance interval sampling.

Autoregressive models have achieved promising results in natural language processing. However, for image generation tasks, they encounter substantial challenges in effectively capturing long-range dependencies, managing computational costs, and most crucially, defining meaningful autoregressive sequences that reflect natural image hierarchies. To address these issues, we present Next-Frequency Image Generation (NFIG), a novel framework that decomposes the image generation process into multiple frequency-guided stages. Our approach first generates low-frequency components to establish global structure with fewer tokens, then progressively adds higher-frequency details, following the natural spectral hierarchy of images. This principled autoregressive sequence not only improves the quality of generated images by better capturing true causal relationships between image components, but also significantly reduces computational overhead during inference. Extensive experiments demonstrate that NFIG achieves state-of-the-art performance with fewer steps, offering a more efficient solution for image generation, with 1.25times speedup compared to VAR-d20 while achieving better performance (FID: 2.81) on the ImageNet-256 benchmark. We hope that our insight of incorporating frequency-domain knowledge to guide autoregressive sequence design will shed light on future research. We will make our code publicly available upon acceptance of the paper.

Prompt tuning for pre-trained masked language models (MLM) has shown promising performance in natural language processing tasks with few labeled examples. It tunes a prompt for the downstream task, and a verbalizer is used to bridge the predicted token and label prediction. Due to the limited training data, prompt initialization is crucial for prompt tuning. Recently, MetaPrompting (Hou et al., 2022) uses meta-learning to learn a shared initialization for all task-specific prompts. However, a single initialization is insufficient to obtain good prompts for all tasks and samples when the tasks are complex. Moreover, MetaPrompting requires tuning the whole MLM, causing a heavy burden on computation and memory as the MLM is usually large. To address these issues, we use a prompt pool to extract more task knowledge and construct instance-dependent prompts via attention. We further propose a novel soft verbalizer (RepVerb) which constructs label embedding from feature embeddings directly. Combining meta-learning the prompt pool and RepVerb, we propose MetaPrompter for effective structured prompting. MetaPrompter is parameter-efficient as only the pool is required to be tuned. Experimental results demonstrate that MetaPrompter performs better than the recent state-of-the-arts and RepVerb outperforms existing soft verbalizers.

Multimodal large language models (MLLMs) have made significant advancements in vision understanding and reasoning. However, the autoregressive Transformer architecture used by MLLMs requries tokenization on input images, which limits their ability to accurately ground objects within the 2D image space. This raises an important question: how can sequential language tokens be improved to better ground objects in 2D spatial space for MLLMs? To address this, we present a spatial representation method for grounding objects, namely GETok, that integrates a specialized vocabulary of learnable tokens into MLLMs. GETok first uses grid tokens to partition the image plane into structured spatial anchors, and then exploits offset tokens to enable precise and iterative refinement of localization predictions. By embedding spatial relationships directly into tokens, GETok significantly advances MLLMs in native 2D space reasoning without modifying the autoregressive architecture. Extensive experiments demonstrate that GETok achieves superior performance over the state-of-the-art methods across various referring tasks in both supervised fine-tuning and reinforcement learning settings.

Vision transformers have recently achieved competitive results across various vision tasks but still suffer from heavy computation costs when processing a large number of tokens. Many advanced approaches have been developed to reduce the total number of tokens in large-scale vision transformers, especially for image classification tasks. Typically, they select a small group of essential tokens according to their relevance with the class token, then fine-tune the weights of the vision transformer. Such fine-tuning is less practical for dense prediction due to the much heavier computation and GPU memory cost than image classification. In this paper, we focus on a more challenging problem, i.e., accelerating large-scale vision transformers for dense prediction without any additional re-training or fine-tuning. In response to the fact that high-resolution representations are necessary for dense prediction, we present two non-parametric operators, a token clustering layer to decrease the number of tokens and a token reconstruction layer to increase the number of tokens. The following steps are performed to achieve this: (i) we use the token clustering layer to cluster the neighboring tokens together, resulting in low-resolution representations that maintain the spatial structures; (ii) we apply the following transformer layers only to these low-resolution representations or clustered tokens; and (iii) we use the token reconstruction layer to re-create the high-resolution representations from the refined low-resolution representations. The results obtained by our method are promising on five dense prediction tasks, including object detection, semantic segmentation, panoptic segmentation, instance segmentation, and depth estimation.

