arXiv subjects

Pengyu Hong

Publications and source records attributed to Pengyu Hong.

At least 19 recordsLinked to original sources

arXiv2026

Boosting Text-to-Image Diffusion Models via Core Token Attention-Based Seed Selection

Text-to-image diffusion models can synthesize high-quality images, yet the outcome is notoriously sensitive to the random seed: different initial seeds often yield large variations in image quality and prompt-image alignment. We revisit this "seed effect" and show that attention dynamics over prompt core tokens, the content-bearing words, measured during the first few denoising steps, strongly predict final generation quality. Building on this observation, we introduce Attention-Based Seed Selection (ABSS), a training-free, plug-and-play method that ranks seeds for a given prompt by leveraging cross-attention to core tokens during the denoising process. ABSS requires no finetuning and does not alter the initial noise; it scores and ranks all candidate seeds, keeps only the top-k for full generation, and discards the rest, without relying on a fixed accept/reject threshold. Operating purely at inference time, ABSS can serve as a lightweight pre-selection add-on for existing seed-optimization pipelines, enabling additional gains. Across three benchmarks, extensive experiments show that ABSS enables consistent improvements in text-image alignment and visual quality for Stable Diffusion variants, as corroborated by human preference and alignment metrics.

cs.CV↗

arXiv2025

Cross-Modality Controlled Molecule Generation with Diffusion Language Model

Current SMILES-based diffusion models for molecule generation typically support only unimodal constraint. They inject conditioning signals at the start of the training process and require retraining a new model from scratch whenever the constraint changes. However, real-world applications often involve multiple constraints across different modalities, and additional constraints may emerge over the course of a study. This raises a challenge: how to extend a pre-trained diffusion model not only to support cross-modality constraints but also to incorporate new ones without retraining. To tackle this problem, we propose the Cross-Modality Controlled Molecule Generation with Diffusion Language Model (CMCM-DLM), demonstrated by two distinct cross modalities: molecular structure and chemical properties. Our approach builds upon a pre-trained diffusion model, incorporating two trainable modules, the Structure Control Module (SCM) and the Property Control Module (PCM), and operates in two distinct phases during the generation process. In Phase I, we employs the SCM to inject structural constraints during the early diffusion steps, effectively anchoring the molecular backbone. Phase II builds on this by further introducing PCM to guide the later stages of inference to refine the generated molecules, ensuring their chemical properties match the specified targets. Experimental results on multiple datasets demonstrate the efficiency and adaptability of our approach, highlighting CMCM-DLM's significant advancement in molecular generation for drug discovery applications.

cs.LG↗

arXiv2025

Doc2Agent: Scalable Generation of Tool-Using Agents from API Documentation

REST APIs play important roles in enriching the action space of web agents, yet most API-based agents rely on curated and uniform toolsets that do not reflect the complexity of real-world APIs. Building tool-using agents for arbitrary domains remains a major challenge, as it requires reading unstructured API documentation, testing APIs and inferring correct parameters. We propose Doc2Agent, a scalable pipeline to build agents that can call Python-based tools generated from API documentation. Doc2Agent generates executable tools from API documentations and iteratively refines them using a code agent. We evaluate our approach on real-world APIs, WebArena APIs, and research APIs, producing validated tools. We achieved a 55\% relative performance improvement with 90\% lower cost compared to direct API calling on WebArena benchmark. A domain-specific agent built for glycomaterial science further demonstrates the pipeline's adaptability to complex, knowledge-rich tasks. Doc2Agent offers a generalizable solution for building tool agents from unstructured API documentation at scale.

