arXiv subjects

Zan Chen

Publications and source records attributed to Zan Chen.

10 recordsLinked to original sources

arXiv2025

A Frequency-Aware Self-Supervised Learning for Ultra-Wide-Field Image Enhancement

Ultra-Wide-Field (UWF) retinal imaging has revolutionized retinal diagnostics by providing a comprehensive view of the retina. However, it often suffers from quality-degrading factors such as blurring and uneven illumination, which obscure fine details and mask pathological information. While numerous retinal image enhancement methods have been proposed for other fundus imageries, they often fail to address the unique requirements in UWF, particularly the need to preserve pathological details. In this paper, we propose a novel frequency-aware self-supervised learning method for UWF image enhancement. It incorporates frequency-decoupled image deblurring and Retinex-guided illumination compensation modules. An asymmetric channel integration operation is introduced in the former module, so as to combine global and local views by leveraging high- and low-frequency information, ensuring the preservation of fine and broader structural details. In addition, a color preservation unit is proposed in the latter Retinex-based module, to provide multi-scale spatial and frequency information, enabling accurate illumination estimation and correction. Experimental results demonstrate that the proposed work not only enhances visualization quality but also improves disease diagnosis performance by restoring and correcting fine local details and uneven intensity. To the best of our knowledge, this work is the first attempt for UWF image enhancement, offering a robust and clinically valuable tool for improving retinal disease management.

cs.CV↗

arXiv2024

TourSynbio-Search: A Large Language Model Driven Agent Framework for Unified Search Method for Protein Engineering

The exponential growth in protein-related databases and scientific literature, combined with increasing demands for efficient biological information retrieval, has created an urgent need for unified and accessible search methods in protein engineering research. We present TourSynbio-Search, a novel bioinformatics search agent framework powered by the TourSynbio-7B protein multimodal large language model (LLM), designed to address the growing challenges of information retrieval across rapidly expanding protein databases and corresponding online research literature. The agent's dual-module architecture consists of PaperSearch and ProteinSearch components, enabling comprehensive exploration of both scientific literature and protein data across multiple biological databases. At its core, TourSynbio-Search employs an intelligent agent system that interprets natural language queries, optimizes search parameters, and executes search operations across major platforms including UniProt, PDB, ArXiv, and BioRxiv. The agent's ability to process intuitive natural language queries reduces technical barriers, allowing researchers to efficiently access and analyze complex biological data without requiring extensive bioinformatics expertise. Through detailed case studies in literature retrieval and protein structure visualization, we demonstrate TourSynbio-Search's effectiveness in streamlining biological information retrieval and enhancing research productivity. This framework represents an advancement in bridging the accessibility gap between complex biological databases and researchers, potentially accelerating progress in protein engineering applications. Our codes are available at: https://github.com/tsynbio/Toursynbio-Search

q-bio.QM↗

arXiv2024

Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab

Recent advancements in Large Language Models (LLMs) have enhanced efficiency across various domains, including protein engineering, where they offer promising opportunities for dry lab and wet lab experiment workflow automation. Previous work, namely TourSynbio-Agent, integrates a protein-specialized multimodal LLM (i.e. TourSynbio-7B) with domain-specific deep learning (DL) models to streamline both computational and experimental protein engineering tasks. While initial validation demonstrated TourSynbio-7B's fundamental protein property understanding, the practical effectiveness of the complete TourSynbio-Agent framework in real-world applications remained unexplored. This study presents a comprehensive validation of TourSynbio-Agent through five diverse case studies spanning both computational (dry lab) and experimental (wet lab) protein engineering. In three computational case studies, we evaluate the TourSynbio-Agent's capabilities in mutation prediction, protein folding, and protein design. Additionally, two wet-lab validations demonstrate TourSynbio-Agent's practical utility: engineering P450 proteins with up to 70% improved selectivity for steroid 19-hydroxylation, and developing reductases with 3.7x enhanced catalytic efficiency for alcohol conversion. Our findings from the five case studies establish that TourSynbio-Agent can effectively automate complex protein engineering workflows through an intuitive conversational interface, potentially accelerating scientific discovery in protein engineering.

