AddressSanitizer, ThreadSanitizer, MemorySanitizer

NEUZZ: Efficient Fuzzing with Neural Program Smoothing

UNIFUZZ: A Holistic and Pragmatic Metrics-Driven Platform for Evaluating Fuzzers

Intel MPX Explained: An Empirical Study of Intel MPX and Software-based Bounds Checking Approaches

CUP: Comprehensive User-Space Protection for C/C++

PROCEEDINGS OF THE 2018 ACM ASIA CONFERENCE ON COMPUTER AND COMMUNICATIONS SECURITY (ASIACCS'18)

VPLanet: The Virtual Planet Simulator

Publications of the Astronomical Society of the Pacific

Sifu - a cybersecurity awareness platform with challenge assessment and intelligent coach

An Exploratory Analysis of Microcode as a Building Block for System Defenses

Ready, set, Go! Data-race detection and the Go language

Taming the War in Memory: A Resilient Mitigation Strategy Against Memory Safety Attacks in CPS

HyCoR: Fault-Tolerant Replicated Containers Based on Checkpoint and Replay


The Full Process Python Package for Robot Learning from Demonstration and Robot Manipulation

Robot Cooking With Stir-Fry: Bimanual Non-Prehensile Manipulation of Semi-Fluid Objects

SoftGPT: Learn Goal-oriented Soft Object Manipulation Skills by Generative Pre-trained Heterogeneous Graph Transformer

BiRP: Learning Robot Generalized Bimanual Coordination using Relative Parameterization Method on Human Demonstration


CARS is a dedicated and open source 3D tool to produce Digital Surface Models from satellite imaging by photogrammetry.

A NEW SATELLITE IMAGERY STEREO PIPELINE DESIGNED FOR SCALABILITY, ROBUSTNESS AND PERFORMANCE

ISPRS annals of the photogrammetry, remote sensing and spatial information sciences

IMPROVING PAIRWISE DSM WITH 3SGM: A SEMANTIC SEGMENTATION FOR SGM USING AN AUTOMATICALLY REFINED NEURAL NETWORK

XXIV ISPRS CONGRESS IMAGING TODAY, FORESEEING TOMORROW, COMMISSION II

AI4GEO: A DATA INTELLIGENCE PLATFORM FOR 3D GEOSPATIAL MAPPING

The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciences


GPU development for the Madgraph5_aMC@NLO event generator software package

Design and engineering of a simplified workflow execution for the MG5aMC event generator on GPUs and vector CPUs

MadFlow: towards the automation of Monte Carlo simulation on GPU for particle physics processes

Developments in Performance and Portability for MadGraph5_aMC@NLO


TCGAbiolinks

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma

Identification of Hub Genes in High-Grade Serous Ovarian Cancer Using Weighted Gene Co-Expression Network Analysis

Medical science monitor : international medical journal of experimental and clinical research

APPBP2 enhances non-small cell lung cancer proliferation and invasiveness through regulating PPM1D and SPOP

CPADS: a web tool for comprehensive pancancer analysis of drug sensitivity


Breakthrough Listen I/O Methods for Python

The Breakthrough Listen Search for Intelligent Life: Observations of 1327 Nearby Stars Over 1.10–3.45GHz

Zenodo (CERN European Organization for Nuclear Research)

The Breakthrough Listen Search for Intelligent Life: Public Data, Formats, Reduction, and Archiving

Analysis of the Breakthrough Listen signal of interest blc1 with a technosignature verification framework

A deep-learning search for technosignatures from 820 nearby stars

The Breakthrough Listen Search for Extraterrestrial Intelligence

Pulsar Based Alternative Timing Source for Grid Synchronization and Operation

Setigen: Simulating Radio Technosignatures for the Search for Extraterrestrial Intelligence


Bayesian learning and inference for state space models

Recurrent Switching Dynamical Systems Models for Multiple Interacting Neural Populations

Neural Latents Benchmark '21: Evaluating latent variable models of neural population activity

Time-varying Autoregression with Low Rank Tensors

Unifying and generalizing models of neural dynamics during decision-making

Limitations of a proposed correction for slow drifts in decision criterion

Propofol Mediated Unconsciousness Disrupts Progression of Sensory Signals through the Cortical Hierarchy

bioRxiv : the preprint server for biology

A layered, hybrid machine learning analytic workflow for mouse risk assessment behavior

Pan-cortical 2-photon mesoscopic imaging and neurobehavioral alignment in awake, behaving mice

Mesoscopic modeling of hidden spiking neurons

Linear Time GPs for Inferring Latent Trajectories from Neural Spike Trains


Tools for working with SAM/BAM data

Pan-cancer whole-genome analyses of metastatic solid tumours

SAMBLASTER: fast duplicate marking and structural variant read extraction

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells

Complete Genome Sequence of Haemophilus influenzae Strain 375 from the Middle Ear of a Pediatric Patient with Otitis Media

Single-Cell Atlas of the Chinese Tongue Sole (Cynoglossus semilaevis) Ovary Reveals Transcriptional Programs of Oogenesis in Fish

Frontiers in cell and developmental biology

Shedding light on dark genes: enhanced targeted resequencing by optimizing the combination of enrichment technology and DNA fragment length

Rap1 regulates TIP60 function during fate transition between two-cell-like and pluripotent states

A Novel Frame-Shift Mutation in SCNN1B Identified in a Chinese Family Characterized by Early-Onset Hypertension

Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China

Animals : an open access journal from MDPI


PyTorch implementation of TabNet paper : https://arxiv.org/pdf/1908.07442.pdf

TabNet: Attentive Interpretable Tabular Learning

TransTab: Learning Transferable Tabular Transformers Across Tables

Predicting and explaining employee turnover intention

International Journal of Data Science and Analytics

SDTR: Soft Decision Tree Regressor for Tabular Data

Towards Cross-Table Masked Pretraining for Web Data Mining

Can Clinical Symptoms and Laboratory Results Predict CT Abnormality? Initial Findings Using Novel Machine Learning Techniques in Children With COVID-19 Infections

Weight Predictor Network with Feature Selection for Small Sample Tabular Biomedical Data

Impact of data-splits on generalization: Identifying COVID-19 from cough and context

Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning

NCART: Neural Classification and Regression Tree for Tabular Data


Jsmn is a world fastest JSON parser/tokenizer. This is the official repo replacing the old one at Bitbucket

SpecFuzz: Bringing Spectre-type vulnerabilities to the surface

Parsing gigabytes of JSON per second

ReplicaTEE: Enabling Seamless Replication of SGX Enclaves in the Cloud

CACTI: Captcha Avoidance via Client-side TEE Integration


Creative Commons Attribution 4.0 International

The consensus GEM for Saccharomyces cerevisiae

Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast

De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts

Genome-scale modeling of yeast metabolism: retrospectives and perspectives

Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production

Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity

Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model

standard-GEM: standardization of open-source genome-scale metabolic models

Author Correction: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models

Saccharomyces cerevisiae as a Host for Chondroitin Production


Toolbox for normative modelling and spatial inference of neuroimaging data. https://pcntoolkit.readthedocs.io/en/latest/

Hierarchical Bayesian Regression for Multi-Site Normative Modeling of Neuroimaging Data

Site effects how-to and when: An overview of retrospective techniques to accommodate site effects in multi-site neuroimaging analyses

A stable and replicable neural signature of lifespan adversity in the adult brain

Revealing Individual Neuroanatomical Heterogeneity in Alzheimer Disease Using Neuroanatomical Normative Modeling

Extreme deviations from the normative model reveal cortical heterogeneity and associations with negative symptom severity in first-episode psychosis from the OPTiMiSE and GAP studies

Estimating cortical thickness trajectories in children across different scanners using transfer learning from normative models

Population-wide cerebellar growth models of children and adolescents

Predictive Clinical Neuroscience Portal (PCNportal): instant online access to research-grade normative models for clinical neuroscientists.

Transformer-based normative modelling for anomaly detection of early schizophrenia


Examples and scripts using Blocks

Blocks and Fuel: Frameworks for deep learning

MED: The LMU System for the SIGMORPHON 2016 Shared Task on Morphological Reinflection

Special Interest Group on Computational Morphology and Phonology Workshop

Single-Model Encoder-Decoder with Explicit Morphological Representation for Reinflection

Neural Morphological Analysis: Encoding-Decoding Canonical Segments

Empirical Methods in Natural Language Processing

Improving Attention Modeling with Implicit Distortion and Fertility for Machine Translation

International Conference on Computational Linguistics

The RWTH Aachen Machine Translation Systems for IWSLT 2017

International Workshop on Spoken Language Translation

A Comparison of Feature-Based and Neural Scansion of Poetry

Recent Advances in Natural Language Processing


[ECCV 2024] Official implementation of the paper "Grounding DINO: Marrying DINO with Grounded Pre-Training for Open-Set Object Detection"

Grounded SAM: Assembling Open-World Models for Diverse Visual Tasks

Segment Any Anomaly without Training via Hybrid Prompt Regularization

Make-A-Protagonist: Generic Video Editing with An Ensemble of Experts

Multimodal Data Curation via Object Detection and Filter Ensembles

Towards Robust Multi-Modal Reasoning via Model Selection


Set of tools to combine multiple power plant databases

PyPSA-Eur: An open optimisation model of the European transmission system

Performing energy modelling exercises in a transparent way the issue of data quality in power plant databases

Classification and Evaluation of Concepts for Improving the Performance of Applied Energy System Optimization Models

PyPSA-Earth. A new global open energy system optimization model demonstrated in Africa

On the means, costs, and system-level impacts of 24/7 carbon-free energy
  procurement


An Open-Source Package for Textual Adversarial Attack.