cs.CL↗

arXiv2025

Multimodal Fusion with Relational Learning for Molecular Property Prediction

Graph based molecular representation learning is essential for accurately predicting molecular properties in drug discovery and materials science; however, it faces significant challenges due to the intricate relationships among molecules and the limited chemical knowledge utilized during training. While contrastive learning is often employed to handle molecular relationships, its reliance on binary metrics is insufficient for capturing the complexity of these interactions. Multimodal fusion has gained attention for property reasoning, but previous work has explored only a limited range of modalities, and the optimal stages for fusing different modalities in molecular property tasks remain underexplored. In this paper, we introduce MMFRL (Multimodal Fusion with Relational Learning for Molecular Property Prediction), a novel framework designed to overcome these limitations. Our method enhances embedding initialization through multimodal pretraining using relational learning. We also conduct a systematic investigation into the impact of modality fusion at different stages such as early, intermediate, and late, highlighting their advantages and shortcomings. Extensive experiments on MoleculeNet benchmarks demonstrate that MMFRL significantly outperforms existing methods. Furthermore, MMFRL enables task-specific optimizations. Additionally, the explainability of MMFRL provides valuable chemical insights, emphasizing its potential to enhance real-world drug discovery applications.

cs.CE↗

arXiv2025

2DNMRGym: An Annotated Experimental Dataset for Atom-Level Molecular Representation Learning in 2D NMR via Surrogate Supervision

Two-dimensional (2D) Nuclear Magnetic Resonance (NMR) spectroscopy, particularly Heteronuclear Single Quantum Coherence (HSQC) spectroscopy, plays a critical role in elucidating molecular structures, interactions, and electronic properties. However, accurately interpreting 2D NMR data remains labor-intensive and error-prone, requiring highly trained domain experts, especially for complex molecules. Machine Learning (ML) holds significant potential in 2D NMR analysis by learning molecular representations and recognizing complex patterns from data. However, progress has been limited by the lack of large-scale and high-quality annotated datasets. In this work, we introduce 2DNMRGym, the first annotated experimental dataset designed for ML-based molecular representation learning in 2D NMR. It includes over 22,000 HSQC spectra, along with the corresponding molecular graphs and SMILES strings. Uniquely, 2DNMRGym adopts a surrogate supervision setup: models are trained using algorithm-generated annotations derived from a previously validated method and evaluated on a held-out set of human-annotated gold-standard labels. This enables rigorous assessment of a model's ability to generalize from imperfect supervision to expert-level interpretation. We provide benchmark results using a series of 2D and 3D GNN and GNN transformer models, establishing a strong foundation for future work. 2DNMRGym supports scalable model training and introduces a chemically meaningful benchmark for evaluating atom-level molecular representations in NMR-guided structural tasks. Our data and code is open-source and available on Huggingface and Github.

cs.LG↗

arXiv2025

Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning

The versatility of multimodal deep learning holds tremendous promise for advancing scientific research and practical applications. As this field continues to evolve, the collective power of cross-modal analysis promises to drive transformative innovations, opening new frontiers in chemical understanding and drug discovery. Hence, we introduce Asymmetric Contrastive Multimodal Learning (ACML), a specifically designed approach to enhance molecular understanding and accelerate advancements in drug discovery. ACML harnesses the power of effective asymmetric contrastive learning to seamlessly transfer information from various chemical modalities to molecular graph representations. By combining pre-trained chemical unimodal encoders and a shallow-designed graph encoder with 5 layers, ACML facilitates the assimilation of coordinated chemical semantics from different modalities, leading to comprehensive representation learning with efficient training. We demonstrate the effectiveness of this framework through large-scale cross-modality retrieval and isomer discrimination tasks. Additionally, ACML enhances interpretability by revealing chemical semantics in graph presentations and bolsters the expressive power of graph neural networks, as evidenced by improved performance in molecular property prediction tasks from MoleculeNet and Therapeutics Data Commons (TDC). Ultimately, ACML exemplifies its potential to revolutionize molecular representational learning, offering deeper insights into the chemical semantics of diverse modalities and paving the way for groundbreaking advancements in chemical research and drug discovery.

cs.LG↗

arXiv2025

ToolFactory: Automating Tool Generation by Leveraging LLM to Understand REST API Documentations

