Author's PyTorch implementation of Randomized Ensembled Double Q-Learning (REDQ) algorithm.

Randomized Ensembled Double Q-Learning: Learning Fast Without a Model

Dropout Q-Functions for Doubly Efficient Reinforcement Learning

Adaptive Ensemble Q-learning: Minimizing Estimation Bias via Error Feedback

Live in the Moment: Learning Dynamics Model Adapted to Evolving Policy

DNS: Determinantal Point Process Based Neural Network Sampler for Ensemble Reinforcement Learning

Off-Policy RL Algorithms Can be Sample-Efficient for Continuous Control via Sample Multiple Reuse

Simplified Temporal Consistency Reinforcement Learning

Balancing Value Underestimation and Overestimationwith Realistic Actor-Critic


Official Pytorch implementation of the ECCV 2022 paper "GIPSO: Geometrically Informed Propagation for Online Adaptation in 3D LiDAR Segmentation"

Segment Any Point Cloud Sequences by Distilling Vision Foundation Models

Annotator: A Generic Active Learning Baseline for LiDAR Semantic Segmentation

Calib3D: Calibrating Model Preferences for Reliable 3D Scene
  Understanding


RayS: A Ray Searching Method for Hard-label Adversarial Attack (KDD2020)

RobustBench: a standardized adversarial robustness benchmark

Reveal of Vision Transformers Robustness against Adversarial Attacks

Efficient Robust Training via Backward Smoothing

Evading Black-box Classifiers Without Breaking Eggs


Functional Map of the World

SatMAE: Pre-training Transformers for Temporal and Multi-Spectral Satellite Imagery

Wild-Time: A Benchmark of in-the-Wild Distribution Shift over Time

Contrastive Adapters for Foundation Model Group Robustness

CSP: Self-Supervised Contrastive Spatial Pre-Training for Geospatial-Visual Representations

Efficient Classification of Very Large Images with Tiny Objects

There Are No Data Like More Data: Datasets for deep learning in Earth observation

IEEE Geoscience and Remote Sensing Magazine


Wide Residual Networks (WideResNets) in PyTorch

Wide Residual Networks

Towards Explaining the Regularization Effect of Initial Large Learning Rate in Training Neural Networks

How Does Learning Rate Decay Help Modern Neural Networks?

Evaluation of Neural Architectures Trained with Square Loss vs Cross-Entropy in Classification Tasks

FreezeOut: Accelerate Training by Progressively Freezing Layers

Data-dependent Sample Complexity of Deep Neural Networks via Lipschitz Augmentation

Improved Sample Complexities for Deep Networks and Robust Classification via an All-Layer Margin

Backbones-Review: Feature Extraction Networks for Deep Learning and Deep Reinforcement Learning Approaches

MultiplexNet: Towards Fully Satisfied Logical Constraints in Neural Networks

Rare Gems: Finding Lottery Tickets at Initialization


[CVPR 2023] VideoMAE V2: Scaling Video Masked Autoencoders with Dual Masking

VideoGLUE: Video General Understanding Evaluation of Foundation Models

VideoEval: Comprehensive Benchmark Suite for Low-Cost Evaluation of Video Foundation Model

HARNet in deep learning approach—a systematic survey


Node Embeddings in Dynamic Graphs

Node embeddings in dynamic graphs

Temporal walk based centrality metric for graph streams

FILDNE: A Framework for Incremental Learning of Dynamic Networks Embeddings

Predicting partially observed processes on temporal networks by Dynamics-Aware Node Embeddings (DyANE)


Independently Recurrent Neural Networks (IndRNN) implemented in pytorch.

Independently Recurrent Neural Network (IndRNN): Building A Longer and Deeper RNN

Deep Independently Recurrent Neural Network (IndRNN)

A Chain Graph Interpretation of Real-World Neural Networks

RNN Training along Locally Optimal Trajectories via Frank-Wolfe Algorithm


Scripts to reproduce TrioBinning manuscript

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle

Twelve quick steps for genome assembly and annotation in the classroom


Bead-based single-cell atac processing

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

Functional inference of gene regulation using single-cell multi-omics

Inference and effects of barcode multiplets in droplet-based single-cell assays

Systematic benchmarking of single-cell ATAC-sequencing protocols


fastlangid, the only language identification package that support cantonese (zh-yue), simplified (zh-hans) and traditional chinese (zh-hant)

Enriching Word Vectors with Subword Information

Bag of Tricks for Efficient Text Classification

FastText.zip: Compressing text classification models

VarDial in the Wild: Industrial Applications of LID Systems for Closely-Related Language Varieties

Workshop on NLP for Similar Languages, Varieties and Dialects


De novo annotation of young retrotransposons

Transposon age and non-CG methylation

Environmental and epigenetic regulation of Rider retrotransposons in tomato

Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants

A pair of effectors encoded on a conditionally dispensable chromosome of Fusarium oxysporum suppress host-specific immunity


This is the official repository for NAACL 2021, "XOR QA: Cross-lingual Open-Retrieval Question Answering".

Dense Passage Retrieval for Open-Domain Question Answering

Learning to Retrieve Reasoning Paths over Wikipedia Graph for Question Answering

One Question Answering Model for Many Languages with Cross-lingual Dense Passage Retrieval

Bridging the Gap Between Indexing and Retrieval for Differentiable Search Index with Query Generation

SimQA: Detecting Simultaneous MT Errors through Word-by-Word Question Answering

Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing

Synthetic Cross-language Information Retrieval Training Data


A stand-alone version of Dehnen's GalaxyPotential code.

The mass distribution and gravitational potential of the Milky Way

Monthly Notices of the Royal Astronomical Society

A dynamically young and perturbed Milky Way disk

Stellar Streams Discovered in the Dark Energy Survey

The Sixth Data Release of the Radial Velocity Experiment (RAVE). I. Survey Description, Spectra, and Radial Velocities

Discovery of a Gamma-Ray Black Widow Pulsar by GPU-accelerated Einstein@Home

Tree-ring structure of Galactic bar resonance

Monthly notices of the Royal Astronomical Society

The Third Fermi Large Area Telescope Catalog of Gamma-Ray Pulsars

The MSPSRπ catalogue: VLBA astrometry of 18 millisecond pulsars

The local rotation curve of the Milky Way based on SEGUE and RAVE data

LAMOST meets Gaia: The Galactic Open Clusters


Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Characterization of an archaeal virus-host system reveals massive genomic rearrangements in a laboratory strain

Phenotypic and genomic assessment of the potential threat of human spaceflight-relevant Staphylococcus capitis isolates under stress conditions

First Report of Colistin-Resistant Escherichia coli Carrying mcr-1 IncI2(delta) and IncX4 Plasmids from Camels (Camelus dromedarius) in the Gulf Region

Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates


Creative Commons Attribution Share Alike 4.0 International

[EMNLP'23] Execution-Based Evaluation for Open Domain Code Generation

Execution-Based Evaluation for Open-Domain Code Generation

An In-depth Look at Gemini's Language Abilities

BigCodeBench: Benchmarking Code Generation with Diverse Function Calls
  and Complex Instructions


Checker for "morally correct" induction proofs about haskell programs

Engaging, Large-Scale Functional Programming Education in Physical and Virtual Space

Check Your (Students') Proofs-With Holes


Flexible Bayesian inference of mutational signatures

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Increased somatic mutation burdens in normal human cells due to defective DNA polymerases

Detection of early seeding of Richter transformation in chronic lymphocytic leukemia

Somatic evolution and global expansion of an ancient transmissible cancer lineage

Computational tools to detect signatures of mutational processes in DNA from tumours: A review and empirical comparison of performance

Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells

Mutational landscape of normal epithelial cells in Lynch Syndrome patients

Clonal origin of KMT2A wild-type lineage-switch leukemia following CAR-T cell and blinatumomab therapy

A comprehensive comparison of tools for fitting mutational signatures


A Python module that implements NAFF Algorithm

Refined betatron tune measurements by mixing beam position data

Identification and characterization of high order incoherent space charge driven structure resonances in the CERN Proton Synchrotron

Resonance identification studies at the CERN PS

Coupling and Space Charge studies at the CERN PSB

Frequency analysis and dynamic aperture studies in a low energy antiproton ring with realistic 3D magnetic fields


normalize the intensities of various MR image modalities

Evaluating the Impact of Intensity Normalization on MR Image Synthesis

Impact of Preprocessing and Harmonization Methods on the Removal of Scanner Effects in Brain MRI Radiomic Features

Harmonization Strategies in Multicenter MRI-Based Radiomics

Radiomics-Based Detection of Radionecrosis Using Harmonized Multiparametric MRI


TE tools for TE RNASeq and smallRNASeq analysis with galaxy

TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids

High Stability of the Epigenome inDrosophilaInterspecific Hybrids


Official PyTorch implementation of GENESIS and GENESIS-V2

GENESIS: Generative Scene Inference and Sampling with Object-Centric Latent Representations

GENESIS-V2: Inferring Unordered Object Representations without Iterative Refinement

RELATE: Physically Plausible Multi-Object Scene Synthesis Using Structured Latent Spaces

Reconstruction Bottlenecks in Object-Centric Generative Models

Unsupervised Object Learning via Common Fate

Learning Foreground-Background Segmentation from Improved Layered GANs

Toward Compositional Generalization in Object-Oriented World Modeling

Autoencoder-based background reconstruction and foreground segmentation with background noise estimation

Weakly supervised learning of multi-object 3D scene decompositions using deep shape priors

Shepherding Slots to Objects: Towards Stable and Robust Object-Centric Learning


Codebase for Evolutionary Reinforcement Learning (ERL) from the paper "Evolution-Guided Policy Gradients in Reinforcement Learning" published at NeurIPS 2018

Soft Actor-Critic: Off-Policy Maximum Entropy Deep Reinforcement Learning with a Stochastic Actor

Evolution-Guided Policy Gradient in Reinforcement Learning

CEM-RL: Combining evolutionary and gradient-based methods for policy search

ERL-Re^2: Efficient Evolutionary Reinforcement Learning with Shared State Representation and Individual Policy Representation

A Surrogate-Assisted Controller for Expensive Evolutionary Reinforcement Learning

Attraction-Repulsion Actor-Critic for Continuous Control Reinforcement Learning

Rethinking Population-assisted Off-policy Reinforcement Learning

Proceedings of the Genetic and Evolutionary Computation Conference


A toolkit for working with piano rolls

Multitask learning for frame-level instrument recognition

A Minimal Template for Interactive Web-based Demonstrations of Musical Machine Learning

Demonstration of PerformanceNet: A Convolutional Neural Network Model for Score-to-Audio Music Generation


Code for the paper "Deep Entity Matching with Pre-trained Language Models"

Deep Entity Matching with Pre-Trained Language Models

PromptEM: Prompt-tuning for Low-resource Generalized Entity Matching

FlexER: Flexible Entity Resolution for Multiple Intents

Ground Truth Inference for Weakly Supervised Entity Matching

A Critical Re-evaluation of Benchmark Datasets for (Deep) Learning-Based Matching Algorithms

Transformer-based Denoising Adversarial Variational Entity Resolution

The Battleship Approach to the Low Resource Entity Matching Problem

Proceedings of the ACM on Management of Data

MultiEM: Efficient and Effective Unsupervised Multi-Table Entity Matching


Verifying Strong Eventual Consistency in Distributed Systems

Proceedings of the ACM on Programming Languages

A Highly-Available Move Operation for Replicated Trees

IEEE Transactions on Parallel and Distributed Systems

Moving elements in list CRDTs


My bioinfo toolbox

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

HaploTypo: a variant-calling pipeline for phased genomes


DeepOnto: A Python Package for Ontology Engineering with Deep Learning

Large language models as oracles for instantiating ontologies with
  domain-specific knowledge

Contextualized Structural Self-supervised Learning for Ontology Matching

PyGraft: Configurable Generation of Synthetic Schemas and Knowledge Graphs at Your Fingertips


R Package to Optimize Windfarm Layouts


Download FASTQ files from SRA or ENA repositories.

