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Sep 10

Regression Transformer: Concurrent sequence regression and generation for molecular language modeling

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

LiDAR-LLM: Exploring the Potential of Large Language Models for 3D LiDAR Understanding

Recently, Large Language Models (LLMs) and Multimodal Large Language Models (MLLMs) have shown promise in instruction following and 2D image understanding. While these models are powerful, they have not yet been developed to comprehend the more challenging 3D physical scenes, especially when it comes to the sparse outdoor LiDAR data. In this paper, we introduce LiDAR-LLM, which takes raw LiDAR data as input and harnesses the remarkable reasoning capabilities of LLMs to gain a comprehensive understanding of outdoor 3D scenes. The central insight of our LiDAR-LLM is the reformulation of 3D outdoor scene cognition as a language modeling problem, encompassing tasks such as 3D captioning, 3D grounding, 3D question answering, etc. Specifically, due to the scarcity of 3D LiDAR-text pairing data, we introduce a three-stage training strategy and generate relevant datasets, progressively aligning the 3D modality with the language embedding space of LLM. Furthermore, we design a View-Aware Transformer (VAT) to connect the 3D encoder with the LLM, which effectively bridges the modality gap and enhances the LLM's spatial orientation comprehension of visual features. Our experiments show that LiDAR-LLM possesses favorable capabilities to comprehend various instructions regarding 3D scenes and engage in complex spatial reasoning. LiDAR-LLM attains a 40.9 BLEU-1 on the 3D captioning task and achieves a 63.1\% classification accuracy and a 14.3\% BEV mIoU on the 3D grounding task. Web page: https://sites.google.com/view/lidar-llm

MeLM, a generative pretrained language modeling framework that solves forward and inverse mechanics problems

We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.

Guaranteed Guess: A Language Modeling Approach for CISC-to-RISC Transpilation with Testing Guarantees

The hardware ecosystem is rapidly evolving, with increasing interest in translating low-level programs across different instruction set architectures (ISAs) in a quick, flexible, and correct way to enhance the portability and longevity of existing code. A particularly challenging class of this transpilation problem is translating between complex- (CISC) and reduced- (RISC) hardware architectures, due to fundamental differences in instruction complexity, memory models, and execution paradigms. In this work, we introduce GG (Guaranteed Guess), an ISA-centric transpilation pipeline that combines the translation power of pre-trained large language models (LLMs) with the rigor of established software testing constructs. Our method generates candidate translations using an LLM from one ISA to another, and embeds such translations within a software-testing framework to build quantifiable confidence in the translation. We evaluate our GG approach over two diverse datasets, enforce high code coverage (>98%) across unit tests, and achieve functional/semantic correctness of 99% on HumanEval programs and 49% on BringupBench programs, respectively. Further, we compare our approach to the state-of-the-art Rosetta 2 framework on Apple Silicon, showcasing 1.73x faster runtime performance, 1.47x better energy efficiency, and 2.41x better memory usage for our transpiled code, demonstrating the effectiveness of GG for real-world CISC-to-RISC translation tasks. We will open-source our codes, data, models, and benchmarks to establish a common foundation for ISA-level code translation research.

Pairing interacting protein sequences using masked language modeling

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

In-Context Pretraining: Language Modeling Beyond Document Boundaries

Large language models (LMs) are currently trained to predict tokens given document prefixes, enabling them to directly perform long-form generation and prompting-style tasks which can be reduced to document completion. Existing pretraining pipelines train LMs by concatenating random sets of short documents to create input contexts but the prior documents provide no signal for predicting the next document. We instead present In-Context Pretraining, a new approach where language models are pretrained on a sequence of related documents, thereby explicitly encouraging them to read and reason across document boundaries. We can do In-Context Pretraining by simply changing the document ordering so that each context contains related documents, and directly applying existing pretraining pipelines. However, this document sorting problem is challenging. There are billions of documents and we would like the sort to maximize contextual similarity for every document without repeating any data. To do this, we introduce approximate algorithms for finding related documents with efficient nearest neighbor search and constructing coherent input contexts with a graph traversal algorithm. Our experiments show In-Context Pretraining offers a simple and scalable approach to significantly enhance LMs'performance: we see notable improvements in tasks that require more complex contextual reasoning, including in-context learning (+8%), reading comprehension (+15%), faithfulness to previous contexts (+16%), long-context reasoning (+5%), and retrieval augmentation (+9%).

MM-Agent: LLM as Agents for Real-world Mathematical Modeling Problem

Mathematical modeling is a cornerstone of scientific discovery and engineering practice, enabling the translation of real-world problems into formal systems across domains such as physics, biology, and economics. Unlike mathematical reasoning, which assumes a predefined formulation, modeling requires open-ended problem analysis, abstraction, and principled formalization. While Large Language Models (LLMs) have shown strong reasoning capabilities, they fall short in rigorous model construction, limiting their utility in real-world problem-solving. To this end, we formalize the task of LLM-powered real-world mathematical modeling, where agents must analyze problems, construct domain-appropriate formulations, and generate complete end-to-end solutions. We introduce MM-Bench, a curated benchmark of 111 problems from the Mathematical Contest in Modeling (MCM/ICM), spanning the years 2000 to 2025 and across ten diverse domains such as physics, biology, and economics. To tackle this task, we propose MM-Agent, an expert-inspired framework that decomposes mathematical modeling into four stages: open-ended problem analysis, structured model formulation, computational problem solving, and report generation. Experiments on MM-Bench show that MM-Agent significantly outperforms baseline agents, achieving an 11.88\% improvement over human expert solutions while requiring only 15 minutes and \$0.88 per task using GPT-4o. Furthermore, under official MCM/ICM protocols, MM-Agent assisted two undergraduate teams in winning the Finalist Award (top 2.0\% among 27,456 teams) in MCM/ICM 2025, demonstrating its practical effectiveness as a modeling copilot. Our code is available at https://github.com/usail-hkust/LLM-MM-Agent

