Repository Index

AlphaFold 3 inference pipeline.

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

• drug-discovery
• quantum-chemistry
• deep-learning
• biology

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

The repository host gives no description.

Open Frontier Biomolecular Intelligence

Bi-Directional Equivariant Long-Range DNA Sequence Modeling

Open source tumor evidence matching for sequencing labs and hospitals without molecular tumor boards. Research prototype; oncologist review required.

• bioinformatics
• cancer-research
• computational-biology
• drug-repurposing

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network

Learning cell communication from spatial graphs of cells

• tensorflow
• gnn
• glm
• cvae

code to run sei and obtain sei and sequence class predictions

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

3D shape analysis using deep learning

• cancer-biology
• cell-biology
• deep-learning
• geometric-deep-learning

Single-cell fluorescence microscopy data analysis

• microscopy
• fluorescence-microscopy-imaging

Interpretable modeling of cellular responses to drug perturbations using cycle consistence learning

DeepAEG: A model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies