arXiv subjects

Guangyong Chen

Publications and source records attributed to Guangyong Chen.

At least 19 recordsLinked to original sources

arXiv2026

InstructPLM-mu: 1-Hour Fine-Tuning of ESM2 Beats ESM3 in Protein Mutation Predictions

Multimodal protein language models deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called InstructPLM-mu and try to answer a question: \textit{Can multimodal fine-tuning of a pretrained, sequence-only protein language model match the performance of models trained end-to-end? } Surprisingly, our experiments show that fine-tuning ESM2 with structural inputs can reach performance comparable to ESM3. To understand how this is achieved, we systematically compare three different feature-fusion designs and fine-tuning recipes. Our results reveal that both the fusion method and the tuning strategy strongly affect final accuracy, indicating that the fine-tuning process is not trivial. We hope this work offers practical guidance for injecting structure into pretrained protein language models and motivates further research on better fusion mechanisms and fine-tuning protocols.

q-bio.QM↗

arXiv2026

Boosting In-Silicon Directed Evolution with Fine-Tuned Protein Language Model and Tree Search

Protein evolution through amino acid mutations is a cornerstone of life sciences. Recent advances in protein language models have shown rich evolutionary patterns, offering unprecedented potential for in-silicon directed evolution. However, existing directed evolution methods largely rely on heuristic evolution strategies and have yet to efficiently integrate the transformative protein language models with advanced optimization techniques, such as reinforcement learning, to adaptively learn superior evolution policies. To bridge this gap, we propose AlphaDE, a novel framework that evolves protein sequences by harnessing the innovative paradigms of large language models, such as fine-tuning and test-time inference. First, AlphaDE fine-tunes pretrained protein language models using masked language modeling on homologous protein sequences to activate the evolutionary plausibility of the interested protein family. Second, AlphaDE introduces test-time inference based on Monte Carlo tree search, which effectively evolves proteins with evolutionary guidance from the fine-tuned protein language model. Extensive benchmark experiments show that AlphaDE remarkably outperforms previous state-of-the-art methods even with few-shot fine-tuning. A case study further demonstrates that AlphaDE supports condensing the protein sequence space of avGFP through computational evolution.

cs.AI↗

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

Excavate the potential of Single-Scale Features: A Decomposition Network for Water-Related Optical Image Enhancement

Underwater image enhancement (UIE) techniques aim to improve visual quality of images captured in aquatic environments by addressing degradation issues caused by light absorption and scattering effects, including color distortion, blurring, and low contrast. Current mainstream solutions predominantly employ multi-scale feature extraction (MSFE) mechanisms to enhance reconstruction quality through multi-resolution feature fusion. However, our extensive experiments demonstrate that high-quality image reconstruction does not necessarily rely on multi-scale feature fusion. Contrary to popular belief, our experiments show that single-scale feature extraction alone can match or surpass the performance of multi-scale methods, significantly reducing complexity. To comprehensively explore single-scale feature potential in underwater enhancement, we propose an innovative Single-Scale Decomposition Network (SSD-Net). This architecture introduces an asymmetrical decomposition mechanism that disentangles input image into clean layer along with degradation layer. The former contains scene-intrinsic information and the latter encodes medium-induced interference. It uniquely combines CNN's local feature extraction capabilities with Transformer's global modeling strengths through two core modules: 1) Parallel Feature Decomposition Block (PFDB), implementing dual-branch feature space decoupling via efficient attention operations and adaptive sparse transformer; 2) Bidirectional Feature Communication Block (BFCB), enabling cross-layer residual interactions for complementary feature mining and fusion. This synergistic design preserves feature decomposition independence while establishing dynamic cross-layer information pathways, effectively enhancing degradation decoupling capacity.

