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Source author record

Xiangxiang Zeng

Xiangxiang Zeng appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

ResearcherUnclaimed source record
Machine LearningArtificial IntelligenceBiomoleculesComputer VisionComputational Engineering, Finance, and Scienceeess.IVOther Quantitative BiologyQuantitative Methods

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Published work

6 published item(s)

preprint2026arXiv

CaptchaMind: Training CAPTCHA Solvers via Reinforcement Learning with Explicit Reasoning Supervision

CAPTCHAs are widely deployed as human verification mechanisms and frequently block intelligent agents from completing end-to-end automation in real-world web environments. Solving modern CAPTCHAs requires robust multi-step visual reasoning and interaction capabilities, yet training-based approaches have remained absent due to the lack of large-scale training data and process-level annotations. We introduce CaptchaBench, the first CAPTCHA benchmark designed to support large-scale training, comprising 16,000 programmatically generated samples across eight task categories with detailed region and process-level annotations. Systematic evaluation on CaptchaBench reveals that existing methods fail consistently on tasks requiring fine-grained visual detail capture and region-level comparison. We therefore present CaptchaMind, an RL-based solver trained with explicit reasoning process supervision, achieving 82.9% average success rate across eight tasks and 71.0% on real-world instances, substantially outperforming all existing methods without closed-source APIs.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

SpecX: A Large-Scale Benchmark for Multi-Modal Spectroscopy and Cross-Paradigm Evaluation

Existing spectral benchmarks are limited in scale, modality alignment, and evaluation scope, and typically focus on either specialized models or multimodal language models (MLLMs). We introduce SpecX, a large-scale benchmark for multi-modal spectroscopy with cross-paradigm evaluation. SpecX contains 1.7M molecules with diverse spectral modalities, including NMR (1H, 13C, HSQC), IR, MS,UV,Raman and FL, and is organized into three tiers: a large-scale dataset for pretraining, an aligned multi-spectral subset for benchmarking, and a high-quality experimental subset for evaluation. SpecX supports a range of tasks such as molecular elucidation, spectrum simulation, and spectral understanding, and enables unified evaluation across both specialized spectral models and MLLMs. Experiments show that specialized models excel at signal-level modeling, while MLLMs exhibit strengths in high-level reasoning but lack precise spectral grounding. SpecX establishes a unified benchmark for spectral intelligence and highlights the need for spectrum-native foundation models.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Deep learning for drug repurposing: methods, databases, and applications

Drug development is time-consuming and expensive. Repurposing existing drugs for new therapies is an attractive solution that accelerates drug development at reduced experimental costs, specifically for Coronavirus Disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, comprehensively obtaining and productively integrating available knowledge and big biomedical data to effectively advance deep learning models is still challenging for drug repurposing in other complex diseases. In this review, we introduce guidelines on how to utilize deep learning methodologies and tools for drug repurposing. We first summarized the commonly used bioinformatics and pharmacogenomics databases for drug repurposing. Next, we discuss recently developed sequence-based and graph-based representation approaches as well as state-of-the-art deep learning-based methods. Finally, we present applications of drug repurposing to fight the COVID-19 pandemic, and outline its future challenges.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Multi-View Substructure Learning for Drug-Drug Interaction Prediction

Drug-drug interaction (DDI) prediction provides a drug combination strategy for systemically effective treatment. Previous studies usually model drug information constrained on a single view such as the drug itself, leading to incomplete and noisy information, which limits the accuracy of DDI prediction. In this work, we propose a novel multi- view drug substructure network for DDI prediction (MSN-DDI), which learns chemical substructures from both the representations of the single drug (intra-view) and the drug pair (inter-view) simultaneously and utilizes the substructures to update the drug representation iteratively. Comprehensive evaluations demonstrate that MSN-DDI has almost solved DDI prediction for existing drugs by achieving a relatively improved accuracy of 19.32% and an over 99% accuracy under the transductive setting. More importantly, MSN-DDI exhibits better generalization ability to unseen drugs with a relatively improved accuracy of 7.07% under more challenging inductive scenarios. Finally, MSN-DDI improves prediction performance for real-world DDI applications to new drugs.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning

There have been more than 850,000 confirmed cases and over 48,000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there are currently no proven effective medications against COVID-19. Drug repurposing offers a promising way for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, genes, pathways, and expressions, from a large scientific corpus of 24 million PubMed publications. Using Amazon AWS computing resources, we identified 41 repurposable drugs (including indomethacin, toremifene and niclosamide) whose therapeutic association with COVID-19 were validated by transcriptomic and proteomic data in SARS-CoV-2 infected human cells and data from ongoing clinical trials. While this study, by no means recommends specific drugs, it demonstrates a powerful deep learning methodology to prioritize existing drugs for further investigation, which holds the potential of accelerating therapeutic development for COVID-19.

0 citations0 reviewsNo code linkedOpen access