ICLR 2025: We propose Atomas, a hierarchical molecular representation learning framework that jointly learns representations from SMILES strings and text. We design a Hierarchical Adaptive Alignment model to automatically learn the fine-grained fragment correspondence between two modalities and align these representations at three semantic level…
☆19Feb 24, 2025Updated last year
Alternatives and similar repositories for Atomas
Users that are interested in Atomas are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction☆17Feb 17, 2025Updated last year
- The official repository for "Multi-channel learning for integrating structural hierarchies into context-dependent molecular representatio…☆15Feb 25, 2025Updated last year
- The official implementation of NeurIPS2024 paper "SubgDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning."☆11May 28, 2025Updated last year
- ☆11Sep 24, 2024Updated last year
- [ICLR 2025] The source code of "MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra"☆20Apr 19, 2025Updated last year
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- ☆11Jun 4, 2021Updated 5 years ago
- [ICLR 2022] The implementation for the paper "Equivariant Graph Mechanics Networks with Constraints".☆66Jun 27, 2024Updated 2 years ago
- ☆19Jun 14, 2025Updated last year
- Code for InstructBioMol, implementing the Nature Machine Intelligence paper "Advancing Biomolecular Understanding and Design Following Hu…☆31Aug 2, 2025Updated 11 months ago
- MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphan…☆11Oct 16, 2022Updated 3 years ago
- [NeurIPS 2022] The implementation for the paper "Equivariant Graph Hierarchy-Based Neural Networks".☆33Oct 5, 2023Updated 2 years ago
- Multi-modal Molecule Structure-text Model for Text-based Editing and Retrieval, Nat Mach Intell 2023 (https://www.nature.com/articles/s42…☆259Jun 27, 2025Updated last year
- [NeurIPS 24] Can LLMs Solve Molecule Puzzles? A Multimodal Benchmark for Molecular Structure Elucidation☆20Jan 2, 2026Updated 6 months ago
- ☆21Feb 19, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A package to draw custom heatmaps on molecular depictions of RDKit☆13Mar 31, 2022Updated 4 years ago
- BridgeDPI: A Novel Graph Neural Network for Predicting Drug-Protein Interactions☆20Dec 25, 2024Updated last year
- Code for the KDD 2022 paper "Interpreting Trajectories from Multiple Views: A Hierarchical Self-Attention Network for Estimating the Time…☆18May 29, 2022Updated 4 years ago
- A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)☆107Jan 11, 2025Updated last year
- Official Code Repository for the paper "Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model"☆32Sep 30, 2025Updated 9 months ago
- 3D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modeling (ICLR 2025)☆19Oct 23, 2025Updated 8 months ago
- The code for "Learning Molecular Representation in a Cell"☆43Mar 6, 2025Updated last year
- Nucleic Acids Research 2024：RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding a…☆71Jul 22, 2024Updated last year
- ActiveDriverDB☆12May 1, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining, ICML'23☆35Mar 29, 2024Updated 2 years ago
- PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes [EMNLP 2024]☆28Nov 18, 2024Updated last year
- ☆14Feb 26, 2024Updated 2 years ago
- ☆39Jun 9, 2025Updated last year
- [ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts☆105Oct 16, 2023Updated 2 years ago
- The official implementation for ICLR23 paper "GNNSafe: Energy-based Out-of-Distribution Detection for Graph Neural Networks"☆84Jul 27, 2023Updated 2 years ago
- Code available for the quantitative pharmacophores☆13Sep 7, 2022Updated 3 years ago
- ☆13Jul 5, 2024Updated 2 years ago
- [WSDM'23] GOOD-D: On Unsupervised Graph Out-Of-Distribution Detection☆45Mar 2, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- [AAAI 2023] The implementation for the paper "Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs"☆33Sep 14, 2024Updated last year
- ☆21Feb 22, 2024Updated 2 years ago
- Codes for "Property-Aware Relation Networks for Few-shot Molecular Property Prediction (NeurIPS 2021)".☆52Feb 22, 2022Updated 4 years ago
- Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)☆218Sep 20, 2022Updated 3 years ago
- Welcome to FLSim_V2, a PyTorch based federated Reinforcement learning simulation framework☆10Dec 15, 2022Updated 3 years ago
- [ICLR 2024] Domain-Agnostic Molecular Generation with Chemical Feedback☆195Dec 17, 2024Updated last year
- Wiener Graph Deconvolutional Network Improves Self-Supervised Learning in AAAI 2023☆18Apr 3, 2024Updated 2 years ago