cs.CV↗

arXiv2025

Accelerating FRB Search: Dataset and Methods

Fast Radio Burst (FRB) is an extremely energetic cosmic phenomenon of short duration. Discovered only recently and with its origin still unknown, FRBs have already started to play a significant role in studying the distribution and evolution of matter in the universe. FRBs can only be observed through radio telescopes, which produce petabytes of data, rendering the search for FRB a challenging task. Traditional techniques are computationally expensive, time-consuming, and generally biased against weak signals. Various machine learning algorithms have been developed and employed, all of which require substantial datasets. We here introduce the FAST dataset for Fast Radio bursts EXploration (FAST-FREX), built upon the observations obtained by the Five-hundred-meter Aperture Spherical radio Telescope (FAST). Our dataset comprises 600 positive samples of observed FRB signals from three sources and 1000 negative samples of noise and Radio Frequency Interference (RFI). Furthermore, we provide a machine learning algorithm, Radio Single-Pulse Detection Algorithm Based on Visual Morphological Features (RaSPDAM), with significant improvements in efficiency and accuracy for FRB search. We also employed the benchmark comparison between conventional single-pulse search softwares, namely PRESTO and Heimdall, and RaSPDAM. RaSPDAMv2 achieves an average precision of 97% and an average recall of 83%, with notable enhancements in computational performance. Future machine learning algorithms can use this as a reference point to measure their performance and help the potential improvements. By enabling more accurate and efficient detection of transient radio events, our work facilitates the FRB and pulsars search pipeline, enhances the potential for discovering new astrophysical phenomena.

astro-ph.IM↗

arXiv2025

ChemMiner: A Large Language Model Agent System for Chemical Literature Data Mining

The development of AI-assisted chemical synthesis tools requires comprehensive datasets covering diverse reaction types, yet current high-throughput experimental (HTE) approaches are expensive and limited in scope. Chemical literature represents a vast, underexplored data source containing thousands of reactions published annually. However, extracting reaction information from literature faces significant challenges including varied writing styles, complex coreference relationships, and multimodal information presentation. This paper proposes ChemMiner, a novel end-to-end framework leveraging multiple agents powered by large language models (LLMs) to extract high-fidelity chemical data from literature. ChemMiner incorporates three specialized agents: a text analysis agent for coreference mapping, a multimodal agent for non-textual information extraction, and a synthesis analysis agent for data generation. Furthermore, we developed a comprehensive benchmark with expert-annotated chemical literature to evaluate both extraction efficiency and precision. Experimental results demonstrate reaction identification rates comparable to human chemists while significantly reducing processing time, with high accuracy, recall, and F1 scores. Our open-sourced benchmark facilitates future research in chemical literature data mining.

cs.IR↗

arXiv2025

Protein Inverse Folding From Structure Feedback

The inverse folding problem, aiming to design amino acid sequences that fold into desired three-dimensional structures, is pivotal for various biotechnological applications. Here, we introduce a novel approach leveraging Direct Preference Optimization (DPO) to fine-tune an inverse folding model using feedback from a protein folding model. Given a target protein structure, we begin by sampling candidate sequences from the inverse-folding model, then predict the three-dimensional structure of each sequence with the folding model to generate pairwise structural-preference labels. These labels are used to fine-tune the inverse-folding model under the DPO objective. Our results on the CATH 4.2 test set demonstrate that DPO fine-tuning not only improves sequence recovery of baseline models but also leads to a significant improvement in average TM-Score from 0.77 to 0.81, indicating enhanced structure similarity. Furthermore, iterative application of our DPO-based method on challenging protein structures yields substantial gains, with an average TM-Score increase of 79.5\% with regard to the baseline model. This work establishes a promising direction for enhancing protein sequence design ability from structure feedback by effectively utilizing preference optimization.

cs.LG↗

arXiv2025

MagicTailor: Component-Controllable Personalization in Text-to-Image Diffusion Models

Text-to-image diffusion models can generate high-quality images but lack fine-grained control of visual concepts, limiting their creativity. Thus, we introduce component-controllable personalization, a new task that enables users to customize and reconfigure individual components within concepts. This task faces two challenges: semantic pollution, where undesired elements disrupt the target concept, and semantic imbalance, which causes disproportionate learning of the target concept and component. To address these, we design MagicTailor, a framework that uses Dynamic Masked Degradation to adaptively perturb unwanted visual semantics and Dual-Stream Balancing for more balanced learning of desired visual semantics. The experimental results show that MagicTailor achieves superior performance in this task and enables more personalized and creative image generation.

