Daniel Liu

uwu. fastest text uwuifier in the west

block-aligner. SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

Java-Machine-Learning. Deep learning library for Java, with fully connected, convolutional, and recurrent layers. Also features many gradient descent optimization algorithms.

cute-nucleotides. Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.

triple_accel. Rust edit distance routines accelerated using SIMD. Supports fast Hamming, Levenshtein, restricted Damerau-Levenshtein, etc. distance calculations and string search.

UMICollapse. Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

Adversarial-point-perturbations-on-3D-objects. New distributional and shape attacks on neural networks that process 3D point cloud data.

3D-Neural-Network-Adversarial-Attacks. Research on adversarial attacks and defenses for deep neural network 3D point cloud classifiers like PointNet and PointNet++.

ANTISEQUENCE. Rust library for processing sequencing reads.

simple-saca. Hardware go brrr bounded context suffix array construction algorithm

dlb-kmer-sampling. Optimal distance lower bound k-mer sampling.

9S. Basic Rust program that uses multiple threads to send and receive pings.

Java-Fuzzy-Search. A general, multi-threaded fuzzy searching language, called fuzzysplit, that is built on top of a fast and flexible Java fuzzy search library. Can be applied to demultiplex and trim DNA.

spliced-aligner. Spliced aligner.

diff-align. Differentiable position-specific probability matrix alignment.

General-Algorithms. A variety of algorithm implementations and short classes, mostly for competitive programming and machine learning.

frfr. Parallelized Ukkonen/Myer's edit distance algorithm, fr fr.

replit_audio. Rust library for playing audio in repl.it.

Maze-Solver. 2D grid-based maze solver that is written in Java. Uses Swing for GUI and contains 8 different methods for solving mazes.

WWDC-2020-Coronavirus-Comparison. Efficiently comparing the 2019 coronavirus genome with a couple of other coronaviruses in Swift.

rust-cloc. Count lines from files in a directory.

simulate-seqs. Simulate sequences.

libsais-rs. rust bindings to libsais

reCall. Interpreter for reCall, a dynamically typed scripting language that emphasizes recursion. Also contains object-oriented and functional features.

diff-bench-paper. Edits to the supplementary data of the difference recurrence alignment paper.

consulting. Consulting website.