Benchmarking Large Language Models for Molecule Prediction Tasks

• URL: http://arxiv.org/abs/2403.05075v1
• Date: Fri, 8 Mar 2024 05:59:56 GMT
• Title: Benchmarking Large Language Models for Molecule Prediction Tasks
• Authors: Zhiqiang Zhong and Kuangyu Zhou and Davide Mottin
• Abstract summary: Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. This paper explores a fundamental question: Can LLMs effectively handle molecule prediction tasks? We identify several classification and regression prediction tasks across six standard molecule datasets. We compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules.
• Score: 7.067145619709089
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

Related papers

• SELF-GUIDE: Better Task-Specific Instruction Following via Self-Synthetic Finetuning [70.21358720599821]
  Large language models (LLMs) hold the promise of solving diverse tasks when provided with appropriate natural language prompts. We propose SELF-GUIDE, a multi-stage mechanism in which we synthesize task-specific input-output pairs from the student LLM. We report an absolute improvement of approximately 15% for classification tasks and 18% for generation tasks in the benchmark's metrics.
  arXiv  Detail & Related papers  (2024-07-16T04:41:58Z)
• The Synergy between Data and Multi-Modal Large Language Models: A Survey from Co-Development Perspective [53.48484062444108]
  We find that the development of models and data is not two separate paths but rather interconnected. On the one hand, vaster and higher-quality data contribute to better performance of MLLMs; on the other hand, MLLMs can facilitate the development of data. To promote the data-model co-development for MLLM community, we systematically review existing works related to MLLMs from the data-model co-development perspective.
  arXiv  Detail & Related papers  (2024-07-11T15:08:11Z)
• Small Models, Big Insights: Leveraging Slim Proxy Models To Decide When and What to Retrieve for LLMs [60.40396361115776]
  This paper introduces a novel collaborative approach, namely SlimPLM, that detects missing knowledge in large language models (LLMs) with a slim proxy model. We employ a proxy model which has far fewer parameters, and take its answers as answers. Heuristic answers are then utilized to predict the knowledge required to answer the user question, as well as the known and unknown knowledge within the LLM.
  arXiv  Detail & Related papers  (2024-02-19T11:11:08Z)
• Large Language Models: A Survey [69.72787936480394]
  Large Language Models (LLMs) have drawn a lot of attention due to their strong performance on a wide range of natural language tasks. LLMs' ability of general-purpose language understanding and generation is acquired by training billions of model's parameters on massive amounts of text data.
  arXiv  Detail & Related papers  (2024-02-09T05:37:09Z)
• Rethinking Interpretability in the Era of Large Language Models [76.1947554386879]
  Large language models (LLMs) have demonstrated remarkable capabilities across a wide array of tasks. The capability to explain in natural language allows LLMs to expand the scale and complexity of patterns that can be given to a human. These new capabilities raise new challenges, such as hallucinated explanations and immense computational costs.
  arXiv  Detail & Related papers  (2024-01-30T17:38:54Z)
• LLM-in-the-loop: Leveraging Large Language Model for Thematic Analysis [18.775126929754833]
  Thematic analysis (TA) has been widely used for analyzing qualitative data in many disciplines and fields. Human coders develop and deepen their data interpretation and coding over multiple iterations, making TA labor-intensive and time-consuming. We propose a human-LLM collaboration framework (i.e., LLM-in-the-loop) to conduct TA with in-context learning (ICL)
  arXiv  Detail & Related papers  (2023-10-23T17:05:59Z)
• Can Large Language Models Empower Molecular Property Prediction? [16.5246941211725]
  Molecular property prediction has gained significant attention due to its transformative potential in scientific disciplines. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules.
  arXiv  Detail & Related papers  (2023-07-14T16:06:42Z)
• LLM-Pruner: On the Structural Pruning of Large Language Models [65.02607075556742]
  Large language models (LLMs) have shown remarkable capabilities in language understanding and generation. We tackle the compression of LLMs within the bound of two constraints: being task-agnostic and minimizing the reliance on the original training dataset. Our method, named LLM-Pruner, adopts structural pruning that selectively removes non-critical coupled structures.
  arXiv  Detail & Related papers  (2023-05-19T12:10:53Z)

This list is automatically generated from the titles and abstracts of the papers in this site.

This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.