arXiv subjects

Heng Ji

Publications and source records attributed to Heng Ji.

At least 73 records · Page 4Linked to original sources

arXiv2026

FARM: Enhancing Molecular Representations with Functional Group Awareness

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key idea behind FARM is the incorporation of functional group (FG) annotations at the atomic level, enabling both FG-enhanced SMILES and FG graphs. In this representation, SMILES strings are enriched with functional group information that identifies the group membership of each atom, while the FG graph captures molecular structure by representing how functional groups are connected. This tokenization injects chemical knowledge into SMILES and expands the effective molecular vocabulary, making the representation more suitable for Transformer-based models and more aligned with natural language structure. FARM learns molecular representations from two complementary perspectives to jointly encode functional and structural information. Masked language modeling on FG-enhanced SMILES captures atom-level features enriched with functional context, while graph neural networks model higher-level molecular topology through functional group connectivity. Contrastive learning is then used to align these two views into a unified embedding space, ensuring that both atom-level detail and functional group structure are jointly represented. We evaluate FARM on the MoleculeNet benchmark and achieve state-of-the-art performance on 8 out of 13 tasks. We further validate its generalization ability on a photostability dataset for quantum mechanical properties. These results demonstrate that FARM improves molecular representation learning, supports strong transfer learning across drug discovery and materials science, and enables broad applications in pharmaceutical research and functional material design.

cs.LG↗

arXiv2026

EMCompress: Video-LLMs with Endomorphic Multimodal Compression

Video-LLMs face a fundamental tension in long-video reasoning: static, sparse frame sampling either dilutes evidence across task-irrelevant segments at significant cost or misses fine-grained temporal semantics altogether. We propose a novel, cognitively-inspired task -- Endomorphic Multimodal Compression (EMC) -- as a structurally-constrained sufficient-statistic problem for VideoQA, and formulate it as an endomorphic transformation F_EMC : (V, Q) -> (v, q) that compresses the multimodal input while preserving answer invariance across reasonable downstream models. The endomorphic form keeps the compressed output in the downstream pipeline's native task space -- a structural mirror of the filter-then-reason mechanism in the cognitive literature motivating EMC -- distinguishing it from latent-code compression (IB / VIB) and making the formulation extensible to other multimodal settings. Under the Markov chain A -> (V, Q) -> (v, q), EMC realizes the classical sufficiency condition I((v, q); A) = I((V, Q); A) in its VideoQA-natural form. As a modular front-end, EMC plugs into both Video Instruction Tuning and Video Question Answering pipelines. We release the first dedicated benchmark and propose ReSimplifyIt, an EMC baseline surpassing prior methods by 0.40 F-1 with competitive query rewriting. Integrating EMC yields relative gains of 7.33% in training and 33.7% in inference for video-language understanding.

cs.CV↗

arXiv2026

SweRank: Software Issue Localization with Code Ranking

Software issue localization, the task of identifying the precise code locations (files, classes, or functions) relevant to a natural language issue description (e.g., bug report, feature request), is a critical yet time-consuming aspect of software development. While recent LLM-based agentic approaches demonstrate promise, they often incur significant latency and cost due to complex multi-step reasoning and relying on closed-source LLMs. Alternatively, traditional code ranking models, typically optimized for query-to-code or code-to-code retrieval, struggle with the verbose and failure-descriptive nature of issue localization queries. To bridge this gap, we introduce SweRank, an efficient and effective retrieve-and-rerank framework for software issue localization. To facilitate training, we construct SweLoc, a large-scale dataset curated from public GitHub repositories, featuring real-world issue descriptions paired with corresponding code modifications. Empirical results on SWE-Bench-Lite and LocBench show that SweRank achieves state-of-the-art performance, outperforming both prior ranking models and costly agent-based systems using closed-source LLMs like Claude-3.5. Further, we demonstrate SweLoc's utility in enhancing various existing retriever and reranker models for issue localization, establishing the dataset as a valuable resource for the community.

cs.SE↗

arXiv2026

The Landscape of Agentic Reinforcement Learning for LLMs: A Survey

The emergence of agentic reinforcement learning (Agentic RL) marks a paradigm shift from conventional reinforcement learning applied to large language models (LLM RL), reframing LLMs from passive sequence generators into autonomous, decision-making agents embedded in complex, dynamic worlds. This survey formalizes this conceptual shift by contrasting the degenerate single-step Markov Decision Processes (MDPs) of LLM-RL with the temporally extended, partially observable Markov decision processes (POMDPs) that define Agentic RL. Building on this foundation, we propose a comprehensive twofold taxonomy: one organized around core agentic capabilities, including planning, tool use, memory, reasoning, self-improvement, and perception, and the other around their applications across diverse task domains. Central to our thesis is that reinforcement learning serves as the critical mechanism for transforming these capabilities from static, heuristic modules into adaptive, robust agentic behavior. To support and accelerate future research, we consolidate the landscape of open-source environments, benchmarks, and frameworks into a practical compendium. By synthesizing over five hundred recent works, this survey charts the contours of this rapidly evolving field and highlights the opportunities and challenges that will shape the development of scalable, general-purpose AI agents.