cs.CV↗

arXiv2025

Chemist-X: Large Language Model-empowered Agent for Reaction Condition Recommendation in Chemical Synthesis

Recent AI research plots a promising future of automatic chemical reactions within the chemistry society. This study proposes Chemist-X, a comprehensive AI agent that automates the reaction condition optimization (RCO) task in chemical synthesis with retrieval-augmented generation (RAG) technology and AI-controlled wet-lab experiment executions. To begin with, as an emulation on how chemical experts solve the RCO task, Chemist-X utilizes a novel RAG scheme to interrogate available molecular and literature databases to narrow the searching space for later processing. The agent then leverages a computer-aided design (CAD) tool we have developed through a large language model (LLM) supervised programming interface. With updated chemical knowledge obtained via RAG, as well as the ability in using CAD tools, our agent significantly outperforms conventional RCO AIs confined to the fixed knowledge within its training data. Finally, Chemist-X interacts with the physical world through an automated robotic system, which can validate the suggested chemical reaction condition without human interventions. The control of the robotic system was achieved with a novel algorithm we have developed for the equipment, which relies on LLMs for reliable script generation. Results of our automatic wet-lab experiments, achieved by fully LLM-supervised end-to-end operation with no human in the lope, prove Chemist-X's ability in self-driving laboratories.

cs.IR↗

arXiv2025

Dual Ensembled Multiagent Q-Learning with Hypernet Regularizer

Overestimation in single-agent reinforcement learning has been extensively studied. In contrast, overestimation in the multiagent setting has received comparatively little attention although it increases with the number of agents and leads to severe learning instability. Previous works concentrate on reducing overestimation in the estimation process of target Q-value. They ignore the follow-up optimization process of online Q-network, thus making it hard to fully address the complex multiagent overestimation problem. To solve this challenge, in this study, we first establish an iterative estimation-optimization analysis framework for multiagent value-mixing Q-learning. Our analysis reveals that multiagent overestimation not only comes from the computation of target Q-value but also accumulates in the online Q-network's optimization. Motivated by it, we propose the Dual Ensembled Multiagent Q-Learning with Hypernet Regularizer algorithm to tackle multiagent overestimation from two aspects. First, we extend the random ensemble technique into the estimation of target individual and global Q-values to derive a lower update target. Second, we propose a novel hypernet regularizer on hypernetwork weights and biases to constrain the optimization of online global Q-network to prevent overestimation accumulation. Extensive experiments in MPE and SMAC show that the proposed method successfully addresses overestimation across various tasks.

cs.MA↗

arXiv2025

Variable Projection Algorithms: Theoretical Insights and A Novel Approach for Problems with Large Residual

This paper delves into an in-depth exploration of the Variable Projection (VP) algorithm, a powerful tool for solving separable nonlinear optimization problems across multiple domains, including system identification, image processing, and machine learning. We first establish a theoretical framework to examine the effect of the approximate treatment of the coupling relationship among parameters on the local convergence of the VP algorithm and theoretically prove that the Kaufman's VP algorithm can achieve a similar convergence rate as the Golub \& Pereyra's form. These studies fill the gap in the existing convergence theory analysis, and provide a solid foundation for understanding the mechanism of VP algorithm and broadening its application horizons. Furthermore, drawing inspiration from these theoretical revelations, we design a refined VP algorithm for handling separable nonlinear optimization problems characterized by large residual, called VPLR, which boosts the convergence performance by addressing the interdependence of parameters within the separable model and by continually correcting the approximated Hessian matrix to counteract the influence of large residual during the iterative process. The effectiveness of this refined algorithm is corroborated through numerical experimentation.