q-bio.QM↗

arXiv2024

AutoProteinEngine: A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering

Protein engineering is important for biomedical applications, but conventional approaches are often inefficient and resource-intensive. While deep learning (DL) models have shown promise, their training or implementation into protein engineering remains challenging for biologists without specialized computational expertise. To address this gap, we propose AutoProteinEngine (AutoPE), an agent framework that leverages large language models (LLMs) for multimodal automated machine learning (AutoML) for protein engineering. AutoPE innovatively allows biologists without DL backgrounds to interact with DL models using natural language, lowering the entry barrier for protein engineering tasks. Our AutoPE uniquely integrates LLMs with AutoML to handle model selection for both protein sequence and graph modalities, automatic hyperparameter optimization, and automated data retrieval from protein databases. We evaluated AutoPE through two real-world protein engineering tasks, demonstrating substantial performance improvements compared to traditional zero-shot and manual fine-tuning approaches. By bridging the gap between DL and biologists' domain expertise, AutoPE empowers researchers to leverage DL without extensive programming knowledge. Our code is available at https://github.com/tsynbio/AutoPE.

q-bio.QM↗

arXiv2024

UniAutoML: A Human-Centered Framework for Unified Discriminative and Generative AutoML with Large Language Models

Automated Machine Learning (AutoML) has simplified complex ML processes such as data pre-processing, model selection, and hyper-parameter searching. However, traditional AutoML frameworks focus solely on discriminative tasks, often falling short in tackling AutoML for generative models. Additionally, these frameworks lack interpretability and user engagement during the training process, primarily due to the absence of human-centered design. It leads to a lack of transparency in final decision-making and limited user control, potentially reducing trust and adoption of AutoML methods. To address these limitations, we introduce UniAutoML, a human-centered AutoML framework that leverages Large Language Models (LLMs) to unify AutoML for both discriminative (e.g., Transformers and CNNs for classification or regression tasks) and generative tasks (e.g., fine-tuning diffusion models or LLMs). The human-centered design of UniAutoML innovatively features a conversational user interface (CUI) that facilitates natural language interactions, providing users with real-time guidance, feedback, and progress updates for better interpretability. This design enhances transparency and user control throughout the AutoML training process, allowing users to seamlessly break down or modify the model being trained. To mitigate potential risks associated with LLM generated content, UniAutoML incorporates a safety guardline that filters inputs and censors outputs. We evaluated UniAutoML's performance and usability through experiments on eight diverse datasets and user studies involving 25 participants, demonstrating that UniAutoML not only enhances performance but also improves user control and trust. Our human-centered design bridges the gap between AutoML capabilities and user understanding, making ML more accessible to a broader audience.

cs.CL↗

arXiv2024

A Survey for Large Language Models in Biomedicine

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model architectures, lacking a comprehensive analysis that integrates the latest advancements across various biomedical domains. This review, based on an analysis of 484 publications sourced from databases including PubMed, Web of Science, and arXiv, provides an in-depth examination of the current landscape, applications, challenges, and prospects of LLMs in biomedicine, distinguishing itself by focusing on the practical implications of these models in real-world biomedical contexts. Firstly, we explore the capabilities of LLMs in zero-shot learning across a broad spectrum of biomedical tasks, including diagnostic assistance, drug discovery, and personalized medicine, among others, with insights drawn from 137 key studies. Then, we discuss adaptation strategies of LLMs, including fine-tuning methods for both uni-modal and multi-modal LLMs to enhance their performance in specialized biomedical contexts where zero-shot fails to achieve, such as medical question answering and efficient processing of biomedical literature. Finally, we discuss the challenges that LLMs face in the biomedicine domain including data privacy concerns, limited model interpretability, issues with dataset quality, and ethics due to the sensitive nature of biomedical data, the need for highly reliable model outputs, and the ethical implications of deploying AI in healthcare. To address these challenges, we also identify future research directions of LLM in biomedicine including federated learning methods to preserve data privacy and integrating explainable AI methodologies to enhance the transparency of LLMs.