cs.AI↗

arXiv2026

Multimodal Policy Internalization for Conversational Agents

Modern conversational agents like ChatGPT and Alexa+ rely on predefined policies specifying metadata, response styles, and tool-usage rules. As these LLM-based systems expand to support diverse business and user queries, such policies, often implemented as in-context prompts, are becoming increasingly complex and lengthy, making faithful adherence difficult and imposing large fixed computational costs. With the rise of multimodal agents, policies that govern visual and multimodal behaviors are critical but remain understudied. Prior prompt-compression work mainly shortens task templates and demonstrations, while existing policy-alignment studies focus only on text-based safety rules. We introduce Multimodal Policy Internalization (MPI), a new task that internalizes reasoning-intensive multimodal policies into model parameters, enabling stronger policy-following without including the policy during inference. MPI poses unique data and algorithmic challenges. We build two datasets spanning synthetic and real-world decision-making and tool-using tasks and propose TriMPI, a three-stage training framework. TriMPI first injects policy knowledge via continual pretraining, then performs supervised finetuning, and finally applies PolicyRollout, a GRPO-style reinforcement learning extension that augments rollouts with policy-aware responses for grounded exploration. TriMPI achieves notable gains in end-to-end accuracy, generalization, and robustness to forgetting. As the first work on multimodal policy internalization, we provide datasets, training recipes, and comprehensive evaluations to foster future research. Project page: https://mikewangwzhl.github.io/TriMPI.

cs.CL↗

arXiv2026

Perception-Aware Policy Optimization for Multimodal Reasoning

Reinforcement Learning with Verifiable Rewards (RLVR) has proven to be a highly effective strategy for endowing Large Language Models (LLMs) with robust multi-step reasoning abilities. However, its design and optimizations remain tailored to purely textual domains, resulting in suboptimal performance when applied to multimodal reasoning tasks. In particular, we observe that a major source of error in current multimodal reasoning lies in the perception of visual inputs. To address this bottleneck, we propose PAPO, a novel policy gradient algorithm that encourages the model to learn to perceive while learning to reason. Specifically, we introduce the Implicit Perception Loss in the form of a KL divergence term, which can be seamlessly plugged into mainstream RLVR algorithms such as GRPO and DAPO. Notably, PAPO does not rely on additional data curation, reward models, or stronger teacher models. To further enhance the training stability of PAPO, we introduce the Double Entropy Loss, which effectively regularizes the new KL objective without compromising performance. Despite its simplicity, PAPO yields significant overall improvements of 4.4%-17.5% on diverse multimodal benchmarks. The improvements are more pronounced, approaching 8.0%-19.1%, on tasks with high vision dependency. We also observe a substantial reduction of 30.5% in perception errors, indicating improved perceptual capabilities with PAPO. Overall, our work introduces a deeper integration of perception-aware supervision into core learning objectives and lays the groundwork for a new RL framework that encourages visually grounded reasoning. Code and data will be made publicly available for research purposes. Project page: https://mikewangwzhl.github.io/PAPO.

cs.CL↗

arXiv2026

Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics

Computing has long served as a cornerstone of scientific discovery. Recently, a paradigm shift has emerged with the rise of large language models (LLMs), introducing autonomous systems, referred to as agents, that accelerate discovery across varying levels of autonomy. These language agents provide a flexible and versatile framework that orchestrates interactions with human scientists, natural language, computer language and code, and physics. This paper presents our view and vision of LLM-based scientific agents and their growing role in transforming the scientific discovery lifecycle, from hypothesis discovery, experimental design and execution, to result analysis and refinement. We critically examine current methodologies, emphasizing key innovations, practical achievements, and outstanding limitations. Additionally, we identify open research challenges and outline promising directions for building more robust, generalizable, and adaptive scientific agents. Our analysis highlights the transformative potential of autonomous agents to accelerate scientific discovery across diverse domains.