OpenAttack: An Open-source Textual Adversarial Attack Toolkit

Triggerless Backdoor Attack for NLP Tasks with Clean Labels

On Robustness and Bias Analysis of BERT-Based Relation Extraction

InterroLang: Exploring NLP Models and Datasets through Dialogue-based Explanations

Rethinking Textual Adversarial Defense for Pre-Trained Language Models

Distinguishing Non-natural from Natural Adversarial Samples for More Robust Pre-trained Language Model

Disentangled Contrastive Learning for Learning Robust Textual Representations

HAT4RD: Hierarchical Adversarial Training for Rumor Detection in Social Media

RMLM: A Flexible Defense Framework for Proactively Mitigating Word-level Adversarial Attacks

Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

Rumor Detection on Social Media with Hierarchical Adversarial Training


Black-box optimization for Julia

First Sagittarius A* Event Horizon Telescope Results. IV. Variability, Morphology, and Black Hole Mass

The tadpole problem

Algorithmically solving the Tadpole Problem

Universal Off-Policy Evaluation

Multi-field inflation in high-slope potentials

Journal of Cosmology and Astroparticle Physics

A new light on the darkest corner of the landscape

Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions

The multi-field, rapid-turn inflationary solution

Architectures of Exoplanetary Systems. II. An Increase in Inner Planetary System Occurrence toward Later Spectral Types for Kepler’s FGK Dwarfs

Rapid-turn inflation in supergravity is rare and tachyonic


Python package for AutoML on Tabular Data with Feature Engineering, Hyper-Parameters Tuning, Explanations and Automatic Documentation

Explainable AI (XAI): A Systematic Meta-Survey of Current Challenges and Future Opportunities

Automated Machine Learning on Graphs: A Survey

Evaluation of Light Gradient Boosted Machine Learning Technique in Large Scale Land Use and Land Cover Classification

AMLB: an AutoML Benchmark

The Technological Emergence of AutoML: A Survey of Performant Software and Applications in the Context of Industry

Prediction of Recurrent Mutations in SARS-CoV-2 Using Artificial Neural Networks

International journal of molecular sciences

Comparison of Automated Machine Learning Tools for SMS Spam Message Filtering

Models including preoperative plasma levels of angiogenic factors, leptin and IL-8 as potential biomarkers of endometrial cancer

AutoDES: AutoML Pipeline Generation of Classification with Dynamic Ensemble Strategy Selection

Diagnosing Hemophagocytic Lymphohistiocytosis with Machine Learning: A Proof of Concept


SmartSim Infrastructure Library.

Using Machine Learning at Scale in HPC Simulations with SmartSim: An Application to Ocean Climate Modeling

Coupling streaming AI and HPC ensembles to achieve 100-1000x faster biomolecular simulations

Achieving 100X faster simulations of complex biological phenomena by coupling ML to HPC ensembles.

Active flow control of a turbulent separation bubble through deep reinforcement learning

In Situ Framework for Coupling Simulation and Machine Learning with Application to CFD

Combining machine learning with computational fluid dynamics using OpenFOAM and SmartSim


Open source pulsar search and analysis toolkit

A repeating fast radio burst

Fast radio bursts

An extreme magneto-ionic environment associated with the fast radio burst source FRB 121102

A repeating fast radio burst source localized to a nearby spiral galaxy

CHIME/FRB Discovery of Eight New Repeating Fast Radio Burst Sources

The Repeating Fast Radio Burst FRB 121102 as Seen on Milliarcsecond Angular Scales

FRB 121102 Bursts Show Complex Time-Frequency Structure

The CHIME Fast Radio Burst Project: System Overview

A repeating fast radio burst source in a globular cluster

A bimodal burst energy distribution of a repeating fast radio burst source


Fast & Simple Resource-Constrained Learning of Deep Network Structure

MorphNet: Fast & Simple Resource-Constrained Structure Learning of Deep Networks

AutoML to Date and Beyond: Challenges and Opportunities

Computationally Efficient Neural Image Compression

Fine-Grained Stochastic Architecture Search


Repository to track the progress in Natural Language Processing (NLP), including the datasets and the current state-of-the-art for the most common NLP tasks.

IndoLEM and IndoBERT: A Benchmark Dataset and Pre-trained Language Model for Indonesian NLP

RECON: Relation Extraction using Knowledge Graph Context in a Graph Neural Network

Falcon 2.0: An Entity and Relation Linking Tool over Wikidata

International Conference on Information and Knowledge Management

Evaluating Text GANs as Language Models

End-to-End NLP Knowledge Graph Construction

The State of the Art of Natural Language Processing—A Systematic Automated Review of NLP Literature Using NLP Techniques

SentimentArcs: A Novel Method for Self-Supervised Sentiment Analysis of Time Series Shows SOTA Transformers Can Struggle Finding Narrative Arcs

An Overview of Indian Language Datasets used for Text Summarization


Multilingual text (NLP) processing toolkit

Dark Patterns at Scale: Findings from a Crawl of 11K Shopping Websites

Proceedings of the ACM on Human-Computer Interaction

We Value Your Privacy ... Now Take Some Cookies: Measuring the GDPR's Impact on Web Privacy

Proceedings 2019 Network and Distributed System Security Symposium

Samanantar: The Largest Publicly Available Parallel Corpora Collection for 11 Indic Languages

DaNE: A Named Entity Resource for Danish

PROCEEDINGS OF THE 12TH INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION (LREC 2020)

LOME: Large Ontology Multilingual Extraction

The Effect of Domain and Diacritics in Yorùbá-English Neural Machine Translation.

Sentiment Analysis by Fusing Text and Location Features of Geo-Tagged Tweets

GTCOM Neural Machine Translation Systems for WMT19

Proceedings of the Fourth Conference on Machine Translation (Volume 2: Shared Task Papers, Day 1)

Challenges and Limitations with the Metrics Measuring the Complexity of Code-Mixed Text

Huawei’s NMT Systems for the WMT 2019 Biomedical Translation Task

Proceedings of the Fourth Conference on Machine Translation (Volume 3: Shared Task Papers, Day 2)


AstroAccelerate is a many-core accelerated software package for processing time-domain radio-astronomy data.

Simultaneous multi-telescope observations of FRB 121102

Monthly notices of the Royal Astronomical Society

A GPU Implementation of the Correlation Technique for Real-time Fourier Domain Pulsar Acceleration Searches

The Astrophysical Journal Supplement Series

First discoveries and localizations of Fast Radio Bursts with MeerTRAP: real-time, commensal MeerKAT survey

Monthly Notices of the Royal Astronomical Society

MeerTRAP in the era of multi-messenger astrophysics

Introduction to the Special Issue on Digital Signal Processing in Radio Astronomy

A polyphase filter for many-core architectures

A MeerKAT, e-MERLIN, H.E.S.S., and Swift search for persistent and transient emission associated with three localized FRBs

Searching for pulsars in extreme orbits -- GPU acceleration of the Fourier domain 'jerk' search.


Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

From Piz Daint to the Stars: Simulation of Stellar Mergers using High-Level Abstractions

Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

octo-tiger: a new, 3D hydrodynamic code for stellar mergers that uses hpx parallelization

Accelerating Octo-Tiger: Stellar Mergers on Intel Knights Landing with HPX

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

From Merging Frameworks to Merging Stars: Experiences using HPX, Kokkos and SIMD Types

From Task-Based GPU Work Aggregation to Stellar Mergers: Turning Fine-Grained CPU Tasks into Portable GPU Kernels

Evaluating HPX and Kokkos on RISC-V using an astrophysics application Octo-Tiger

Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis

Betelgeuse as a Merger of a Massive Star with a Companion

Hydrodynamic simulations of WD-WD mergers and the origin of RCB stars


Public Workflows at GNPS

Feature-based Molecular Networking in the GNPS Analysis Environment

Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment

Ion Identity Molecular Networking in the GNPS Environment

foodMASST: A Mass Spectrometry Search Tool for Foods and Beverages.


A framework for data augmentation for 2D and 3D image classification and segmentation

nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation

nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation

The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge

Automated brain extraction of multisequence MRI using artificial neural networks

TractSeg - Fast and accurate white matter tract segmentation

No New-Net

nnU-Net for Brain Tumor Segmentation

nnU-Net: Breaking the Spell on Successful Medical Image Segmentation.

MIScnn: a framework for medical image segmentation with convolutional neural networks and deep learning

Combined tract segmentation and orientation mapping for bundle-specific tractography


Fairness Testing: A Comprehensive Survey and Analysis of Trends

SenSeI: Sensitive Set Invariance for Enforcing Individual Fairness

Machine Learning Suites for Online Toxicity Detection

Automatic Fairness Testing of Neural Classifiers Through Adversarial Sampling

Finding Good Representations of Emotions for Text Classification

An Empirical Study of the Downstream Reliability of Pre-Trained Word Embeddings

International Conference on Computational Linguistics

Don't Just Clean It, Proxy Clean It: Mitigating Bias by Proxy in Pre-Trained Models

Findings of the Association for Computational Linguistics: EMNLP 2022


extract and tweak data from electrochemical tests of cells


QuickCheck inspired property-based testing for OCaml.

Automatic and scalable detection of logical errors in functional programming assignments

Proceedings of the ACM on Programming Languages

Random testing of a higher-order blockchain language (experience report)

Proceedings of the ACM on programming languages

Formalizing Date Arithmetic and Statically Detecting Ambiguities for the Law


Neural Collaborative Filtering

Variational Autoencoders for Collaborative Filtering

Content-based recommendations with Poisson factorization

Scalable Recommendation with Poisson Factorization

Bilateral Variational Autoencoder for Collaborative Filtering

Cornac: A Comparative Framework for Multimodal Recommender Systems

The Simpson's Paradox in the Offline Evaluation of Recommendation Systems

Explainable Recommendation with Comparative Constraints on Product Aspects

MMRec: Simplifying Multimodal Recommendation

Multimodal Recommender Systems: A Survey


Benchmarking various AD tools.

