arXiv subjects

Fang Wu

Publications and source records attributed to Fang Wu.

At least 55 records · Page 3Linked to original sources

arXiv2026

Surface-based Molecular Design with Multi-modal Flow Matching

Therapeutic peptides show promise in targeting previously undruggable binding sites, with recent advancements in deep generative models enabling full-atom peptide co-design for specific protein receptors. However, the critical role of molecular surfaces in protein-protein interactions (PPIs) has been underexplored. To bridge this gap, we propose an omni-design peptides generation paradigm, called SurfFlow, a novel surface-based generative algorithm that enables comprehensive co-design of sequence, structure, and surface for peptides. SurfFlow employs a multi-modality conditional flow matching (CFM) architecture to learn distributions of surface geometries and biochemical properties, enhancing peptide binding accuracy. Evaluated on the comprehensive PepMerge benchmark, SurfFlow consistently outperforms full-atom baselines across all metrics. These results highlight the advantages of considering molecular surfaces in de novo peptide discovery and demonstrate the potential of integrating multiple protein modalities for more effective therapeutic peptide discovery.

cs.LG↗

arXiv2026

A Semi-supervised Molecular Learning Framework for Activity Cliff Estimation

Machine learning (ML) enables accurate and fast molecular property predictions, which are of interest in drug discovery and material design. Their success is based on the principle of similarity at its heart, assuming that similar molecules exhibit close properties. However, activity cliffs challenge this principle, and their presence leads to a sharp decline in the performance of existing ML algorithms, particularly graph-based methods. To overcome this obstacle under a low-data scenario, we propose a novel semi-supervised learning (SSL) method dubbed SemiMol, which employs predictions on numerous unannotated data as pseudo-signals for subsequent training. Specifically, we introduce an additional instructor model to evaluate the accuracy and trustworthiness of proxy labels because existing pseudo-labeling approaches require probabilistic outputs to reveal the model's confidence and fail to be applied in regression tasks. Moreover, we design a self-adaptive curriculum learning algorithm to progressively move the target model toward hard samples at a controllable pace. Extensive experiments on 30 activity cliff datasets demonstrate that SemiMol significantly enhances graph-based ML architectures and outpasses state-of-the-art pretraining and SSL baselines.

cs.CE↗

arXiv2026

Dynamics-inspired Structure Hallucination for Protein-protein Interaction Modeling

Protein-protein interaction (PPI) represents a central challenge within the biology field, and accurately predicting the consequences of mutations in this context is crucial for drug design and protein engineering. Deep learning (DL) has shown promise in forecasting the effects of such mutations, but is hindered by two primary constraints. First, the structures of mutant proteins are often elusive to acquire. Secondly, PPI takes place dynamically, which is rarely integrated into the DL architecture design. To address these obstacles, we present a novel framework named Refine-PPI with two key enhancements. First, we introduce a structure refinement module trained by a mask mutation modeling (MMM) task on available wild-type structures, which is then transferred to produce the inaccessible mutant structures. Second, we employ a new kind of geometric network, called the probability density cloud network (PDC-Net), to capture 3D dynamic variations and encode the atomic uncertainty associated with PPI. Comprehensive experiments on SKEMPI.v2 substantiate the superiority of Refine-PPI over all existing tools for predicting free energy change. These findings underscore the effectiveness of our hallucination strategy and the PDC module in addressing the absence of mutant protein structure and modeling geometric uncertainty.

cs.LG↗

arXiv2026

InsertGNN: Can Graph Neural Networks Outperform Humans in TOEFL Sentence Insertion Problem?

The integration of sentences poses an intriguing challenge within the realm of NLP, but it has not garnered the attention it deserves. Existing methods that focus on sentence arrangement, textual consistency, and question answering are inadequate in addressing this issue. To bridge this gap, we introduce InsertGNN, which conceptualizes the problem as a graph and employs a hierarchical Graph Neural Network (GNN) to comprehend the interplay between sentences. Our approach was rigorously evaluated on a TOEFL dataset, and its efficacy was further validated on the expansive arXiv dataset using cross-domain learning. Thorough experimentation unequivocally establishes InsertGNN's superiority over all comparative benchmarks, achieving an impressive 70% accuracy, a performance on par with average human test scores.