cs.AI↗

arXiv2026

Benchmarking Multi-turn Medical Diagnosis: Hold, Lure, and Self-Correction

Large language models (LLMs) achieve high accuracy in medical diagnosis when all clinical information is provided in a single turn, yet how they behave under multi-turn evidence accumulation closer to real clinical reasoning remains unexplored. We introduce MINT (Medical Incremental N-Turn Benchmark), a high-fidelity, multi-turn medical diagnosis benchmark comprising 1,035 cases with clinically labeled evidence shards, controlled turn granularity, and information-preserving decomposition. Through systematic evaluation of 11 LLMs on MINT, we uncover three persistent behavioral patterns that significantly impact diagnostic decisions: (1) intent to answer, models rush to answer before sufficient evidence has been observed, with over 55% of answers committed within the first two turns; (2) self-correction, incorrect-to-correct answer revisions occur at up to 10.6 times the rate of correct-to-incorrect flips, revealing a latent capacity for self-correction that premature commitment forecloses; and (3) strong lures, clinically salient information such as laboratory results trigger premature answering even when models are explicitly instructed to wait. We translate these findings into clinically actionable guidance: deferring the diagnostic question to later turns reduces premature answering and improves accuracy at the first point of commitment by up to 62.6%, while reserving salient clinical evidence for later turns prevents a catastrophic accuracy drop of up to 23.3% caused by premature commitment. Our work provides both a controlled evaluation framework and concrete recommendations for improving the reliability of LLMs in multi-turn medical diagnosis.

cs.CL↗

arXiv2026

Must Read: A Comprehensive Survey of Computational Persuasion

Persuasion is a fundamental aspect of communication, influencing decision-making across diverse contexts, from everyday conversations to high-stakes scenarios such as politics, marketing, and law. The rise of conversational AI systems has significantly expanded the scope of persuasion, introducing both opportunities and risks. AI-driven persuasion can be leveraged for beneficial applications, but also poses threats through unethical influence. Moreover, AI systems are not only persuaders, but also susceptible to persuasion, making them vulnerable to adversarial attacks and bias reinforcement. Despite rapid advancements in AI-generated persuasive content, our understanding of what makes persuasion effective remains limited due to its inherently subjective and context-dependent nature. In this survey, we provide a comprehensive overview of persuasion, structured around three key perspectives: (1) AI as a Persuader, which explores AI-generated persuasive content and its applications; (2) AI as a Persuadee, which examines AI's susceptibility to influence and manipulation; and (3) AI as a Persuasion Judge, which analyzes AI's role in evaluating persuasive strategies, detecting manipulation, and ensuring ethical persuasion. We introduce a taxonomy for persuasion research and discuss key challenges for future research to enhance the safety, fairness, and effectiveness of AI-powered persuasion while addressing the risks posed by increasingly capable language models.

cs.CL↗

arXiv2026

The Future of Artificial Intelligence and the Mathematical and Physical Sciences (AI+MPS)

This community paper developed out of the NSF Workshop on the Future of Artificial Intelligence (AI) and the Mathematical and Physics Sciences (MPS), which was held in March 2025 with the goal of understanding how the MPS domains (Astronomy, Chemistry, Materials Research, Mathematical Sciences, and Physics) can best capitalize on, and contribute to, the future of AI. We present here a summary and snapshot of the MPS community's perspective, as of Spring/Summer 2025, in a rapidly developing field. The link between AI and MPS is becoming increasingly inextricable; now is a crucial moment to strengthen the link between AI and Science by pursuing a strategy that proactively and thoughtfully leverages the potential of AI for scientific discovery and optimizes opportunities to impact the development of AI by applying concepts from fundamental science. To achieve this, we propose activities and strategic priorities that: (1) enable AI+MPS research in both directions; (2) build up an interdisciplinary community of AI+MPS researchers; and (3) foster education and workforce development in AI for MPS researchers and students. We conclude with a summary of suggested priorities for funding agencies, educational institutions, and individual researchers to help position the MPS community to be a leader in, and take full advantage of, the transformative potential of AI+MPS.