A Benchmark of Selected Algorithmic Differentiation Tools on Some Problems in Computer Vision and Machine Learning

Hashing Modulo Alpha-Equivalence

AD for an Array Language with Nested Parallelism


Atomistic Spin Simulation Framework

Emergence of zero-field non-synthetic single and interchained antiferromagnetic skyrmions in thin films

Magnetic domain walls of the van der Waals material Fe3GeTe2

Micromagnetic description of twisted spin spirals in the B20 chiral magnet FeGe from first principles

The AiiDA-Spirit Plugin for Automated Spin-Dynamics Simulations and Multi-Scale Modeling Based on First-Principles Calculations

Intrinsic antiferromagnetic multimeronic Néel spin-textures in ultrathin films


Bias Auditing & Fair ML Toolkit

Retiring Adult: New Datasets for Fair Machine Learning

Aequitas: A Bias and Fairness Audit Toolkit

Amazon SageMaker Clarify: Machine Learning Bias Detection and Explainability in the Cloud

Dealing with Bias and Fairness in Data Science Systems: A Practical Hands-on Tutorial

Turning the Tables: Biased, Imbalanced, Dynamic Tabular Datasets for ML Evaluation

Towards a multi-stakeholder value-based assessment framework for algorithmic systems

Conference on Fairness, Accountability and Transparency

Building Trustworthy AI Solutions: A Case for Practical Solutions for Small Businesses

IEEE Transactions on Artificial Intelligence

The Technological Emergence of AutoML: A Survey of Performant Software and Applications in the Context of Industry

The Right Tool for the Job: Open-Source Auditing Tools in Machine Learning

Data quality dimensions for fair AI


结巴中文分词

CSI: A Hybrid Deep Model for Fake News Detection

International Conference on Information and Knowledge Management

Massively Multilingual Sentence Embeddings for Zero-Shot Cross-Lingual Transfer and Beyond

Achieving Human Parity on Automatic Chinese to English News Translation

VATEX: A Large-Scale, High-Quality Multilingual Dataset for Video-and-Language Research

The United Nations Parallel Corpus v1.0

SHINE: Signed Heterogeneous Information Network Embedding for Sentiment Link Prediction

Automated Phrase Mining from Massive Text Corpora

Overview for the Second Shared Task on Language Identification in Code-Switched Data

Hybrid Retrieval-Generation Reinforced Agent for Medical Image Report Generation

Wikipedia2Vec: An Efficient Toolkit for Learning and Visualizing the Embeddings of Words and Entities from Wikipedia


PYthon For Homomorphic Encryption Libraries, perform encrypted computations such as sum, mult, scalar product or matrix multiplication in Python, with NumPy compatibility. Uses SEAL/PALISADE as backends, implemented using Cython.

A systematic review of homomorphic encryption and its contributions in healthcare industry

FLASHE: Additively Symmetric Homomorphic Encryption for Cross-Silo Federated Learning

A Privacy-Preserving Distributed Architecture for Deep-Learning-as-a-Service

A Review of Homomorphic Encryption for Privacy-Preserving Biometrics

Reputation Systems for Supply Chains: The Challenge of Achieving Privacy Preservation

Reinforcement Learning on Encrypted Data

A Review on Searchable Encryption Functionality and the Evaluation of Homomorphic Encryption


Repository for suggesting new lineages that should be added to the current scheme

SARS-CoV-2 variants, spike mutations and immune escape

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas

Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant

Convergent Evolution in SARS-CoV-2 Spike Creates a Variant Soup from Which New COVID-19 Waves Emerge

International journal of molecular sciences

Culture and identification of a “Deltamicron” SARS‐CoV‐2 in a three cases cluster in southern France

Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 synergistically enhances antibody evasion and ACE2 binding

SARS-CoV-2 Delta–Omicron Recombinant Viruses, United States

Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

Molnupiravir: From Hope to Epic Fail?


Conversion of IPCC documents into semantic form


Guidelines and forecasts for a collaborative U.S. influenza forecasting project.

A collaborative multiyear, multimodel assessment of seasonal influenza forecasting in the United States

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

A Collaborative Multi-Model Ensemble for Real-Time Influenza Season Forecasting in the U.S

An extended note on the multibin logarithmic score used in the FluSight competitions

Correction: Evaluating epidemic forecasts in an interval format


AutoML tools chain

AutoML: A survey of the state-of-the-art

CurveLane-NAS: Unifying Lane-Sensitive Architecture Search and Adaptive Point Blending

Neural Architecture Generator Optimization

VEGA: Towards an End-to-End Configurable AutoML Pipeline

An Asymptotically Optimal Multi-Armed Bandit Algorithm and Hyperparameter Optimization


Fast and memory-efficient exact attention

FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness

Efficient Memory Management for Large Language Model Serving with PagedAttention

FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning


Avatars for Zoom, Skype and other video-conferencing apps.

The Creation and Detection of Deepfakes: A Survey

Zooming Into Video Conferencing Privacy

FakeBuster: A DeepFakes Detection Tool for Video Conferencing Scenarios

The practice of technological deception in videoconferencing systems for distance learning and ways to counter it

Deepfake CAPTCHA: A Method for Preventing Fake Calls

Detection of Real-time DeepFakes in Video Conferencing with Active Probing and Corneal Reflection

Discussion Paper: The Threat of Real Time Deepfakes


Advanced AI Explainability for computer vision.  Support for CNNs, Vision Transformers, Classification, Object detection, Segmentation, Image similarity and more.

Grad-CAM: Visual Explanations from Deep Networks via Gradient-Based Localization

International Journal of Computer Vision

Grad-CAM++: Improved Visual Explanations for Deep Convolutional Networks

Workshop on Applications of Computer Vision

Score-CAM: Score-Weighted Visual Explanations for Convolutional Neural Networks

LayerCAM: Exploring Hierarchical Class Activation Maps for Localization

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

Grad-CAM: Why did you say that?

Ablation-CAM: Visual Explanations for Deep Convolutional Network via Gradient-free Localization

Eigen-CAM: Class Activation Map using Principal Components

International Joint Conference on Neural Network

Full-Gradient Representation for Neural Network Visualization

Axiom-based Grad-CAM: Towards Accurate Visualization and Explanation of CNNs

Last Layer Re-Training is Sufficient for Robustness to Spurious Correlations


Scikit-learn style model finetuning for NLP

BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding

RoBERTa: A Robustly Optimized BERT Pretraining Approach

Convolutional Neural Networks for Sentence Classification

Transfer Learning for Risk Classification of Social Media Posts: Model Evaluation Study


Reservoir computing utilities for scientific machine learning (SciML)

Data-driven prediction of a multi-scale Lorenz 96 chaotic system using deep learning methods: Reservoir computing, ANN, and RNN-LSTM

Reservoir Computing using Cellular Automata

ReservoirComputing.jl: An Efficient and Modular Library for Reservoir Computing Models

Measuring chaos in the Lorenz and Rössler models: Fidelity tests for reservoir computing


Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Nextclade: clade assignment, mutation calling and quality control for viral genomes

Zenodo (CERN European Organization for Nuclear Research)

Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York

Rapid screening for SARS-CoV-2 variants of concern in clinical and environmental samples using nested RT-PCR assays targeting key mutations of the spike protein

SARS-CoV-2 Reinfection in a Healthcare Worker Despite the Presence of Detectable Neutralizing Antibodies

Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation

Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay

Evolving strategy for an evolving virus: Development of real-time PCR assays for detecting all SARS-CoV-2 variants of concern

Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland

Rapid and Flexible RT-qPCR Surveillance Platforms To Detect SARS-CoV-2 Mutations


Home of the Renovate CLI: Cross-platform Dependency Automation by Mend.io

The GitHub Development Workflow Automation Ecosystems

Is ChatGPT a Good Software Librarian? An Exploratory Study on the Use of
  ChatGPT for Software Library Recommendations

When conversations turn into work: a taxonomy of converted discussions and issues in GitHub


Multi-vector Simulation Tool assessing and optimizing Local Energy Systems (LES) for the E-LAND project


Machine learning, statistics, and data mining for astronomy and astrophysics

Astronomy in the Big Data Era

Precise radial velocities of giant stars IX. HD 59686 Ab: a massive circumstellar planet orbiting a giant star in a ~13.6 au eccentric binary system

Monte Carlo method for calculating oxygen abundances and their uncertainties from strong-line flux measurements

VISION - Vienna Survey in Orion


About moja global and How We Work


Python and JavaScript bindings for calling the Earth Engine API.

AGGREGATING CLOUD-FREE SENTINEL-2 IMAGES WITH GOOGLE EARTH ENGINE

ISPRS annals of the photogrammetry, remote sensing and spatial information sciences

sUAS Remote Sensing of Vineyard Evapotranspiration Quantifies Spatiotemporal Uncertainty in Satellite-Borne ET Estimates

CLOUD-DESKTOP REMOTE SENSING DATA MANAGEMENT TO ENSURE TIME SERIES ANALYSIS, INTEGRATION OF QGIS AND GOOGLE EARTH ENGINE

The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciences

Improving the congruency of satellite-based fertilizer maps with field-operable units using pneumatic spreaders


light NN client

Deep Sets

MLaaS4HEP: Machine Learning as a Service for HEP

HL-LHC Computing Review: Common Tools and Community Software

C++ Code Generation for Fast Inference of Deep Learning Models in ROOT/TMVA

Machine Learning as a Service for HEP


Code for Bayesian Analysis

Cosmological parameters from the BOSS galaxy power spectrum

Journal of Cosmology and Astroparticle Physics

Early dark energy does not restore cosmological concordance

General cosmography model with spatial curvature

Monthly notices of the Royal Astronomical Society

Nonlinear perturbation theory extension of the Boltzmann code CLASS

Modified Gravity and Cosmology: An Update by the CANTATA Network

Atacama Cosmology Telescope: Constraints on prerecombination early dark energy

CosmoPower: emulating cosmological power spectra for accelerated Bayesian inference from next-generation surveys

Monthly Notices of the Royal Astronomical Society

CMB lensing from Planck PR4 maps

Constraints on primordial gravitational waves from the cosmic microwave background

Testing the effect of H-0 on f sigma(8) tension using a Gaussian process method


XACC - eXtreme-scale Accelerator programming framework

Open source software in quantum computing

A Quantum Computing View on Unitary Coupled Cluster Theory

A Language and Hardware Independent Approach to Quantum-Classical Computing

Enabling Pulse-level Programming, Compilation, and Execution in XACC


netCDF Operators


Croissant is a high-level format for machine learning datasets that brings together four rich layers.

Croissant: A Metadata Format for ML-Ready Datasets

DMLR: Data-centric Machine Learning Research -- Past, Present and Future

Data Acquisition: A New Frontier in Data-centric AI

Retrospective for the Dynamic Sensorium Competition for predicting large-scale mouse primary visual cortex activity from videos

Synthesizing Sentiment-Controlled Feedback For Multimodal Text and Image
  Data


HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Cohesin residency determines chromatin loop patterns

Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin

Multidimensional profiling reveals GATA1-modulated stage-specific chromatin states and functional associations during human erythropoiesis

Revisiting the Use of Structural Similarity Index in Hi-C

Light control of three‐dimensional chromatin organization in soybean

Flowering genes identification, network analysis, and database construction for 837 plants


Official home of genome aligner based upon notion of Cactus graphs

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Cactus: Algorithms for genome multiple sequence alignment

A comparative genomics multitool for scientific discovery and conservation

HAL: a hierarchical format for storing and analyzing multiple genome alignments

Cactus Graphs for Genome Comparisons

Research in Computational Molecular Biology

The mosaic oat genome gives insights into a uniquely healthy cereal crop

Sequence tube maps: making graph genomes intuitive to commuters

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers

SegAlign: A Scalable GPU-Based Whole Genome Aligner

PROCEEDINGS OF SC20: THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC20)


Identify and quantify MHC eluted peptides from mass spectrometry raw data

The nf-core framework for community-curated bioinformatics pipelines

MHCflurry: open-source class I MHC binding affinity prediction

A Deeper Look into Comet—Implementation and Features

Journal of the American Society for Mass Spectrometry

An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics

High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets

MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

FRED 2: an immunoinformatics framework for Python


:sparkles: new shiny website built with svelte :heart: for dust and noise measuring project :point_right:  https://sensor.community


Synthetic data generators for structured and unstructured text, featuring differentially private learning.

