GitHub
https://github.com/kundajelab/retina-design
Designing AAV sequences for retinal cell types (with scATAC-seq models)
https://github.com/kundajelab/apricot
apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly.
https://github.com/kundajelab/alzheimers_parkinsons
Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis
https://github.com/kundajelab/1kg_ld_utils
utils/notes for LD calculation from 1000 genomes panel
https://github.com/kunpai/acadhashiru
The Expert Orchestrator AI: Dynamically Adapting, Budget-Aware, and Precisely Tailored to Your Needs
https://github.com/kundajelab/pybigwig
A python extension for quick access to bigWig files
https://github.com/kundajelab/neural_motif_discovery
Framework for interrogating transcription-factor motifs and their syntax/grammars from neural-network interpretations
https://github.com/kundajelab/chromdragonn
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
https://github.com/kundajelab/3dchromatin_replicateqc
Software to compute reproducibility and quality scores for Hi-C data
https://github.com/kundajelab/coessentiality
Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)
https://github.com/kundajelab/synapse-backup-syncer
Create and sync backups to Synapse
https://github.com/kundajelab/pylearn2
A Machine Learning library based on Theano
https://github.com/kunpai/llm-inference-cpp
Script to run LLM inference using C++
https://github.com/kunpai/ecs272-final-project
Final project for ECS272 class - InfoVis
https://github.com/kurokida/jspsych
A JavaScript library for creating and running behavioral experiments in a web browser
https://github.com/kunpengren/zclaim
Cross-chain private transactions between Zcash chains
https://github.com/kunpengren/sui-networks
A local multiple validator nodes sui network with fauce service
https://github.com/kunpengren/slimchain
Source code for the VLDB21 paper "SlimChain: Scaling Blockchain Transactions through Off-Chain Storage and Parallel Processing"
https://github.com/kunpengren/ethlocal
Build a local private Ethereum Network by docker container
https://github.com/kunzaatko/boundarylayerproblem
Resources and Beamer presentation for a talk about perturbation methods that leads to solving a non-linear differential equation with a boundary layer.
https://github.com/kunzaatko/promptingtools.jl
Streamline your life using PromptingTools.jl, the Julia package that simplifies interacting with large language models.
https://github.com/kurokio/soso-spase
For creating Science On Schema.Org (SOSO) markup in dataset landing pages to improve data discovery through search engines.
https://github.com/kurokio/spase-datacite
For creating and updating DataCite DOIs for SPASE records.
https://github.com/kurokio/ivoa-presentation-files
Contains the schema.org and DataCite JSONs resulting from new mappings with SPASE
https://github.com/lamastex/expositions
This is a set of mathematical, statistical and computational expositions
https://github.com/lamastex/jpautogradercomps
This is a repository for various components developed around semi/auto-grading a jupyter .ipynb notebook
https://github.com/lamastex/hawkesprocessesonmedia
Master's thesis of Alfred Lindstr\"om, Mathematics, Uppsala University, 2021 (exjobb of Combient Mix AB)
https://github.com/lamastex/2023-mastersthesis-axelsandstedt
Axel Sandstedt's Masters thesis
https://github.com/lamastex/spark-trend-calculus
To detect trends in time series using Andrew Morgan's trend calculus algorithms in Apache Spark and Scala from Antoine Amend's initial implementation
https://github.com/lamastex/scadamale
Scalable Data Science and Distributed Machine Learning Course Book written by Raazesh Sainudiin and his WASP AI-Track PhD Students
https://github.com/lczech/come_2017
Some sample files for the CoME2017 course to play around with.
https://github.com/lczech/ratatosk
Snakemake pipeline for phylogenetic placement of metagenomic sequences
https://github.com/lczech/grenepilot-paper
Scripts and analyses for the GrENE-net pilot dataset
https://github.com/lczech/grenedalf-paper
Code for tests and benchmarks of our paper on grenedalf
https://github.com/lesunb/jss-2022-replication-package
Replication package of the paper titled "An Architecture for Mission Coordination of Heterogeneous Robots"
https://github.com/lesunb/bsn_seams24
Body Sensor Network (BSN): a prototype for exercising dependable adaptation in healthcare domain.
https://github.com/lesunb/bsn_rome_24
Body Sensor Network (BSN): a prototype for exercising dependable adaptation in healthcare domain.
https://github.com/lesunb/implied_scenarios
Relevant files used for the project 'Characterization of Implied Scenarios as Families of Common Behavior'.
https://github.com/linux-cpp-lisp/pytorch_geometric
Geometric Deep Learning Extension Library for PyTorch
https://github.com/linux-cpp-lisp/opt_einsum
⚡️Optimizing einsum functions in NumPy, Tensorflow, Dask, and more with contraction order optimization.
https://github.com/linux-cpp-lisp/litmatter
Rapid experimentation and scaling of deep learning models on molecular and crystal graphs.
pyOMA2: A Python module for conducting operational modal analysis
pyOMA2: A Python module for conducting operational modal analysis - Published in JOSS (2025)
tmmax
A fast transfer matrix method written in jax for modelling optical multilayer thin films
NonSysId: Nonlinear System Identification with Improved Model Term Selection for NARMAX Models
NonSysId: Nonlinear System Identification with Improved Model Term Selection for NARMAX Models - Published in JOSS (2025)
THz Image Explorer - An Interactive Cross-Platform Open-Source THz Image Analysis Tool
THz Image Explorer - An Interactive Cross-Platform Open-Source THz Image Analysis Tool - Published in JOSS (2025)
PyDrugLogics: A Python Package for Predicting Drug Synergies Using Boolean Models
PyDrugLogics: A Python Package for Predicting Drug Synergies Using Boolean Models - Published in JOSS (2025)
MetaSpread: A cancer growth and metastatic spread simulation program in Python
MetaSpread: A cancer growth and metastatic spread simulation program in Python - Published in JOSS (2025)
mlr3extralearners: Expanding the mlr3 Ecosystem with Community-Driven Learner Integration
mlr3extralearners: Expanding the mlr3 Ecosystem with Community-Driven Learner Integration - Published in JOSS (2025)
deepinv
DeepInverse: a PyTorch library for solving imaging inverse problems using deep learning
mlgidGUI - an annotation program for 2D scattering data
mlgidGUI - an annotation program for 2D scattering data - Published in JOSS (2025)
STON: SofTware for petrOgraphic visualisatioN
STON: SofTware for petrOgraphic visualisatioN - Published in JOSS (2025)
optimeo
OPTIMEO is a package doubled by a web application that helps you optimize your experimental process by generating a Design of Experiment, generating new experiments using Bayesian Optimization (BO), and analyzing the results of your experiments using Machine Learning models.
PathFinder: A Matlab/Octave package for oscillatory integration
PathFinder: A Matlab/Octave package for oscillatory integration - Published in JOSS (2025)
NeuroCAPs
NeuroCAPs: A Python Package for Performing Co-Activation Patterns Analyses on Resting-State and Task-Based fMRI Data - Published in JOSS (2025)
ActiSleep Tracker
ActiSleep Tracker: a Python-based dashboard for adjusting automatic sleep predictions of actigraphy data - Published in JOSS (2025)
HINA
HINA: A Learning Analytics Tool for Heterogenous Interaction Network Analysis in Python - Published in JOSS (2025)
PANKH: An unsteady potential flow solver for hovering airfoils
PANKH: An unsteady potential flow solver for hovering airfoils - Published in JOSS (2025)
elasticipy
A python toolkit to perform common tensor operations in Continuum Mechanics
eitprocessing
Software for electrical impedance tomography data loading, visualization and processing