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Plassembler: an automated bacterial plasmid assembly tool

Drug resistance prediction for Mycobacterium tuberculosis with reference graphs


A simple library for Fréchet Audio Distance (FAD) calculation

FMA: A Dataset For Music Analysis

Adapting Frechet Audio Distance for Generative Music Evaluation

Generating Speakers by Prompting Listener Impressions for Pre-trained Multi-Speaker Text-to-Speech Systems


Reproduction of 'Analysing Mathematical Reasoning Abilities of Neural Models' Saxton et. al. 2019

Do NLP Models Know Numbers? Probing Numeracy in Embeddings

AllenNLP Interpret: A Framework for Explaining Predictions of NLP Models

Attending to Mathematical Language with Transformers


Proteomics Toolset for Integrative Data Analysis

ESCRT-dependent STING degradation inhibits steady-state and cGAMP-induced signalling

Proteomic profiling reveals CDK6 upregulation as a targetable resistance mechanism for lenalidomide in multiple myeloma

Mitochondria preserve an autarkic one-carbon cycle to confer growth-independent cancer cell migration and metastasis

Cyclin-Dependent Kinase 18 Controls Trafficking of Aquaporin-2 and Its Abundance through Ubiquitin Ligase STUB1, Which Functions as an AKAP

Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues

Pan-claudin family interactome analysis reveals shared and specific interactions.

Inhibition of MYC translation through targeting of the newly identified PHB-eIF4F complex as a therapeutic strategy in CLL

Deep Proteome Profiling Reveals Signatures of Age and Sex Differences in Paw Skin and Sciatic Nerve of Naïve Mice

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics


Julia package to Compare Graph Embeddings

An Unsupervised Framework for Comparing Graph Embeddings

Evaluating Node Embeddings of Complex Networks

A multi-purposed unsupervised framework for comparing embeddings of undirected and directed graphs

Artificial Benchmark for Community Detection with Outliers (ABCD+o)

Survey of Generative Methods for Social Media Analysis

Unsupervised Framework for Evaluating and Explaining Structural Node Embeddings of Graphs


A Knowledge Graph for Relational Learning On Biological Data

A unified drug–target interaction prediction framework based on knowledge graph and recommendation system

A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge
  Graph Perspective

Knowledge Graph Embeddings in the Biomedical Domain: Are They Useful? A Look at Link Prediction, Rule Learning, and Downstream Polypharmacy Tasks

BioBLP: A Modular Framework for Learning on Multimodal Biomedical Knowledge Graphs


The UK National Grid historical demand for electricity


Artificial Benchmark for Community Detection (ABCD) - A Fast Random Graph Model with Community Structure

Artificial Benchmark for Community Detection (ABCD)—Fast random graph model with community structure

Modularity of the ABCD Random Graph Model with Community Structure

Hypergraph Artificial Benchmark for Community Detection (h-ABCD)

Properties and Performance of the ABCDe Random Graph Model with Community Structure

Self-similarity of Communities of the ABCD Model

Modularity Based Community Detection in Hypergraphs


Safety Verification of Deep Neural Networks

Algorithms for Verifying Deep Neural Networks

Verification for Machine Learning, Autonomy, and Neural Networks Survey

A Review of Formal Methods applied to Machine Learning


Estimate metagenomic coverage and sequence diversity

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

Estimating coverage in metagenomic data sets and why it matters


Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.

wgd—simple command line tools for the analysis of ancient whole-genome duplications

Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades

Comparative Genomic Analysis and Metabolic Potential Profiling of a Novel Culinary-Medicinal Mushroom, Hericium rajendrae (Basidiomycota)

The First Whole Genome Sequencing of Agaricus bitorquis and Its Metabolite Profiling

Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Isoseq and Illumina Sequencing

Genome-Wide Comparison and Functional Characterization of HMGR Gene Family Associated with Shikonin Biosynthesis in Lithospermum erythrorhizon

International journal of molecular sciences

Gapless Genome Assembly of Puccinia triticina Provides Insights into Chromosome Evolution in Pucciniales


Frame Semantic Parser based on T5 and FrameNet

Frame-Semantic Parsing with Softmax-Margin Segmental RNNs and a Syntactic Scaffold

Open-Domain Frame Semantic Parsing Using Transformers

Open-source Frame Semantic Parsing


A fastai/PyTorch package for unpaired image-to-image translation.

Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks

DualGAN: Unsupervised Dual Learning for Image-to-Image Translation

GANILLA: Generative Adversarial Networks for Image to Illustration Translation

Automatic Diagnosis of COVID-19 from CT Images using CycleGAN and Transfer Learning


caliver: CALIbration and VERification of gridded fire danger models

ERA5-based global meteorological wildfire danger maps

A 1980–2018 global fire danger re-analysis dataset for the Canadian Fire Weather Indices

Using machine learning to predict fire-ignition occurrences from lightning forecasts

Caliver: An R package for CALIbration and VERification of forest fire gridded model outputs


Language Modelling Makes Sense - WSD (and more) with Contextual Embeddings

Language Modelling Makes Sense: Propagating Representations through WordNet for Full-Coverage Word Sense Disambiguation

LMMS reloaded: Transformer-based sense embeddings for disambiguation and beyond

Sense Embeddings are also Biased – Evaluating Social Biases in Static and Contextualised Sense Embeddings

LIAAD at SemDeep-5 Challenge: Word-in-Context (WiC)

Don't Neglect the Obvious: On the Role of Unambiguous Words in Word Sense Disambiguation

Decomposing Word Embedding with the Capsule Network

Can Word Sense Distribution Detect Semantic Changes of Words?

Together We Make Sense -- Learning Meta-Sense Embeddings from Pretrained Static Sense Embeddings

On the Curious Case of ℓ_2 norm of Sense Embeddings

Definition generation for lexical semantic change detection


Code for comparison of multimodal VAE models

Multimodal Generative Models for Scalable Weakly-Supervised Learning

Variational Mixture-of-Experts Autoencoders for Multi-Modal Deep Generative Models


Pyproffit is a Python code for the analysis of X-ray brightness profiles from clusters of galaxies

Low-scatter galaxy cluster mass proxies for the eROSITA all-sky survey

HSC-XXL: Baryon budget of the 136 XXL groups and clusters

Toward a characterization of X-ray galaxy clusters for cosmology

The Planck clusters in the LOFAR sky. III. LoTSS-DR2: Dynamic states and density fluctuations of the intracluster medium

The XXL Survey XLIV. Sunyaev-Zel'dovich mapping of a low-mass cluster at z~1: a multi-wavelength approach

HAL (Le Centre pour la Communication Scientifique Directe)

Setting the scene for BUFFALO: A study of the matter distribution in the
  HFF galaxy cluster MACS J0416.1-2403 and its parallel field

The complex intracluster medium of Abell 1569 and its interaction with central radio galaxies

Re-energisation of AGN head-tail radio galaxies in the galaxy cluster ZwCl0634.1+47474

Scaling relations of X-ray luminous clusters in the Hyper Suprime-Cam Subaru Strategic Program field


The main repo of Penglai Enclave based on RISC-V Trapped Virtual Memory (TVM).


MSDNet

Multi-Scale Dense Networks for Resource Efficient Image Classification

Window-Based Early-Exit Cascades for Uncertainty Estimation: When Deep Ensembles are More Efficient than Single Models

Inplace knowledge distillation with teacher assistant for improved training of flexible deep neural networks

A Closer Look at Branch Classifiers of Multi-exit Architectures


Microstructure Diffusion Toolbox

Challenges for biophysical modeling of microstructure

Multimodal and multicontrast image fusion via deep generative models

Sleep quality relates to emotional reactivity via intracortical myelination

Reliability on multiband diffusion NODDI models: A test retest study on children and adults

Neurite Orientation Dispersion and Density Imaging in Multiple Sclerosis: A Systematic Review

Journal of magnetic resonance imaging : JMRI

GAMER-MRI in Multiple Sclerosis Identifies the Diffusion-Based Microstructural Measures That Are Most Sensitive to Focal Damage: A Deep-Learning-Based Analysis and Clinico-Biological Validation

Multishell diffusion MRI reveals whole‐brain white matter changes in HIV

Fast quantification of uncertainty in non-linear diffusion MRI models for artifact detection and more power in group studies


Cold pool area and temperature data products for the eastern Bering Sea from NOAA/AFSC/RACE Groundfish Assessment Program's summer trawl surveys


Technology agnostic long read analysis pipeline for transcriptomes

Accurate isoform discovery with IsoQuant using long reads

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

bioRxiv : the preprint server for biology

Characterizing nascent transcription patterns of PROMPTs, eRNAs, and readthrough transcripts in the ENCODE4 deeply profiled cell lines


Simod is a tool for automated BPS model discovery

Automated discovery of business process simulation models from event logs

Discovering generative models from event logs: data-driven simulation vs deep learning

Discovering Business Process Simulation Models in the Presence of Multitasking


Unified MultiWOZ evaluation scripts for the context-to-response task.

Shades of BLEU, Flavours of Success: The Case of MultiWOZ

TOD-Flow: Modeling the Structure of Task-Oriented Dialogues


Surveillance System Against Violence

You Only Look Once: Unified, Real-Time Object Detection

Two-Stream Convolutional Networks for Action Recognition in Videos

Temporal Segment Networks: Towards Good Practices for Deep Action Recognition

Action Recognition with Trajectory-Pooled Deep-Convolutional Descriptors


Capacity Expansion Problem Formulation for Julia

On representation of temporal variability in electricity capacity planning models

CapacityExpansion: A capacity expansion modeling framework in Julia


Package for Simulation, Tomography and Analysis of Quantum Computers

The ITensor Software Library for Tensor Network Calculations

Provably efficient machine learning for quantum many-body problems

Classical variational simulation of the Quantum Approximate Optimization Algorithm

Quantum HyperNetworks: Training Binary Neural Networks in Quantum Superposition

QXTools: A Julia framework for distributed quantum circuit simulation

Quantum-Inspired Machine Learning: a Survey


1D, super-resolution brightness profile reconstruction for interferometric sources

frankenstein: protoplanetary disc brightness profile reconstruction at sub-beam resolution with a rapid Gaussian process

A super-resolution analysis of the DSHARP survey: Substructure is common in the inner 30 au

Dust traps and the formation of cavities in transition discs: a millimetre to sub-millimetre comparison survey

Inner edges of planetesimal belts: collisionally eroded or truncated?