Subword Regularization: Improving Neural Network Translation Models with Multiple Subword Candidates

Privacy and Utility of Private Synthetic Data for Medical Data Analyses

TSGM: A Flexible Framework for Generative Modeling of Synthetic Time Series


The Community Earth System Model

Understanding processes that control dust spatial distributions with global climate models and satellite observations

Assessment of Equilibrium Climate Sensitivity of the Community Earth System Model Version 2 Through Simulation of the Last Glacial Maximum

Differences in the quasi-biennial oscillation response to stratospheric aerosol modification depending on injection strategy and species

Dependence of strategic solar climate intervention on background scenario and model physics

Specified dynamics scheme impacts on wave-mean flow dynamics, convection, and tracer transport in CESM2 (WACCM6)

Summer atmospheric circulation over Greenland in response to Arctic amplification and diminished spring snow cover

Interannual and Seasonal Drivers of Carbon Cycle Variability Represented by the Community Earth System Model (CESM2)

Comparison of Urban Air Quality Simulations During the KORUS‐AQ Campaign With Regionally Refined Versus Global Uniform Grids in the Multi‐Scale Infrastructure for Chemistry and Aerosols (MUSICA) Version 0

Journal of Advances in Modeling Earth Systems

Diffuse Radiation Forcing Constraints on Gross Primary Productivity and Global Terrestrial Evapotranspiration

Submesoscale Effects on Changes to Export Production Under Global Warming


A Python library for amortized Bayesian workflows using generative neural networks.

BayesFlow: Learning complex stochastic models with invertible neural networks

Amortized Bayesian model comparison with evidential deep learning

Detecting Model Misspecification in Amortized Bayesian Inference with Neural Networks

JANA: Jointly Amortized Neural Approximation of Complex Bayesian Models

A General Integrative Neurocognitive Modeling Framework to Jointly Describe EEG and Decision-making on Single Trials

BayesFlow: Amortized Bayesian Workflows With Neural Networks

Neural Superstatistics for Bayesian Estimation of Dynamic Cognitive Models


Ground Control Station for Android Devices

Low Cost and Flexible UAV Deployment of Sensors

ChimpCheck: property-based randomized test generation for interactive apps

SIGPLAN symposium on New ideas, new paradigms, and reflections on programming and software

An Overview of the Drone Open-Source Ecosystem


A Python nearest neighbor descent for approximate nearest neighbors

ANN-Benchmarks: A Benchmarking Tool for Approximate Nearest Neighbor Algorithms

A General Framework For Detecting Anomalous Inputs to DNN Classifiers

LANNS: A Web-Scale Approximate Nearest Neighbor Lookup System

K-Nearest Neighbor Approximation Via the Friend-of-a-Friend Principle

TopoAct: Exploring the Shape of Activations in Deep Learning

Empirical complexity of comparator-based nearest neighbor descent

An Efficient Content-based Time Series Retrieval System

A Survey on Efficient Processing of Similarity Queries over Neural Embeddings

Fast Single-Core K-Nearest Neighbor Graph Computation

CEnt: An Entropy-based Model-agnostic Explainability Framework to Contrast Classifiers' Decisions


Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

bioRxiv : the preprint server for biology

Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic

Identifying SARS-CoV-2 regional introductions and transmission clusters in real time

Pandemic-scale phylogenetics

Systematic Guidelines for Effective Utilization of COVID-19 Databases in Genomic, Epidemiologic, and Clinical Research


【PyTorch】Easy-to-use,Modular and Extendible package of deep-learning based CTR models.

Wide & Deep Learning for Recommender Systems

An Overview of Multi-Task Learning in Deep Neural Networks

DeepFM: A Factorization-Machine based Neural Network for CTR Prediction

Deep Interest Network for Click-Through Rate Prediction

Neural Factorization Machines for Sparse Predictive Analytics

Deep & Cross Network for Ad Click Predictions

xDeepFM: Combining Explicit and Implicit Feature Interactions for Recommender Systems

Deep Interest Evolution Network for Click-Through Rate Prediction

Modeling Task Relationships in Multi-task Learning with Multi-gate Mixture-of-Experts

Attentional Factorization Machines: Learning the Weight of Feature Interactions via Attention Networks


Cyclops Tensor Framework: parallel arithmetic on multidimensional arrays

Red-blue pebbling revisited: near optimal parallel matrix-matrix multiplication

DISTAL: the distributed tensor algebra compiler

Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation

SpDISTAL: Compiling Distributed Sparse Tensor Computations

Deinsum: Practically I/O Optimal Multi-Linear Algebra


Stream summarizer and cardinality estimator.

Automatic test improvement with DSpot: a study with ten mature open-source projects

Scaling Graph-based Semi Supervised Learning to Large Number of Labels Using Count-Min Sketch

Refactoring for Reuse: An Empirical Study

A Synopses Data Engine for Interactive Extreme-Scale Analytics


AIRR Community Data Standards

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data

AIRR Community Standardized Representations for Annotated Immune Repertoires

The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons


Qanary a methodology to construct and share resources to build QA systems

The Qanary Ecosystem: Getting New Insights by Composing Question Answering Pipelines

Systematic review of question answering over knowledge bases

CBench: Towards Better Evaluation of Question Answering Over Knowledge Graphs


Library for Semi-Automated Data Science

Lale: Consistent Automated Machine Learning

Mining Documentation to Extract Hyperparameter Schemas

Type Safety with JSON Subschema

Gradual AutoML using Lale

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

An Empirical Study of Modular Bias Mitigators and Ensembles

Type-Driven Automated Learning with Lale

A Suite of Fairness Datasets for Tabular Classification


A fast medical imaging analysis library in Python with algorithms for registration, segmentation, and more.

TransMorph: Transformer for unsupervised medical image registration

ViT-V-Net: Vision Transformer for Unsupervised Volumetric Medical Image Registration

Recommendations for Processing Head CT Data

NODEO: A Neural Ordinary Differential Equation Based Optimization Framework for Deformable Image Registration

Deep learning-based quantification of temporalis muscle has prognostic value in patients with glioblastoma

NEURO-DRAM: a 3D recurrent visual attention model for interpretable neuroimaging classification

Cross-Modality Multi-Atlas Segmentation via Deep Registration and Label Fusion

Unified Multi-Modal Image Synthesis for Missing Modality Imputation

Aligning Multi-Sequence CMR Towards Fully Automated Myocardial Pathology Segmentation

Unsupervised Multi-Modality Registration Network based on Spatially Encoded Gradient Information


Stanford Network Analysis Platform (SNAP) is a general purpose network analysis and graph mining library.

Inferring Networks of Substitutable and Complementary Products

Inductive Representation Learning on Temporal Graphs

Overlapping Community Detection with Graph Neural Networks

Billion-scale Network Embedding with Iterative Random Projection

CIMTDetect: A Community Infused Matrix-Tensor Coupled Factorization Based Method for Fake News Detection

PecanPy: a fast, efficient and parallelized Python implementation of node2vec

Graph Classification with 2D Convolutional Neural Networks

An End-to-End Framework for Cold Question Routing in Community Question Answering Services

InGram: Inductive Knowledge Graph Embedding via Relation Graphs

Classifying Graphs as Images with Convolutional Neural Networks.


Benchmark datasets, data loaders, and evaluators for graph machine learning

Open Graph Benchmark: Datasets for Machine Learning on Graphs

Do Transformers Really Perform Bad for Graph Representation?

SIGN: Scalable Inception Graph Neural Networks

OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs

Anomaly Detection on Attributed Networks via Contrastive Self-Supervised Learning

IEEE transactions on neural networks and learning systems

Weisfeiler and Lehman Go Cellular: CW Networks

Exploring the Potential of Large Language Models (LLMs)in Learning on Graphs

G-Mixup: Graph Data Augmentation for Graph Classification

Rethinking pooling in graph neural networks

Local Augmentation for Graph Neural Networks


The Real-time COVID-19 Status in Australia

Covid-19: Open-Data Resources for Monitoring, Modeling, and Forecasting the Epidemic

Open Data Resources for Fighting COVID-19


Common repository for example datasets used by Vega-related projects

MultiVision: Designing Analytical Dashboards with Deep Learning Based Recommendation

LIDA: A Tool for Automatic Generation of Grammar-Agnostic Visualizations and Infographics using Large Language Models

An Evaluation-Focused Framework for Visualization Recommendation Algorithms

DashBot: Insight-Driven Dashboard Generation Based on Deep Reinforcement Learning

Why is AI not a Panacea for Data Workers? An Interview Study on Human-AI Collaboration in Data Storytelling

Notable: On-the-fly Assistant for Data Storytelling in Computational Notebooks

Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems

Agnostic Visual Recommendation Systems: Open Challenges and Future Directions.

Metrics-Based Evaluation and Comparison of Visualization Notations


CERN PyHEADTAIL macro-particle code for simulating beam dynamics in particle accelerators with collective effects.

Impedance modelling and collective effects in the Future Circular e+e− Collider with 4 IPs

Interim report for the International Muon Collider Collaboration (IMCC)


Tree based hydrologic and hydraulic routing


Response of Extreme Precipitating Cell Structures to Atmospheric Warming

Journal of geophysical research. Atmospheres : JGR

Nonprecipitating Shallow Cumulus Convection Is Intrinsically Unstable to Length Scale Growth

The diurnal stratocumulus-to-cumulus transition over land in southern West Africa

Why Does Fog Deepen? An Analytical Perspective

Explicit aerosol–cloud interactions in the Dutch Atmospheric Large-Eddy Simulation model DALES4.1-M7

Assessing uncertainties from physical parameters and modelling choices in an atmospheric large eddy simulation model

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Cloud Botany: Shallow Cumulus Clouds in an Ensemble of Idealized Large‐Domain Large‐Eddy Simulations of the Trades

Aerosol-cloud-turbulence interactions in well-coupled Arctic boundary layers over open water

Clouds dissipate quickly during solar eclipses as the land surface cools

Zenodo (CERN European Organization for Nuclear Research)


Utility functions for handling MIDI data in a nice/intuitive way.

