Challenge: Deep learning models are often inefficient and resource-intensive for biologists without specialized computational expertise.
Approach: They propose an agent framework that leverages large language models for multimodal automated machine learning (AutoML) in protein engineering.
Outcome: The proposed framework demonstrates significant improvements in performance over previous approaches in two real-world protein engineering tasks.

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Challenge: Large Language Model (LLM) agents have demonstrated remarkable capabilities in task automation and intelligent decision-making.
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Protein Large Language Models: A Comprehensive Survey (2025.findings-emnlp)

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Challenge: Existing studies focus on specific aspects or applications, but this study provides a comprehensive overview of Protein-specific large language models.
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AgentGym: Evaluating and Training Large Language Model-based Agents across Diverse Environments (2025.acl-long)

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Challenge: Large language models (LLMs) are promising foundations to build generally-capable agents . however, the community lacks a unified interactive framework that covers diverse environments for comprehensive evaluation of agents.
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Automated Molecular Concept Generation and Labeling with Large Language Models (2025.coling-main)

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Challenge: Concept-based models lack explainability and need predefined concepts and manual labeling in molecular science.
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Towards large language model-based personal agents in the enterprise: Current trends and open problems (2023.findings-emnlp)

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Challenge: Existing large language models (LLMs) are brittle to input changes and can produce inconsistent results for the same inputs.
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AutoML for NLP (2023.eacl-tutorials)

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Challenge: Automated Machine Learning (AutoML) is an emerging field that has potential to impact how we build models in NLP.
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Foundation Model for Biomedical Graphs: Integrating Knowledge Graphs and Protein Structures to Large Language Models (2024.acl-srw)

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Challenge: Transformer model has been a de-facto standard in natural language processing, but it is limited to images, text, and/or sequence data.
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MLCopilot: Unleashing the Power of Large Language Models in Solving Machine Learning Tasks (2024.eacl-long)

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Challenge: Existing approaches to automating ML are time-consuming and difficult to understand for human developers.
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Small LLMs Are Weak Tool Learners: A Multi-LLM Agent (2024.emnlp-main)

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Challenge: Large Language Models (LLMs) have revolutionized natural language processing with impressive capabilities, but they lack domain specificity, real-time information and face challenges in solving specialized problems.
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BioTool: A Comprehensive Tool-Calling Dataset for Enhancing Biomedical Capabilities of Large Language Models (2026.acl-long)

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Challenge: despite the success of large language models, their performance in highly specialized domains remains unsatisfactory.
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