Deprojecting and constraining the vertical thickness of exoKuiper belts


Synthesis Format Conversion Tool

A High-Level LTL Synthesis Format: TLSF v1.0

The 4th Reactive Synthesis Competition (SYNTCOMP 2017): Benchmarks, Participants & Results

The 3rd Reactive Synthesis Competition (SYNTCOMP 2016): Benchmarks, Participants & Results

The Reactive Synthesis Competition: SYNTCOMP 2016 and Beyond

The Temporal Logic Synthesis Format TLSF v1.2

Synthesis of Compact Strategies for Coordination Programs

Tools and Algorithms for the Construction and Analysis of Systems


A Python wrapper for PaDEL-Descriptor software

A Database Framework for Rapid Screening of Structure-Function Relationships in PFAS Chemistry

MOOMIN: Deep Molecular Omics Network for Anti-Cancer Drug Combination Therapy

From intuition to AI: evolution of small molecule representations in drug discovery

Virtual Screening of Small Molecules Targeting BCL2 with Machine Learning, Molecular Docking, and MD Simulation


Source code of FUMA GWAS web application

Functional mapping and annotation of genetic associations with FUMA

Association of Polygenic Variants with Type 2 Diabetes Risk and Their Interaction with Lifestyles in Asians

Association of Polygenic Variants Involved in Immunity and Inflammation with Duodenal Ulcer Risk and Their Interaction with Irregular Eating Habits

Height-Related Polygenic Variants Are Associated with Metabolic Syndrome Risk and Interact with Energy Intake and a Rice-Main Diet to Influence Height in KoGES

Independent Genomic Sources of Brain Structure and Function


Boltzmann Generators and Normalizing Flows in PyTorch

Equivariant flow matching

Temperature Steerable Flows and Boltzmann Generators

Skipping the Replica Exchange Ladder with Normalizing Flows

Reaction coordinate flows for model reduction of molecular kinetics

Normalizing flows as an enhanced sampling method for atomistic
  supercooled liquids


Collection of tools to support submissions to the 3rd VIPriors workshop challenges

VIPriors 1: Visual Inductive Priors for Data-Efficient Deep Learning Challenges

VIPriors 2: Visual Inductive Priors for Data-Efficient Deep Learning Challenges

EfficientSeg: An Efficient Semantic Segmentation Network

VIPriors 3: Visual Inductive Priors for Data-Efficient Deep Learning Challenges


Diffusion MRI Simulation Toolbox in Matlab

Challenges for biophysical modeling of microstructure

SpinDoctor: A MATLAB toolbox for diffusion MRI simulation

Diffusion MRI simulation of realistic neurons with SpinDoctor and the Neuron Module

Practical computation of the diffusion MRI signal of realistic neurons based on Laplace eigenfunctions


A CF-compliant Earth Science data analysis library


FrEDI estimates annual physical and economic impacts from climate change to the U.S., through the 21st century


Experiments with experimental rule-based models to go along with imodels.

Hierarchical Shrinkage: improving the accuracy and interpretability of tree-based methods

MDI+: A Flexible Random Forest-Based Feature Importance Framework

Fast Interpretable Greedy-Tree Sums

Group Probability-Weighted Tree Sums for Interpretable Modeling of Heterogeneous Data


SARS-CoV-2 workflow for nanopore sequence data

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

SARS-CoV-2 Causes Severe Epithelial Inflammation and Barrier Dysfunction

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing

Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany

Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay

Molecular epidemiology of SARS-CoV-2 - a regional to global perspective


An open large-scale dataset for training high-resolution physics emulators in hybrid multi-scale climate simulators.

ClimSim: A large multi-scale dataset for hybrid physics-ML climate emulation


museval - source separation evaluation tools for python

Music Source Separation with Band-split RNN

Demucs: Deep Extractor for Music Sources with extra unlabeled data remixed

Investigating U-Nets with various Intermediate Blocks for Spectrogram-based Singing Voice Separation

Class-conditional embeddings for music source separation

Denoising Auto-encoder with Recurrent Skip Connections and Residual Regression for Music Source Separation

Dilated Convolution with Dilated GRU for Music Source Separation

LaSAFT: Latent Source Attentive Frequency Transformation for Conditioned Source Separation

Diffiner: A Versatile Diffusion-based Generative Refiner for Speech Enhancement

Universal Source Separation with Weakly Labelled Data

Switching Independent Vector Analysis and its Extension to Blind and Spatially Guided Convolutional Beamforming Algorithms


Beta-RecSys: Build, Evaluate and Tune Automated Recommender Systems

Neural Graph Collaborative Filtering

PROCEEDINGS OF THE 42ND INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL (SIGIR '19)

BERT4Rec: Sequential Recommendation with Bidirectional Encoder Representations from Transformer

KGAT: Knowledge Graph Attention Network for Recommendation

Personalized Top-N Sequential Recommendation via Convolutional Sequence Embedding

Variational Autoencoders for Collaborative Filtering

A Simple Convolutional Generative Network for Next Item Recommendation

Collaborative Memory Network for Recommendation Systems

International ACM SIGIR Conference on Research and Development in Information Retrieval

Representing and Recommending Shopping Baskets with Complementarity, Compatibility and Loyalty

International Conference on Information and Knowledge Management

BETA-Rec: Build, Evaluate and Tune Automated Recommender Systems

RECSYS 2020: 14TH ACM CONFERENCE ON RECOMMENDER SYSTEMS


Accelerated Quality-Diversity

evosax: JAX-based Evolution Strategies

Neuroevolution is a Competitive Alternative to Reinforcement Learning for Skill Discovery

Accelerated Quality-Diversity through Massive Parallelism

Benchmarking Quality-Diversity Algorithms on Neuroevolution for Reinforcement Learning

QDax: A Library for Quality-Diversity and Population-based Algorithms with Hardware Acceleration

Assessing Quality-Diversity Neuro-Evolution Algorithms Performance in Hard Exploration Problems

Evolving Populations of Diverse RL Agents with MAP-Elites

Benchmark Tasks for Quality-Diversity Applied to Uncertain Domains


A tool for light curve extraction from the TESS FFIs.

eleanor: An Open-source Tool for Extracting Light Curves from the TESS Full-frame Images

Publications of the Astronomical Society of the Pacific

The μ Tau Association: A 60 Myr Old Coeval Group at 150 pc from the Sun

A search for young exoplanets in Sectors 1-5 of the TESS full-frame images

TOI-3984 A b and TOI-5293 A b: Two Temperate Gas Giants Transiting Mid-M Dwarfs in Wide Binary Systems

TFAW survey - I. Wavelet-based denoising of K2 light curves. Discovery and validation of two new Earth-sized planets in K2 campaign 1

Detection and characterization of planets orbiting oscillating red-giant stars with NASA's TESS mission

A Comparative Study of TESS Light-curve Extraction Methods Applied to Blazars


Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

Federated Learning Enables Big Data for Rare Cancer Boundary Detection

The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: advanced MRI, clinical, genomics, & radiomics

The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)

Multi-institutional noninvasive in vivo characterization of IDH, 1p/19q, and EGFRvIII in glioma using neuro-Cancer Imaging Phenomics Toolkit (neuro-CaPTk)


Generalization without systematicity: On the compositional skills of sequence-to-sequence recurrent networks

StylePTB: A Compositional Benchmark for Fine-grained Controllable Text Style Transfer

Sequence-to-Sequence Learning with Latent Neural Grammars


CUDD: CU Decision Diagram package - unofficial git mirror of https://web.archive.org/web/20180127051756/http://vlsi.colorado.edu/~fabio/CUDD/html/index.html (intro: https://web.archive.org/web/20150215010018/http://vlsi.colorado.edu/~fabio/CUDD/cuddIntro.html)

The probabilistic model checker Storm

DPMC: Weighted Model Counting by Dynamic Programming on Project-Join Trees

Cache Persistence Analysis: Finally Exact

Solving Bitvectors with MCSAT: Explanations from Bits and Pieces

MAP Inference for Probabilistic Logic Programming

Theory and Practice of Logic Programming

Core Challenge 2023: Solver and Graph Descriptions

Symbolic Search for Optimal Planning with Expressive Extensions

Parametric Verification: An Introduction

Transactions on Petri Nets and Other Models of Concurrency XIV

On Deciding Feature Membership in Explanations of SDD & Related Classifiers

Quantum State Preparation Using an Exact CNOT Synthesis Formulation


SR based on LLMs.

End-to-end symbolic regression with transformers

Interpretable scientific discovery with symbolic regression: a review

Transformer-based Planning for Symbolic Regression

The Causal Chambers: Real Physical Systems as a Testbed for AI
  Methodology


Code for building and experimenting on saliency maps for RL agents.

Dueling Network Architectures for Deep Reinforcement Learning

Visualizing and Understanding Atari Agents

Transparency and Explanation in Deep Reinforcement Learning Neural Networks

Exploratory Not Explanatory: Counterfactual Analysis of Saliency Maps for Deep Reinforcement Learning

ToyBox: Better Atari Environments for Testing Reinforcement Learning Agents


AutoFIS: Automatic  Feature Interaction Selection in Factorization  Models for  Click-Through Rate Prediction

User Response Prediction in Online Advertising

FIVES: Feature Interaction Via Edge Search for Large-Scale Tabular Data

Optimizing Feature Set for Click-Through Rate Prediction

Towards Hybrid-grained Feature Interaction Selection for Deep Sparse Network


R scripts for performing co-occurrence analyses

Soil bacterial networks are less stable under drought than fungal networks

The capacity of wastewater treatment plants drives bacterial community structure and its assembly

Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate Forests

Characterization of a nifH-Harboring Bacterial Community in the Soil-Limited Gotjawal Forest


Python routines for computing Navarro-Frenk-White halo properties

Measuring the Circumgalactic and Intergalactic Baryon Contents with Fast Radio Bursts

Weak-lensing calibration of a stellar mass-based mass proxy for redMaPPer and Voronoi Tessellation clusters in SDSS Stripe 82

Monthly Notices of the Royal Astronomical Society

Velocity dispersion and dynamical masses for 388 Galaxy Clusters and groups. Calibrating the M_ SZ–M_ dyn scaling relation for the PSZ2 sample

CLUSTER-LENSING: A PYTHON PACKAGE FOR GALAXY CLUSTERS AND MISCENTERING

NFW: NFW v0.1


Source for Action Schema Networks paper (AAAI'18)

Action Schema Networks: Generalised Policies with Deep Learning

ASNets: Deep Learning for Generalised Planning

Journal of Artificial Intelligence Research

Reinforcement learning on graphs: A survey


A GAN based framework for artifacts and noise removal

TomoGAN: low-dose synchrotron x-ray tomography with generative adversarial networks: discussion.