Lead Sheet Generation and Arrangement by Conditional Generative Adversarial Network

MIDI-Sheet Music Alignment Using Bootleg Score Synthesis

Melody Generation for Pop Music via Word Representation of Musical Properties

Multimodal Lyrics-Rhythm Matching

Musical Score Following and Audio Alignment


A PyTorch library entirely dedicated to neural differential equations, implicit models and related numerical methods

On Neural Differential Equations

GalaxyFlow: Upsampling Hydrodynamical Simulations for Realistic Gaia Mock Catalogs

Neural Contractive Dynamical Systems


Harrell Miscellaneous

Predicted Shifts in Small Mammal Distributions and Biodiversity in the Altered Future Environment of Alaska: An Open Access Data and Machine Learning Perspective

Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals

Selfish chromosomal drive shapes recent centromeric histone evolution in monkeyflowers

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia

Alternative dietary protein and water temperature influence the skin and gut microbial communities of yellowtail kingfish (Seriola lalandi)

Growth faltering regardless of chronic diarrhea is associated with mucosal immune dysfunction and microbial dysbiosis in the gut lumen

Genome-Wide Network of lncRNA–mRNA During Ovine Oocyte Development From Germinal Vesicle to Metaphase II in vitro

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface

Frontiers in cellular and infection microbiology


Program for analysing NGS data.

Reconstructing the Deep Population History of Central and South America

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

The Genomic Footprints of the Fall and Recovery of the Crested Ibis

Inferring Balancing Selection From Genome-Scale Data

Authentication and Assessment of Contamination in Ancient DNA

Methods in molecular biology (Clifton, N.J.)

Origin and mobility of Iron Age Gaulish groups in present-day France revealed through archaeogenomics

Testing the ‘caves as islands’ model in two cave-obligate invertebrates with a genomic approach


The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

Genomic insights into the 2016–2017 cholera epidemic in Yemen

The Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin Expression

Rapid multi-locus sequence typing direct from uncorrected long reads using Krocus

Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory

Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum

Contrasting approaches to genome-wide association studies impact the detection of resistance mechanisms in Staphylococcus aureus

Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings


Brain Dynamics Programming in Python

BrainPy: a flexible, integrative, efficient, and extensible framework towards general-purpose brain dynamics programming

A Just-In-Time Compilation Approach for Neural Dynamics Simulation

A differentiable brain simulator bridging brain simulation and brain-inspired computing

A Differentiable Approach to Multi-scale Brain Modeling


Code for the paper Hybrid Spectrogram and Waveform Source Separation

Conv-TasNet: Surpassing Ideal Time–Frequency Magnitude Masking for Speech Separation

IEEE/ACM transactions on audio, speech, and language processing

Music Source Separation in the Waveform Domain

Hybrid Transformers for Music Source Separation

Seamless: Multilingual Expressive and Streaming Speech Translation

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

CWS-PResUNet: Music Source Separation with Channel-wise Subband Phase-aware ResUNet

SingFake: Singing Voice Deepfake Detection

The Sound Demixing Challenge 2023 x2013 Music Demixing Track

Multi-Task Audio Source Separation


Experimental implementation of Cubical Type Theory

Cubical Type Theory: a constructive interpretation of the univalence axiom

On Higher Inductive Types in Cubical Type Theory

Guarded Cubical Type Theory

Canonicity for Cubical Type Theory

An introduction to univalent foundations for mathematicians

Bulletin of the American Mathematical Society

Homotopy Type Theory in Lean

On the Formalization of Higher Inductive Types and Synthetic Homotopy Theory

The RedPRL Proof Assistant (Invited Paper)

Bicategories in Univalent Foundations

Guarded Cubical Type Theory: Path Equality for Guarded Recursion


Python Script to download hundreds of images from 'Google Images'. It is a ready-to-run code!

Waste detection in Pomerania: non-profit project for detecting waste in environment.

EncoderMI: Membership Inference against Pre-trained Encoders in Contrastive Learning

Hate Speech in Pixels: Detection of Offensive Memes towards Automatic Moderation

Improving Adversarial Robustness via Unlabeled Out-of-Domain Data

Efficient Super Resolution For Large-Scale Images Using Attentional GAN

Best of both worlds: local and global explanations with human-understandable concepts

Task-Agnostic Object Recognition for Mobile Robots through Few-Shot Image Matching

An Application for Aesthetic Quality Assessment in Photography with Interpretability Features

Investigating response time and accuracy in online classifier learning for multimedia publish-subscribe systems

Semantics Preserving Hierarchy based Retrieval of Indian heritage monuments


A Python interface for https://github.com/fplll/fplll

Sparse Recovery With Integrality Constraints

Déjà Vu: Side-Channel Analysis of Mozilla's NSS

Conference on Computer and Communications Security

HyperDegrade: From GHz to MHz Effective CPU Frequencies

Improved attacks on knapsack problem with their variants and a knapsack type ID-scheme

Advances in Mathematics of Communications

Lattice attack on group ring NTRU: The case of the dihedral group


Machine Learning for Health python package

BMI-adjusted adipose tissue volumes exhibit depot-specific and divergent associations with cardiometabolic diseases

Patient contrastive learning: A performant, expressive, and practical approach to electrocardiogram modeling

Cross-modal autoencoder framework learns holistic representations of cardiovascular state

Selection of 51 predictors from 13,782 candidate multimodal features using machine learning improves coronary artery disease prediction

Silhouette images enable estimation of body fat distribution and associated cardiometabolic risk

Deep learning to estimate cardiac magnetic resonance–derived left ventricular mass


Pytorch-based framework for solving parametric constrained optimization problems, physics-informed system identification, and parametric model predictive control.

Learning Constrained Adaptive Differentiable Predictive Control Policies With Guarantees

Neural Ordinary Differential Equations for Nonlinear System Identification

Learning Stochastic Parametric Differentiable Predictive Control Policies

Koopman-based Differentiable Predictive Control for the Dynamics-Aware Economic Dispatch Problem

Differentiable Predictive Control with Safety Guarantees: A Control Barrier Function Approach

Learning for CasADi: Data-driven Models in Numerical Optimization

Finite basis Kolmogorov-Arnold networks: domain decomposition for
  data-driven and physics-informed problems

Towards Practical Physics-Informed ML Design and Evaluation for Power Grid

Neuro-physical dynamic load modeling using differentiable parametric optimization

A Robust, Efficient Predictive Safety Filter


DeepFlame: A deep learning empowered open-source platform for reacting flow simulations

An integrated framework for accelerating reactive flow simulation using GPU and machine learning models


Shadow is a discrete-event network simulator that directly executes real application code, enabling you to simulate distributed systems with thousands of network-connected processes in realistic and scalable private network experiments using your laptop, desktop, or server running Linux.

Avoiding The Man on the Wire: Improving Tor's Security with Trust-Aware Path Selection

Once is Never Enough: Foundations for Sound Statistical Inference in Tor Network Experimentation

B-Tor: Anonymous communication system based on consortium blockchain


Pyroomacoustics is a package for audio signal processing for indoor applications. It was developed as a fast prototyping platform for beamforming algorithms in indoor scenarios.

Pyroomacoustics: A Python Package for Audio Room Simulation and Array Processing Algorithms

International Conference on Acoustics, Speech, and Signal Processing

ASVspoof 2021: Towards Spoofed and Deepfake Speech Detection in the Wild

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

Far-Field Automatic Speech Recognition

MASS: Microphone Array Speech Simulator in Room Acoustic Environment for Multi-Channel Speech Coding and Enhancement

L-SpEx: Localized Target Speaker Extraction

A study on more realistic room simulation for far-field keyword spotting

The NPU-ASLP System for Audio-Visual Speech Recognition in MISP 2022 Challenge

MLCA-AVSR: Multi-Layer Cross Attention Fusion based Audio-Visual Speech Recognition

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

Focus on the Sound around You: Monaural Target Speaker Extraction via Distance and Speaker Information


Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research

Reverb: A Framework For Experience Replay

When should agents explore?

QuaRL: Quantization for Fast and Environmentally Sustainable Reinforcement Learning

Return-based Scaling: Yet Another Normalisation Trick for Deep RL

Training a First-Order Theorem Prover from Synthetic Data

The Architectural Implications of Distributed Reinforcement Learning on CPU-GPU Systems


LLM based autonomous agent that conducts in-depth web research on any given topic

Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks

Plan-and-Solve Prompting: Improving Zero-Shot Chain-of-Thought Reasoning by Large Language Models

Exploring Large Language Model based Intelligent Agents: Definitions, Methods, and Prospects

Assisting in Writing Wikipedia-like Articles From Scratch with Large
  Language Models


A faster pytorch implementation of faster r-cnn

CutMix: Regularization Strategy to Train Strong Classifiers with Localizable Features

Rethinking the Value of Network Pruning

Graph R-CNN for Scene Graph Generation

Unbiased Mean Teacher for Cross-domain Object Detection

Towards Universal Object Detection by Domain Attention

Co-Separating Sounds of Visual Objects

Differentiable Learning-to-Normalize via Switchable Normalization

Borrow from Anywhere: Pseudo Multi-modal Object Detection in Thermal Imagery

Probabilistic Object Detection: Definition and Evaluation

Pedestrian Detection in Thermal Images using Saliency Maps


Grid2Op a testbed platform to model sequential decision making in power systems.