MLP Memory: Language Modeling with Retriever-pretrained External Memory

While modern decoder-only LLMs achieve superior performance across various domains, hallucinations have risen to be a common problem in their generated text, hindering their application in knowledge-intensive tasks. Retriever-augmented generation (RAG) offers a solution, but the non-parametric nature of the retriever hinders its deep interaction with LLM. In this work, we propose to decouple memorization from the LLM decoder using a pretrained, differentiable external memory. The external memory is an MLP pretrained by imitating the behavior of a retriever on the entire pretraining dataset. Our resulting architecture, which comprises a transformer decoder and an external MLP memory pretrained on language modeling and retriever imitation respectively, demonstrates strong perplexity and performance on downstream tasks. Experiments show our architecture exhibits steeper power-law scaling with model size, achieving 17.5% and 24.1% improvement on WikiText-103 and Web datasets compared to decoder-only models while benefiting from added training without overfitting. We demonstrate superior performance on three hallucination benchmarks and nine memory-intensive tasks. Additionally, our approach delivers 80times speedup over kNN-LM (500M tokens) and 1.3times faster inference than decoder-only models. Unlike kNN-LM, which impairs reasoning, our MLP memory improves StrategyQA performance. We will open-source our code and models in the future.

GenSE: Generative Speech Enhancement via Language Models using Hierarchical Modeling

Semantic information refers to the meaning conveyed through words, phrases, and contextual relationships within a given linguistic structure. Humans can leverage semantic information, such as familiar linguistic patterns and contextual cues, to reconstruct incomplete or masked speech signals in noisy environments. However, existing speech enhancement (SE) approaches often overlook the rich semantic information embedded in speech, which is crucial for improving intelligibility, speaker consistency, and overall quality of enhanced speech signals. To enrich the SE model with semantic information, we employ language models as an efficient semantic learner and propose a comprehensive framework tailored for language model-based speech enhancement, called GenSE. Specifically, we approach SE as a conditional language modeling task rather than a continuous signal regression problem defined in existing works. This is achieved by tokenizing speech signals into semantic tokens using a pre-trained self-supervised model and into acoustic tokens using a custom-designed single-quantizer neural codec model. To improve the stability of language model predictions, we propose a hierarchical modeling method that decouples the generation of clean semantic tokens and clean acoustic tokens into two distinct stages. Moreover, we introduce a token chain prompting mechanism during the acoustic token generation stage to ensure timbre consistency throughout the speech enhancement process. Experimental results on benchmark datasets demonstrate that our proposed approach outperforms state-of-the-art SE systems in terms of speech quality and generalization capability.

Selective Token Generation for Few-shot Natural Language Generation

Natural language modeling with limited training data is a challenging problem, and many algorithms make use of large-scale pretrained language models (PLMs) for this due to its great generalization ability. Among them, additive learning that incorporates a task-specific adapter on top of the fixed large-scale PLM has been popularly used in the few-shot setting. However, this added adapter is still easy to disregard the knowledge of the PLM especially for few-shot natural language generation (NLG) since an entire sequence is usually generated by only the newly trained adapter. Therefore, in this work, we develop a novel additive learning algorithm based on reinforcement learning (RL) that selectively outputs language tokens between the task-general PLM and the task-specific adapter during both training and inference. This output token selection over the two generators allows the adapter to take into account solely the task-relevant parts in sequence generation, and therefore makes it more robust to overfitting as well as more stable in RL training. In addition, to obtain the complementary adapter from the PLM for each few-shot task, we exploit a separate selecting module that is also simultaneously trained using RL. Experimental results on various few-shot NLG tasks including question answering, data-to-text generation and text summarization demonstrate that the proposed selective token generation significantly outperforms the previous additive learning algorithms based on the PLMs.

Fourier Head: Helping Large Language Models Learn Complex Probability Distributions

As the quality of large language models has improved, there has been increased interest in using them to model non-linguistic tokens. For example, the Decision Transformer recasts agentic decision making as a sequence modeling problem, using a decoder-only LLM to model the distribution over the discrete action space for an Atari agent. However, when adapting LLMs to non-linguistic domains, it remains unclear if softmax over discrete bins captures the continuous structure of the tokens and the potentially complex distributions needed for high quality token generation. We introduce a neural network layer, constructed using Fourier series, which we can easily substitute for any linear layer if we want the outputs to have a more continuous structure. We perform extensive analysis on synthetic datasets, as well as on large-scale decision making and time series forecasting tasks. We also provide theoretical evidence that this layer can better learn signal from data while ignoring high-frequency noise. All of our results support the effectiveness of our proposed Fourier head in scenarios where the underlying data distribution has a natural continuous structure. For example, the Fourier head improves a Decision Transformer agent's returns by 46% on the Atari Seaquest game, and increases a state-of-the-art times series foundation model's forecasting performance by 3.5% across 20 benchmarks unseen during training.

