Computational Chemistry
ChemDFM-X architecture showing five modalities (2D graphs, 3D conformations, images, MS2 spectra, IR spectra) feeding through separate encoders into unified LLM decoder

ChemDFM-X: Large Multimodal Model for Chemistry

Multimodal chemical model integrating 5 modalities (2D graphs, 3D conformations, images, MS2/IR spectra) trained on 7.6M …

Computational Biology
DynamicFlow illustration showing the transformation from apo pocket to holo pocket with ligand molecule generation

DynamicFlow: Integrating Protein Dynamics into Drug Design

Flow matching model that co-generates ligands and flexible protein pockets, addressing rigid-receptor limitations in …

Computational Chemistry
Comparative analysis of image-to-sequence OCSR methods

Image-to-Sequence OCSR: A Comparative Analysis

Comparative analysis of image-to-sequence OCSR methods across architecture, output format, training data, and compute …

Computational Chemistry
InstructMol architecture showing molecular graph and text inputs feeding through two-stage training to produce property predictions, descriptions, and reactions

InstructMol: Multi-Modal Molecular Assistant

A multi-modal LLM aligning 2D molecular graphs with text via two-stage instruction tuning for drug discovery tasks.

Computational Biology
InvMSAFold generates diverse protein sequences from structure using a Potts model

InvMSAFold: Fast & Diverse Inverse Folding

A fast, diverse inverse folding method combining deep learning with Potts models to capture full sequence landscapes.

Computational Chemistry
MOFFlow assembles metal nodes and organic linkers into Metal-Organic Framework structures

MOFFlow: Flow Matching for MOF Structure Prediction

A Riemannian flow matching framework for generating Metal-Organic Framework structures by treating building blocks as …

Computational Chemistry
Diagram showing text, molecular structures, and reactions feeding into a multimodal index and search system that outputs passages with context

Multimodal Search in Chemical Documents

A multimodal search engine that integrates text passages, molecular diagrams, and reaction data to enable passage-level …

Computational Chemistry
Diagram showing molecular structure passing through a neural network to produce IUPAC chemical nomenclature document

STOUT V2.0: SMILES to IUPAC Name Conversion

A Transformer-based model for translating SMILES to IUPAC names, trained on ~1 billion molecules, achieving ~99% …

Computational Chemistry
Vintage wooden device labeled 'The Molecular Interpreter - Model 1974' with vacuum tubes, showing SMILES to IUPAC name translation

STOUT: SMILES to IUPAC names using NMT

A deep-learning neural machine translation approach to translate between SMILES strings and IUPAC names using the STOUT …

Computational Chemistry
Diagram showing Struct2IUPAC workflow: molecular structure (SMILES) passing through Transformer to generate IUPAC name, with round-trip verification loop

Struct2IUPAC: Transformers for SMILES to IUPAC

A Transformer-based model for translating between SMILES strings and IUPAC names, trained on 47M PubChem examples, …

Computational Chemistry
Transformer encoder-decoder architecture processing InChI string character-by-character to produce IUPAC chemical name

Translating InChI to IUPAC Names with Transformers

Sequence-to-sequence Transformer translating InChI identifiers to IUPAC names with 91% accuracy on organic compounds.

Computational Chemistry
AtomLenz learns atom-level detection from hand-drawn molecular images with weak supervision

AtomLenz: Atom-Level OCSR with Limited Supervision

Weakly supervised OCSR framework combining object detection and graph construction to recognize chemical structures from …