Reinforcement Learning for Selective Key Applications in Power Systems: Recent Advances and Future Challenges

Learning to run a Power Network Challenge: a Retrospective Analysis

Reinforcement Learning for Electricity Network Operation

Exploring grid topology reconfiguration using a simple deep reinforcement learning approach

Learning to run a power network with trust

PowerGym: A Reinforcement Learning Environment for Volt-Var Control in Power Distribution Systems

Deep Reinforcement Learning-Based Approach for Autonomous Power Flow Control Using Only Topology Changes

Power Grid Congestion Management via Topology Optimization with AlphaZero

Curriculum Based Reinforcement Learning of Grid Topology Controllers to Prevent Thermal Cascading

Managing power grids through topology actions: A comparative study between advanced rule-based and reinforcement learning agents


Community-provided extensions to Seurat

Inferring and perturbing cell fate regulomes in human brain organoids

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair

CSS: cluster similarity spectrum integration of single-cell genomics data

Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum

Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq

SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis

Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells

Dynamic single-cell regulomes characterize human peripheral blood innate lymphoid cell subpopulations


Microbiome analysis

Defects in microvillus crosslinking sensitize to colitis and inflammatory bowel disease

The nasal microbiome in patients suffering from non-steroidal anti-inflammatory drugs-exacerbated respiratory disease in absence of corticosteroids

Is Autologous Fecal Microbiota Transfer after Exclusive Enteral Nutrition in Pediatric Crohn’s Disease Patients Rational and Feasible? Data from a Feasibility Test


Toolkit for Machine Learning, Natural Language Processing, and Text Generation, in TensorFlow.  This is part of the CASL project: http://casl-project.ai/

Toward Controlled Generation of Text

Unsupervised Text Style Transfer using Language Models as Discriminators

Explaining The Efficacy of Counterfactually Augmented Data

Texar: A Modularized, Versatile, and Extensible Toolkit for Text Generation

Enhancing Content Preservation in Text Style Transfer Using Reverse Attention and Conditional Layer Normalization

Structured Content Preservation for Unsupervised Text Style Transfer

Connecting the Dots Between MLE and RL for Sequence Prediction

DialogueBERT: A Self-Supervised Learning based Dialogue Pre-training Encoder

trie-nlg: trie context augmentation to improve personalized query auto-completion for short and unseen prefixes


The xAPI Specification describes communication about learner activity and experiences between technologies.

A Cloud Game-Based Educative Platform Architecture: The CyberScratch Project

Parametrizable exercise generation from authentic texts: Effectively targeting the language means on the curriculum

Workshop on Innovative Use of NLP for Building Educational Applications

Learning Analytics Made in France: The METALproject

Taking Informed Action on Student Activity in MOOCs

PROCEEDINGS OF THE FOURTH (2017) ACM CONFERENCE ON LEARNING @ SCALE (L@S'17)

A framework to foster analysis skill for self-directed activities in data-rich environment

Research and Practice in Technology Enhanced Learning

Enriching context descriptions for enhanced LA scalability: a case study

Dataset of user interactions across four large pilots on the use of augmented reality in learning experiences


Location for summaries and analysis of data related to n-CoV 2019, first reported in Wuhan, China

Effectiveness of isolation, testing, contact tracing, and physical distancing on reducing transmission of SARS-CoV-2 in different settings: a mathematical modelling study

Artificial Intelligence and COVID-19: Deep Learning Approaches for Diagnosis and Treatment

IEEE access : practical innovations, open solutions

Epidemiological data from the COVID-19 outbreak, real-time case information

Deep-LSTM ensemble framework to forecast Covid-19: an insight to the global pandemic

International journal of information technology : an official journal of Bharati Vidyapeeth's Institute of Computer Applications and Management

Data Science and Machine Learning Integrated Implementation Patterns for Cavernous Knowledge Discovery from COVID-19 Data

IOP Conference Series: Materials Science and Engineering

Deep convolutional neural network–based image classification for COVID-19 diagnosis

Machine Learning Approaches to Identify Patient Comorbidities and Symptoms That Increased Risk of Mortality in COVID-19

Modeling the Coronavirus Disease 2019 Incubation Period: Impact on Quarantine Policy

CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties

medRxiv : the preprint server for health sciences

Risk Factors Associated with Mortality Among Patients with Novel Coronavirus Disease (COVID-19) in Africa

Journal of racial and ethnic health disparities


Implementation of paper - YOLOv7: Trainable bag-of-freebies sets new state-of-the-art for real-time object detectors

Benchmarking YOLOv5 and YOLOv7 models with DeepSORT for droplet tracking applications

Evaluation of YOLO Object Detectors for Weed Detection in Different Turfgrass Scenarios

Deep Learning YOLO-Based Solution for Grape Bunch Detection and Assessment of Biophysical Lesions

An open dataset for intelligent recognition and classification of abnormal condition in longwall mining

Optimizing YOLOv7 for Semiconductor Defect Detection

Automatic 3D Building Reconstruction from OpenStreetMap and LiDAR Using Convolutional Neural Networks

Road Damages Detection and Classification with YOLOv7

Non-destructive detection of single-seed viability in maize using hyperspectral imaging technology and multi-scale 3D convolutional neural network

Assessing the performance of YOLOv5, YOLOv6, and YOLOv7 in road defect detection and classification: a comparative study

Bulletin of Electrical Engineering and Informatics


BoxMOT: pluggable SOTA tracking modules for segmentation, object detection and pose estimation models

YOLOv4: Optimal Speed and Accuracy of Object Detection

Simple Online and Realtime Tracking with a Deep Association Metric

ByteTrack: Multi-Object Tracking by Associating Every Detection Box

Omni-Scale Feature Learning for Person Re-Identification

StrongSORT: Make DeepSORT Great Again

Observation-Centric SORT: Rethinking SORT for Robust Multi-Object Tracking

BoT-SORT: Robust Associations Multi-Pedestrian Tracking

Deep OC-SORT: Multi-Pedestrian Tracking by Adaptive Re-Identification

CLIP-ReID: Exploiting Vision-Language Model for Image Re-Identification without Concrete Text Labels

Lightweight Multi-Branch Network for Person Re-Identification


A Fast Implementation of Random Forests

Global terrestrial carbon fluxes of 1999–2019 estimated by upscaling eddy covariance data with a random forest

Machine Learning and Deep Learning -- A review for Ecologists

Synthesis of L-Band SAR and Forest Heights Derived from TanDEM-X DEM and 3 Digital Terrain Models for Biomass Mapping

Application of Machine Learning Classification to Improve the Performance of Vancomycin Therapeutic Drug Monitoring

Review on Real Time Background Extraction: Models, Applications, Environments, Challenges and Evaluation Approaches

International Journal of Online and Biomedical Engineering (iJOE)

Discrete-time survival forests with Hellinger distance decision trees

Identifying Recent Cholera Infections Using a Multiplex Bead Serological Assay

Analysis and Prediction of Vehicle Kilometers Traveled: A Case Study in Spain

International journal of environmental research and public health


Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

Whole genome characterization of sequence diversity of 15,220 Icelanders

A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis

Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies

Genetic variants associated with platelet count are predictive of human disease and physiological markers

A truncating mutation in EPOR leads to hypo-responsiveness to erythropoietin with normal haemoglobin

Population-level deficit of homozygosity unveils CPSF3 as an intellectual disability syndrome gene

Whole-exome sequencing analysis to identify novel potential pathogenetic mutations in fetuses with abnormal brain structure


ARCH models in Python

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

Scalable Bayesian dynamic covariance modeling with variational Wishart and inverse Wishart processes

Forecasting Bitcoin volatility spikes from whale transactions and CryptoQuant data using Synthesizer Transformer models

Estimating value at risk: LSTM vs. GARCH

Sector Volatility Prediction Performance Using GARCH Models and Artificial Neural Networks


The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.

The Human Phenotype Ontology in 2021

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease

dictyBase and the Dicty Stock Center (version 2.0) - a progress report.

The International journal of developmental biology

Transforming the study of organisms: Phenomic data models and knowledge bases

Quantitative analysis of proteins which are members of the same protein complex but cause locus heterogeneity in disease

Choosing preferable labels for the Japanese translation of the Human Phenotype Ontology


Repository for the Parallel Ice Sheet Model (PISM)

Contribution of the Greenland Ice Sheet to sea level over the next millennium

Antarctic sub-shelf melt rates via PICO

Glacial-cycle simulations of the Antarctic Ice Sheet with the Parallel Ice Sheet Model (PISM) – Part 2: Parameter ensemble analysis

Glacial-cycle simulations of the Antarctic Ice Sheet with the Parallel Ice Sheet Model (PISM) – Part 1: Boundary conditions and climatic forcing

From cyclic ice streaming to Heinrich-like events: the grow-and-surge instability in the Parallel Ice Sheet Model

A salty deep ocean as a prerequisite for glacial termination

Dynamic regimes of the Greenland Ice Sheet emerging from interacting melt-elevation and glacial isostatic adjustment feedbacks

Climate intervention on a high-emissions pathway could delay but not prevent West Antarctic Ice Sheet demise

Simulating interactive ice sheets in the multi-resolution AWI-ESM 1.2: A case study using SCOPE 1.0

Future sea level contribution from Antarctica inferred from CMIP5 model forcing and its dependence on precipitation ansatz


QUICsand: Quantifying QUIC Reconnaissance Scans and DoS Flooding Events

PROCEEDINGS OF THE 2021 ACM INTERNET MEASUREMENT CONFERENCE, IMC 2021

Revisiting QUIC attacks: a comprehensive review on QUIC security and a hands-on study

On the interplay between TLS certificates and QUIC performance

Proceedings of the 18th International Conference on emerging Networking EXperiments and Technologies

QUIC Hunter: Finding QUIC Deployments and Identifying Server Libraries Across the Internet

ECN with QUIC: Challenges in the Wild

Proceedings of the 2023 ACM on Internet Measurement Conference


A multi-scale, python-based library for the modelling of solar cells and semiconductor materials


Software package for assigning SARS-CoV-2 genome sequences to global lineages.

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

T cell responses to SARS-CoV-2 spike cross-recognize Omicron

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study

SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion

Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York

bioRxiv : the preprint server for biology

Detection of B.1.351 SARS-CoV-2 Variant Strain — Zambia, December 2020

MMWR. Morbidity and mortality weekly report


MISP (core software) - Open Source Threat Intelligence and Sharing Platform

Investigating Sharing of Cyber Threat Intelligence and Proposing A New Data Model for Enabling Automation in Knowledge Representation and Exchange

Open Dataset of Phishing and Tor Hidden Services Screen-captures

Collaborative Information Sharing for ML-Based Threat Detection

Carl-Hauser - Open Source Image Matching Algorithms Benchmarking Framework


A library to extract Code Property Graphs from C/C++, Java, Go, Python, Ruby and every other language through LLVM-IR.

Cloud Property Graph: Connecting Cloud Security Assessments with Static Code Analysis

International Conference on Cloud Computing

Privacy Property Graph: Towards Automated Privacy Threat Modeling via Static Graph-based Analysis

Proceedings on Privacy Enhancing Technologies

A Language-Independent Analysis Platform for Source Code

A Uniform Representation of Classical and Quantum Source Code for Static Code Analysis

Representing LLVM-IR in a Code Property Graph


AdelaiDet is an open source toolbox for multiple instance-level detection and recognition tasks.

