Baltimore, MD

Daniel Baker

Expert
@dnbaker

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

dashing. Fast and accurate genomic distances using HyperLogLog

162

sketch. C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings

156

dashing2. Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.

77

bonsai. Bonsai: Fast, flexible taxonomic analysis and classification

70

frp. FRP: Fast Random Projections

43

minicore. Fast and memory-efficient clustering + coreset construction, including fast distance kernels for Bregman and f-divergences.

33

bioseq. Tokenizers and Machine Learning Models for biological sequence data

25

aesctr. C++ implementation of AES-CTR PRNG using SIMD, based on Samuel Neves' Implementation

12

vec. Type-generic SIMD library for optimized generic code generation

12

wmh. Weighted Minhash Code

5

stochasticSVM. SVM trained by the PEGASOS Stochastic Subgradient Descent algorithm

4

libsimdsampling. Data- and processor- parallelism for fast weighted sampling

4

mcl. Markov Clustering

4

fastiota. Fast std::iota for contiguous memory using SIMD operations

4

khset. Simple wrappers around khset/map

3

fgc. C++

3

libkl. Kernels for fast vectorized KL divergence + related

3

10xdash. Pairwise similarity metrics for 10x barcoded RNASeq datasets

3

fftwrapper. RAII-based C++ wrapper of FFTW

3

valptr. Stores a pointer and a value using unused bits in the pointer

3

fpwrap. Wrap zstd/gzip/std::FILE * generically in one class template.

2

CircularQueue. Circular Queue for minimizing memory allocations in deque applications

2

SimpleUtilities. Miscellaneous utilities: zhead, reverse-complement, tab6

2

libtorch-kseq-demo. Demo using libtorch and one-hot encoding for fastx files

2

dashing2-experiments. Shell

2

DCI. Dynamic Continuous Indexing

2

gds. Graph Data Structures: Generic, Space-efficient Graph Algorithms

2

alias_sampler. C++

2

kspp. C++/RAII port of kstring_t from klib

2

scavenger. Rust spatial/single-cell genomics

1

Stream-Data-Compactor. Burrows-Wheeler Transform for Data Compression

1

Prodigal. Prodigal Gene Prediction Software

1

mdn. Mixture Density Networks in pytorch

1

scVI. Deep generative modeling for single-cell transcriptomics

1

diskmat. mmap-backed blaze matrices

1

squeakr. Squeakr: An Exact and Approximate k -mer Counting System

1

tilt. Biased dataloaders for PyTorch and related utilities

1

minicore-experiments. Experiments for minicore: fast scRNA-seq clustering with various distances

1

comanche. Component-based development framework for memory-centric storage systems

1

fastmod. A C/C++ header file for fast 32-bit division remainders (and divisibility tests) on 64-bit hardware.

1

clhash. C library implementing the ridiculously fast CLHash hashing function

1

klib. A standalone and lightweight C library

1

distance. Distance and Meaning

1

lazy-fisher-yates. A class offering lazy iteration over a shuffled sequence.

1

sv. Sparse Vector Implementation

1

dashing2-binaries. Binaries for releases for Dashing2

1

lazy. Lazy container for reduced memory footprint and optional initialization

1
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