brianhie

scanorama

Panoramic stitching of single cell data

efficient-evolution

Efficient evolution from protein language models

viral-mutation

Language modeling of viral evolution

evolocity

Evolutionary velocity with protein language models

geosketch

Geometry-preserving random sampling

uncertainty

Learning with uncertainty for biological discovery and design

trajectorama

Multi-study integration of cellular trajectories

secure-dti

Realizing private and practical pharmacological collaboration

mutational-semantics-neurips2020

Learning mutational semantics

flash-attention

Fast and memory-efficient exact attention

brianhie.github.com

DGraphDTA

a novel DTA predition method using graph neural network

evovdss

orf-fold-website

protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

schema

Framework for integrating heterogeneous modalities of data

scib

Benchmarking analysis of data integration tools

atac-diverge

causaldag

Python package for the creation, manipulation, and learning of Causal DAGs

causaldag_examples

Example usage of https://github.com/uhlerlab/causaldag

CellBench_data

This contains the dataset for comparing scRNA-seq analysis methods

ggb

Graph-Guided Banding of the Covariance Matrix

icml18-jtnn

Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)

led-website

louvain-igraph

Implementation of the Louvain algorithm for community detection with various methods for use with igraph in python.

Megatron-LM

Ongoing research training transformer models at scale

prosodic

PROSODIC: a metrical-phonological parser, written in Python. For English and Finnish, with flexible language support.

stripedhyena

Repository for StripedHyena-7B, a state-of-the-art beyond Transformer model

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