Agents Play Thousands of 3D Video Games

We present PORTAL, a novel framework for developing artificial intelligence agents capable of playing thousands of 3D video games through language-guided policy generation. By transforming decision-making problems into language modeling tasks, our approach leverages large language models (LLMs) to generate behavior trees represented in domain-specific language (DSL). This method eliminates the computational burden associated with traditional reinforcement learning approaches while preserving strategic depth and rapid adaptability. Our framework introduces a hybrid policy structure that combines rule-based nodes with neural network components, enabling both high-level strategic reasoning and precise low-level control. A dual-feedback mechanism incorporating quantitative game metrics and vision-language model analysis facilitates iterative policy improvement at both tactical and strategic levels. The resulting policies are instantaneously deployable, human-interpretable, and capable of generalizing across diverse gaming environments. Experimental results demonstrate PORTAL's effectiveness across thousands of first-person shooter (FPS) games, showcasing significant improvements in development efficiency, policy generalization, and behavior diversity compared to traditional approaches. PORTAL represents a significant advancement in game AI development, offering a practical solution for creating sophisticated agents that can operate across thousands of commercial video games with minimal development overhead. Experiment results on the 3D video games are best viewed on https://zhongwen.one/projects/portal .

FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning

Scaling Transformers to longer sequence lengths has been a major problem in the last several years, promising to improve performance in language modeling and high-resolution image understanding, as well as to unlock new applications in code, audio, and video generation. The attention layer is the main bottleneck in scaling to longer sequences, as its runtime and memory increase quadratically in the sequence length. FlashAttention exploits the asymmetric GPU memory hierarchy to bring significant memory saving (linear instead of quadratic) and runtime speedup (2-4times compared to optimized baselines), with no approximation. However, FlashAttention is still not nearly as fast as optimized matrix-multiply (GEMM) operations, reaching only 25-40\% of the theoretical maximum FLOPs/s. We observe that the inefficiency is due to suboptimal work partitioning between different thread blocks and warps on the GPU, causing either low-occupancy or unnecessary shared memory reads/writes. We propose FlashAttention-2, with better work partitioning to address these issues. In particular, we (1) tweak the algorithm to reduce the number of non-matmul FLOPs (2) parallelize the attention computation, even for a single head, across different thread blocks to increase occupancy, and (3) within each thread block, distribute the work between warps to reduce communication through shared memory. These yield around 2times speedup compared to FlashAttention, reaching 50-73\% of the theoretical maximum FLOPs/s on A100 and getting close to the efficiency of GEMM operations. We empirically validate that when used end-to-end to train GPT-style models, FlashAttention-2 reaches training speed of up to 225 TFLOPs/s per A100 GPU (72\% model FLOPs utilization).

Transformer-Based Models Are Not Yet Perfect At Learning to Emulate Structural Recursion

This paper investigates the ability of transformer-based models to learn structural recursion from examples. Recursion is a universal concept in both natural and formal languages. Structural recursion is central to the programming language and formal mathematics tasks where symbolic tools currently excel beyond neural models, such as inferring semantic relations between datatypes and emulating program behavior. We introduce a general framework that nicely connects the abstract concepts of structural recursion in the programming language domain to concrete sequence modeling problems and learned models' behavior. The framework includes a representation that captures the general syntax of structural recursion, coupled with two different frameworks for understanding their semantics -- one that is more natural from a programming languages perspective and one that helps bridge that perspective with a mechanistic understanding of the underlying transformer architecture. With our framework as a powerful conceptual tool, we identify different issues under various set-ups. The models trained to emulate recursive computations cannot fully capture the recursion yet instead fit short-cut algorithms and thus cannot solve certain edge cases that are under-represented in the training distribution. In addition, it is difficult for state-of-the-art large language models (LLMs) to mine recursive rules from in-context demonstrations. Meanwhile, these LLMs fail in interesting ways when emulating reduction (step-wise computation) of the recursive function.

SciPrompt: Knowledge-augmented Prompting for Fine-grained Categorization of Scientific Topics

Prompt-based fine-tuning has become an essential method for eliciting information encoded in pre-trained language models for a variety of tasks, including text classification. For multi-class classification tasks, prompt-based fine-tuning under low-resource scenarios has resulted in performance levels comparable to those of fully fine-tuning methods. Previous studies have used crafted prompt templates and verbalizers, mapping from the label terms space to the class space, to solve the classification problem as a masked language modeling task. However, cross-domain and fine-grained prompt-based fine-tuning with an automatically enriched verbalizer remains unexplored, mainly due to the difficulty and costs of manually selecting domain label terms for the verbalizer, which requires humans with domain expertise. To address this challenge, we introduce SciPrompt, a framework designed to automatically retrieve scientific topic-related terms for low-resource text classification tasks. To this end, we select semantically correlated and domain-specific label terms within the context of scientific literature for verbalizer augmentation. Furthermore, we propose a new verbalization strategy that uses correlation scores as additional weights to enhance the prediction performance of the language model during model tuning. Our method outperforms state-of-the-art, prompt-based fine-tuning methods on scientific text classification tasks under few and zero-shot settings, especially in classifying fine-grained and emerging scientific topics.