math.OC↗

arXiv2024

Point Cloud Understanding via Attention-Driven Contrastive Learning

Recently Transformer-based models have advanced point cloud understanding by leveraging self-attention mechanisms, however, these methods often overlook latent information in less prominent regions, leading to increased sensitivity to perturbations and limited global comprehension. To solve this issue, we introduce PointACL, an attention-driven contrastive learning framework designed to address these limitations. Our method employs an attention-driven dynamic masking strategy that guides the model to focus on under-attended regions, enhancing the understanding of global structures within the point cloud. Then we combine the original pre-training loss with a contrastive learning loss, improving feature discrimination and generalization. Extensive experiments validate the effectiveness of PointACL, as it achieves state-of-the-art performance across a variety of 3D understanding tasks, including object classification, part segmentation, and few-shot learning. Specifically, when integrated with different Transformer backbones like Point-MAE and PointGPT, PointACL demonstrates improved performance on datasets such as ScanObjectNN, ModelNet40, and ShapeNetPart. This highlights its superior capability in capturing both global and local features, as well as its enhanced robustness against perturbations and incomplete data.

cs.CV↗

arXiv2024

LLM-Assisted Multi-Teacher Continual Learning for Visual Question Answering in Robotic Surgery

Visual question answering (VQA) is crucial for promoting surgical education. In practice, the needs of trainees are constantly evolving, such as learning more surgical types, adapting to different robots, and learning new surgical instruments and techniques for various surgeries. However, patient data privacy often restricts the availability of old data when updating the model, necessitating an exemplar-free continual learning (CL) setup. Prior CL studies overlooked two vital problems in the surgical domain: 1) large domain shifts from diverse surgical operations collected from multiple sources, and 2) severe data imbalance arising from the uneven presence of surgical instruments or activities. This paper proposes addressing these problems with a multimodal large language model (LLM) and an adaptive weight assignment methodology. We first develop a new multi-teacher CL framework that leverages a multimodal LLM as the additional teacher. The strong generalization ability of the LLM can bridge the knowledge gap when domain shifts and data imbalances occur. We then put forth a novel data processing method that transforms complex LLM embeddings into logits compatible with our CL framework. We further design an adaptive weight assignment approach that balances the generalization ability of the LLM and the domain expertise of the old CL model. Finally, to comprehensively test the effectiveness of our proposed method, we have also constructed two new surgical VQA datasets that are largely different from existing ones and could be valuable resources for future research. Extensive experimental results on the tested datasets demonstrate the superiority of our method to other advanced CL schemes.

cs.IR↗

arXiv2024

SeaDAG: Semi-autoregressive Diffusion for Conditional Directed Acyclic Graph Generation

We introduce SeaDAG, a semi-autoregressive diffusion model for conditional generation of Directed Acyclic Graphs (DAGs). Considering their inherent layer-wise structure, we simulate layer-wise autoregressive generation by designing different denoising speed for different layers. Unlike conventional autoregressive generation that lacks a global graph structure view, our method maintains a complete graph structure at each diffusion step, enabling operations such as property control that require the full graph structure. Leveraging this capability, we evaluate the DAG properties during training by employing a graph property decoder. We explicitly train the model to learn graph conditioning with a condition loss, which enhances the diffusion model's capacity to generate graphs that are both realistic and aligned with specified properties. We evaluate our method on two representative conditional DAG generation tasks: (1) circuit generation from truth tables, where precise DAG structures are crucial for realizing circuit functionality, and (2) molecule generation based on quantum properties. Our approach demonstrates promising results, generating high-quality and realistic DAGs that closely align with given conditions.

cs.LG↗

arXiv2024

Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries

In the realm of drug discovery, DNA-encoded library (DEL) screening technology has emerged as an efficient method for identifying high-affinity compounds. However, DEL screening faces a significant challenge: noise arising from nonspecific interactions within complex biological systems. Neural networks trained on DEL libraries have been employed to extract compound features, aiming to denoise the data and uncover potential binders to the desired therapeutic target. Nevertheless, the inherent structure of DEL, constrained by the limited diversity of building blocks, impacts the performance of compound encoders. Moreover, existing methods only capture compound features at a single level, further limiting the effectiveness of the denoising strategy. To mitigate these issues, we propose a Multimodal Pretraining DEL-Fusion model (MPDF) that enhances encoder capabilities through pretraining and integrates compound features across various scales. We develop pretraining tasks applying contrastive objectives between different compound representations and their text descriptions, enhancing the compound encoders' ability to acquire generic features. Furthermore, we propose a novel DEL-fusion framework that amalgamates compound information at the atomic, submolecular, and molecular levels, as captured by various compound encoders. The synergy of these innovations equips MPDF with enriched, multi-scale features, enabling comprehensive downstream denoising. Evaluated on three DEL datasets, MPDF demonstrates superior performance in data processing and analysis for validation tasks. Notably, MPDF offers novel insights into identifying high-affinity molecules, paving the way for improved DEL utility in drug discovery.