The cross-lingual language models are typically pretrained with masked language modeling on multilingual text or parallel sentences. In this paper, we introduce denoising word alignment as a new cross-lingual pre-training task. Specifically, the model first self-labels word alignments for parallel sentences. Then we randomly mask tokens in a bitext pair. Given a masked token, the model uses a pointer network to predict the aligned token in the other language. We alternately perform the above two steps in an expectation-maximization manner. Experimental results show that our method improves cross-lingual transferability on various datasets, especially on the token-level tasks, such as question answering, and structured prediction. Moreover, the model can serve as a pretrained word aligner, which achieves reasonably low error rates on the alignment benchmarks. The code and pretrained parameters are available at https://github.com/CZWin32768/XLM-Align.

In-context learning (ICL) -- the capacity of a model to infer and apply abstract patterns from examples provided within its input -- has been extensively studied in large language models trained for next-token prediction on human text. In fact, prior work often attributes this emergent behavior to distinctive statistical properties in human language. This raises a fundamental question: can ICL arise organically in other sequence domains purely through large-scale predictive training? To explore this, we turn to genomic sequences, an alternative symbolic domain rich in statistical structure. Specifically, we study the Evo2 genomic model, trained predominantly on next-nucleotide (A/T/C/G) prediction, at a scale comparable to mid-sized LLMs. We develop a controlled experimental framework comprising symbolic reasoning tasks instantiated in both linguistic and genomic forms, enabling direct comparison of ICL across genomic and linguistic models. Our results show that genomic models, like their linguistic counterparts, exhibit log-linear gains in pattern induction as the number of in-context demonstrations increases. To the best of our knowledge, this is the first evidence of organically emergent ICL in genomic sequences, supporting the hypothesis that ICL arises as a consequence of large-scale predictive modeling over rich data. These findings extend emergent meta-learning beyond language, pointing toward a unified, modality-agnostic view of in-context learning.

Recent advances in natural language processing highlight two key factors for improving reasoning in large language models (LLMs): (i) allocating more test-time compute tends to help on harder problems but often introduces redundancy in the reasoning trace, and (ii) compute is most effective when reasoning is systematic and incremental, forming structured chains of thought (CoTs) akin to human problem-solving. To study these factors in isolation, we introduce a controlled setting based on shortest-path tasks in layered graphs. We train decoder-only transformers on question-trace-answer triples using a custom tokenizer, comparing models trained on optimal bottom-up dynamic programming traces with those trained on longer, valid traces involving backtracking. Surprisingly, with the same training-token budget, models trained on inefficient traces generalize better to unseen graphs. This benefit is not due to length alone-injecting arbitrary redundancy into reasoning traces fails to help and can even hurt performance. Instead, we find that generalization correlates with the model's confidence in next-token prediction, suggesting that long, coherent, and locally incremental traces make the training signal easier to optimize.

Large Language Models (LLMs) have become foundational to modern AI agent systems, enabling autonomous agents to reason and plan. In most existing systems, inter-agent communication relies primarily on natural language. While this design supports interpretability and human oversight, we argue that it introduces fundamental limitations in agent-to-agent coordination. The semantic space of natural language is structurally misaligned with the high-dimensional vector spaces in which LLMs operate, resulting in information loss and behavioral drift. Beyond surface-level inefficiencies, we highlight a deeper architectural limitation: current LLMs were not trained with the objective of supporting agentic behavior. As such, they lack mechanisms for modeling role continuity, task boundaries, and multi-agent dependencies. The standard next-token prediction paradigm fails to support the structural alignment required for robust, scalable agent coordination. Based on this, we argue that two core questions deserve careful examination: first, given that AI agents fundamentally operate in high-dimensional vector spaces, should they rely on a language system originally designed for human cognition as their communication medium? Second, should we consider developing a new model construction paradigm that builds models from the ground up to natively support structured communication, shared intentionality, and task alignment in multi-role, multi-agent environments? This paper calls for a reconsideration not only of how agents should communicate, but also of what it fundamentally means to train a model that natively supports multi-agent coordination and communication.