Journal of the Optical Society of America. A, Optics, image science, and vision

Deep Learning Accelerated Light Source Experiments

Scientific Image Restoration Anywhere

Joint ptycho-tomography with deep generative priors


The Fortran 77 codes for the open-loop  and the closed-loop simulations for the Tennessee Eastman process (TEP) as well as the training and testing data files used for evaluating the data-driven methods (PCA, PLS, FDA, and CVA).

Knowledge-Based Regularization in Generative Modeling

PROCEEDINGS OF THE TWENTY-NINTH INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE

Three-layer Approach to Detect Anomalies in Industrial Environments based on Machine Learning

High-Efficiency Generative Adversarial Network Model for Chemical Process Fault Diagnosis


GlossBERT: BERT for Word Sense Disambiguation with Gloss Knowledge (EMNLP 2019)

Foundation Models for Natural Language Processing -- Pre-trained Language Models Integrating Media

WiC-TSV: An Evaluation Benchmark for Target Sense Verification of Words in Context


Yuck is a local-search constraint solver with FlatZinc interface

A Framework for Generating Informative Benchmark Instances

Generating Local Search Neighborhood with Synthesized Logic Programs


Rust library for fast multi-pattern searching.

Fast Multiple String Matching Using Streaming SIMD Extensions Technology

String Processing and Information Retrieval

Optimal Packed String Matching

IARCS ANNUAL CONFERENCE ON FOUNDATIONS OF SOFTWARE TECHNOLOGY AND THEORETICAL COMPUTER SCIENCE (FSTTCS 2011)

Fast and flexible packed string matching

Towards optimal packed string matching


Minimum Bayes Risk Decoding for Hugging Face Transformers

Epsilon Sampling Rocks: Investigating Sampling Strategies for Minimum Bayes Risk Decoding for Machine Translation

It's MBR All the Way Down: Modern Generation Techniques Through the Lens of Minimum Bayes Risk

Linear-time Minimum Bayes Risk Decoding with Reference Aggregation


NeurIPS 2019 Paper: RUBi : Reducing Unimodal Biases for Visual Question Answering

RUBi: Reducing Unimodal Biases in Visual Question Answering

Introspective Distillation for Robust Question Answering

Accuracy vs. Complexity: A Trade-off in Visual Question Answering Models

Language Prior Is Not the Only Shortcut: A Benchmark for Shortcut Learning in VQA


Source code of paper "Differentially Private Generative Adversarial Network"

Differentially Private Synthetic Medical Data Generation using Convolutional GANs

DataLens: Scalable Privacy Preserving Training via Gradient Compression and Aggregation

Conference on Computer and Communications Security

Differentially Private Generation of Small Images

A Unified View of Differentially Private Deep Generative Modeling


QuickerADC is an implementation of highly-efficient product quantizers leveraging SIMD shuffle instructions integrated into FAISS

Product Quantization for Nearest Neighbor Search

IEEE transactions on pattern analysis and machine intelligence

Efficient and Robust Approximate Nearest Neighbor Search Using Hierarchical Navigable Small World Graphs

The Inverted Multi-Index

Accelerated Nearest Neighbor Search with Quick ADC

PROCEEDINGS OF THE 2017 ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA RETRIEVAL (ICMR'17)

Quicker ADC : Unlocking the Hidden Potential of Product Quantization With SIMD


AAAI 2020. Spatial-Temporal Synchronous Graph Convolutional Networks: A New Framework for Spatial-Temporal Network Data Forecasting

THIRTY-FOURTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, THE THIRTY-SECOND INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE AND THE TENTH AAAI SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE

Deep Learning on Traffic Prediction: Methods, Analysis and Future Directions

IEEE Transactions on Intelligent Transportation Systems

Spatio-Temporal Graph Neural Networks for Predictive Learning in Urban Computing: A Survey

A Comprehensive Survey on Traffic Prediction.

Graph Neural Networks for Intelligent Transportation Systems: A Survey

Do We Really Need Graph Neural Networks for Traffic Forecasting?

Graph Neural Rough Differential Equations for Traffic Forecasting

Graph-based Multi-ODE Neural Networks for Spatio-Temporal Traffic Forecasting

KITS: Inductive Spatio-Temporal Kriging with Increment Training Strategy

Revealing the Power of Masked Autoencoders in Traffic Forecasting


Code for "Label-Consistent Backdoor Attacks"

Label-Consistent Backdoor Attacks

Adversarial Neuron Pruning Purifies Backdoored Deep Models

Narcissus: A Practical Clean-Label Backdoor Attack with Limited Information

SPECTRE: Defending Against Backdoor Attacks Using Robust Statistics

Training with More Confidence: Mitigating Injected and Natural Backdoors During Training

How to Sift Out a Clean Data Subset in the Presence of Data Poisoning?

Trap and Replace: Defending Backdoor Attacks by Trapping Them into an Easy-to-Replace Subnetwork

Rethinking Backdoor Data Poisoning Attacks in the Context of Semi-Supervised Learning

UltraClean: A Simple Framework to Train Robust Neural Networks against Backdoor Attacks


SparseP is the first open-source Sparse Matrix Vector Multiplication (SpMV) software package for real-world Processing-In-Memory (PIM) architectures. SparseP is developed to evaluate and characterize the first publicly-available real-world PIM architecture, the UPMEM PIM architecture. Described by C. Giannoula et al. [https://arxiv.org/abs/2201.05072]

A Modern Primer on Processing in Memory

Towards Efficient Sparse Matrix Vector Multiplication on Real Processing-In-Memory Architectures

Measurement and Modeling of Computer Systems

SparseP

Proceedings of the ACM on Measurement and Analysis of Computing Systems

SparseP: Towards Efficient Sparse Matrix Vector Multiplication on Real Processing-In-Memory Systems

Accelerating irregular applications via efficient synchronization and data access techniques


PyTorch Wrapper for Earth-Mover-Distance (EMD) for 3D point cloud regression

LION: Latent Point Diffusion Models for 3D Shape Generation

MPED: Quantifying Point Cloud Distortion Based on Multiscale Potential Energy Discrepancy

Mosaic-SDF for 3D Generative Models


Implementation of Graph Neural Tangent Kernel (NeurIPS 2019)

Graph Neural Tangent Kernel: Fusing Graph Neural Networks with Graph Kernels

Towards Deepening Graph Neural Networks: A GNTK-based Optimization Perspective

State of the Art and Potentialities of Graph-level Learning


[SDM 2022] Towards Similarity-Aware Time-Series Classification

Data-centric Artificial Intelligence: A Survey

A Survey on Graph Neural Networks for Time Series: Forecasting, Classification, Imputation, and Anomaly Detection


Defending graph neural networks against adversarial attacks (NeurIPS 2020)

GNNGuard: Defending Graph Neural Networks against Adversarial Attacks

Are Defenses for Graph Neural Networks Robust?

EvenNet: Ignoring Odd-Hop Neighbors Improves Robustness of Graph Neural Networks

How does Heterophily Impact the Robustness of Graph Neural Networks? Theoretical Connections and Practical Implications

Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining

Robust Graph Representation Learning for Local Corruption Recovery

A Simple and Yet Fairly Effective Defense for Graph Neural Networks


Learning from History: Modeling Temporal Knowledge Graphs with Sequential Copy-Generation Networks

TimeTraveler: Reinforcement Learning for Temporal Knowledge Graph Forecasting

Temporal Knowledge Graph Forecasting with Neural ODE

xERTE: Explainable Reasoning on Temporal Knowledge Graphs for Forecasting Future Links

zrLLM: Zero-Shot Relational Learning on Temporal Knowledge Graphs with Large Language Models


ASCEND Chinese-English code-switching dataset

ASCEND: A Spontaneous Chinese-English Dataset for Code-switching in Multi-turn Conversation

Adapting the adapters for code-switching in multilingual ASR

Improving Zero-Shot Chinese-English Code-Switching ASR with kNN-CTC and
  Gated Monolingual Datastores


Collection of simple anti-debugging tricks for Linux

Evaluating Dynamic Binary Instrumentation Systems for Conspicuous Features and Artifacts

Follow the WhiteRabbit: Towards Consolidation of On-the-Fly Virtualization and Virtual Machine Introspection


PyTorch Language Modeling Toolkit for Fast Weight Programmers

Linear Transformers Are Secretly Fast Weight Programmers

Going Beyond Linear Transformers with Recurrent Fast Weight Programmers

Transformer with Fourier Integral Attentions

Mitigating Over-smoothing in Transformers via Regularized Nonlocal Functionals

PIDformer: Transformer Meets Control Theory


remef: Remove Partial Effects

The eye-voice span during reading aloud

Linked linear mixed models: A joint analysis of fixation locations and fixation durations in natural reading

Speed-Accuracy Tradeoffs in Brain and Behavior: Testing the Independence of P300 and N400 Related Processes in Behavioral Responses to Sentence Categorization

Positive Psychology Broadens Readers’ Attentional Scope During L2 Reading: Evidence From Eye Movements

Human and computer estimations of Predictability of words in written language

Cross-Linguistic Word Recognition Development Among Chinese Children: A Multilevel Linear Mixed-Effects Modeling Approach

Predictive pre-activation of orthographic and lexical-semantic representations facilitates visual word recognition

Predicting Known Sentences: Neural Basis of Proverb Reading Using Non-parametric Statistical Testing and Mixed-Effects Models

Object Properties Influence Visual Guidance of Motor Actions


Sarus implementation of classical ML models. The models are implemented using the Keras API of tensorflow 2. Vizualization are implemented and can be seen in tensorboard.

Large Scale GAN Training for High Fidelity Natural Image Synthesis

Stochastic Gradient VB and the Variational Auto-Encoder

Neural Discrete Representation Learning

Pixel Recurrent Neural Networks

Conditional Image Generation with PixelCNN Decoders

PixelCNN++: Improving the PixelCNN with Discretized Logistic Mixture Likelihood and Other Modifications

Conditional Neural Processes

PixelSNAIL: An Improved Autoregressive Generative Model


Code to read/write tables of rotation measures following the proposed standard.

