# InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery

arXiv: https://arxiv.org/abs/2311.16208 · HTML: https://mlsanity.com/paper/2311.16208/

## Key facts

- Cited by 86 papers in the map (data through 14 Oct 2026).
- Builds on 60 of its 100 references that are in the map.
- First posted on arXiv 27 Nov 2023.

## Builds on (most cited first, 30 of 60)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models](https://mlsanity.com/paper/2301.12597/) (2023)
- [Improved Baselines with Visual Instruction Tuning](https://mlsanity.com/paper/2310.03744/) (2023)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Flamingo: a Visual Language Model for Few-Shot Learning](https://mlsanity.com/paper/2204.14198/) (2022)
- [Finetuned Language Models Are Zero-Shot Learners](https://mlsanity.com/paper/2109.01652/) (2021)
- [InstructBLIP: Towards General-purpose Vision-Language Models with Instruction Tuning](https://mlsanity.com/paper/2305.06500/) (2023)
- [MiniGPT-4: Enhancing Vision-Language Understanding with Advanced Large Language Models](https://mlsanity.com/paper/2304.10592/) (2023)
- [ViLBERT: Pretraining Task-Agnostic Visiolinguistic Representations for Vision-and-Language Tasks](https://mlsanity.com/paper/1908.02265/) (2019)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [PaLM 2 Technical Report](https://mlsanity.com/paper/2305.10403/) (2023)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [mPLUG-Owl: Modularization Empowers Large Language Models with Multimodality](https://mlsanity.com/paper/2304.14178/) (2023)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [A Survey on Multimodal Large Language Models](https://mlsanity.com/paper/2306.13549/) (2023)
- [GLM-130B: An Open Bilingual Pre-trained Model](https://mlsanity.com/paper/2210.02414/) (2022)

## Built on by (most cited first, 30 of 86)

- [A Survey on Knowledge Distillation of Large Language Models](https://mlsanity.com/paper/2402.13116/) (2024)
- [Continual Learning of Large Language Models: A Comprehensive Survey](https://mlsanity.com/paper/2404.16789/) (2024)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)
- [A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery](https://mlsanity.com/paper/2406.10833/) (2024)
- [From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery](https://mlsanity.com/paper/2508.14111/) (2025)
- [A Survey of Large Language Models for Graphs](https://mlsanity.com/paper/2405.08011/) (2024)
- [A Comprehensive Survey of Foundation Models in Medicine](https://mlsanity.com/paper/2406.10729/) (2024)
- [BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning](https://mlsanity.com/paper/2402.17810/) (2024)
- [Developing ChemDFM as a large language foundation model for chemistry](https://mlsanity.com/paper/2401.14818/) (2024)
- [A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers](https://mlsanity.com/paper/2508.21148/) (2025)
- [Scientists' First Exam: Probing Cognitive Abilities of MLLM via Perception, Understanding, and Reasoning](https://mlsanity.com/paper/2506.10521/) (2025)
- [ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback](https://mlsanity.com/paper/2402.10980/) (2024)
- [Graph Machine Learning in the Era of Large Language Models (LLMs)](https://mlsanity.com/paper/2404.14928/) (2024)
- [Position: Multimodal Large Language Models Can Significantly Advance Scientific Reasoning](https://mlsanity.com/paper/2502.02871/) (2025)
- [How Do Large Language Models Understand Graph Patterns? A Benchmark for Graph Pattern Comprehension](https://mlsanity.com/paper/2410.05298/) (2024)
- [UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation](https://mlsanity.com/paper/2408.00863/) (2024)
- [LLaMo: Large Language Model-based Molecular Graph Assistant](https://mlsanity.com/paper/2411.00871/) (2024)
- [L+M-24: Building a Dataset for Language + Molecules @ ACL 2024](https://mlsanity.com/paper/2403.00791/) (2024)
- [Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey](https://mlsanity.com/paper/2403.01528/) (2024)
- [HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment](https://mlsanity.com/paper/2406.14021/) (2024)
- [Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model](https://mlsanity.com/paper/2502.13449/) (2025)
- [ChemMLLM: Chemical Multimodal Large Language Model](https://mlsanity.com/paper/2505.16326/) (2025)
- [PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes](https://mlsanity.com/paper/2406.13193/) (2024)
- [Graph2text or Graph2token: A Perspective of Large Language Models for Graph Learning](https://mlsanity.com/paper/2501.01124/) (2025)
- [Learning on Graphs with Large Language Models(LLMs): A Deep Dive into Model Robustness](https://mlsanity.com/paper/2407.12068/) (2024)
- [Regression with Large Language Models for Materials and Molecular Property Prediction](https://mlsanity.com/paper/2409.06080/) (2024)
- [Structural Reasoning Improves Molecular Understanding of LLM](https://mlsanity.com/paper/2410.05610/) (2024)
- [From Generalist to Specialist: A Survey of Large Language Models for Chemistry](https://mlsanity.com/paper/2412.19994/) (2024)
- [Geometry Informed Tokenization of Molecules for Language Model Generation](https://mlsanity.com/paper/2408.10120/) (2024)
- [Advancing biomolecular understanding and design following human instructions](https://mlsanity.com/paper/2410.07919/) (2024)

## Abstract (arXiv)

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.