LLM-based tool agents offer natural language interfaces, enabling users to seamlessly interact with computing services. While REST APIs are valuable resources for building such agents, they must first be transformed into AI-compatible tools. Automatically generating AI-compatible tools from REST API documents can greatly streamline tool agent development and minimize user learning curves. However, API documentation often suffers from a lack of standardization, inconsistent schemas, and incomplete information. To address these issues, we developed \textbf{ToolFactory}, an open-source pipeline for automating tool generation from unstructured API documents. To enhance the reliability of the developed tools, we implemented an evaluation method to diagnose errors. Furthermore, we built a knowledge base of verified tools, which we leveraged to infer missing information from poorly documented APIs. We developed the API Extraction Benchmark, comprising 167 API documents and 744 endpoints in various formats, and designed a JSON schema to annotate them. This annotated dataset was utilized to train and validate ToolFactory. The experimental results highlight the effectiveness of ToolFactory. We also demonstrated ToolFactory by creating a domain-specific AI agent for glycomaterials research. ToolFactory exhibits significant potential for facilitating the seamless integration of scientific REST APIs into AI workflows.

cs.LG↗

arXiv2025

Multiple Abstraction Level Retrieve Augment Generation

A Retrieval-Augmented Generation (RAG) model powered by a large language model (LLM) provides a faster and more cost-effective solution for adapting to new data and knowledge. It also delivers more specialized responses compared to pre-trained LLMs. However, most existing approaches rely on retrieving prefix-sized chunks as references to support question-answering (Q/A). This approach is often deployed to address information needs at a single level of abstraction, as it struggles to generate answers across multiple levels of abstraction. In an RAG setting, while LLMs can summarize and answer questions effectively when provided with sufficient details, retrieving excessive information often leads to the 'lost in the middle' problem and exceeds token limitations. We propose a novel RAG approach that uses chunks of multiple abstraction levels (MAL), including multi-sentence-level, paragraph-level, section-level, and document-level. The effectiveness of our approach is demonstrated in an under-explored scientific domain of Glycoscience. Compared to traditional single-level RAG approaches, our approach improves AI evaluated answer correctness of Q/A by 25.739\% on Glyco-related papers.

cs.CL↗

arXiv2025

Reflections from the 2024 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research.

cs.LG↗

arXiv2024

TransPeakNet: Solvent-Aware 2D NMR Prediction via Multi-Task Pre-Training and Unsupervised Learning

Nuclear Magnetic Resonance (NMR) spectroscopy is essential for revealing molecular structure, electronic environment, and dynamics. Accurate NMR shift prediction allows researchers to validate structures by comparing predicted and observed shifts. While Machine Learning (ML) has improved one-dimensional (1D) NMR shift prediction, predicting 2D NMR remains challenging due to limited annotated data. To address this, we introduce an unsupervised training framework for predicting cross-peaks in 2D NMR, specifically Heteronuclear Single Quantum Coherence (HSQC).Our approach pretrains an ML model on an annotated 1D dataset of 1H and 13C shifts, then finetunes it in an unsupervised manner using unlabeled HSQC data, which simultaneously generates cross-peak annotations. Our model also adjusts for solvent effects. Evaluation on 479 expert-annotated HSQC spectra demonstrates our model's superiority over traditional methods (ChemDraw and Mestrenova), achieving Mean Absolute Errors (MAEs) of 2.05 ppm and 0.165 ppm for 13C shifts and 1H shifts respectively. Our algorithmic annotations show a 95.21% concordance with experts' assignments, underscoring the approach's potential for structural elucidation in fields like organic chemistry, pharmaceuticals, and natural products.

cs.LG↗

arXiv2024

Counterpart Fairness -- Addressing Systematic between-group Differences in Fairness Evaluation

When using machine learning to aid decision-making, it is critical to ensure that an algorithmic decision is fair and does not discriminate against specific individuals/groups, particularly those from underprivileged populations. Existing group fairness methods aim to ensure equal outcomes (such as loan approval rates) across groups delineated by protected variables like race or gender. However, in cases where systematic differences between groups play a significant role in outcomes, these methods may overlook the influence of non-protected variables that can systematically vary across groups. These confounding factors can affect fairness evaluations, making it challenging to assess whether disparities are due to discrimination or inherent differences. Therefore, we recommend a more refined and comprehensive fairness index that accounts for both the systematic differences within groups and the multifaceted, intertwined confounding effects. The proposed index evaluates fairness on counterparts (pairs of individuals who are similar with respect to the task of interest but from different groups), whose group identities cannot be distinguished algorithmically by exploring confounding factors. To identify counterparts, we developed a two-step matching method inspired by propensity score and metric learning. In addition, we introduced a counterpart-based statistical fairness index, called Counterpart Fairness (CFair), to assess the fairness of machine learning models. Empirical results on the MIMIC and COMPAS datasets indicate that standard group-based fairness metrics may not adequately inform about the degree of unfairness present in predictions, as revealed through CFair.