Synthesizing mixed-integer linear programming models from natural language descriptions

Numerous real-world decision-making problems can be formulated and solved using Mixed-Integer Linear Programming (MILP) models. However, the transformation of these problems into MILP models heavily relies on expertise in operations research and mathematical optimization, which restricts non-experts' accessibility to MILP. To address this challenge, we propose a framework for automatically formulating MILP models from unstructured natural language descriptions of decision problems, which integrates Large Language Models (LLMs) and mathematical modeling techniques. This framework consists of three phases: i) identification of decision variables, ii) classification of objective and constraints, and iii) finally, generation of MILP models. In this study, we present a constraint classification scheme and a set of constraint templates that can guide the LLMs in synthesizing a complete MILP model. After fine-tuning LLMs, our approach can identify and synthesize logic constraints in addition to classic demand and resource constraints. The logic constraints have not been studied in existing work. To evaluate the performance of the proposed framework, we extend the NL4Opt dataset with more problem descriptions and constraint types, and with the new dataset, we compare our framework with one-step model generation methods offered by LLMs. The experimental results reveal that with respect to the accuracies of generating the correct model, objective, and constraints, our method which integrates constraint classification and templates with LLMs significantly outperforms the others. The prototype system that we developed has a great potential to capture more constraints for more complex MILPs. It opens up opportunities for developing training tools for operations research practitioners and has the potential to be a powerful tool for automatic decision problem modeling and solving in practice.

Natural Language Generation from Visual Events: Challenges and Future Directions

The ability to use natural language to talk about visual events is at the core of human intelligence and a crucial feature of any artificial intelligence system. In recent years, a substantial body of work in visually grounded NLP has focused on describing content depicted in single images. By contrast, comparatively less attention has been devoted to exhaustively modeling scenarios in which natural language is employed to interpret and talk about events presented through videos or sequences of images. In this position paper, we argue that any NLG task dealing with sequences of images or frames is an instance of the broader, more general problem of modeling the intricate relationships between visual events unfolding over time and the features of the language used to interpret, describe, or narrate them. Therefore, solving these tasks requires models to be capable of identifying and managing such intricacies. We consider five seemingly different tasks, which we argue are compelling instances of this broader multimodal problem. Consistently, we claim that these tasks pose a common set of challenges and share similarities in terms of modeling and evaluation approaches. Building on this perspective, we identify key open questions and propose several research directions for future investigation. We claim that improving language-and-vision models' understanding of visual events is both timely and essential, given their growing applications. Additionally, this challenge offers significant scientific insight, advancing model development through principles of human cognition and language use.

Knowledge Graph Modeling-Driven Large Language Model Operating System (LLM OS) for Task Automation in Process Engineering Problem-Solving

We present the Process Engineering Operations Assistant (PEOA), an AI-driven framework designed to solve complex problems in the chemical and process industries. The framework employs a modular architecture orchestrated by a meta-agent, which serves as the central coordinator, managing an action generator and instruction-tuned small-scale language models (expert models). The action generator decomposes complex problems into sub-tasks and identifies suitable expert models to execute each, delivering precise solutions for multi-step problem-solving. Key techniques include advanced knowledge modeling using property graphs for improved information retrieval, facilitating more accurate and contextually relevant solutions. Additionally, the framework utilizes a teacher-student transfer-learning approach with GPT-4 (Omni) to fine-tune the action generator and expert models for domain adaptation, alongside an iterative problem-solving mechanism with sophisticated error handling. Custom datasets were developed to evaluate the framework against leading proprietary language models on various engineering tasks. The results demonstrate the framework effectiveness in automating calculations, accelerating prototyping, and providing AI-augmented decision support for industrial processes, marking a significant advancement in process engineering capabilities.

3D-GPT: Procedural 3D Modeling with Large Language Models

In the pursuit of efficient automated content creation, procedural generation, leveraging modifiable parameters and rule-based systems, emerges as a promising approach. Nonetheless, it could be a demanding endeavor, given its intricate nature necessitating a deep understanding of rules, algorithms, and parameters. To reduce workload, we introduce 3D-GPT, a framework utilizing large language models~(LLMs) for instruction-driven 3D modeling. 3D-GPT positions LLMs as proficient problem solvers, dissecting the procedural 3D modeling tasks into accessible segments and appointing the apt agent for each task. 3D-GPT integrates three core agents: the task dispatch agent, the conceptualization agent, and the modeling agent. They collaboratively achieve two objectives. First, it enhances concise initial scene descriptions, evolving them into detailed forms while dynamically adapting the text based on subsequent instructions. Second, it integrates procedural generation, extracting parameter values from enriched text to effortlessly interface with 3D software for asset creation. Our empirical investigations confirm that 3D-GPT not only interprets and executes instructions, delivering reliable results but also collaborates effectively with human designers. Furthermore, it seamlessly integrates with Blender, unlocking expanded manipulation possibilities. Our work highlights the potential of LLMs in 3D modeling, offering a basic framework for future advancements in scene generation and animation.

Automated Optimization Modeling through Expert-Guided Large Language Model Reasoning

Optimization Modeling (OM) is essential for solving complex decision-making problems. However, the process remains time-consuming and error-prone, heavily relying on domain experts. While Large Language Models (LLMs) show promise in addressing these challenges through their natural language understanding and reasoning capabilities, current approaches face three critical limitations: high benchmark labeling error rates reaching up to 42%, narrow evaluation scope that only considers optimal values, and computational inefficiency due to heavy reliance on multi-agent systems or model fine-tuning. In this work, we first enhance existing datasets through systematic error correction and more comprehensive annotation. Additionally, we introduce LogiOR, a new optimization modeling benchmark from the logistics domain, containing more complex problems with standardized annotations. Furthermore, we present ORThought, a novel framework that leverages expert-level optimization modeling principles through chain-of-thought reasoning to automate the OM process. Through extensive empirical evaluation, we demonstrate that ORThought outperforms existing approaches, including multi-agent frameworks, with particularly significant advantages on complex optimization problems. Finally, we provide a systematic analysis of our method, identifying critical success factors and failure modes, providing valuable insights for future research on LLM-based optimization modeling.

