# SciCore-Mol: Augmenting Large Language Models with Pluggable Molecular Cognition Modules

arXiv: https://arxiv.org/abs/2605.22287 · HTML: https://mlsanity.com/paper/2605.22287/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 39 of its 55 references that are in the map.
- First posted on arXiv 21 May 2026.

## Builds on (most cited first, 30 of 39)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [OpenAI GPT-5 System Card](https://mlsanity.com/paper/2601.03267/) (2025)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [Do Transformers Really Perform Bad for Graph Representation?](https://mlsanity.com/paper/2106.05234/) (2021)
- [Learning from Protein Structure with Geometric Vector Perceptrons](https://mlsanity.com/paper/2009.01411/) (2020)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)
- [MoFlow: An Invertible Flow Model for Generating Molecular Graphs](https://mlsanity.com/paper/2006.10137/) (2020)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [Nemotron-CC: Transforming Common Crawl into a Refined Long-Horizon Pretraining Dataset](https://mlsanity.com/paper/2412.02595/) (2024)
- [Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models](https://mlsanity.com/paper/2306.08018/) (2023)
- [MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter](https://mlsanity.com/paper/2310.12798/) (2023)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)
- [ChemBERTa-2: Towards Chemical Foundation Models](https://mlsanity.com/paper/2209.01712/) (2022)

## Abstract (arXiv)

Large Language Models (LLMs) are central to the one-for-all intelligent paradigm, but they face a fundamental challenge when dealing with heterogeneous scientific data such as molecules: the inherent gap between discrete linguistic symbols and topological molecular or continuous reaction data leads to significant information loss and semantic noise in text-based reasoning. We propose SciCore-Mol, a modular framework that bridges this gap through three deeply integrated pluggable cognitive modules: a topology-aware perception module, a latent diffusion-based molecular generation module, and a reaction-aware reasoning module. Each module is coupled to the LLM backbone through learned representation interfaces, enabling richer information exchange than is possible with text-only tool feedback. Our experiments on diverse chemical tasks demonstrate that SciCore-Mol achieves strong comprehensive performance across molecular understanding, generation, reaction prediction, and general chemistry knowledge, with an 8B-parameter open-source system that is competitive with and in several dimensions surpasses proprietary large models. This work provides a systematic blueprint for equipping LLMs with scientific expertise through decoupled, pluggable, and flexibly orchestrated modules, with direct implications for drug design, chemical synthesis, and broader scientific discovery.