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled sequence-only (e.g., SMILES or SELFIES) generalist molecular LLMs, and researchers are now exploring multimodal approaches that incorporate molecular structural information for further gains. However, a genuinely multimodal, generalist LLM that covers a broad spectrum of molecular tasks has yet to be fully investigated. We observe that naive next token prediction training ignores graph-structural information, limiting an LLM's ability to exploit molecular graphs. To address this, we propose (i) Molecular structure Preference Optimization (MolPO), which facilitates graph usage by optimizing preferences between pairs of correct and perturbed molecular structures, and (ii) an advanced graph encoder with a tailored pre-training strategy to improve the effect of graph utilization by MolPO. Building on these contributions, we introduce Mol-LLM, the first multimodal generalist model that (a) handles a broad spectrum of molecular tasks among molecular LLMs, (b) explicitly leverages molecular-structure information, and (c) takes advantage of extensive instruction tuning. Mol-LLM attains state-of-the-art or comparable results across the most comprehensive molecular-LLM benchmark-even on out-of-distribution datasets for reaction and property prediction, where it surpasses prior generalist molecular LLMs by a large margin.

Autoregressive (AR) language models and Diffusion Language Models (DLMs) constitute the two principal paradigms of large language models. However, both paradigms suffer from insufficient reasoning capabilities. Human reasoning inherently relies on causal knowledge and thought, which are reflected in natural language. But in the AR paradigm, language is modeled as next token prediction (a strictly left-to-right, token-by-token order), whereas natural language itself exhibits more flexible causal structures. In the DLM paradigm, the attention mechanism is fully connected, which entirely disregards causal order. To fill this gap, we propose a \textbf{C}ausal \textbf{C}oncept-Guided \textbf{D}iffusion \textbf{L}anguage \textbf{M}odel (C^2DLM). Starting from DLM's fully connected attention, C^2DLM first obtains a concept-level causal graph from the teacher model, and then explicitly guides attention to learn causal relationships between concepts. By focusing on causal relationships and avoiding interference from difficult subgoals involving causal inversion, C^2DLM improves 12\% with about 3.2 times training speedup in the COT-OrderPerturb task, and achieves an average gain of 1.31\% across six downstream reasoning tasks. More details in the repository ~https://github.com/Kairong-Han/C-2-DLM{here}.

While LLMs are powerful embedding backbones, their application in training-free settings faces two structural challenges: causal attention restricts early tokens from accessing subsequent context, and the next-token prediction objective biases representations toward generation rather than semantic compression. To address these limitations, we propose KV-Embedding, a framework that activates the latent representation power of frozen LLMs. Our method leverages the observation that the key-value (KV) states of the final token at each layer encode a compressed view of the sequence. By re-routing these states as a prepended prefix, we enable all tokens to access sequence-level context within a single forward pass. To ensure model-agnostic applicability, we introduce an automated layer selection strategy based on intrinsic dimensionality. Evaluations on MTEB across Qwen, Mistral, and Llama backbones show that KV-Embedding outperforms existing training-free baselines by up to 10%, while maintaining robust performance on sequences up to 4,096 tokens. These results demonstrate that internal state manipulation offers an efficient alternative to input modification, and we hope this work encourages further exploration of LLM internals for representation learning.

Time series analysis is crucial in diverse scenarios. Beyond forecasting, considerable real-world tasks are categorized into classification, imputation, and anomaly detection, underscoring different capabilities termed time series understanding in this paper. While GPT-style models have been positioned as foundation models for time series forecasting, the BERT-style architecture, which has made significant advances in natural language understanding, has not been fully unlocked for time series understanding, possibly attributed to the undesirable dropout of essential elements of BERT. In this paper, inspired by the shared multi-granularity structure between multivariate time series and multisentence documents, we design TimesBERT to learn generic representations of time series including temporal patterns and variate-centric characteristics. In addition to a natural adaptation of masked modeling, we propose a parallel task of functional token prediction to embody vital multi-granularity structures. Our model is pre-trained on 260 billion time points across diverse domains. Leveraging multi-granularity representations, TimesBERT achieves state-of-the-art performance across four typical downstream understanding tasks, outperforming task-specific models and language pre-trained backbones, positioning it as a versatile foundation model for time series understanding.