cs.CL↗

arXiv2026

Discovering the Representation Bottleneck of Graph Neural Networks

Graph neural networks (GNNs) rely mainly on the message-passing paradigm to propagate node features and build interactions, and different graph learning problems require different ranges of node interactions. In this work, we explore the capacity of GNNs to capture node interactions under contexts of different complexities. We discover that GNNs usually fail to capture the most informative kinds of interaction styles for diverse graph learning tasks, and thus name this phenomenon GNNs' representation bottleneck. As a response, we demonstrate that the inductive bias introduced by existing graph construction mechanisms can result in this representation bottleneck, \emph{i.e.}, preventing GNNs from learning interactions of the most appropriate complexity. To address that limitation, we propose a novel graph rewiring approach based on interaction patterns learned by GNNs to dynamically adjust each node's receptive fields. Extensive experiments on both real-world and synthetic datasets prove the effectiveness of our algorithm in alleviating the representation bottleneck and its superiority in enhancing the performance of GNNs over state-of-the-art graph rewiring baselines.

cs.LG↗

arXiv2026

Instructor-inspired Machine Learning for Robust Molecular Property Prediction

Machine learning catalyzes a revolution in chemical and biological science. However, its efficacy heavily depends on the availability of labeled data, and annotating biochemical data is extremely laborious. To surmount this data sparsity challenge, we present an instructive learning algorithm named InstructMol to measure pseudo-labels' reliability and help the target model leverage large-scale unlabeled data. InstructMol does not require transferring knowledge between multiple domains, which avoids the potential gap between the pretraining and fine-tuning stages. We demonstrated the high accuracy of InstructMol on several real-world molecular datasets and out-of-distribution (OOD) benchmarks. Code is available at~ https://github.com/smiles724/InstructMol.

cs.LG↗

arXiv2026

Toward Global Large Language Models in Medicine

Despite continuous advances in medical technology, the global distribution of health care resources remains uneven. The development of large language models (LLMs) has transformed the landscape of medicine and holds promise for improving health care quality and expanding access to medical information globally. However, existing LLMs are primarily trained on high-resource languages, limiting their applicability in global medical scenarios. To address this gap, we constructed GlobMed, a large multilingual medical dataset, containing over 500,000 entries spanning 12 languages, including four low-resource languages. Building on this, we established GlobMed-Bench, which systematically assesses 56 state-of-the-art proprietary and open-weight LLMs across multiple multilingual medical tasks, revealing significant performance disparities across languages, particularly for low-resource languages. Additionally, we introduced GlobMed-LLMs, a suite of multilingual medical LLMs trained on GlobMed, with parameters ranging from 1.7B to 8B. GlobMed-LLMs achieved an average performance improvement of over 40% relative to baseline models, with a more than threefold increase in performance on low-resource languages. Together, these resources provide an important foundation for advancing the equitable development and application of LLMs globally, enabling broader language communities to benefit from technological advances.

cs.CL↗

arXiv2025

Diagnose, Localize, Align: A Full-Stack Framework for Reliable LLM Multi-Agent Systems under Instruction Conflicts

Large Language Model (LLM)-powered multi-agent systems (MAS) have rapidly advanced collaborative reasoning, tool use, and role-specialized coordination in complex tasks. However, reliability-critical deployment remains hindered by a systemic failure mode: hierarchical compliance under instruction conflicts (system-user, peer-peer), where agents misprioritize system-level rules in the presence of competing demands. Moreover, widely used macro-level metrics (e.g., pass@k) obscure these micro-level violations and offer little actionable guidance for remedy. In this work, we present a full-stack, three-stage framework: (1) Diagnose - Contextualized Role Adherence Score (CRAS), a query-wise, context-aware scoring metric that decomposes role adherence into four measurable dimensions; (2) Localize - attention drift analysis revealing that instruction conflicts are resolved by attention heads that are largely concentrated in middle layers; (3) Align - Surgical Alignment of Instruction Layers (SAIL), which installs LoRA only on the localized focal layers and optimizes a token-weighted DPO-style preference objective that credits tokens by their focal attentional contribution. Across standard benchmarks and MAS frameworks, our surgical approach improves instruction hierarchy compliance (e.g., +5.60% with AutoGen on MedQA) without full-model finetuning.