cs.LG↗

arXiv2024

Theoretical Corrections and the Leveraging of Reinforcement Learning to Enhance Triangle Attack

Adversarial examples represent a serious issue for the application of machine learning models in many sensitive domains. For generating adversarial examples, decision based black-box attacks are one of the most practical techniques as they only require query access to the model. One of the most recently proposed state-of-the-art decision based black-box attacks is Triangle Attack (TA). In this paper, we offer a high-level description of TA and explain potential theoretical limitations. We then propose a new decision based black-box attack, Triangle Attack with Reinforcement Learning (TARL). Our new attack addresses the limits of TA by leveraging reinforcement learning. This creates an attack that can achieve similar, if not better, attack accuracy than TA with half as many queries on state-of-the-art classifiers and defenses across ImageNet and CIFAR-10.

cs.LG↗

arXiv2024

Uncertainty Quantification for Clinical Outcome Predictions with (Large) Language Models

To facilitate healthcare delivery, language models (LMs) have significant potential for clinical prediction tasks using electronic health records (EHRs). However, in these high-stakes applications, unreliable decisions can result in high costs due to compromised patient safety and ethical concerns, thus increasing the need for good uncertainty modeling of automated clinical predictions. To address this, we consider the uncertainty quantification of LMs for EHR tasks in white- and black-box settings. We first quantify uncertainty in white-box models, where we can access model parameters and output logits. We show that an effective reduction of model uncertainty can be achieved by using the proposed multi-tasking and ensemble methods in EHRs. Continuing with this idea, we extend our approach to black-box settings, including popular proprietary LMs such as GPT-4. We validate our framework using longitudinal clinical data from more than 6,000 patients in ten clinical prediction tasks. Results show that ensembling methods and multi-task prediction prompts reduce uncertainty across different scenarios. These findings increase the transparency of the model in white-box and black-box settings, thus advancing reliable AI healthcare.

cs.CL↗

arXiv2024

Question Rephrasing for Quantifying Uncertainty in Large Language Models: Applications in Molecular Chemistry Tasks

Uncertainty quantification enables users to assess the reliability of responses generated by large language models (LLMs). We present a novel Question Rephrasing technique to evaluate the input uncertainty of LLMs, which refers to the uncertainty arising from equivalent variations of the inputs provided to LLMs. This technique is integrated with sampling methods that measure the output uncertainty of LLMs, thereby offering a more comprehensive uncertainty assessment. We validated our approach on property prediction and reaction prediction for molecular chemistry tasks.

cs.CL↗

arXiv2024

Enhancing Peak Assignment in 13C NMR Spectroscopy: A Novel Approach Using Multimodal Alignment

Nuclear magnetic resonance (NMR) spectroscopy plays an essential role in deciphering molecular structure and dynamic behaviors. While AI-enhanced NMR prediction models hold promise, challenges still persist in tasks such as molecular retrieval, isomer recognition, and peak assignment. In response, this paper introduces a novel solution, Multi-Level Multimodal Alignment with Knowledge-Guided Instance-Wise Discrimination (K-M3AID), which establishes correspondences between two heterogeneous modalities: molecular graphs and NMR spectra. K-M3AID employs a dual-coordinated contrastive learning architecture with three key modules: a graph-level alignment module, a node-level alignment module, and a communication channel. Notably, K-M3AID introduces knowledge-guided instance-wise discrimination into contrastive learning within the node-level alignment module. In addition, K-M3AID demonstrates that skills acquired during node-level alignment have a positive impact on graph-level alignment, acknowledging meta-learning as an inherent property. Empirical validation underscores K-M3AID's effectiveness in multiple zero-shot tasks.