JiuZhang 2.0: A Unified Chinese Pre-trained Language Model for Multi-task Mathematical Problem Solving

Although pre-trained language models~(PLMs) have recently advanced the research progress in mathematical reasoning, they are not specially designed as a capable multi-task solver, suffering from high cost for multi-task deployment (\eg a model copy for a task) and inferior performance on complex mathematical problems in practical applications. To address these issues, in this paper, we propose JiuZhang~2.0, a unified Chinese PLM specially for multi-task mathematical problem solving. Our idea is to maintain a moderate-sized model and employ the cross-task knowledge sharing to improve the model capacity in a multi-task setting. Specially, we construct a Mixture-of-Experts~(MoE) architecture for modeling mathematical text, so as to capture the common mathematical knowledge across tasks. For optimizing the MoE architecture, we design multi-task continual pre-training and multi-task fine-tuning strategies for multi-task adaptation. These training strategies can effectively decompose the knowledge from the task data and establish the cross-task sharing via expert networks. In order to further improve the general capacity of solving different complex tasks, we leverage large language models~(LLMs) as complementary models to iteratively refine the generated solution by our PLM, via in-context learning. Extensive experiments have demonstrated the effectiveness of our model.

MechAgents: Large language model multi-agent collaborations can solve mechanics problems, generate new data, and integrate knowledge

Solving mechanics problems using numerical methods requires comprehensive intelligent capability of retrieving relevant knowledge and theory, constructing and executing codes, analyzing the results, a task that has thus far mainly been reserved for humans. While emerging AI methods can provide effective approaches to solve end-to-end problems, for instance via the use of deep surrogate models or various data analytics strategies, they often lack physical intuition since knowledge is baked into the parametric complement through training, offering less flexibility when it comes to incorporating mathematical or physical insights. By leveraging diverse capabilities of multiple dynamically interacting large language models (LLMs), we can overcome the limitations of conventional approaches and develop a new class of physics-inspired generative machine learning platform, here referred to as MechAgents. A set of AI agents can solve mechanics tasks, here demonstrated for elasticity problems, via autonomous collaborations. A two-agent team can effectively write, execute and self-correct code, in order to apply finite element methods to solve classical elasticity problems in various flavors (different boundary conditions, domain geometries, meshes, small/finite deformation and linear/hyper-elastic constitutive laws, and others). For more complex tasks, we construct a larger group of agents with enhanced division of labor among planning, formulating, coding, executing and criticizing the process and results. The agents mutually correct each other to improve the overall team-work performance in understanding, formulating and validating the solution. Our framework shows the potential of synergizing the intelligence of language models, the reliability of physics-based modeling, and the dynamic collaborations among diverse agents, opening novel avenues for automation of solving engineering problems.

OptiBench Meets ReSocratic: Measure and Improve LLMs for Optimization Modeling

Large language models (LLMs) have exhibited their problem-solving abilities in mathematical reasoning. Solving realistic optimization (OPT) problems in application scenarios requires advanced and applied mathematics ability. However, current OPT benchmarks that merely solve linear programming are far from complex realistic situations. In this work, we propose OptiBench, a benchmark for End-to-end optimization problem-solving with human-readable inputs and outputs. OptiBench contains rich optimization problems, including linear and nonlinear programming with or without tabular data, which can comprehensively evaluate LLMs' solving ability. In our benchmark, LLMs are required to call a code solver to provide precise numerical answers. Furthermore, to alleviate the data scarcity for optimization problems, and to bridge the gap between open-source LLMs on a small scale (e.g., Llama-3-8b) and closed-source LLMs (e.g., GPT-4), we further propose a data synthesis method namely ReSocratic. Unlike general data synthesis methods that proceed from questions to answers, \ReSocratic first incrementally synthesizes formatted optimization demonstration with mathematical formulations step by step and then back-translates the generated demonstrations into questions. Based on this, we synthesize the ReSocratic-29k dataset. We further conduct supervised fine-tuning with ReSocratic-29k on multiple open-source models. Experimental results show that ReSocratic-29k significantly improves the performance of open-source models.

Learning Traffic Crashes as Language: Datasets, Benchmarks, and What-if Causal Analyses

The increasing rate of road accidents worldwide results not only in significant loss of life but also imposes billions financial burdens on societies. Current research in traffic crash frequency modeling and analysis has predominantly approached the problem as classification tasks, focusing mainly on learning-based classification or ensemble learning methods. These approaches often overlook the intricate relationships among the complex infrastructure, environmental, human and contextual factors related to traffic crashes and risky situations. In contrast, we initially propose a large-scale traffic crash language dataset, named CrashEvent, summarizing 19,340 real-world crash reports and incorporating infrastructure data, environmental and traffic textual and visual information in Washington State. Leveraging this rich dataset, we further formulate the crash event feature learning as a novel text reasoning problem and further fine-tune various large language models (LLMs) to predict detailed accident outcomes, such as crash types, severity and number of injuries, based on contextual and environmental factors. The proposed model, CrashLLM, distinguishes itself from existing solutions by leveraging the inherent text reasoning capabilities of LLMs to parse and learn from complex, unstructured data, thereby enabling a more nuanced analysis of contributing factors. Our experiments results shows that our LLM-based approach not only predicts the severity of accidents but also classifies different types of accidents and predicts injury outcomes, all with averaged F1 score boosted from 34.9% to 53.8%. Furthermore, CrashLLM can provide valuable insights for numerous open-world what-if situational-awareness traffic safety analyses with learned reasoning features, which existing models cannot offer. We make our benchmark, datasets, and model public available for further exploration.