FCOS: Fully Convolutional One-Stage Object Detection

Enhancing Geometric Factors in Model Learning and Inference for Object Detection and Instance Segmentation

SOLO: Segmenting Objects by Locations

Conditional Convolutions for Instance Segmentation

BlendMask: Top-Down Meets Bottom-Up for Instance Segmentation

ABCNet: Real-time Scene Text Spotting with Adaptive Bezier-Curve Network

Read Like Humans: Autonomous, Bidirectional and Iterative Language Modeling for Scene Text Recognition

BoxInst: High-Performance Instance Segmentation with Box Annotations

Mask Encoding for Single Shot Instance Segmentation

DirectPose: Direct End-to-End Multi-Person Pose Estimation


A scalable and versatile library to generate representations for atomic-scale learning

Physics-Inspired Structural Representations for Molecules and Materials

Efficient implementation of atom-density representations

Optimal radial basis for density-based atomic representations

Local invertibility and sensitivity of atomic structure-feature mappings

scikit-matter : A Suite of Generalisable Machine Learning Methods Born out of Chemistry and Materials Science

Comment on "Manifolds of quasi-constant SOAP and ACSF fingerprints and the resulting failure to machine learn four-body interactions" [J. Chem. Phys. 156, 034302 (2022)].

Ranking the synthesizability of hypothetical zeolites with the sorting hat


A Python-based toolbox of various methods in decision making, uncertainty quantification and statistical emulation: multi-fidelity, experimental design, Bayesian optimisation, Bayesian quadrature, etc.

BoTorch: A Framework for Efficient Monte-Carlo Bayesian Optimization

Deep Gaussian Processes for Multi-fidelity Modeling

Emulation of physical processes with Emukit

BOFFIN TTS: Few-Shot Speaker Adaptation by Bayesian Optimization

Meta-Surrogate Benchmarking for Hyperparameter Optimization

A Multi-Fidelity Emulator for the Matter Power Spectrum using Gaussian Processes

Preferential Batch Bayesian Optimization

Hyperparameter Transfer Learning with Adaptive Complexity

Residual Gaussian Process: A Tractable Nonparametric Bayesian Emulator for Multi-fidelity Simulations

Bayesian Optimisation for Sequential Experimental Design with Applications in Additive Manufacturing


Python 3 framework to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.

EasyVVUQ: A Library for Verification, Validation and Uncertainty Quantification in High Performance Computing

VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Uncertainty Quantification for Multiscale Fusion Plasma Simulations with VECMA Toolkit

Assessing uncertainties from physical parameters and modelling choices in an atmospheric large eddy simulation model

Epistemic and Aleatoric Uncertainty Quantification and Surrogate Modelling in High-Performance Multiscale Plasma Physics Simulations


ProjectQ: An open source software framework for quantum computing

Full-Stack, Real-System Quantum Computer Studies: Architectural Comparisons and Design Insights

QBugs: A Collection of Reproducible Bugs in Quantum Algorithms and a Supporting Infrastructure to Enable Controlled Quantum Software Testing and Debugging Experiments

Quantum computing with Qiskit

Efficient Implementation of PRESENT and GIFT on Quantum Computers


LightSeq: A High Performance Library for Sequence Processing and Generation

LightSeq: A High Performance Inference Library for Transformers

LightSeq2: Accelerated Training for Transformer-Based Models on GPUs

A Survey on Efficient Training of Transformers

Xiaomingbot: A Multilingual Robot News Reporter

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

The VolcTrans System for WMT22 Multilingual Machine Translation Task


:floppy_disk: C++ & Python API for Scientific I/O

Modeling of advanced accelerator concepts

Snowmass21 Accelerator Modeling Community White Paper

From Compact Plasma Particle Sources to Advanced Accelerators with Modeling at Exascale

Enabling High-Throughput Parallel I/O in Particle-in-Cell Monte Carlo
  Simulations with openPMD and Darshan I/O Monitoring


Reduce the environmental footprint of your software programs with SonarQube


Technical Analysis Library using Pandas and Numpy

A Hybrid Framework Using PCA, EMD and LSTM Methods for Stock Market Price Prediction with Sentiment Analysis

Deep Prediction of Investor Interest: a Supervised Clustering Approach

Improving Portfolio Performance Using a Novel Method for Predicting Financial Regimes


C library for finding and handling crystal symmetries

: a software library for crystal symmetry search

Expansion of the Materials Cloud 2D Database

Two-dimensional altermagnets from high throughput computational screening: Symmetry requirements, chiral magnons, and spin-orbit effects

Algorithms for magnetic symmetry operation search and identification of magnetic space group from magnetic crystal structure

Algorithm for spin symmetry operation search


A set of extension codes, utilities, and scripts for the enterprise PTA analysis framework.

Common-red-signal analysis with 24-yr high-precision timing of the European Pulsar Timing Array: inferences in the stochastic gravitational-wave background search

Monthly Notices of the Royal Astronomical Society

Astrophysics Milestones for Pulsar Timing Array Gravitational-wave Detection

Primordial gravitational waves in the nano-Hertz regime and PTA data — towards solving the GW inverse problem

Non-tensorial gravitational wave background in NANOGrav 12.5-year data set

中国科学. 物理学 力学 天文学

Noise analysis in the European Pulsar Timing Array data release 2 and its implications on the gravitational-wave background search

Fast Bayesian analysis of individual binaries in pulsar timing array data

Null energy condition violation during inflation and pulsar timing array observations

The NANOGrav 12.5 yr Data Set: Search for Gravitational Wave Memory

The NANOGrav 12.5 yr Data Set: A Computationally Efficient Eccentric Binary Search Pipeline and Constraints on an Eccentric Supermassive Binary Candidate in 3C 66B

Measuring kinematic anisotropies with pulsar timing arrays


FFCV: Fast Forward Computer Vision (and other ML workloads!)

A Cookbook of Self-Supervised Learning

Datamodels: Predicting Predictions from Training Data

The Effects of Regularization and Data Augmentation are Class Dependent

Distilling Model Failures as Directions in Latent Space

FFCV: Accelerating Training by Removing Data Bottlenecks

Matryoshka Representation Learning

A Data-Based Perspective on Transfer Learning

Compute-Efficient Deep Learning: Algorithmic Trends and Opportunities

On the Symmetries of Deep Learning Models and their Internal Representations

Guillotine Regularization: Why removing layers is needed to improve generalization in Self-Supervised Learning


Plant-for-the-Planet App allows you to plant trees with over 100 reforestation projects around the world.


A domain specific language for neuron and synapse models in spiking neural network simulation

NESTML: a modeling language for spiking neurons

Code Generation in Computational Neuroscience: A Review of Tools and Techniques

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

On Distribution Shift in Learning-based Bug Detectors

Automatically Selecting a Suitable Integration Scheme for Systems of Differential Equations in Neuron Models

Brain signal predictions from multi-scale networks using a linearized framework


Quantum Technology Toolbox https://qtt.readthedocs.io/

Quantum logic with spin qubits crossing the surface code threshold

Qubits made by advanced semiconductor manufacturing

Nagaoka ferromagnetism observed in a quantum dot plaquette

Loading a quantum-dot based “Qubyte” register

Electron cascade for distant spin readout


Stellarator Equilibrium and Optimization Suite

The DESC stellarator code suite Part 3: Quasi-symmetry optimization

The DESC Stellarator Code Suite Part I: Quick and accurate equilibria computations

The DESC Stellarator Code Suite Part II: Perturbation and continuation methods


HElib is an open-source software library that implements homomorphic encryption. It supports the BGV scheme with bootstrapping and the Approximate Number CKKS scheme. HElib also includes optimizations for efficient homomorphic evaluation, focusing on effective use of ciphertext packing techniques and on the Gentry-Halevi-Smart optimizations.

Advances and Open Problems in Federated Learning

F1: A Fast and Programmable Accelerator for Fully Homomorphic Encryption

PROCEEDINGS OF 54TH ANNUAL IEEE/ACM INTERNATIONAL SYMPOSIUM ON MICROARCHITECTURE, MICRO 2021

Homomorphic Encryption for Machine Learning in Medicine and Bioinformatics

EVA: an encrypted vector arithmetic language and compiler for efficient homomorphic computation

Programming Language Design and Implementation

Encrypted Control for Networked Systems: An Illustrative Introduction and Current Challenges

Survey on Fully Homomorphic Encryption, Theory, and Applications

FAB: An FPGA-based Accelerator for Bootstrappable Fully Homomorphic Encryption

Glyph: Fast and Accurately Training Deep Neural Networks on Encrypted Data

Accelerating Fully Homomorphic Encryption Through Architecture-Centric Analysis and Optimization

Effective Activation Functions for Homomorphic Evaluation of Deep Neural Networks


Extend cloud computing, data and service seamlessly to edge devices.

Convergence of Edge Computing and Deep Learning: A Comprehensive Survey

IEEE Communications Surveys and Tutorials

Fog Function: Serverless Fog Computing for Data Intensive IoT Services

Tailored Learning-Based Scheduling for Kubernetes-Oriented Edge-Cloud System

AI Augmented Edge and Fog Computing: Trends and Challenges

Computing Power Network: A Survey

Collaborative Learning-Based Scheduling for Kubernetes-Oriented Edge-Cloud Network


THIS REPOSITORY HAS MOVED TO github.com/nvidia/cub, WHICH IS AUTOMATICALLY MIRRORED HERE.

TurboTransformers: An Efficient GPU Serving System For Transformer Models

A Memory Bandwidth-Efficient Hybrid Radix Sort on GPUs

SIGMOD'17: PROCEEDINGS OF THE 2017 ACM INTERNATIONAL CONFERENCE ON MANAGEMENT OF DATA

Snap ML: A Hierarchical Framework for Machine Learning

Specifying and Testing GPU Workgroup Progress Models

Proceedings of the ACM on Programming Languages

MPU: Towards Bandwidth-abundant SIMT Processor via Near-bank Computing

MPU: Memory-centric SIMT Processor via In-DRAM Near-bank Computing

ACM Transactions on Architecture and Code Optimization (TACO)


Reach Biomedical Information Extraction

Large-scale automated machine reading discovers new cancer-driving mechanisms

Database : the journal of biological databases and curation

Automated assembly of molecular mechanisms at scale from text mining and curated databases

Automated detection of discourse segment and experimental types from the text of cancer pathway results sections

INDRA-IPM: interactive pathway modeling using natural language with automated assembly

Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining

This before That: Causal Precedence in the Biomedical Domain

Sieve-based Coreference Resolution in the Biomedical Domain

Swanson linking revisited: Accelerating literature-based discovery across domains using a conceptual influence graph

PROCEEDINGS OF THE 55TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS (ACL 2017): SYSTEM DEMONSTRATIONS

Learning what to read: Focused machine reading

Neural Architectures for Biological Inter-Sentence Relation Extraction


Laboratory automation for the behavioral and social sciences; human culture on a chip.