cs.CL↗

arXiv2025

FieldSeer I: Physics-Guided World Models for Long-Horizon Electromagnetic Dynamics under Partial Observability

We introduce FieldSeer I, a geometry-aware world model that forecasts electromagnetic field dynamics from partial observations in 2-D TE waveguides. The model assimilates a short prefix of observed fields, conditions on a scalar source action and structure/material map, and generates closed-loop rollouts in the physical domain. Training in a symmetric-log domain ensures numerical stability. Evaluated on a reproducible FDTD benchmark (200 unique simulations, structure-wise split), FieldSeer I achieves higher suffix fidelity than GRU and deterministic baselines across three practical settings: (i) software-in-the-loop filtering (64x64, P=80->Q=80), (ii) offline single-file rollouts (80x140, P=240->Q=40), and (iii) offline multi-structure rollouts (80x140, P=180->Q=100). Crucially, it enables edit-after-prefix geometry modifications without re-assimilation. Results demonstrate that geometry-conditioned world models provide a practical path toward interactive digital twins for photonic design.

physics.optics↗

arXiv2025

Joint Design of Protein Surface and Structure Using a Diffusion Bridge Model

Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement target receptors remains a significant challenge in computational protein design. In this work, we introduce PepBridge, a novel framework for the joint design of protein surface and structure that seamlessly integrates receptor surface geometry and biochemical properties. Starting with a receptor surface represented as a 3D point cloud, PepBridge generates complete protein structures through a multi-step process. First, it employs denoising diffusion bridge models (DDBMs) to map receptor surfaces to ligand surfaces. Next, a multi-model diffusion model predicts the corresponding structure, while Shape-Frame Matching Networks ensure alignment between surface geometry and backbone architecture. This integrated approach facilitates surface complementarity, conformational stability, and chemical feasibility. Extensive validation across diverse protein design scenarios demonstrates PepBridge's efficacy in generating structurally viable proteins, representing a significant advancement in the joint design of top-down protein structure.

cs.LG↗

arXiv2025

Agent KB: Leveraging Cross-Domain Experience for Agentic Problem Solving

AI agent frameworks operate in isolation, forcing agents to rediscover solutions and repeat mistakes across different systems. Despite valuable problem-solving experiences accumulated by frameworks like smolagents, OpenHands, and OWL, this knowledge remains trapped within individual systems, preventing the emergence of collective intelligence. Current memory systems focus on individual agents or framework-specific demonstrations, failing to enable cross-architecture knowledge transfer. We introduce AGENT KB, a universal memory infrastructure enabling seamless experience sharing across heterogeneous agent frameworks without retraining. AGENT KB aggregates trajectories into a structured knowledge base and serves lightweight APIs. At inference time, hybrid retrieval operates through two stages: planning seeds agents with cross-domain workflows, while feedback applies targeted diagnostic fixes. A disagreement gate ensures retrieved knowledge enhances rather than disrupts reasoning, addressing knowledge interference in cross-framework transfer. We validate AGENT KB across major frameworks on GAIA, Humanity's Last Exam, GPQA, and SWE-bench. Results show substantial improvements across diverse model families: compared to baseline pass@1, smolagents with AGENT KB achieve up to 18.7pp gains at pass@3 (55.2% -> 73.9%), while OpenHands improves 4.0pp on SWE-bench pass@1 (24.3% -> 28.3%). Similar improvements are observed across all base model families. Ablations confirm that hybrid retrieval and feedback stages are essential, with automatically generated experiences matching manual curation. This establishes the foundation for collective agent intelligence through shared memory infrastructures.