Distributional semantic modeling: a revised technique to train term/word vector space models applying the ontology-related approach

We design a new technique for the distributional semantic modeling with a neural network-based approach to learn distributed term representations (or term embeddings) - term vector space models as a result, inspired by the recent ontology-related approach (using different types of contextual knowledge such as syntactic knowledge, terminological knowledge, semantic knowledge, etc.) to the identification of terms (term extraction) and relations between them (relation extraction) called semantic pre-processing technology - SPT. Our method relies on automatic term extraction from the natural language texts and subsequent formation of the problem-oriented or application-oriented (also deeply annotated) text corpora where the fundamental entity is the term (includes non-compositional and compositional terms). This gives us an opportunity to changeover from distributed word representations (or word embeddings) to distributed term representations (or term embeddings). This transition will allow to generate more accurate semantic maps of different subject domains (also, of relations between input terms - it is useful to explore clusters and oppositions, or to test your hypotheses about them). The semantic map can be represented as a graph using Vec2graph - a Python library for visualizing word embeddings (term embeddings in our case) as dynamic and interactive graphs. The Vec2graph library coupled with term embeddings will not only improve accuracy in solving standard NLP tasks, but also update the conventional concept of automated ontology development. The main practical result of our work is the development kit (set of toolkits represented as web service APIs and web application), which provides all necessary routines for the basic linguistic pre-processing and the semantic pre-processing of the natural language texts in Ukrainian for future training of term vector space models.

TransliCo: A Contrastive Learning Framework to Address the Script Barrier in Multilingual Pretrained Language Models

The world's more than 7000 languages are written in at least 293 scripts. Due to various reasons, many closely related languages use different scripts, which poses a difficulty for multilingual pretrained language models (mPLMs) in learning crosslingual knowledge through lexical overlap. As a consequence, mPLMs are faced with a script barrier: representations from different scripts are located in different subspaces, which can result in crosslingual transfer involving languages of different scripts performing suboptimally. To address this problem, we propose TransliCo, a framework that optimizes the Transliteration Contrastive Modeling (TCM) objective to fine-tune an mPLM by contrasting sentences in its training data and their transliterations in a unified script (in our case Latin), which enhances uniformity in the representation space for different scripts. Using Glot500-m, an mPLM pretrained on over 500 languages, as our source model, we fine-tune it on a small portion (5%) of its training data, and refer to the resulting model as Furina. We show that Furina not only better aligns representations from distinct scripts but also outperforms the original Glot500-m on various zero-shot crosslingual transfer tasks. Additionally, we achieve consistent improvement in a case study on the Indic group where the languages exhibit areal features but use different scripts. We make our code and models publicly available.

CAB: Comprehensive Attention Benchmarking on Long Sequence Modeling

Transformer has achieved remarkable success in language, image, and speech processing. Recently, various efficient attention architectures have been proposed to improve transformer's efficiency while largely preserving its efficacy, especially in modeling long sequences. A widely-used benchmark to test these efficient methods' capability on long-range modeling is Long Range Arena (LRA). However, LRA only focuses on the standard bidirectional (or noncausal) self attention, and completely ignores cross attentions and unidirectional (or causal) attentions, which are equally important to downstream applications. Although designing cross and causal variants of an attention method is straightforward for vanilla attention, it is often challenging for efficient attentions with subquadratic time and memory complexity. In this paper, we propose Comprehensive Attention Benchmark (CAB) under a fine-grained attention taxonomy with four distinguishable attention patterns, namely, noncausal self, causal self, noncausal cross, and causal cross attentions. CAB collects seven real-world tasks from different research areas to evaluate efficient attentions under the four attention patterns. Among these tasks, CAB validates efficient attentions in eight backbone networks to show their generalization across neural architectures. We conduct exhaustive experiments to benchmark the performances of nine widely-used efficient attention architectures designed with different philosophies on CAB. Extensive experimental results also shed light on the fundamental problems of efficient attentions, such as efficiency length against vanilla attention, performance consistency across attention patterns, the benefit of attention mechanisms, and interpolation/extrapolation on long-context language modeling.

OptMATH: A Scalable Bidirectional Data Synthesis Framework for Optimization Modeling

Despite the rapid development of large language models (LLMs), a fundamental challenge persists: the lack of high-quality optimization modeling datasets hampers LLMs' robust modeling of practical optimization problems from natural language descriptions (NL). This data scarcity also contributes to the generalization difficulties experienced by learning-based methods. To address these challenges, we propose a scalable framework for synthesizing a high-quality dataset, named OptMATH. Starting from curated seed data with mathematical formulations (MF), this framework automatically generates problem data (PD) with controllable complexity. Then, a back-translation step is employed to obtain NL. To verify the correspondence between the NL and the PD, a forward modeling step followed by rejection sampling is used. The accepted pairs constitute the training part of OptMATH. Then a collection of rejected pairs is identified and further filtered. This collection serves as a new benchmark for optimization modeling, containing difficult instances whose lengths are much longer than these of NL4OPT and MAMO. Through extensive experiments, we demonstrate that models of various sizes (0.5B-32B parameters) trained on OptMATH achieve superior results on multiple modeling benchmarks, thereby validating the effectiveness and scalability of our approach. Our dataset is publicly available at https://github.com/AuroraLHL/OptMATH.