The Galactic Faraday rotation sky 2020

Magnetism Science with the Square Kilometre Array

The POlarised GLEAM Survey (POGS) II: Results from an all-sky rotation measure synthesis survey at long wavelengths

Publications of the Astronomical Society of Australia

Discovery of ASKAP J173608.2–321635 as a Highly Polarized Transient Point Source with the Australian SKA Pathfinder

The Faraday Rotation Measure Grid of the LOFAR Two-metre Sky Survey: Data Release 2

Revisiting Rotation Measures from the Canadian Galactic Plane Survey: the Magnetic Field in the Disk of the Outer Galaxy

The Astrophysical Journal Supplement Series

RMTable2023 and PolSpectra2023: Standards for Reporting Polarization and Faraday Rotation Measurements of Radio Sources

The Rapid ASKAP Continuum Survey III: Spectra and Polarisation In Cutouts of Extragalactic Sources (SPICE-RACS) first data release

The Global Magneto-Ionic Medium Survey (GMIMS): the brightest polarized region in the southern sky at 75 cm and its implications for Radio Loop II

Deep Synoptic Array Science: Polarimetry of 25 New Fast Radio Bursts Provides Insights into Their Origins


The Open Lab Book: A collection of freely distributable scientific protocols

Dissection of Root Transcriptional Responses to Low pH, Aluminum Toxicity and Iron Excess Under Pi-Limiting Conditions in Arabidopsis Wild-Type and stop1 Seedlings

A transition phase in late mouse oogenesis impacts DNA methylation of the early embryo

ROOT PENETRATION INDEX 3, a major quantitative trait locus (QTL) associated with root system penetrability in Arabidopsis


Code for the CVPR 2020 [ORAL] paper "SAM: The Sensitivity of Attribution Methods to Hyperparameters"

Deep Residual Learning for Image Recognition

Going Deeper with Convolutions

Adversarial Robustness as a Prior for Learned Representations


Neural Temporal Point Processes For Modelling Electronic Health Records

Modeling Inter-Dependence Between Time and Mark in Multivariate Temporal Point Processes

Proceedings of the 31st ACM International Conference on Information & Knowledge Management

Concurrent Multi-Label Prediction in Event Streams

Proceedings of the AAAI Conference on Artificial Intelligence

On the Predictive Accuracy of Neural Temporal Point Process Models for Continuous-time Event Data


Rank Minimization for Snapshot Compressive Imaging (TPAMI'19)

Snapshot Compressive Imaging: Theory, Algorithms, and Applications

Plug-and-Play Algorithms for Large-scale Snapshot Compressive Imaging

Non-local Meets Global: An Iterative Paradigm for Hyperspectral Image Restoration

Plug-and-Play Algorithms for Video Snapshot Compressive Imaging

Fast Hyperspectral Image Recovery via Non-iterative Fusion of Dual-Camera Compressive Hyperspectral Imaging


Zero-shot dialogue state tracking (DST)

Leveraging Slot Descriptions for Zero-Shot Cross-Domain Dialogue State Tracking

Zero-Shot Dialogue State Tracking via Cross-Task Transfer


A Python library for blind source separation.

Stable and fast update rules for independent vector analysis based on auxiliary function technique

Workshop on Applications of Signal Processing to Audio and Acoustics

Determined Blind Source Separation Unifying Independent Vector Analysis and Nonnegative Matrix Factorization

IEEE/ACM Transactions on Audio, Speech, and Language Processing

An auxiliary-function approach to online independent vector analysis for real-time blind source separation

Joint Workshop on Hands-free Speech Communication and Microphone Arrays

Fast Multichannel Source Separation Based on Jointly Diagonalizable Spatial Covariance Matrices


Code for paper "Poisoned classifiers are not only backdoored, they are fundamentally broken"

BadNets: Identifying Vulnerabilities in the Machine Learning Model Supply Chain

Hidden Trigger Backdoor Attacks

Denoised Smoothing: A Provable Defense for Pretrained Classifiers


Transformer-XL: Attentive Language Models Beyond a Fixed-Length Context

Regularizing and Optimizing LSTM Language Models

Creative GANs for generating poems, lyrics, and metaphors


GTNet:Guided Transformer Network for Detecting Human-Object Interactions

VSGNet: Spatial Attention Network for Detecting Human Object Interactions Using Graph Convolutions

HOI Analysis: Integrating and Decomposing Human-Object Interaction

ConsNet: Learning Consistency Graph for Zero-Shot Human-Object Interaction Detection

MM '20: PROCEEDINGS OF THE 28TH ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA


The official Tensorflow implementation for ICCV'19 paper 'Attributing Fake Images to GANs: Learning and Analyzing GAN Fingerprints'

Leveraging Frequency Analysis for Deep Fake Image Recognition

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

RepMix: Representation Mixing for Robust Attribution of Synthesized Images

Towards Robust Gan-Generated Image Detection: A Multi-View Completion Representation


Temporal-Relational CrossTransformers (CVPR 2021)

Temporal-Relational CrossTransformers for Few-Shot Action Recognition

Rethinking matching-based few-shot action recognition

Few-shot Action Recognition via Intra- and Inter-Video Information Maximization


This repository contains the codes to run the nuclei segmentation pipeline of the BIOMAG group inspired by Kaggle's Data Science Bowl 2018 competition

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

A deep learning framework for nucleus segmentation using image style transfer

Regression plane concept for analysing continuous cellular processes with machine learning


FuSeBMC is a novel Energy-Efficient Test Generator that exploits fuzzing and BMC engines to detect security vulnerabilities in real-world C programs.

FuSeBMC: A White-Box Fuzzer for Finding Security Vulnerabilities in C Programs (Competition Contribution)

FuSeBMC v.4: Smart Seed Generation for Hybrid Fuzzing

FuSeBMC v4: Improving code coverage with smart seeds via BMC, fuzzing and static analysis


DTVNet: Dynamic Time-lapse Video Generation via Single Still Image, ECCV'20 Spotlight.

Learning to Generate Time-Lapse Videos Using Multi-Stage Dynamic Generative Adversarial Networks

Stochastic Image-to-Video Synthesis using cINNs


Code for "Unpaired Sentiment-to-Sentiment Translation: A Cycled Reinforcement Learning Approach" (ACL  2018)

Mask and Infill: Applying Masked Language Model for Sentiment Transfer

International Joint Conference on Artificial Intelligence

"Mask and Infill" : Applying Masked Language Model to Sentiment Transfer


UniAudio: An Audio Foundation Model Toward Universal Audio Generation

Neural Target Speech Extraction: An Overview

Listen only to me! How well can target speech extraction handle false alarms?

Target Speech Extraction with Conditional Diffusion Model

Weakly-Supervised Speech Pre-training: A Case Study on Target Speech Recognition

Typing to Listen at the Cocktail Party: Text-Guided Target Speaker Extraction

Target Speech Extraction with Pre-trained Self-supervised Learning
  Models

Beamformer-Guided Target Speaker Extraction

Speaker-Aware Mixture of Mixtures Training for Weakly Supervised Speaker Extraction

Analysis of Impact of Emotions on Target Speech Extraction and Speech Separation


Generates input data for energy models on renewable energy in arbitrary world regions using public datasets. Written in Julia 1.x.

An autopilot for energy models -- automatic generation of renewable supply curves, hourly capacity factors and hourly synthetic electricity demand for arbitrary world regions

OSeMOSYS Global: An open-source, open data global electricity system model generator

MENA compared to Europe: The influence of land use, nuclear power, and transmission expansion on renewable electricity system costs


Data and analysis scripts for our Embryo Timecourse paper.

Stalled developmental programs at the root of pediatric brain tumors

Transcriptomic entropy benchmarks stem cell-derived cardiomyocyte maturation against endogenous tissue at single cell level

Defining totipotency using criteria of increasing stringency

A single-cell time-lapse of mouse prenatal development from gastrula to birth


Official PyTorch implementation of "SPACE: Unsupervised Object-Oriented Scene Representation via Spatial Attention and Decomposition"

SlotFormer: Unsupervised Visual Dynamics Simulation with Object-Centric Models

Unsupervised Object Learning via Common Fate

Refactoring Policy for Compositional Generalizability using Self-Supervised Object Proposals

Unsupervised Learning of Compositional Scene Representations from Multiple Unspecified Viewpoints

GMAIR: Unsupervised Object Detection Based on Spatial Attention and Gaussian Mixture Model

Computational intelligence and neuroscience


The official implementation of ACL 2020, "Logic-Guided Data Augmentation and Regularization for Consistent Question Answering".

PIQA: Reasoning about Physical Commonsense in Natural Language

Fine-Tuning Pretrained Language Models: Weight Initializations, Data Orders, and Early Stopping

WIQA: A dataset for "What if..." reasoning over procedural text


Safety Score for Pre-Trained Language Models

Baichuan 2: Open Large-scale Language Models

Textbooks Are All You Need II: phi-1.5 technical report

An Empirical Study of Metrics to Measure Representational Harms in Pre-Trained Language Models

Examining Forgetting in Continual Pre-training of Aligned Large Language Models


NanigoNet — Language detector for code-mixed input supporting 150+19 human+programming languages using deep neural networks

Deep Residual Learning for Image Recognition

Language Modeling with Gated Convolutional Networks

GitHub Typo Corpus: A Large-Scale Multilingual Dataset of Misspellings and Grammatical Errors


A multi-planet Radial Velocity and Transit modelling software

pyaneti: a fast and powerful software suite for multiplanet radial velocity and transit fitting

Monthly notices of the Royal Astronomical Society

The transiting multi-planet system HD3167: a 5.7 MEarth Super-Earth and a 8.3 MEarth mini-Neptune

PYANETI - II. A multidimensional Gaussian process approach to analysing spectroscopic time-series

Two Intermediate-mass Transiting Brown Dwarfs from the TESS Mission

Super-Earth of 8 Mearth in a 2.2-day orbit around the K5V star K2-216

One year of AU Mic with HARPS – I. Measuring the masses of the two transiting planets

Monthly Notices of the Royal Astronomical Society

Greening of the Brown Dwarf Desert. EPIC 212036875 b – a 51 M_J object in a 5 day orbit around an F7 V star

K2-139 b: A low-mass warm Jupiter on a 29-d orbit transiting an active K0 V star

Detection and Doppler monitoring of K2-285 (EPIC 246471491), a system of four transiting planets smaller than Neptune

Statistical Methods for Exoplanet Detection with Radial Velocities

Annual Review of Statistics and Its Application


Code for the paper "Offline Reinforcement Learning as One Big Sequence Modeling Problem"

Bootstrapped Transformer for Offline Reinforcement Learning

Efficient Planning in a Compact Latent Action Space

Addressing Optimism Bias in Sequence Modeling for Reinforcement Learning

Deep Generative Models for Decision-Making and Control


Optimized Utilities for PyTorch

Datamodels: Predicting Predictions from Training Data

TRAK: Attributing Model Behavior at Scale

Characterizing Datapoints via Second-Split Forgetting

Rethinking Backdoor Attacks

ModelDiff: A Framework for Comparing Learning Algorithms

A Simple and Efficient Baseline for Data Attribution on Images


Data Programming by Demonstration (DPBD) for Document Classification

Snorkel: Rapid Training Data Creation with Weak Supervision

Data Programming: Creating Large Training Sets, Quickly

Ruler: Data Programming by Demonstration for Document Labeling

Data Programming by Demonstration: A Framework for Interactively Learning Labeling Functions


Code accompanying the paper Pretraining Language Models with Human Preferences

RealToxicityPrompts: Evaluating Neural Toxic Degeneration in Language Models


AAAI 2020 - ASAP: Adaptive Structure Aware Pooling for Learning Hierarchical Graph Representations

State of the Art and Potentialities of Graph-level Learning

Learning to Pool in Graph Neural Networks for Extrapolation


ChatMed: 中文医疗大模型，善于在线回答患者/用户的日常医疗相关问题！

CMB: A Comprehensive Medical Benchmark in Chinese

PromptCBLUE: A Chinese Prompt Tuning Benchmark for the Medical Domain

Datasets for Large Language Models: A Comprehensive Survey

AI Hospital: Benchmarking Large Language Models in a Multi-agent Medical Interaction Simulator

MedBench: A Large-Scale Chinese Benchmark for Evaluating Medical Large Language Models

Overview of the PromptCBLUE Shared Task in CHIP2023

A Survey on Medical Large Language Models: Technology, Application,
  Trustworthiness, and Future Directions

A Survey on Large Language Models from General Purpose to Medical
  Applications: Datasets, Methodologies, and Evaluations

Text2MDT: Extracting Medical Decision Trees from Medical Texts

Quantifying Self-diagnostic Atomic Knowledge in Chinese Medical Foundation Model: A Computational Analysis


Toy datasets to evaluate algorithms for domain generalization and invariance learning.

