nealgravindra

cluster2celltype

Using biological priors (previously selected important features or "markers"), assign cell types to clusters based on differential discriminability of cell type markers

CONDENSE

CONditional DENSity Embedding for unsupervised characterization of gene dynamics

covid_severity_index

CSI developed in the early days, published in https://www.annemergmed.com/article/S0196-0644(20)30588-6/fulltext

cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

diffuse_profile

How to diffuse a profile into a shared space for recommendations? Should we use supervised learning and feature attribution or variance metrics for perturbation profiles? How to evaluate this approach?

readinglist

need to read more papers gahhh

scGAT

Code to reproduce results in Ravindra NG* & Sehanobish A* et al. 2020, "Disease State Prediction From Single-Cell Data Using Graph Attention Networks" to appear in ACM Proceedings. <https://arxiv.org/abs/2002.07128>

scnd

neurodegeneration and single-cell omics

self-supervsed_edge_feats

code for "Self-supervised edge features for improved Graph Neural Network training", <arxivlink>

wearables

nealgravindra/self-supervsed_edge_feats

code for "Self-supervised edge features for improved Graph Neural Network training", <arxivlink>

nealgravindra/readinglist

need to read more papers gahhh

nealgravindra/wearables

nealgravindra/scnd

neurodegeneration and single-cell omics

nealgravindra/cluster2celltype

Using biological priors (previously selected important features or "markers"), assign cell types to clusters based on differential discriminability of cell type markers

nealgravindra/covid_severity_index

CSI developed in the early days, published in https://www.annemergmed.com/article/S0196-0644(20)30588-6/fulltext

nealgravindra/cpa

The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.

nealgravindra/diffuse_profile

How to diffuse a profile into a shared space for recommendations? Should we use supervised learning and feature attribution or variance metrics for perturbation profiles? How to evaluate this approach?

nealgravindra/distributional_encoder

use of a permutation invariant network to encode probability distributions

nealgravindra/DLmodules

3 month-ish thematic modules to keep up with new developments in other fields -- blogging, writing a textbook, implementing code from scratch

nealgravindra/fromscratch

implementations of papers from scratch

nealgravindra/GenePT

nealgravindra/gnn_scgexa

GNN-based single-cell gene expression analysis

nealgravindra/graphtransormer

nealgravindra/harmonized-toolkit

The Harmonized Pre-processing Toolkit for Dementia Bank

nealgravindra/lungmap

nealgravindra/nalab

nealgravindra/new2dev

Playground for new computational implementations in order to appropriately tweak and transition to personal prj dev

nealgravindra/pytorch_geometric

Geometric Deep Learning Extension Library for PyTorch

nealgravindra/rl4xai

nealgravindra/scFormer

nealgravindra/scgat_scnd

tutorial for Cell paper

nealgravindra/scGPT

copy of bo wang lab scGPT repo from 240604

nealgravindra/seq2gex

Learning how life's languages are expressed

nealgravindra/simpletopics

composite scores for indexed descriptions to target document(s)

nealgravindra/single-cell_neurodegeneration

Code to reproduce results of Tejwani L* and Ravindra NG* et al. 2020

nealgravindra/stuck_in_plat

for the ave. apex legends player that needs to scheme to rank up

nealgravindra/talks

nealgravindra/torch_accelerated_skeleton

based on a talk by Sebastian Rascka at CVPR, finally gonna use fabric

nealgravindra/transformers

🤗Transformers: State-of-the-art Natural Language Processing for Pytorch and TensorFlow 2.0.