TreePO: Bridging the Gap of Policy Optimization and Efficacy and Inference Efficiency with Heuristic Tree-based Modeling

Recent advancements in aligning large language models via reinforcement learning have achieved remarkable gains in solving complex reasoning problems, but at the cost of expensive on-policy rollouts and limited exploration of diverse reasoning paths. In this work, we introduce TreePO, involving a self-guided rollout algorithm that views sequence generation as a tree-structured searching process. Composed of dynamic tree sampling policy and fixed-length segment decoding, TreePO leverages local uncertainty to warrant additional branches. By amortizing computation across common prefixes and pruning low-value paths early, TreePO essentially reduces the per-update compute burden while preserving or enhancing exploration diversity. Key contributions include: (1) a segment-wise sampling algorithm that alleviates the KV cache burden through contiguous segments and spawns new branches along with an early-stop mechanism; (2) a tree-based segment-level advantage estimation that considers both global and local proximal policy optimization. and (3) analysis on the effectiveness of probability and quality-driven dynamic divergence and fallback strategy. We empirically validate the performance gain of TreePO on a set reasoning benchmarks and the efficiency saving of GPU hours from 22\% up to 43\% of the sampling design for the trained models, meanwhile showing up to 40\% reduction at trajectory-level and 35\% at token-level sampling compute for the existing models. While offering a free lunch of inference efficiency, TreePO reveals a practical path toward scaling RL-based post-training with fewer samples and less compute. Home page locates at https://m-a-p.ai/TreePO.

Writing-Zero: Bridge the Gap Between Non-verifiable Problems and Verifiable Rewards

Reinforcement learning with verifiable rewards (RLVR) has enabled large language models (LLMs) to achieve remarkable breakthroughs in reasoning tasks with objective ground-truth answers, such as mathematics and code generation. However, a significant gap remains for non-verifiable tasks, like creative writing and open-ended dialogue, where quality assessment is inherently subjective and lacks definitive references. Existing approaches for these domains often rely on scalar reward models trained with human preferences, which suffer from limited generalization and are prone to reward hacking, such as over-explanation and length bias. In this work, we propose a unified RLVR-based training paradigm that bridges the gap between non-verifiable tasks and verifiable rewards. We introduce a writing-principle-based pairwise Generative Reward Model (GenRM) and a novel Bootstrapped Relative Policy Optimization (BRPO) algorithm. The pairwise writing GenRM leverages self-principled critique to transform subjective assessments into reliable, verifiable rewards, while BRPO enables dynamic, reference-free pairwise comparison by leveraging a bootstrapped response as temporary reference from within group rollouts during RL training. Our approach empowers LLMs to develop robust writing capabilities without supervised fine-tuning, as demonstrated by Writing-Zero, which shows consistent improvement and strong resistance to reward hacking compared to scalar reward baselines. Furthermore, our method achieves competitive results on both in-house and open-source writing benchmarks. Our findings suggest the potential to unify rule-based, reference-based, and reference-free reward modeling under the RLVR framework, thus paving the way for a comprehensive and scalable RL training paradigm applicable across all language tasks.

Testing the Limits of Unified Sequence to Sequence LLM Pretraining on Diverse Table Data Tasks

Tables stored in databases and tables which are present in web pages and articles account for a large part of semi-structured data that is available on the internet. It then becomes pertinent to develop a modeling approach with large language models (LLMs) that can be used to solve diverse table tasks such as semantic parsing, question answering as well as classification problems. Traditionally, there existed separate models specialized for each task individually. It raises the question of how far can we go to build a unified model that works well on some table tasks without significant degradation on others. To that end, we attempt at creating a shared modeling approach in the pretraining stage with encoder-decoder style LLMs that can cater to diverse tasks. We evaluate our approach that continually pretrains and finetunes different model families of T5 with data from tables and surrounding context, on these downstream tasks at different model scales. Through multiple ablation studies, we observe that our pretraining with self-supervised objectives can significantly boost the performance of the models on these tasks. As an example of one improvement, we observe that the instruction finetuned public models which come specialized on text question answering (QA) and have been trained on table data still have room for improvement when it comes to table specific QA. Our work is the first attempt at studying the advantages of a unified approach to table specific pretraining when scaled from 770M to 11B sequence to sequence models while also comparing the instruction finetuned variants of the models.

Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Novel Proteins

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Exploring Transformer Backbones for Heterogeneous Treatment Effect Estimation

Previous works on Treatment Effect Estimation (TEE) are not in widespread use because they are predominantly theoretical, where strong parametric assumptions are made but untractable for practical application. Recent work uses multilayer perceptron (MLP) for modeling casual relationships, however, MLPs lag far behind recent advances in ML methodology, which limits their applicability and generalizability. To extend beyond the single domain formulation and towards more realistic learning scenarios, we explore model design spaces beyond MLPs, i.e., transformer backbones, which provide flexibility where attention layers govern interactions among treatments and covariates to exploit structural similarities of potential outcomes for confounding control. Through careful model design, Transformers as Treatment Effect Estimators (TransTEE) is proposed. We show empirically that TransTEE can: (1) serve as a general purpose treatment effect estimator that significantly outperforms competitive baselines in a variety of challenging TEE problems (e.g., discrete, continuous, structured, or dosage-associated treatments) and is applicable to both when covariates are tabular and when they consist of structural data (e.g., texts, graphs); (2) yield multiple advantages: compatibility with propensity score modeling, parameter efficiency, robustness to continuous treatment value distribution shifts, explainable in covariate adjustment, and real-world utility in auditing pre-trained language models

Future Token Prediction -- Causal Language Modelling with Per-Token Semantic State Vector for Multi-Token Prediction