cs.CL↗

arXiv2024

TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering

The structural similarities between protein sequences and natural languages have led to parallel advancements in deep learning across both domains. While large language models (LLMs) have achieved much progress in the domain of natural language processing, their potential in protein engineering remains largely unexplored. Previous approaches have equipped LLMs with protein understanding capabilities by incorporating external protein encoders, but this fails to fully leverage the inherent similarities between protein sequences and natural languages, resulting in sub-optimal performance and increased model complexity. To address this gap, we present TourSynbio-7B, the first multi-modal large model specifically designed for protein engineering tasks without external protein encoders. TourSynbio-7B demonstrates that LLMs can inherently learn to understand proteins as language. The model is post-trained and instruction fine-tuned on InternLM2-7B using ProteinLMDataset, a dataset comprising 17.46 billion tokens of text and protein sequence for self-supervised pretraining and 893K instructions for supervised fine-tuning. TourSynbio-7B outperforms GPT-4 on the ProteinLMBench, a benchmark of 944 manually verified multiple-choice questions, with 62.18% accuracy. Leveraging TourSynbio-7B's enhanced protein sequence understanding capability, we introduce TourSynbio-Agent, an innovative framework capable of performing various protein engineering tasks, including mutation analysis, inverse folding, protein folding, and visualization. TourSynbio-Agent integrates previously disconnected deep learning models in the protein engineering domain, offering a unified conversational user interface for improved usability. Finally, we demonstrate the efficacy of TourSynbio-7B and TourSynbio-Agent through two wet lab case studies on vanilla key enzyme modification and steroid compound catalysis.

q-bio.BM↗

arXiv2024

A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score.

q-bio.QM↗

arXiv2024

DeepMpMRI: Tensor-decomposition Regularized Learning for Fast and High-Fidelity Multi-Parametric Microstructural MR Imaging

Deep learning has emerged as a promising approach for learning the nonlinear mapping between diffusion-weighted MR images and tissue parameters, which enables automatic and deep understanding of the brain microstructures. However, the efficiency and accuracy in estimating multiple microstructural parameters derived from multiple diffusion models are still limited since previous studies tend to estimate parameter maps from distinct models with isolated signal modeling and dense sampling. This paper proposes DeepMpMRI, an efficient framework for fast and high-fidelity multiple microstructural parameter estimation from multiple models using highly sparse sampled q-space data. DeepMpMRI is equipped with a newly designed tensor-decomposition-based regularizer to effectively capture fine details by exploiting the high-dimensional correlation across microstructural parameters. In addition, we introduce a Nesterov-based adaptive learning algorithm that optimizes the regularization parameter dynamically to enhance the performance. DeepMpMRI is an extendable framework capable of incorporating flexible network architecture. Experimental results on the HCP dataset and the Alzheimer's disease dataset both demonstrate the superiority of our approach over 5 state-of-the-art methods in simultaneously estimating multi-model microstructural parameter maps for DKI and NODDI model with fine-grained details both quantitatively and qualitatively, achieving 4.5 - 15 $\times$ acceleration compared to the dense sampling of a total of 270 diffusion gradients.

cs.CV↗

arXiv2020

Cognitive computation of brain disorders based primarily on ocular responses

The present review presents multiple techniques in which ocular assessments may serve as a noninvasive approach for the early diagnoses of various cognitive and psychiatric disorders, such as Alzheimer's disease (AD), autism spectrum disorder (ASD), schizophrenia (SZ), and major depressive disorder (MDD). Real-time ocular responses are tightly associated with emotional and cognitive processing within the central nervous system. Patterns seen in saccades, pupillary responses, and blinking, as well as retinal microvasculature and morphology visualized via office-based ophthalmic imaging, are potential biomarkers for the screening and evaluation of cognitive and psychiatric disorders. Additionally, rapid advances in artificial intelligence (AI) present a growing opportunity to use machine-learning-based AI, especially deep-learning neural networks, to shed new light on the field of cognitive neuroscience, which may lead to novel evaluations and interventions via ocular approaches for cognitive and psychiatric disorders.

q-bio.NC↗