Invariance Principle Meets Information Bottleneck for Out-of-Distribution Generalization

When is invariance useful in an Out-of-Distribution Generalization problem ?

Linear unit-tests for invariance discovery

Decorr: Environment Partitioning for Invariant Learning and OOD Generalization

Counterfactual Supervision-based Information Bottleneck for Out-of-Distribution Generalization

Invariant-Feature Subspace Recovery: A New Class of Provable Domain Generalization Algorithms


Implementation of the paper "NetGAN: Generating Graphs via Random Walks".

A Comprehensive Survey on Graph Neural Networks

IEEE transactions on neural networks and learning systems

Graph Neural Networks: A Review of Methods and Applications

Deep Learning on Graphs: A Survey

Deep Graph Generators: A Survey

State of the Art and Potentialities of Graph-level Learning

GenCAT: Generating Attributed Graphs with Controlled Relationships between Classes, Attributes, and Topology

SaGess: Sampling Graph Denoising Diffusion Model for Scalable Graph Generation

FLOWGEN: Fast and slow graph generation

Generating a Doppelganger Graph: Resembling but Distinct


[MedIA2022]WORD: A large scale dataset, benchmark and clinical applicable study for abdominal organ segmentation from CT image

WORD: Revisiting Organs Segmentation in the Whole Abdominal Region.

One Model to Rule them All: Towards Universal Segmentation for Medical Images with Text Prompts

UFPS: A unified framework for partially annotated federated segmentation in heterogeneous data distribution


Implementation of Federated Learning to Person Re-identification (Code for ACMMM 2020 paper)

Performance Optimization of Federated Person Re-identification via Benchmark Analysis

EasyFL: A Low-Code Federated Learning Platform for Dummies

Optimizing Performance of Federated Person Re-identification: Benchmarking and Analysis

ACM Transactions on Multimedia Computing, Communications, and Applications


Code of NIPS18 Paper: BRITS: Bidirectional Recurrent Imputation for Time Series

SAITS: Self-Attention-based Imputation for Time Series

Filling the G_ap_s: Multivariate Time Series Imputation by Graph Neural Networks

A Survey on Principles, Models and Methods for Learning from Irregularly Sampled Time Series: From Discretization to Attention and Invariance.

Networked Time Series Imputation via Position-aware Graph Enhanced Variational Autoencoders

Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining

Gradient Importance Learning for Incomplete Observations

PulseImpute: A Novel Benchmark Task for Pulsative Physiological Signal Imputation

SRI-EEG: State-Based Recurrent Imputation for EEG Artifact Correction

Graph-based Virtual Sensing from Sparse and Partial Multivariate
  Observations


Efficient baselines for autocurricula in JAX.

Domain Randomization for Transferring Deep Neural Networks from Simulation to the Real World

Emergent Complexity and Zero-shot Transfer via Unsupervised Environment Design

Prioritized Level Replay

Evolving Curricula with Regret-Based Environment Design

Replay-Guided Adversarial Environment Design

minimax: Efficient Baselines for Autocurricula in JAX


Pipeline for the Semantic Segmentation (i.e., classification) of Remote Sensing Imagery

Low-Shot Learning for the Semantic Segmentation of Remote Sensing Imagery

A tutorial on modelling and inference in undirected graphical models for hyperspectral image analysis

EarthMapper: A Tool Box for the Semantic Segmentation of Remote Sensing Imagery


ChartQA: A Benchmark for Question Answering about Charts with Visual and Logical Reasoning

Beyond LLaVA-HD: Diving into High-Resolution Large Multimodal Models

Chart-based Reasoning: Transferring Capabilities from LLMs to VLMs

Do LLMs Work on Charts? Designing Few-Shot Prompts for Chart Question Answering and Summarization

Program Synthesis for Complex QA on Charts via Probabilistic Grammar Based Filtered Iterative Back-Translation

Findings of the Association for Computational Linguistics: EACL 2023

Enhancing Question Answering on Charts Through Effective Pre-training Tasks


The PyTorch implementation of STGCN.

Spatio-Temporal Graph Convolutional Networks: A Deep Learning Framework for Traffic Forecasting

PROCEEDINGS OF THE TWENTY-SEVENTH INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE

Deep learning for dynamic graphs: models and benchmarks

Graph-Free Learning in Graph-Structured Data: A More Efficient and Accurate Spatiotemporal Learning Perspective

Survey of Graph Neural Network for Internet of Things and NextG Networks


An Unsupervised Distance Learning Framework for Multimedia Retrieval

Multimedia Retrieval Through Unsupervised Hypergraph-Based Manifold Ranking

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

A BFS-Tree of ranking references for unsupervised manifold learning

Efficient Rank-Based Diffusion Process with Assured Convergence

Rank Flow Embedding for Unsupervised and Semi-Supervised Manifold Learning


Learning multiple visual domains with residual adapters

Efficient parametrization of multi-domain deep neural networks

Multi-domain Learning for Updating Face Anti-spoofing Models


ICLR 2022 Paper, SOTA Table Pre-training Model, TAPEX: Table Pre-training via Learning a Neural SQL Executor

BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension

On the Potential of Lexico-logical Alignments for Semantic Parsing to SQL Queries

Table-based Fact Verification with Self-labeled Keypoint Alignment

International Conference on Computational Linguistics


EEG Pre-Processing Pipeline

The HAPPE plus Event-Related (HAPPE+ER) software: A standardized preprocessing pipeline for event-related potential analyses

HAPPILEE: HAPPE In Low Electrode Electroencephalography, a standardized pre-processing software for lower density recordings

The HAPPE plus Event-Related (HAPPE+ER) Software: A Standardized Processing Pipeline for Event-Related Potential Analyses

HAPPILEE: The Harvard Automated Processing Pipeline In Low Electrode Electroencephalography, a standardized software for low density EEG and ERP data


Large scale Blast Score Ratio (BSR) analysis

Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics

Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives

Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation

Distribution of papA and papG Variants among Escherichia coli Genotypes: Association with Major Extraintestinal Pathogenic Lineages

International Journal of Molecular Sciences


Liver transcriptomic networks reveal main biological processes associated with feed efficiency in beef cattle

Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation

Proceedings of the National Academy of Sciences of the United States of America

SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing

International Conference on Bioinformatics

Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda

High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing

The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family

Arbuscular Mycorrhizal Symbiosis Leads to Differential Regulation of Drought-Responsive Genes in Tissue-Specific Root Cells of Common Bean

Diapause in a tropical oil-collecting bee: molecular basis unveiled by RNA-Seq

Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes

Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis


This repository contains data used in the NAACL 2015 paper "Personalized Page Rank for Named Entity Disambiguation" by Maria Pershina, Yifan He, Ralph Grishman.

North American Chapter of the Association for Computational Linguistics

ELDEN: Improved Entity Linking Using Densified Knowledge Graphs

Alleviating Poor Context with Background Knowledge for Named Entity Disambiguation

PROCEEDINGS OF THE 54TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS, VOL 1

SpEL: Structured Prediction for Entity Linking

Entity Linking with a Paraphrase Flavor


Can we use Planet high-resolution imagery and machine learning to assess snow cover?


soliDMFT allows to perform charge self-consistent DFT+DMFT calculations by utilizing the triqs library and VASP.

Effect of charge self-consistency in DFT+DMFT calculations for complex transition metal oxides

Oxygen vacancies in strontium titanate: A DFT+DMFT study

Correlation-Induced Octahedral Rotations in SrMoO_3

Charge disproportionation and Hund's insulating behavior in a five-orbital Hubbard model applicable to d^4 perovskites

Charge self-consistency and double-counting in DFT+DMFT calculations for complex transition metal oxides


Code and data of the EMNLP 2022 paper "Why Should Adversarial Perturbations be Imperceptible? Rethink the Research Paradigm in Adversarial NLP".

TARGET: Template-Transferable Backdoor Attack Against Prompt-based NLP Models via GPT4

On the Intrinsic Self-Correction Capability of LLMs: Uncertainty and Latent Concept


Do What The F*ck You Want To Public License

A very long list of English profanity.

A Telegram Corpus for Hate Speech, Offensive Language, and Online Harm

The Telegram Chronicles of Online Harm

Battling Hateful Content in Indic Languages HASOC '21

Not All Counterhate Tweets Elicit the Same Replies: A Fine-Grained Analysis

Proceedings of the 12th Joint Conference on Lexical and Computational Semantics (*SEM 2023)

Detox Browser -- Towards Filtering Sensitive Content On the Web


Oink, an implementation of modern parity game solvers

Oink: An Implementation and Evaluation of Modern Parity Game Solvers

Tools and Algorithms for Construction and Analysis of Systems

Attracting Tangles to Solve Parity Games

Simple Fixpoint Iteration To Solve Parity Games

A Parity Game Tale of Two Counters


Minimax Estimation of Conditional Moment Models

On Instrumental Variable Regression for Deep Offline Policy Evaluation

Instrumental Variables in Causal Inference and Machine Learning: A Survey


Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks

SSD: Single Shot MultiBox Detector

YOLOv3: An Incremental Improvement

End-to-End Object Detection with Transformers

Unmanned Aerial Vehicle Visual Detection and Tracking using Deep Neural Networks: A Performance Benchmark


Calculates the Word Error Rate between two text files

Dialect Text Normalization to Normative Standard Finnish

Empirical Methods in Natural Language Processing

Dialect-to-Standard Normalization: A Large-Scale Multilingual Evaluation

Findings of the Association for Computational Linguistics: EMNLP 2023

Murreviikko - A Dialectologically Annotated and Normalized Dataset of Finnish Tweets

Workshop on NLP for Similar Languages, Varieties and Dialects

Help from the Neighbors: Estonian Dialect Normalization Using a Finnish Dialect Generator

Workshop on Deep Learning Approaches for Low-Resource Natural Language Processing

Dialect Representation Learning with Neural Dialect-to-Standard Normalization

Automated Prediction of Medieval Arabic Diacritics


USAD: UnSupervised Anomaly Detection on Multivariate Time Series

OneShotSTL: One-Shot Seasonal-Trend Decomposition For Online Time Series Anomaly Detection And Forecasting

Generative Optimization Networks for Memory Efficient Data Generation

A Survey of Time Series Anomaly Detection Methods in the AIOps Domain

Time Series Anomaly Detection via Reinforcement Learning-Based Model Selection

LPC-AD: Fast and Accurate Multivariate Time Series Anomaly Detection via Latent Predictive Coding


This repository implements our ACL Findings 2022 research paper RelationPrompt: Leveraging Prompts to Generate Synthetic Data for Zero-Shot Relation Triplet Extraction. The goal of Zero-Shot Relation Triplet Extraction (ZeroRTE) is to extract relation triplets of the format (head entity, tail entity, relation), despite not having annotated data for the test relation labels.