Causal decoder-only transformer models used for generative language modelling, such as Generative Pre-trained Transformers (GPT), are trained to predict the next token in a sequence based only on its previous tokens. Despite this simple training objective, they have proved to be powerful AI tools. However, only predicting the next token results in top layer embedding vectors that are highly token-focused. There may be benefits in generating embedding vectors at each token position that better capture the overall meaning of longer sequences of future text. Recent studies matching brain scans with deep language models suggest that humans also predict upcoming words when listening or reading but consider multiple future tokens rather than just one. This research investigates a new pretraining method called Future Token Prediction (FTP). In FTP, a large transformer encoder generates top layer embedding vectors for each token position, which, instead of being passed to a language head, are linearly and expansively projected to a pseudo-sequence, which is cross attended to by a small transformer decoder to predict the next N tokens forward from that position in the sequence. The top layer embedding vectors from FTP models exhibit distinct properties compared to those from standard GPT models, varying smoothly along a text sequence as measured by cosine similarity between adjacent tokens. Text generated by FTP models show improved topic coherence compared to standard GPT-like models trained with the same prediction perplexity for the next single token. The vectors are shown to better represent the topic of text based on the results of text classification examples. On a toy, but complex, coding problem, FTP networks produce significantly better results than GPT networks.

Unifying Molecular and Textual Representations via Multi-task Language Modelling

The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to optimize laboratory operations and fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose a multi-domain, multi-task language model to solve a wide range of tasks in both the chemical and natural language domains. By leveraging multi-task learning, our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.

Scaling Autoregressive Models for Content-Rich Text-to-Image Generation

We present the Pathways Autoregressive Text-to-Image (Parti) model, which generates high-fidelity photorealistic images and supports content-rich synthesis involving complex compositions and world knowledge. Parti treats text-to-image generation as a sequence-to-sequence modeling problem, akin to machine translation, with sequences of image tokens as the target outputs rather than text tokens in another language. This strategy can naturally tap into the rich body of prior work on large language models, which have seen continued advances in capabilities and performance through scaling data and model sizes. Our approach is simple: First, Parti uses a Transformer-based image tokenizer, ViT-VQGAN, to encode images as sequences of discrete tokens. Second, we achieve consistent quality improvements by scaling the encoder-decoder Transformer model up to 20B parameters, with a new state-of-the-art zero-shot FID score of 7.23 and finetuned FID score of 3.22 on MS-COCO. Our detailed analysis on Localized Narratives as well as PartiPrompts (P2), a new holistic benchmark of over 1600 English prompts, demonstrate the effectiveness of Parti across a wide variety of categories and difficulty aspects. We also explore and highlight limitations of our models in order to define and exemplify key areas of focus for further improvements. See https://parti.research.google/ for high-resolution images.

CP-Bench: Evaluating Large Language Models for Constraint Modelling

Combinatorial problems are present in a wide range of industries. Constraint Programming (CP) is a well-suited problem-solving paradigm, but its core process, namely constraint modelling, is a bottleneck for wider adoption. Aiming to alleviate this bottleneck, recent studies have explored using Large Language Models (LLMs) as modelling assistants, transforming combinatorial problem descriptions to executable constraint models, similar to coding assistants. However, the existing evaluation datasets for constraint modelling are often limited to small, homogeneous, or domain-specific instances, which do not capture the diversity of real-world scenarios. This work addresses this gap by introducing CP-Bench, a novel benchmark dataset that includes a diverse set of well-known combinatorial problem classes sourced from the CP community, structured explicitly for evaluating LLM-driven CP modelling. With this dataset, and given the variety of constraint modelling frameworks, we compare and evaluate the modelling capabilities of LLMs for three distinct constraint modelling systems, which vary in abstraction level and underlying syntax: the high-level MiniZinc language and Python-based CPMpy library, and the lower-level Python interface of the OR-Tools CP-SAT solver. In order to enhance the ability of LLMs to produce valid constraint models, we systematically evaluate the use of prompt-based and inference-time compute methods adapted from existing LLM-based code generation research. Our results underscore the modelling convenience provided by Python-based frameworks, as well as the effectiveness of documentation-rich system prompts, which, augmented with repeated sampling and self-verification, achieve further improvements, reaching up to 70\% accuracy on this new, highly challenging benchmark.

GUI-R1 : A Generalist R1-Style Vision-Language Action Model For GUI Agents

Existing efforts in building Graphical User Interface (GUI) agents largely rely on the training paradigm of supervised fine-tuning on Large Vision-Language Models (LVLMs). However, this approach not only demands extensive amounts of training data but also struggles to effectively understand GUI screenshots and generalize to unseen interfaces. The issue significantly limits its application in real-world scenarios, especially for high-level tasks. Inspired by Reinforcement Fine-Tuning (RFT) in large reasoning models (e.g., DeepSeek-R1), which efficiently enhances the problem-solving capabilities of large language models in real-world settings, we propose \name, the first reinforcement learning framework designed to enhance the GUI capabilities of LVLMs in high-level real-world task scenarios, through unified action space rule modeling. By leveraging a small amount of carefully curated high-quality data across multiple platforms (including Windows, Linux, MacOS, Android, and Web) and employing policy optimization algorithms such as Group Relative Policy Optimization (GRPO) to update the model, \name achieves superior performance using only 0.02\% of the data (3K vs. 13M) compared to previous state-of-the-art methods like OS-Atlas across eight benchmarks spanning three different platforms (mobile, desktop, and web). These results demonstrate the immense potential of reinforcement learning based on unified action space rule modeling in improving the execution capabilities of LVLMs for real-world GUI agent tasks.