cs.CL↗

arXiv2025

RiboPO: Preference Optimization for Structure- and Stability-Aware RNA Design

Designing RNA sequences that reliably adopt specified three-dimensional structures while maintaining thermodynamic stability remains challenging for synthetic biology and therapeutics. Current inverse folding approaches optimize for sequence recovery or single structural metrics, failing to simultaneously ensure global geometry, local accuracy, and ensemble stability-three interdependent requirements for functional RNA design. This gap becomes critical when designed sequences encounter dynamic biological environments. We introduce RiboPO, a Ribonucleic acid Preference Optimization framework that addresses this multi-objective challenge through reinforcement learning from physical feedback (RLPF). RiboPO fine-tunes gRNAde by constructing preference pairs from composite physical criteria that couple global 3D fidelity and thermodynamic stability. Preferences are formed using structural gates, PLDDT geometry assessments, and thermostability proxies with variability-aware margins, and the policy is updated with Direct Preference Optimization (DPO). On RNA inverse folding benchmarks, RiboPO demonstrates a superior balance of structural accuracy and stability. Compared to the best non-overlap baselines, our multi-round model improves Minimum Free Energy (MFE) by 12.3% and increases secondary-structure self-consistency (EternaFold scMCC) by 20%, while maintaining competitive 3D quality and high sequence diversity. In sampling efficiency, RiboPO achieves 11% higher pass@64 than the gRNAde base under the conjunction of multiple requirements. A multi-round variant with preference-pair reconstruction delivers additional gains on unseen RNA structures. These results establish RLPF as an effective paradigm for structure-accurate and ensemble-robust RNA design, providing a foundation for extending to complex biological objectives.

q-bio.BM↗

arXiv2025

L^2M^3OF: A Large Language Multimodal Model for Metal-Organic Frameworks

Large language models have demonstrated remarkable reasoning capabilities across diverse natural language tasks. However, comparable breakthroughs in scientific discovery are more limited, because understanding complex physical phenomena demands multifaceted representations far beyond language alone. A compelling example is the design of functional materials such as MOFs-critical for a range of impactful applications like carbon capture and hydrogen storage. Navigating their vast and intricate design space in language-based representations interpretable by LLMs is challenging due to the numerous possible three-dimensional atomic arrangements and strict reticular rules of coordination geometry and topology. Despite promising early results in LLM-assisted discovery for simpler materials systems, MOF design remains heavily reliant on tacit human expertise rarely codified in textual information alone. To overcome this barrier, we introduce L2M3OF, the first multimodal LLM for MOFs. L2M3OF integrates crystal representation learning with language understanding to process structural, textual, and knowledge modalities jointly. L2M3OF employs a pre-trained crystal encoder with a lightweight projection layer to compress structural information into a token space, enabling efficient alignment with language instructions. To facilitate training and evaluation, we curate a structure-property-knowledge database of crystalline materials and benchmark L2M3OF against state-of-the-art closed-source LLMs such as GPT-5, Gemini-2.5-Pro and DeepSeek-R1. Experiments show that L2M3OF outperforms leading text-based closed-source LLMs in property prediction and knowledge generation tasks, despite using far fewer parameters. These results highlight the importance of multimodal approaches for porous material understanding and establish L2M3OF as a foundation for next-generation AI systems in materials discovery.

cs.LG↗

arXiv2025

From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?

Protein language models (PLMs) have advanced computational protein science through large-scale pretraining and scalable architectures. In parallel, reinforcement learning (RL) has broadened exploration and enabled precise multi-objective optimization in protein design. Yet whether RL can push PLMs beyond their pretraining priors to uncover latent sequence-structure-function rules remains unclear. We address this by pairing RL with PLMs across four domains: antimicrobial peptide design, kinase variant optimization, antibody engineering, and inverse folding. Using diverse RL algorithms and model classes, we ask if RL improves sampling efficiency and, more importantly, if it reveals capabilities not captured by supervised learning. Across benchmarks, RL consistently boosts success rates and sample efficiency. Performance follows a three-factor interaction: task headroom, reward fidelity, and policy capacity jointly determine gains. When rewards are accurate and informative, policies have sufficient capacity, and tasks leave room beyond supervised baselines, improvements scale; when rewards are noisy or capacity is constrained, gains saturate despite exploration. This view yields practical guidance for RL in protein design: prioritize reward modeling and calibration before scaling policy size, match algorithm and regularization strength to task difficulty, and allocate capacity where marginal gains are largest. Implementation is available at https://github.com/chq1155/RL-PLM.