Gibbs Sampling with People

Exploring emotional prototypes in a high dimensional TTS latent space

Predicting Human Similarity Judgments Using Large Language Models

VoiceMe: Personalized voice generation in TTS

Timbral effects on consonance disentangle psychoacoustic mechanisms and suggest perceptual origins for musical scales

Putting the Con in Context: Identifying Deceptive Actors in the Game of Mafia

Fair group decisions via non-deterministic proportional consensus


:movie_camera: Python and OpenCV-based scene cut/transition detection program & library.

Stable Video Diffusion: Scaling Latent Video Diffusion Models to Large Datasets

Robots Learn Social Skills: End-to-End Learning of Co-Speech Gesture Generation for Humanoid Robots

Spot the conversation: speaker diarisation in the wild

LAVIE: High-Quality Video Generation with Cascaded Latent Diffusion Models

InternVid: A Large-scale Video-Text Dataset for Multimodal Understanding and Generation

Generic Event Boundary Detection: A Benchmark for Event Segmentation

Online Detection of Action Start in Untrimmed, Streaming Videos

A Deep Ranking Model for Spatio-Temporal Highlight Detection from a 360 Video

GIFdroid: Automated Replay of Visual Bug Reports for Android Apps

Partially Relevant Video Retrieval

Proceedings of the 30th ACM International Conference on Multimedia


NoSQL Redis and Memcache traffic generation and benchmarking tool.

Memory DoS Attacks in Multi-tenant Clouds: Severity and Mitigation

Trust Management as a Service: Enabling Trusted Execution in the Face of Byzantine Stakeholders

Kollaps: Decentralized and Dynamic Topology Emulation

TEEMon: A continuous performance monitoring framework for TEEs

Concerto: Dynamic Processor Scaling for Distributed Data Systems with Replication

Application-Oriented Data Migration to Accelerate In-Memory Database on Hybrid Memory

Async-fork: Mitigating Query Latency Spikes Incurred by the Fork-based Snapshot Mechanism from the OS Level

ROVN: Replica placement for distributed data system with heterogeneous memory devices

WELES: Policy-driven Runtime Integrity Enforcement of Virtual Machines

Design and Implementation of Burst Buffer Over-Subscription Scheme for HPC Storage Systems


:bar_chart: A universal enrichment tool for interpreting omics data

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

PRMD: an integrated database for plant RNA modifications

Effects of sex and aging on the immune cell landscape as assessed by single-cell transcriptomic analysis

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

clusterProfiler: An universal enrichment tool for functional and comparative study

Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma

De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar ‘Tieguanyin’ compared with cultivar ‘Benshan’

Integrated Analysis to Evaluate the Prognostic Value of Signature mRNAs in Glioblastoma Multiforme

Single-cell profiling reveals pathogenic role and differentiation trajectory of granzyme K+CD8+ T cells in primary Sjögren’s syndrome

Profiling mouse cochlear cell maturation using 10× Genomics single-cell transcriptomics

Radiation increases COL1A1, COL3A1, and COL1A2 expression in breast cancer


Construction and Comparison of High-Dimensional Sobol' Generators

Application of Quasi-Monte Carlo Methods to Elliptic PDEs with Random Diffusion Coefficients: A Survey of Analysis and Implementation

Algorithm 958

ACM Transactions on Mathematical Software

Guaranteed Conservative Fixed Width Confidence Intervals Via Monte Carlo Sampling

Quasi-Monte Carlo Software


Rayleigh: Pseudo-spectral MHD

Equatorially trapped convection in a rapidly rotating shallow shell

Constraining Global Solar Models through Helioseismic Analysis

Perspectives on Reproducibility and Sustainability of Open-Source Scientific Software from Seven Years of the Dedalus Project

MagIC v5.10: a two-dimensional message-passing interface (MPI) distribution for pseudo-spectral magnetohydrodynamics simulations in spherical geometry

Dataset for ApJ Letter: Confinement of the Solar Tachocline by Dynamo Action in the Radiative Interior

Zenodo (CERN European Organization for Nuclear Research)

Simulation data-set for ApJ Article: "Confinement of the Solar Tachocline by a Non-Axisymmetric Dynamo"


The Identity Overlay Network (ION) is a DID Method implementation using the Sidetree protocol atop Bitcoin

A Taxonomic Approach to Understanding Emerging Blockchain Identity Management Systems

A Tutorial on the Interoperability of Self-sovereign Identities

Digital identity architectures: comparing goals and vulnerabilities


An open source python package for implementing and developing standard methods for calculating normalized metered energy consumption and avoided energy use.

Empirical Estimation of the Energy Impacts of Projects Installed through Residential Property Assessed Clean Energy Financing Programs in California


Reed-Solomon Erasure Coding in Go

InfiniCache: Exploiting Ephemeral Serverless Functions to Build a Cost-Effective Memory Cache

Adding Forward Erasure Correction to QUIC

Leopard: Towards High Throughput-Preserving BFT for Large-scale Systems

JUMBO: Fully Asynchronous BFT Consensus Made Truly Scalable

BFT-DSN: A Byzantine Fault Tolerant Decentralized Storage Network


Image Super-Resolution for Anime-Style Art

Image Super-Resolution Using Deep Convolutional Networks

U-GAT-IT: Unsupervised Generative Attentional Networks with Adaptive Layer-Instance Normalization for Image-to-Image Translation

MontageGAN: Generation and Assembly of Multiple Components by GANs


Amplicon sequencing analysis workflow using DADA2 and QIIME2

DADA2: High-resolution sample inference from Illumina amplicon data

The nf-core framework for community-curated bioinformatics pipelines

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline

Arsenic mobilization by anaerobic iron-dependent methane oxidation

Identification of Bull Semen Microbiome by 16S Sequencing and Possible Relationships with Fertility

Prokaryotic and eukaryotic microbial diversity from three soda lakes in the East African Rift Valley determined by amplicon sequencing

Bacterial diversity in semen from stallions in three European countries evaluated by 16S sequencing

In Vitro Incubations Do Not Reflect In Vivo Differences Based on Ranking of Low and High Methane Emitters in Dairy Cows

Animals : an open access journal from MDPI

Diversity Profiling of Seed Associated Endophytic Microbiome in Important Species of Caricaceae Family


A lightweight parameter server interface

Parallel Distributed Logistic Regression for Vertical Federated Learning without Third-Party Coordinator

HET: Scaling out Huge Embedding Model Training via Cache-enabled Distributed Framework

MiCS: Near-linear Scaling for Training Gigantic Model on Public Cloud

Feature-Distributed SVRG for High-Dimensional Linear Classification


CMS Offline Software

Looking Inside Jets: An Introduction to Jet Substructure and Boosted-object Phenomenology

Jet flavour classification using DeepJet

Precise Simulation of Electromagnetic Calorimeter Showers Using a Wasserstein Generative Adversarial Network

9.6 Million Links in Source Code Comments: Purpose, Evolution, and Decay

FPGA-Accelerated Machine Learning Inference as a Service for Particle Physics Computing

GeantV: Results from the prototype of concurrent vector particle transport simulation in HEP

Observation of triple J/ψ meson production in proton-proton collisions

Strategic Plan for a Scientific Software Innovation Institute (S2I2) for High Energy Physics

Top tagging: an analytical perspective

Exploiting Apache Spark platform for CMS computing analytics


This tool lets you search your gadgets on your binaries to facilitate your ROP exploitation. ROPgadget supports ELF, PE and Mach-O format on x86, x64, ARM, ARM64, PowerPC, SPARC, MIPS, RISC-V 64, and RISC-V Compressed architectures.

Return-Oriented Programming on RISC-V

Analyzing the Gadgets Towards a Metric to Measure Gadget Quality

Tackling imbalanced data in cybersecurity with transfer learning: a case with ROP payload detection

A TOCTOU Attack on DICE Attestation

Proceedings of the Twelfth ACM Conference on Data and Application Security and Privacy

Reins to the Cloud: Compromising Cloud Systems via the Data Plane

Thwarting Code-Reuse and Side-Channel Attacks in Embedded Systems

From MMU to MPU: Adaptation of the Pip Kernel to Constrained Devices

Artificial Intelligence, Soft Computing and Applications

MAJORCA: Multi-Architecture JOP and ROP Chain Assembler


OWL API main repository

An ontology-guided semantic data integration framework to support integrative data analysis of cancer survival

BMC medical informatics and decision making

Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools

Methods in molecular biology (Clifton, N.J.)

A Rule-Based Reasoner for Underwater Robots Using OWL and SWRL

Development Experience of a Context-Aware System for Smart Irrigation Using CASO and IRRIG Ontologies

The CaLiGraph Ontology as a Challenge for OWL Reasoners

Integroly: Automatic Knowledge Graph Population from Social Big Data in the Political Marketing Domain

OWLSIZ: An isiZulu CNL for structured knowledge validation

Leveraging Algorithms to Improve Decision-Making Workflows for Genomic Data Access and Management

When one Logic is Not Enough: Integrating First-order Annotations in OWL Ontologies

An Alignment-Based Implementation of a Holistic Ontology Integration Method


Non-Metric Space Library (NMSLIB): An efficient similarity search library and a toolkit for evaluation of k-NN methods for generic non-metric spaces.

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

Approximate Nearest Neighbor Search on High Dimensional Data — Experiments, Analyses, and Improvement

IEEE Transactions on Knowledge and Data Engineering

Fast Approximate Nearest Neighbor Search With The Navigating Spreading-out Graph

Consensus-Driven Propagation in Massive Unlabeled Data for Face Recognition

Optimization of Indexing Based on k-Nearest Neighbor Graph for Proximity Search in High-dimensional Data

Off the Beaten Path: Let's Replace Term-Based Retrieval with k-NN Search

International Conference on Information and Knowledge Management

Permutation Search Methods are Efficient, Yet Faster Search is Possible

Extreme Multi-label Learning for Semantic Matching in Product Search

High Dimensional Similarity Search with Satellite System Graph: Efficiency, Scalability, and Unindexed Query Compatibility

FreshDiskANN: A Fast and Accurate Graph-Based ANN Index for Streaming Similarity Search