Schema-aware Reference as Prompt Improves Data-Efficient Knowledge Graph Construction


PoSeiDon: positive selection detection and recombination analysis pipeline

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Evolution and Antiviral Specificities of Interferon-Induced Mx Proteins of Bats against Ebola, Influenza, and Other RNA Viruses

PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection

Determining the International Spread of B.1.1.523 SARS-CoV-2 Lineage with a Set of Mutations Highly Associated with Reduced Immune Neutralization

Determining international spread of novel B.1.1.523 SARS-CoV-2 lineage


QE-GIPAW for Quantum-Espresso (official repository)

Probing the Coherence of Solid-State Qubits at Avoided Crossings

Substrate-controlled dynamics of spin qubits in low dimensional van der Waals materials

Depth-dependent study of time-reversal symmetry-breaking in the kagome
  superconductor AV_3Sb_5


The second data release from the European Pulsar Timing Array

KiDS-1000 Cosmology: Multi-probe weak gravitational lensing and spectroscopic galaxy clustering constraints

Dark Energy Survey Year 3 results: Cosmology from cosmic shear and robustness to modeling uncertainty

Assessing tension metrics with dark energy survey and Planck data

Monthly Notices of the Royal Astronomical Society

Dark Energy Survey Year 3 results: Cosmological constraints from galaxy clustering and galaxy-galaxy lensing using the MagLim lens sample

Cosmological implications of the full shape of anisotropic clustering measurements in BOSS and eBOSS

Non-Gaussian estimates of tensions in cosmological parameters

Comparing recent PTA results on the nanohertz stochastic gravitational wave background

Hyper Suprime-Cam Year 3 results: Cosmology from galaxy clustering and weak lensing with HSC and SDSS using the emulator based halo model

Comparing Recent Pulsar Timing Array Results on the Nanohertz Stochastic Gravitational-wave Background


V2X simulator

Performance Analysis of Sidelink 5G-V2X Mode 2 Through an Open-Source Simulator

A Methodology for Abstracting the Physical Layer of Direct V2X Communications Technologies

Performance analysis of IEEE 802.11p preamble insertion in C-V2X sidelink signals for co-channel coexistence

Adaptive Repetition Strategies in IEEE 802.11bd V2X Networks

Analysis of Co-Channel Coexistence Mitigation Methods Applied to IEEE 802.11p and 5G NR-V2X Sidelink


OpenP5: An Open-Source Platform for Developing, Training, and Evaluating LLM-based Recommender Systems

Recommendation as Language Processing (RLP): A Unified Pretrain, Personalized Prompt & Predict Paradigm (P5)

How to Index Item IDs for Recommendation Foundation Models

Proceedings of the Annual International ACM SIGIR Conference on Research and Development in Information Retrieval in the Asia Pacific Region

SLMRec: Empowering Small Language Models for Sequential Recommendation


[ICLR 2021 Spotlight] Code release for "Long-tailed Recognition by Routing Diverse Distribution-Aware Experts."

CUDA: Curriculum of Data Augmentation for Long-Tailed Recognition

Decoupled Training for Long-Tailed Classification With Stochastic Representations


10x Genomics Reads Simulator

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads

Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding


记录GitHub热门仓库，每小时更新，按天归档。

High-Resolution Image Synthesis with Latent Diffusion Models

Masked Autoencoders Are Scalable Vision Learners

DreamBooth: Fine Tuning Text-to-Image Diffusion Models for Subject-Driven Generation

You Only Learn One Representation: Unified Network for Multiple Tasks

DiffusionDet: Diffusion Model for Object Detection


Parity and time-reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks

pystablemotifs: Python library for attractor identification and control in Boolean networks

Global stabilizing control of large-scale biomolecular regulatory networks

Phenotype control techniques for Boolean gene regulatory networks

bioRxiv : the preprint server for biology

Translocating proteins compartment-specifically alter the fate of epithelial-mesenchymal transition in a compartmentalized Boolean network model


Python 2.7 implementation of network-based stratification (NBS) algorithm from Hofree et al (Nature Methods 2013)

Unsupervised Multi-Omics Data Integration Methods: A Comprehensive Review

pyNBS: a Python implementation for network-based stratification of tumor mutations

Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment


Python package for dealing with the Halo Model

The galaxy-halo connection in the VIDEO survey at 0.5 < z < 1.7

TheHaloMod: An online calculator for the halo model

Intensity mapping cross-correlations II: HI halo models including shot noise

The halo model for cosmology: a pedagogical review

The environment and host haloes of the brightest z ∼ 6 Lyman-break galaxies

Extracting H I astrophysics from interferometric intensity mapping

Subaru High-z Exploration of Low-luminosity Quasars (SHELLQs). XVIII. The Dark Matter Halo Mass of Quasars at z ∼ 6

Comparing galaxy clustering in Horizon-AGN simulated light-cone mocks and VIDEO observations


Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium.  These files can be used as standard resource of BED files for use with GA4GH benchmarking tools such as hap.py to stratify true positive, false positive, and false negative variant calls based on genomic context.

A draft human pangenome reference

Best practices for benchmarking germline small-variant calls in human genomes

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

Application of long-read sequencing to elucidate complex pharmacogenomic regions: a proof of principle

Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment

GCparagon: evaluating and correcting GC biases in cell-free DNA at the fragment level


This is a modified version of the L-PICOLA code extending the COLA approach for simulating cosmological structure formation to theories that exhibit scale-dependent growth. It can compute matter power-spectra (CDM and total), redshift-space multipole power-spectra P0,P2,P4 and do halofinding on the fly. It can also include the effects of massive neutrinos on structure formation.

COLA with scale-dependent growth: applications to screened modified gravity models

Journal of Cosmology and Astroparticle Physics

COLA with massive neutrinos

Cosmological constraints on the gravitational constant

Euclid: Modelling massive neutrinos in cosmology – a code comparison

Assessing non-linear models for galaxy clustering III: theoretical accuracy for stage IV surveys

Nonlinear cosmological structure with ultralight bosons via modified gravity

Sesame: A power spectrum emulator pipeline for beyond-ΛCDM models


paprica - PAthway PRediction by phylogenetIC plAcement

Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula

Sensitivity of the mangrove-estuarine microbial community to aquaculture effluent

Machine Learning Predicts Biogeochemistry from Microbial Community Structure in a Complex Model System

Understanding Microbial Community Dynamics in Up-Flow Bioreactors to Improve Mitigation Strategies for Oil Souring

From microbial community structure to metabolic inference using paprica

Detection of Sulfate-Reducing Bacteria as an Indicator for Successful Mitigation of Sulfide Production


SiSEC MUS 2018 Submission System

Demucs: Deep Extractor for Music Sources with extra unlabeled data remixed

Investigating U-Nets with various Intermediate Blocks for Spectrogram-based Singing Voice Separation

Denoising Auto-encoder with Recurrent Skip Connections and Residual Regression for Music Source Separation

Dilated Convolution with Dilated GRU for Music Source Separation


Accurate Condition Synthesis

Precise Condition Synthesis for Program Repair

Attention Please: Consider Mockito when Evaluating Newly Proposed Automated Program Repair Techniques

Multi-Location Program Repair Strategies Learned from Successful Experience (S)


Simple code to read mangle masks, calculate ids and weights, and generate random points

Updated results on the galaxy–halo connection from satellite kinematics in SDSS

The dependence of galaxy clustering on tidal environment in the Sloan Digital Sky Survey

Brightest galaxies as halo centre tracers in SDSS DR7

Maturing satellite kinematics into a competitive probe of the galaxy–halo connection

Full forward model of galaxy clustering statistics with AbacusSummit lightcones


R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

A single-cell atlas of the human healthy airways

Resolving the immune landscape of human prostate at a single-cell level in health and cancer

A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche

Aging-related olfactory loss is associated with olfactory stem cell transcriptional alterations in humans

Selective Vulnerability of Layer 5a Corticostriatal Neurons in Huntington’s Disease

Combined lineage tracing and scRNA-seq reveals unexpected first heart field predominance of human iPSC differentiation

Effects of hyperinsulinemia on pancreatic cancer development and the immune microenvironment revealed through single-cell transcriptomics

Drugs of abuse hijack a mesolimbic pathway that processes homeostatic need


Tools for producing high-quality hourly generation and emissions data for U.S. electric grids


scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network

From single- to multi-omics: future research trends in medicinal plants

Deep Learning in Single-Cell Analysis

Reference-free Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network


A JavaScript bilingual text realizer for web development

JSrealB: A Bilingual Text Realizer for Web Programming

The jsRealB Text Realizer: Organization and Use Cases -- Revised version


A Julia/JuMP Package for Maximizing Algebraic Connectivity of Undirected Weighted Graphs

On maximizing algebraic connectivity of networks for various engineering applications

Synthesizing Robust Communication Networks for Unmanned Aerial Vehicles With Resource Constraints

Volume 1: Adaptive Control; Advanced Vehicle Propulsion Systems; Aerospace Systems; Autonomous Systems; Battery Modeling; Biochemical Systems; Control Over Networks; Control Systems Design; Cooperativ

Optimal Robust Network Design: Formulations and Algorithms for Maximizing Algebraic Connectivity


Deep generative models of 3D grids for structure-based drug discovery

Generating 3D molecules conditional on receptor binding sites with deep generative models

Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models

Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models

Docking-based generative approaches in the search for new drug candidates

Learning Subpocket Prototypes for Generalizable Structure-based Drug Design


The DRAT-trim proof checker

Guiding High-Performance SAT Solvers with Unsat-Core Predictions

Efficient Certified RAT Verification

Efficient Verified (UN)SAT Certificate Checking

Efficient Certified Resolution Proof Checking

Trimming Graphs Using Clausal Proof Optimization

Unsatisfiability Proofs for Distributed Clause-Sharing SAT Solvers

Tools and Algorithms for the Construction and Analysis of Systems

Towards the shortest DRAT proof of the Pigeonhole Principle


Working directory for dynamics learning for experimental robots.

Deep Reinforcement Learning in a Handful of Trials using Probabilistic Dynamics Models

Neural Network Dynamics for Model-Based Deep Reinforcement Learning with Model-Free Fine-Tuning

PIPPS: Flexible Model-Based Policy Search Robust to the Curse of Chaos


Program for generating load curves for residential consumers. Agentbased and extremly detailed.

