dnbaker

I write fast, memory-efficient software for scientific applications.

@langmead-lab Baltimore, MD

Pinned Repositories

BMFtools
Barcoded Molecular Families
Language:C++22 20 318
aesctr
C++ implementation of AES-CTR PRNG using SIMD, based on Samuel Neves' Implementation
Language:C++11 2 00
bioseq
Tokenizers and Machine Learning Models for biological sequence data
Language:C++22 4 22
bonsai
Bonsai: Fast, flexible taxonomic analysis and classification
Language:C++70 9 411
dashing
Fast and accurate genomic distances using HyperLogLog
Language:C++160 11 6411
dashing2
Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.
Language:C++62 5 257
frp
FRP: Fast Random Projections
Language:C++43 4 66
minicore
Fast and memory-efficient clustering + coreset construction, including fast distance kernels for Bregman and f-divergences.
Language:C++33 3 16
sketch
C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings
Language:C++153 8 1213
vec
Type-generic SIMD library for optimized generic code generation
Language:C++12 2 00

dnbaker's Repositories

dnbaker/dashing
Fast and accurate genomic distances using HyperLogLog
Language:C++160 11 6411
dnbaker/sketch
C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings
Language:C++153 8 1213
dnbaker/bonsai
Bonsai: Fast, flexible taxonomic analysis and classification
Language:C++70 9 411
dnbaker/dashing2
Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.
Language:C++62 5 257
dnbaker/minicore
Fast and memory-efficient clustering + coreset construction, including fast distance kernels for Bregman and f-divergences.
Language:C++33 3 16
dnbaker/bioseq
Tokenizers and Machine Learning Models for biological sequence data
Language:C++22 4 22
dnbaker/vec
Type-generic SIMD library for optimized generic code generation
Language:C++12 2 00
dnbaker/aesctr
C++ implementation of AES-CTR PRNG using SIMD, based on Samuel Neves' Implementation
Language:C++11 2 00
dnbaker/wmh
Weighted Minhash Code
Language:C++5 2 0
dnbaker/fastiota
Fast std::iota for contiguous memory using SIMD operations
Language:C4 2 01
dnbaker/libsimdsampling
Data- and processor- parallelism for fast weighted sampling
Language:C++4 2 0
dnbaker/fgc
Language:C++3 2 0
dnbaker/libkl
Kernels for fast vectorized KL divergence + related
Language:C3 2 0
dnbaker/dashing2-experiments
Language:Shell2 2 0
dnbaker/libtorch-kseq-demo
Demo using libtorch and one-hot encoding for fastx files
Language:C++2 2 0
dnbaker/dashing2-binaries
Binaries for releases for Dashing2
1 2 2
dnbaker/minicore-experiments
Experiments for minicore: fast scRNA-seq clustering with various distances
Language:Python1 2 0
dnbaker/scavenger
Rust spatial/single-cell genomics
Language:Rust1 1 0
dnbaker/tilt
Biased dataloaders for PyTorch and related utilities
Language:Python1 2 0
dnbaker/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell1 0
dnbaker/dashing-binaries
2 0
dnbaker/distmat
2-dimensional distance matrix for holding distances of arbitrary types.
Language:C++2 01
dnbaker/dnbaker
1
dnbaker/einops
Simplistic API for deep learning tensor operations
Language:Rust1 0
dnbaker/FFHT
Fast Fast Hadamard Transform
Language:C1 03
dnbaker/megadepth
BigWig and BAM utilities
Language:C++1 0
dnbaker/minilsh
Python bindings for Locality-Sensitive Hashers, built on the minicore C++ library.
Language:C++2 0
dnbaker/pathml
Tools for computational pathology
Language:Python1 0
dnbaker/ProtTrans
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
Language:Jupyter Notebook1 0
dnbaker/rust-tokenizers
Rust-tokenizer offers high-performance tokenizers for modern language models, including WordPiece, Byte-Pair Encoding (BPE) and Unigram (SentencePiece) models
Language:Rust1 0