cs.LG↗

arXiv2025

BroRL: Scaling Reinforcement Learning via Broadened Exploration

Reinforcement Learning with Verifiable Rewards (RLVR) has emerged as a key ingredient for unlocking complex reasoning capabilities in large language models. Recent work ProRL has shown promise in scaling RL by increasing the number of training steps. However, performance plateaus after thousands of steps, with clear diminishing returns from allocating more computation to additional training. In this work, we investigate a complementary paradigm for scaling RL, BroR-Lincreasing the number of rollouts per example to hundreds to exhaustively Broaden exploration, which yields continuous performance gains beyond the saturation point observed in ProRL when scaling the number of training steps. Our approach is motivated by a mass balance equation analysis allowing us to characterize the rate of change in probability mass for correct and incorrect tokens during the reinforcement process. We show that under a one-step RL assumption, sampled rollout tokens always contribute to correct-mass expansion, while unsampled tokens outside rollouts may lead to gains or losses depending on their distribution and the net reward balance. Importantly, as the number of rollouts per example N increases, the effect of unsampled terms diminishes, ensuring overall correct-mass expansion. To validate our theoretical analysis, we conduct simulations under more relaxed conditions and find that a sufficiently large rollout size N-corresponding to ample exploration-guarantees an increase in the probability mass of all correct tokens. Empirically, BroRL revives models saturated after 3K ProRL training steps and demonstrates robust, continuous improvement, achieving state-of-the-art results for the 1.5B model across diverse benchmarks.

cs.LG↗

arXiv2025

A deep reinforcement learning platform for antibiotic discovery

Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep-learning framework for de novo design of antibiotics that couples a 6.4-billion-parameter protein language model with reinforcement learning. The model is first fine-tuned on curated peptide data to capture antimicrobial sequence regularities, then optimised with proximal policy optimization against a composite reward that combines predictions from a learned minimum inhibitory concentration (MIC) classifier with differentiable physicochemical objectives. In vitro evaluation of 100 designed peptides showed low MIC values (nanomolar range in some cases) for all candidates (100% hit rate). Moreover, 99 our of 100 compounds exhibited broad-spectrum antimicrobial activity against at least two clinically relevant bacteria. The lead molecules killed bacteria primarily by potently targeting the cytoplasmic membrane. By unifying generation, scoring and multi-objective optimization with deep reinforcement learning in a single pipeline, our approach rapidly produces diverse, potent candidates, offering a scalable route to peptide antibiotics and a platform for iterative steering toward potency and developability within hours.

cs.LG↗

arXiv2025

Trading-R1: Financial Trading with LLM Reasoning via Reinforcement Learning

Developing professional, structured reasoning on par with human financial analysts and traders remains a central challenge in AI for finance, where markets demand interpretability and trust. Traditional time-series models lack explainability, while LLMs face challenges in turning natural-language analysis into disciplined, executable trades. Although reasoning LLMs have advanced in step-by-step planning and verification, their application to risk-sensitive financial decisions is underexplored. We present Trading-R1, a financially-aware model that incorporates strategic thinking and planning for comprehensive thesis composition, facts-grounded analysis, and volatility-adjusted decision making. Trading-R1 aligns reasoning with trading principles through supervised fine-tuning and reinforcement learning with a three-stage easy-to-hard curriculum. Training uses Tauric-TR1-DB, a 100k-sample corpus spanning 18 months, 14 equities, and five heterogeneous financial data sources. Evaluated on six major equities and ETFs, Trading-R1 demonstrates improved risk-adjusted returns and lower drawdowns compared to both open-source and proprietary instruction-following models as well as reasoning models. The system generates structured, evidence-based investment theses that support disciplined and interpretable trading decisions. Trading-R1 Terminal will be released at https://github.com/TauricResearch/Trading-R1.

q-fin.TR↗

arXiv2025

Puzzle Game: Prediction and Classification of Wordle Solution Words

We study the prediction and classification of Wordle solution words. After cleaning the public results log, we fit an ARIMA model to forecast the daily volume of reported outcomes through March 1, 2023. For each solution word, we compute three interpretable attributes: usage frequency (FREQ), word information entropy (WIE), and the number of repeated letters (NRE), and analyze their correlations with the empirical attempt distribution (1-6 attempts plus failure, coded as 7). We then train an XGBoost regressor to predict the full 1-7 outcome distribution for unseen words; a case study of "EERIE" illustrates the model's behavior. To categorize difficulty, we cluster words into three tiers (simple, moderate, difficult) via K-means and train a decision-tree classifier that maps FREQ, WIE, and NRE to these tiers, yielding interpretable rules. For each word, we also report the share of players requiring three or more attempts. Sensitivity analyses and full modeling details are provided in the appendix.

math.NA↗