LoadProfileGenerator: An Agent-Based Behavior Simulation for Generating Residential Load Profiles

The Role of Hydrogen in German Residential Buildings


Intelligence Task Ontology (ITO)

A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks

A critical analysis of metrics used for measuring progress in artificial intelligence

Mapping global dynamics of benchmark creation and saturation in artificial intelligence

A global analysis of metrics used for measuring performance in natural language processing

Benchmark datasets driving artificial intelligence development fail to capture the needs of medical professionals


Train neural networks based on geographic species occurrences, environmental data and existing IUCN Red List assessments to predict the conservation status of "Not Evaluated" species, for any taxon or geographic region of interest. https://iucnn.github.io/IUCNN/

Automated conservation assessment of the orchid family with deep learning

Zenodo (CERN European Organization for Nuclear Research)

IUCNN – Deep learning approaches to approximate species' extinction risk


PyTorch implementation of COVID-Net https://github.com/lindawangg/COVID-Net

COVID-Net: A Tailored Deep Convolutional Neural Network Design for Detection of COVID-19 Cases from Chest X-Ray Images

COVID-CT-Dataset: A CT Scan Dataset about COVID-19

Artificial Intelligence applied to chest X-Ray images for the automatic detection of COVID-19. A thoughtful evaluation approach

CovFrameNet: An Enhanced Deep Learning Framework for COVID-19 Detection

IEEE access : practical innovations, open solutions

Ebola Optimization Search Algorithm (EOSA): A new metaheuristic algorithm based on the propagation model of Ebola virus disease


Streaming over lightweight data transformations

Multimodal Machine Learning-based Knee Osteoarthritis Progression Prediction from Plain Radiographs and Clinical Data

KNEEL: Knee Anatomical Landmark Localization Using Hourglass Networks

Semixup: In- and Out-of-Manifold Regularization for Deep Semi-Supervised Knee Osteoarthritis Severity Grading from Plain Radiographs

Automatic Grading of Individual Knee Osteoarthritis Features in Plain Radiographs using Deep Convolutional Neural Networks

Automated analysis of rabbit knee calcified cartilage morphology using micro‐computed tomography and deep learning

Deep-Learning for Tidemark Segmentation in Human Osteochondral Tissues Imaged with Micro-computed Tomography

DALib: A Curated Repository of Libraries for Data Augmentation in Computer Vision


Chatbot Arena meets multi-modality! Multi-Modality Arena allows you to benchmark vision-language models side-by-side while providing images as inputs. Supports MiniGPT-4, LLaMA-Adapter V2, LLaVA, BLIP-2, and many more!

Judging LLM-as-a-Judge with MT-Bench and Chatbot Arena

LVLM-eHub: A Comprehensive Evaluation Benchmark for Large Vision-Language Models

Tiny LVLM-eHub: Early Multimodal Experiments with Bard

OmniMedVQA: A New Large-Scale Comprehensive Evaluation Benchmark for
  Medical LVLM

GMAI-MMBench: A Comprehensive Multimodal Evaluation Benchmark Towards General Medical AI


A comprehensive library for implementing LLMs, including a unified training pipeline and comprehensive model evaluation.

What Makes Good In-Context Examples for GPT-3?

Fantastically Ordered Prompts and Where to Find Them: Overcoming Few-Shot Prompt Order Sensitivity

Least-to-Most Prompting Enables Complex Reasoning in Large Language Models

Large Language Models Are Human-Level Prompt Engineers

PAL: Program-aided Language Models

GPQA: A Graduate-Level Google-Proof Q&A Benchmark


A Python library that encapsulates various methods for neuron interpretation and analysis in Deep NLP models.

What Is One Grain of Sand in the Desert? Analyzing Individual Neurons in Deep NLP Models

NeuroX: A Toolkit for Analyzing Individual Neurons in Neural Networks

Discovering Salient Neurons in Deep NLP Models

NeuroX Library for Neuron Analysis of Deep NLP Models

Redundancy and Concept Analysis for Code-trained Language Models


A Cloud Model for Exoplanets and Brown Dwarfs

Early Release Science of the exoplanet WASP-39b with JWST NIRISS

JWST-TST DREAMS: Quartz Clouds in the Atmosphere of WASP-17b

Cloudy and Cloud-free Thermal Phase Curves with PICASO: Applications to WASP-43b

Cloud Parameterizations and their Effect on Retrievals of Exoplanet Reflection Spectroscopy

The Emission Spectrum of the Hot Jupiter WASP-79b from HST/WFC3

Data availability and requirements relevant for the Ariel space mission
  and other exoplanet atmosphere applications


Utilities for astronomical spectral energy distributions

Stellar Population Inference with Prospector

The Astrophysical Journal Supplement Series

High-redshift JWST predictions from IllustrisTNG: dust modelling and galaxy luminosity functions

Monthly notices of the Royal Astronomical Society

High-redshift JWST predictions from IllustrisTNG: II. Galaxy line and continuum spectral indices and dust attenuation curves

High redshift JWST predictions from IllustrisTNG: III. Infrared luminosity functions, obscured star formation and dust temperature of high-redshift galaxies.

The SPHINX Public Data Release: Forward Modelling High-Redshift JWST Observations with Cosmological Radiation Hydrodynamics Simulations

The Dragonfly Wide Field Survey. II. Accurate Total Luminosities and Colors of Nearby Massive Galaxies and Implications for the Galaxy Stellar-mass Function

Starduster: A Multiwavelength SED Model Based on Radiative Transfer Simulations and Deep Learning


A Coq formalization of information theory and linear error-correcting codes

A trustful monad for axiomatic reasoning with probability and nondeterminism

Extending Equational Monadic Reasoning with Monad Transformers

Formal Adventures in Convex and Conical Spaces


:bullettrain_front: Fast orthogonal polynomial transforms :surfer:

Fast algorithms using orthogonal polynomials

Fast and backward stable transforms between spherical harmonic expansions and bivariate Fourier series

A sparse spectral method on triangles

A fast and accurate algorithm for spherical harmonic analysis on HEALPix grids with applications to the cosmic microwave background radiation

Polynomial and rational measure modifications of orthogonal polynomials via infinite-dimensional banded matrix factorizations

Fast associated classical orthogonal polynomial transforms


A Mechanical Turk Interface (amti)

GENIE: Toward Reproducible and Standardized Human Evaluation for Text Generation

Easy, Reproducible and Quality-Controlled Data Collection with CROWDAQ

EasyTurk: A User-Friendly Interface for High-Quality Linguistic Annotation with Amazon Mechanical Turk

EACL 2021: THE 16TH CONFERENCE OF THE EUROPEAN CHAPTER OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS: PROCEEDINGS OF THE SYSTEM DEMONSTRATIONS


Expectation-Maximization algorithm for Allele-Specific Expression

Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice

Hierarchical Analysis of Multi-mapping RNA-Seq Reads Improves the Accuracy of Allele-specific Expression

Variation in histone configurations correlates with gene expression across nine inbred strains of mice


GPU Framework for Radio Astronomical Image Synthesis

Dust Unveils the Formation of a Mini-Neptune Planet in a Protoplanetary Ring

Long Baseline Observations of the HD 100546 Protoplanetary Disk with ALMA

Multi-GPU maximum entropy image synthesis for radio astronomy

Spirals and Clumps in V960 Mon: Signs of Planet Formation via Gravitational Instability around an FU Ori Star?

Visualizing the Kinematics of Planet Formation

Radio-continuum decrements associated to shadowing from the central warp in transition disc DoAr44


An R package for water quality thresholds and index calculation for British Columbia


An Automata Learning Library Written in Python

AALpy: an active automata learning library

Active vs. Passive: A Comparison of Automata Learning Paradigms for Network Protocols

FlexFringe: Modeling Software Behavior by Learning Probabilistic Automata

Learning Task Automata for Reinforcement Learning using Hidden Markov Models


Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition

Improved Methods for Acetocarmine and Haematoxylin Staining to Visualize Chromosomes in the Filamentous Green Alga Zygnema (Charophyta)

Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage

Comparative genomics of the genus Pseudomonas reveals host- and environment-specific evolution

Metatranscriptomic analysis of the gut microbiome of black soldier fly larvae reared on lignocellulose-rich fiber diets unveils key lignocellulolytic enzymes

Genetic and functional diversity help explain pathogenic, weakly pathogenic, and commensal lifestyles in the genusXanthomonas

Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed

Taxonomic and functional stability overrules seasonality in polar benthic microbiomes

Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco


Repository of the open-source RAMP model for generating multi-energy loads profiles


Web scraper for Atlantic and east Pacific hurricanes and tropical storms


cgat-flow repository

IL-1-driven stromal–neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies

Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism

Interleukin-17A Causes Osteoarthritis-Like Transcriptional Changes in Human Osteoarthritis-Derived Chondrocytes and Synovial Fibroblasts In Vitro

IL-33 promotes anemia during chronic inflammation by inhibiting differentiation of erythroid progenitors

Electrospun Scaffold Micro-Architecture Induces an Activated Transcriptional Phenotype within Tendon Fibroblasts

Frontiers in bioengineering and biotechnology


ImageD11 is a python code for identifying individual grains in spotty area detector X-ray diffraction images.

Scanning 3DXRD Measurement of Grain Growth, Stress, and Formation of Cu6Sn5 around a Tin Whisker during Heat Treatment

Intragranular strain estimation in far-field scanning X-ray diffraction using a Gaussian process

In situ synchrotron X-ray multimodal experiment to study polycrystal plasticity

Per-grain and neighbourhood stress interactions during deformation of a ferritic steel obtained using three-dimensional X-ray diffraction

Non-destructive determination of phase, size, and strain of individual grains in polycrystalline photovoltaic materials

Textures Induced by the Coesite‐Stishovite Transition and Implications for the Visibility of the X‐Discontinuity

CNN-Based Laue Spot Morphology Predictor for Reliable Crystallographic Descriptor Estimation

Implementing and evaluating far-field 3D X-ray diffraction at the I12 JEEP beamline, Diamond Light Source

In situ analysis of cast irons mechanical behaviour using synchrotron x-ray tomography and 3DXRD

IOP Conference Series: Materials Science and Engineering


PopPUNK  (POPulation Partitioning Using Nucleotide Kmers)

Fast and flexible bacterial genomic epidemiology with PopPUNK

The Mobilome-Enriched Genome of the Competence-Deficient Streptococcus pneumoniae BM6001, the Original Host of Integrative Conjugative Element Tn5253, Is Phylogenetically Distinct from Historical Pneumococcal Genomes

Genealogical inference and more flexible sequence clustering using iterative PopPUNK


EQTransformer, a python package for earthquake signal detection and phase picking using AI.

Earthquake transformer—an attentive deep-learning model for simultaneous earthquake detection and phase picking

Comparison of Deep Learning Techniques for the Investigation of a Seismic Sequence: An Application to the 2019, Mw 4.5 Mugello (Italy) Earthquake

Journal of Geophysical Research: Solid Earth

Small Magnitude Events Highlight the Correlation Between Hydraulic Fracturing Injection Parameters, Geological Factors, and Earthquake Occurrence


Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments

Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life

Distribution and Implications of Haloarchaeal Plasmids Disseminated in Self-Encoded Plasmid Vesicles