q-bio.QM↗

arXiv2024

Distribution-Aware Calibration for Object Detection with Noisy Bounding Boxes

Large-scale well-annotated datasets are of great importance for training an effective object detector. However, obtaining accurate bounding box annotations is laborious and demanding. Unfortunately, the resultant noisy bounding boxes could cause corrupt supervision signals and thus diminish detection performance. Motivated by the observation that the real ground-truth is usually situated in the aggregation region of the proposals assigned to a noisy ground-truth, we propose DIStribution-aware CalibratiOn (DISCO) to model the spatial distribution of proposals for calibrating supervision signals. In DISCO, spatial distribution modeling is performed to statistically extract the potential locations of objects. Based on the modeled distribution, three distribution-aware techniques, i.e., distribution-aware proposal augmentation (DA-Aug), distribution-aware box refinement (DA-Ref), and distribution-aware confidence estimation (DA-Est), are developed to improve classification, localization, and interpretability, respectively. Extensive experiments on large-scale noisy image datasets (i.e., Pascal VOC and MS-COCO) demonstrate that DISCO can achieve state-of-the-art detection performance, especially at high noise levels. Code is available at https://github.com/Correr-Zhou/DISCO.

cs.CV↗

arXiv2024

MM-Mixing: Multi-Modal Mixing Alignment for 3D Understanding

We introduce MM-Mixing, a multi-modal mixing alignment framework for 3D understanding. MM-Mixing applies mixing-based methods to multi-modal data, preserving and optimizing cross-modal connections while enhancing diversity and improving alignment across modalities. Our proposed two-stage training pipeline combines feature-level and input-level mixing to optimize the 3D encoder. The first stage employs feature-level mixing with contrastive learning to align 3D features with their corresponding modalities. The second stage incorporates both feature-level and input-level mixing, introducing mixed point cloud inputs to further refine 3D feature representations. MM-Mixing enhances intermodality relationships, promotes generalization, and ensures feature consistency while providing diverse and realistic training samples. We demonstrate that MM-Mixing significantly improves baseline performance across various learning scenarios, including zero-shot 3D classification, linear probing 3D classification, and cross-modal 3D shape retrieval. Notably, we improved the zero-shot classification accuracy on ScanObjectNN from 51.3% to 61.9%, and on Objaverse-LVIS from 46.8% to 51.4%. Our findings highlight the potential of multi-modal mixing-based alignment to significantly advance 3D object recognition and understanding while remaining straightforward to implement and integrate into existing frameworks.

cs.CV↗

arXiv2024

Text-Anchored Score Composition: Tackling Condition Misalignment in Text-to-Image Diffusion Models

Text-to-image diffusion models have advanced towards more controllable generation via supporting various additional conditions (e.g.,depth map, bounding box) beyond text. However, these models are learned based on the premise of perfect alignment between the text and extra conditions. If this alignment is not satisfied, the final output could be either dominated by one condition, or ambiguity may arise, failing to meet user expectations. To address this issue, we present a training free approach called Text-Anchored Score Composition (TASC) to further improve the controllability of existing models when provided with partially aligned conditions. The TASC firstly separates conditions based on pair relationships, computing the result individually for each pair. This ensures that each pair no longer has conflicting conditions. Then we propose an attention realignment operation to realign these independently calculated results via a cross-attention mechanism to avoid new conflicts when combining them back. Both qualitative and quantitative results demonstrate the effectiveness of our approach in handling unaligned conditions, which performs favorably against recent methods and more importantly adds flexibility to the controllable image generation process. Our code will be available at: https://github.com/EnVision-Research/Decompose-and-Realign.

cs.CV↗