cs.AI↗

arXiv2026

Adaptation of Agentic AI: A Survey of Post-Training, Memory, and Skills

Large language model (LLM) agents are moving beyond prompting alone. ChatGPT marked the rise of general-purpose LLM assistants, DeepSeek showed that on-policy reinforcement learning with verifiable rewards can improve reasoning and tool use, and OpenClaw highlights a newer direction in which agents accumulate persistent memory and reusable skills. Yet the research landscape remains fragmented across post-training, retrieval, memory, and skill systems. This survey studies these developments under a single notion of \emph{adaptation}: improving an agent, its tools, or their interaction after pretraining. We organize the field with a four-paradigm framework spanning agent adaptation and tool adaptation. On the agent side, A1 (tool-execution-signaled) and A2 (agent-output-signaled) improve the agent itself through supervised fine-tuning, preference optimization, and reinforcement learning with verifiable rewards. On the tool side, T1 (agent-agnostic) provides reusable pre-trained modules any agent can call, while T2 (agent-supervised) uses the agent's outputs to train memory systems, skill libraries, or lightweight subagents. Using this framework, we review post-training methods, adaptive memory architectures, and agent skills; compare their trade-offs in cost, flexibility, and generalization; and summarize evaluation practices across deep research, software development, computer use, and drug discovery. We conclude by outlining open problems in agent-tool co-adaptation, continual learning, safety, and efficient deployment.

cs.AI↗

arXiv2026

OSExpert: Computer-Use Agents Learning Professional Skills via Exploration

General-purpose computer-use agents have shown impressive performance across diverse digital environments. However, our new benchmark, OSExpert-Eval, indicates they remain far less helpful than human experts. Although inference-time scaling enables adaptation, these agents complete complex tasks inefficiently with degraded performance, transfer poorly to unseen UIs, and struggle with fine-grained action sequences. To solve the problem, we introduce a GUI-based depth-first search (GUI-DFS) exploration algorithm to comprehensively explore and verify an environment's unit functions. The agent then exploits compositionality between unit skills to self-construct a curriculum for composite tasks. To support fine-grained actions, we curate a database of action primitives for agents to discover during exploration; these are saved as a skill set once the exploration is complete. We use the learned skills to improve the agent's performance and efficiency by (1) enriching agents with ready-to-use procedural knowledge, allowing them to plan only once for long trajectories and generate accurate actions, and (2) enabling them to end inference-time scaling earlier by realizing their boundary of capabilities. Extensive experiments show that our environment-learned agent takes a meaningful step toward expert-level computer use, achieving a around 20 percent performance gain on OSExpert-Eval and closing the efficiency gap to humans by around 80 percent

cs.AI↗

arXiv2026

RM-R1: Reward Modeling as Reasoning

Reward modeling is essential for aligning large language models with human preferences through reinforcement learning. To provide accurate reward signals, a reward model (RM) should stimulate deep thinking and conduct interpretable reasoning before assigning a score or a judgment. Inspired by recent advances of long chain-of-thought on reasoning-intensive tasks, we hypothesize and validate that integrating reasoning into reward modeling significantly enhances RM's interpretability and performance. We introduce a new class of generative reward models, Reasoning Reward Models (ReasRMs), which formulate reward modeling as a reasoning task. We propose a reasoning-oriented training pipeline and train a family of ReasRMs, RM-R1. RM-R1 features a chain-of-rubrics (CoR) mechanism -- self-generating sample-level chat rubrics or math/code solutions, and evaluating candidate responses against them. The training of RM-R1 consists of two key stages: (1) distillation of high-quality reasoning chains and (2) reinforcement learning with verifiable rewards. Empirically, our models achieve superior performance across three reward model benchmarks on average, outperforming much larger open-weight models (e.g., INF-ORM-Llama3.1-70B) and proprietary ones (e.g., GPT-4o) by up to 4.9%. Beyond final performance, we perform thorough analyses to understand the key ingredients of successful ReasRM training.

cs.CL↗

arXiv2026

From Word to World: Can Large Language Models be Implicit Text-based World Models?

Agentic reinforcement learning increasingly relies on experience-driven scaling, yet real-world environments remain non-adaptive, limited in coverage, and difficult to scale. World models offer a potential way to improve learning efficiency through simulated experience, but it remains unclear whether large language models can reliably serve this role and under what conditions they meaningfully benefit agents. We study these questions in text-based environments, which provide a controlled setting to reinterpret language modeling as next-state prediction under interaction. We introduce a three-level framework for evaluating LLM-based world models: (i) fidelity and consistency, (ii) scalability and robustness, and (iii) agent utility. Across five representative environments, we find that sufficiently trained world models maintain coherent latent state, scale predictably with data and model size, and improve agent performance via action verification, synthetic trajectory generation, and warm-starting reinforcement learning. Meanwhile, these gains depend critically on behavioral coverage and environment complexity, delineating clear boundry on when world modeling effectively supports agent learning.