cs.LG↗

arXiv2024

Deep-learning Optical Flow Outperforms PIV in Obtaining Velocity Fields from Active Nematics

Deep learning-based optical flow (DLOF) extracts features in adjacent video frames with deep convolutional neural networks. It uses those features to estimate the inter-frame motions of objects at the pixel level. In this article, we evaluate the ability of optical flow to quantify the spontaneous flows of MT-based active nematics under different labeling conditions. We compare DLOF against the commonly used technique, particle imaging velocimetry (PIV). We obtain flow velocity ground truths either by performing semi-automated particle tracking on samples with sparsely labeled filaments, or from passive tracer beads. We find that DLOF produces significantly more accurate velocity fields than PIV for densely labeled samples. We show that the breakdown of PIV arises because the algorithm cannot reliably distinguish contrast variations at high densities, particularly in directions parallel to the nematic director. DLOF overcomes this limitation. For sparsely labeled samples, DLOF and PIV produce results with similar accuracy, but DLOF gives higher-resolution fields. Our work establishes DLOF as a versatile tool for measuring fluid flows in a broad class of active, soft, and biophysical systems.

cond-mat.soft↗

arXiv2024

Graph Multi-Similarity Learning for Molecular Property Prediction

Enhancing accurate molecular property prediction relies on effective and proficient representation learning. It is crucial to incorporate diverse molecular relationships characterized by multi-similarity (self-similarity and relative similarities) between molecules. However, current molecular representation learning methods fall short in exploring multi-similarity and often underestimate the complexity of relationships between molecules. Additionally, previous multi-similarity approaches require the specification of positive and negative pairs to attribute distinct predefined weights to different relative similarities, which can introduce potential bias. In this work, we introduce Graph Multi-Similarity Learning for Molecular Property Prediction (GraphMSL) framework, along with a novel approach to formulate a generalized multi-similarity metric without the need to define positive and negative pairs. In each of the chemical modality spaces (e.g.,molecular depiction image, fingerprint, NMR, and SMILES) under consideration, we first define a self-similarity metric (i.e., similarity between an anchor molecule and another molecule), and then transform it into a generalized multi-similarity metric for the anchor through a pair weighting function. GraphMSL validates the efficacy of the multi-similarity metric across MoleculeNet datasets. Furthermore, these metrics of all modalities are integrated into a multimodal multi-similarity metric, which showcases the potential to improve the performance. Moreover, the focus of the model can be redirected or customized by altering the fusion function. Last but not least, GraphMSL proves effective in drug discovery evaluations through post-hoc analyses of the learnt representations.

cs.LG↗

arXiv2023

A Machine Learning Approach to Robustly Determine Director Fields and Analyze Defects in Active Nematics

Active nematics are dense systems of rodlike particles that consume energy to drive motion at the level of the individual particles. They exist in natural systems like biological tissues and artificial materials such as suspensions of self-propelled colloidal particles or synthetic microswimmers. Active nematics have attracted significant attention in recent years due to their spectacular nonequilibrium collective spatiotemporal dynamics, which may enable applications in fields such as robotics, drug delivery, and materials science. The director field, which measures the direction and degree of alignment of the local nematic orientation, is a crucial characteristic of active nematic and is essential for studying topological defects. However, determining the director field is a significant challenge in many experimental systems. Although director fields can be derived from images of active nematics using traditional imaging processing methods, the accuracy of such methods are highly sensitive to the settings of the algorithms. These settings must be tuned from image-to-image due to experimental noise, intrinsic noise of the imaging technology, and perturbations caused by changes in experimental conditions. This sensitivity currently limits automatic analysis of active nematics. To address this, we developed a machine learning model for extracting reliable director fields from raw experimental images, which enables accurate analysis of topological defects. Application of the algorithm to experimental data demonstrates that the approach is robust and highly generalizable to experimental settings that are different from those in the training data. It could be a promising tool for investigating active nematics and may be generalized to other active matter systems.

cond-mat.soft↗