Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for
Large Language Models
- URL: http://arxiv.org/abs/2306.08018v5
- Date: Mon, 4 Mar 2024 12:49:31 GMT
- Title: Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for
Large Language Models
- Authors: Yin Fang, Xiaozhuan Liang, Ningyu Zhang, Kangwei Liu, Rui Huang, Zhuo
Chen, Xiaohui Fan, Huajun Chen
- Abstract summary: Mol-Instructions is a comprehensive instruction dataset designed for the biomolecular domain.
Each component aims to improve the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors.
We demonstrate the effectiveness of Mol-Instructions in enhancing large models' performance in the intricate realm of biomolecular studies.
- Score: 44.41299105569085
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: Large Language Models (LLMs), with their remarkable task-handling
capabilities and innovative outputs, have catalyzed significant advancements
across a spectrum of fields. However, their proficiency within specialized
domains such as biomolecular studies remains limited. To address this
challenge, we introduce Mol-Instructions, a comprehensive instruction dataset
designed for the biomolecular domain. Mol-Instructions encompasses three key
components: molecule-oriented instructions, protein-oriented instructions, and
biomolecular text instructions. Each component aims to improve the
understanding and prediction capabilities of LLMs concerning biomolecular
features and behaviors. Through extensive instruction tuning experiments on
LLMs, we demonstrate the effectiveness of Mol-Instructions in enhancing large
models' performance in the intricate realm of biomolecular studies, thus
fostering progress in the biomolecular research community. Mol-Instructions is
publicly available for ongoing research and will undergo regular updates to
enhance its applicability.
Related papers
- MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction [44.27112553103388]
We present Molecule Caption Arena: the first comprehensive benchmark of large language models (LLMs)augmented molecular property prediction.
We evaluate over twenty LLMs, including both general-purpose and domain-specific molecule captioners, across diverse prediction tasks.
Our findings confirm the ability of LLM-extracted knowledge to enhance state-of-the-art molecular representations.
arXiv Detail & Related papers (2024-11-01T17:03:16Z) - MolX: Enhancing Large Language Models for Molecular Learning with A Multi-Modal Extension [34.586861881519134]
Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields.
This study seeks to enhance the ability of LLMs to comprehend molecules by equipping them with a multi-modal external module, namely MolX.
In particular, instead of directly using a SMILES string to represent a molecule, we utilize specific encoders to extract fine-grained features from both SMILES string and 2D molecular graph representations.
arXiv Detail & Related papers (2024-06-10T20:25:18Z) - Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model [49.64512917330373]
We introduce a multi-constraint molecular generation large language model, TSMMG, akin to a student.
To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers'
We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements.
arXiv Detail & Related papers (2024-03-20T02:15:55Z) - Leveraging Biomolecule and Natural Language through Multi-Modal
Learning: A Survey [75.47055414002571]
The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology.
We provide an analysis of recent advancements achieved through cross modeling of biomolecules and natural language.
arXiv Detail & Related papers (2024-03-03T14:59:47Z) - Interactive Molecular Discovery with Natural Language [69.89287960545903]
We propose the conversational molecular design, a novel task adopting natural language for describing and editing target molecules.
To better accomplish this task, we design ChatMol, a knowledgeable and versatile generative pre-trained model, enhanced by injecting experimental property information.
arXiv Detail & Related papers (2023-06-21T02:05:48Z) - Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective [53.300288393173204]
Large Language Models (LLMs) have shown remarkable performance in various cross-modal tasks.
In this work, we propose an In-context Few-Shot Molecule Learning paradigm for molecule-caption translation.
We evaluate the effectiveness of MolReGPT on molecule-caption translation, including molecule understanding and text-based molecule generation.
arXiv Detail & Related papers (2023-06-11T08:16:25Z) - MolFM: A Multimodal Molecular Foundation Model [9.934141536012596]
MolFM is a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs.
We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule.
On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively.
arXiv Detail & Related papers (2023-06-06T12:45:15Z) - Domain-Agnostic Molecular Generation with Chemical Feedback [44.063584808910896]
MolGen is a pre-trained molecular language model tailored specifically for molecule generation.
It internalizes structural and grammatical insights through the reconstruction of over 100 million molecular SELFIES.
Our chemical feedback paradigm steers the model away from molecular hallucinations, ensuring alignment between the model's estimated probabilities and real-world chemical preferences.
arXiv Detail & Related papers (2023-01-26T17:52:56Z) - A Molecular Multimodal Foundation Model Associating Molecule Graphs with
Natural Language [63.60376252491507]
We propose a molecular multimodal foundation model which is pretrained from molecular graphs and their semantically related textual data.
We believe that our model would have a broad impact on AI-empowered fields across disciplines such as biology, chemistry, materials, environment, and medicine.
arXiv Detail & Related papers (2022-09-12T00:56:57Z)
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.