cs.CL↗

arXiv2026

A Rubric-Supervised Critic from Sparse Real-World Outcomes

Academic benchmarks for coding agents tend to reward autonomous task completion, measured by verifiable rewards such as unit-test success. In contrast, real-world coding agents operate with humans in the loop, where success signals are typically noisy, delayed, and sparse. How can we bridge this gap? In this paper, we propose a process to learn a "critic" model from sparse and noisy interaction data, which can then be used both as a reward model for either RL-based training or inference-time scaling. Specifically, we introduce Critic Rubrics, a rubric-based supervision framework with 24 behavioral features that can be derived from human-agent interaction traces alone. Using a semi-supervised objective, we can then jointly predict these rubrics and sparse human feedback (when present). In experiments, we demonstrate that, despite being trained primarily from trace-observable rubrics and sparse real-world outcome proxies, these critics improve best-of-N reranking on SWE-bench (Best@8 +15.9 over Random@8 over the rerankable subset of trajectories), enable early stopping (+17.7 with 83% fewer attempts), and support training-time data curation via critic-selected trajectories.

cs.AI↗

arXiv2026

mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Molecules

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never compatible with automated synthesis approaches. To better enable the discovery of functional small molecules, LLMs need to learn a new molecular language that is more effective in predicting properties and inherently synced with automated synthesis technology. Current molecule LLMs are limited by representing molecules based on atoms. In this paper, we argue that just like tokenizing texts into meaning-bearing (sub-)word tokens instead of characters, molecules should be tokenized at the level of functional building blocks, i.e., parts of molecules that bring unique functions and serve as effective building blocks for real-world automated laboratory synthesis. This motivates us to propose mCLM, a modular Chemical-Language Model that comprises a bilingual language model that understands both natural language descriptions of functions and molecular blocks. mCLM front-loads synthesizability considerations while improving the predicted functions of molecules in a principled manner. Experiments on FDA-approved drugs showed that mCLM is capable of significantly improving chemical functions. mCLM, with only 3B parameters, also achieves improvements in synthetic accessibility relative to 7 other leading generative AI methods including GPT-5. When tested on 122 out-of-distribution medicines using only building blocks/tokens that are compatible with automated modular synthesis, mCLM outperforms all baselines in property scores and synthetic accessibility. mCLM can also reason on multiple functions and iteratively self-improve to rescue drug candidates that failed late in clinical trials ("fallen angels").

cs.AI↗

arXiv2026

Protein Language Models Diverge from Natural Language: Comparative Analysis and Improved Inference

Modern Protein Language Models (PLMs) apply transformer-based model architectures from natural language processing to biological sequences, predicting a variety of protein functions and properties. However, protein language has key differences from natural language, such as a rich functional space despite a vocabulary of only 20 amino acids. These differences motivate research into how transformer-based architectures operate differently in the protein domain and how we can better leverage PLMs to solve protein-related tasks. In this work, we begin by directly comparing how the distribution of information stored across layers of attention heads differs between the protein and natural language domain. Furthermore, we adapt a simple early-exit technique-originally used in the natural language domain to improve efficiency at the cost of performance-to achieve both increased accuracy and substantial efficiency gains in protein non-structural property prediction by allowing the model to automatically select protein representations from the intermediate layers of the PLMs for the specific task and protein at hand. We achieve performance gains ranging from 0.4 to 7.01 percentage points while simultaneously improving efficiency by over 10 percent across models and non-structural prediction tasks. Our work opens up an area of research directly comparing how language models change behavior when moved into the protein domain and advances language modeling in biological domains.

cs.LG↗

arXiv2026

Tool-R0: Self-Evolving LLM Agents for Tool-Learning from Zero Data

Large language models (LLMs) are becoming the foundation for autonomous agents that can use tools to solve complex tasks. Reinforcement learning (RL) has emerged as a common approach for injecting such agentic capabilities, but typically under tightly controlled training setups. It often depends on carefully constructed task-solution pairs and substantial human supervision, which creates a fundamental obstacle to open-ended self-evolution toward superintelligent systems. In this paper, we propose Tool-R0 framework for training general purpose tool-calling agents from scratch with self-play RL, under a zero-data assumption. Initialized from the same base LLM, Tool-R0 co-evolves a Generator and a Solver with complementary rewards: one proposes targeted challenging tasks at the other's competence frontier and the other learns to solve them with real-world tool calls. This creates a self-evolving cycle that requires no pre-existing tasks or datasets. Evaluation on different tool-use benchmarks show that Tool-R0 yields 92.5 relative improvement over the base model and surpasses fully supervised tool-calling baselines under the same setting. Our work further provides empirical insights into self-play LLM agents by analyzing co-evolution, curriculum dynamics, and scaling behavior.

cs.LG↗