qFit: Automated and unbiased multi-conformer models from X-ray and EM maps.

Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

Ligand binding remodels protein side chain conformational heterogeneity

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.

qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data

bioRxiv : the preprint server for biology


Mutation Identification Pipeline. Read the latest documentation:

Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26

Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism

Rare variants in the outcome of social skills group training for autism

Novel Cysteine-Sparing Hypomorphic NOTCH3 A1604T Mutation Observed in a Family With Migraine and White Matter Lesions

Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis


Repository for nvCOMP docs and examples. nvCOMP is a library for fast lossless compression/decompression on the GPU that can be downloaded from https://developer.nvidia.com/nvcomp.

MGARD: A multigrid framework for high-performance, error-controlled data compression and refactoring

Accelerating GPU-Based Out-of-Core Stencil Computation with On-the-Fly Compression

FZ-GPU: A Fast and High-Ratio Lossy Compressor for Scientific Computing Applications on GPUs

Proceedings of the 32nd International Symposium on High-Performance Parallel and Distributed Computing

GPULZ: Optimizing LZSS Lossless Compression for Multi-byte Data on Modern GPUs

A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications

FCBench: Cross-Domain Benchmarking of Lossless Compression for Floating-Point Data

L3: Accelerator-Friendly Lossless Image Format for High-Resolution, High-Throughput DNN Training


lumpy: a general probabilistic framework for structural variant discovery

LUMPY: a probabilistic framework for structural variant discovery

One-step generation of complete gene knockout mice and monkeys by CRISPR/Cas9-mediated gene editing with multiple sgRNAs

Whole-genome CNV analysis: advances in computational approaches

CRISPR/Cas9-mediated targeted chromosome elimination

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features

Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections

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

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy

Parliament2: Accurate structural variant calling at scale

Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia


Shed Skin is a restricted-Python-to-C++ compiler. Read the introduction below to learn about the restrictions.

Svar: A Tiny C++ Header Brings Unified Interface for Multiple programming Languages

Efficient and Accurate Automatic Python Bindings with cppyy & Cling


CLIP-like model evaluation

LAION-5B: An open large-scale dataset for training next generation image-text models

LiT: Zero-Shot Transfer with Locked-image text Tuning

Scaling Language-Image Pre-training via Masking

What does a platypus look like? Generating customized prompts for zero-shot image classification

AltCLIP: Altering the Language Encoder in CLIP for Extended Language Capabilities

CiT: Curation in Training for Effective Vision-Language Data

NLLB-CLIP -- train performant multilingual image retrieval model on a budget

LOVM: Language-Only Vision Model Selection

Babel-ImageNet: Massively Multilingual Evaluation of Vision-and-Language Representations


Code for the TCAV ML interpretability project

Interpretability Beyond Feature Attribution: Quantitative Testing with Concept Activation Vectors (TCAV)

Explainable AI Methods - A Brief Overview

Survey of Explainable AI Techniques in Healthcare

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

TCAV: Relative concept importance testing with Linear Concept Activation Vectors


Mt-KaHyPar (Multi-Threaded Karlsruhe Hypergraph Partitioner) is a shared-memory multilevel graph and hypergraph partitioner equipped with parallel implementations of techniques used in the best sequential partitioning algorithms. Mt-KaHyPar can partition extremely large hypergraphs very fast and with high quality.

Shared-Memory n-level Hypergraph Partitioning

Parallel Flow-Based Hypergraph Partitioning

Scalable High-Quality Hypergraph Partitioning

Parallel Unconstrained Local Search for Partitioning Irregular Graphs


Code for the paper "Language Models are Unsupervised Multitask Learners"

Generating Sentiment-Preserving Fake Online Reviews Using Neural Language Models and Their Human- and Machine-based Detection

Generating Counter Narratives against Online Hate Speech: Data and Strategies

Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues

Workshop on Biomedical Natural Language Processing

Can Machines Tell Stories? A Comparative Study of Deep Neural Language Models and Metrics

Training Optimus Prime, M.D.: Generating Medical Certification Items by Fine-Tuning OpenAI's gpt2 Transformer Model


[vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium

Peptide–MHC Class I Tetramers Can Fail To Detect Relevant Functional T Cell Clonotypes and Underestimate Antigen-Reactive T Cell Populations

Inferring the T cell repertoire dynamics of healthy individuals

Predicting recognition between T cell receptors and epitopes using contextualized motifs


Implementation of various string similarity and distance algorithms: Levenshtein, Jaro-winkler, n-Gram, Q-Gram, Jaccard index, Longest Common Subsequence edit distance, cosine similarity ...

Ontology Alignment Based on Word Embedding and Random Forest Classification

MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2018, PT I

Towards Anticipation of Architectural Smells using Link Prediction Techniques

Learning to Diagnose: Assimilating Clinical Narratives using Deep Reinforcement Learning

International Joint Conference on Natural Language Processing

Visualizing test diversity to support test optimisation

Using mutation testing to measure behavioural test diversity

International Conference on Software Testing, Verification and Validation Workshops

Estimating Uniqueness of I-Vector Representation of Human Voice

Too Slow to Be Useful? On Incorporating Humans in the Loop of Smart Speakers

Ensemble-Based Relationship Discovery in Relational Databases


An open-source tool-augmented conversational language model from Fudan University

A Survey of Large Language Models

CodeGen: An Open Large Language Model for Code with Multi-Turn Program Synthesis

C-Eval: A Multi-Level Multi-Discipline Chinese Evaluation Suite for Foundation Models

VisionLLM: Large Language Model is also an Open-Ended Decoder for Vision-Centric Tasks

Instruction Tuning for Large Language Models: A Survey

VideoChat: Chat-Centric Video Understanding

GPT4RoI: Instruction Tuning Large Language Model on Region-of-Interest

LLM-Blender: Ensembling Large Language Models with Pairwise Ranking and Generative Fusion

Skywork: A More Open Bilingual Foundation Model

InternGPT: Solving Vision-Centric Tasks by Interacting with ChatGPT Beyond Language


A Unified Framework for Surface Reconstruction

Viewpoint Textual Inversion: Unleashing Novel View Synthesis with Pretrained 2D Diffusion Models

Neural digital twins: reconstructing complex medical environments for spatial planning in virtual reality

International journal of computer assisted radiology and surgery

Active Neural 3D Reconstruction with Colorized Surface Voxel-based View Selection

The Sky's the Limit: Re-lightable Outdoor Scenes via a Sky-pixel Constrained Illumination Prior and Outside-In Visibility


Foundation Architecture for (M)LLMs

Language Is Not All You Need: Aligning Perception with Language Models

Retentive Network: A Successor to Transformer for Large Language Models

DeepNet: Scaling Transformers to 1,000 Layers

LongNet: Scaling Transformers to 1,000,000,000 Tokens

A Length-Extrapolatable Transformer

On the Representation Collapse of Sparse Mixture of Experts

Adapting Large Language Models via Reading Comprehension

Stabilizing Transformer Training by Preventing Attention Entropy Collapse

Foundation Transformers

TorchScale: Transformers at Scale


a fast and user-friendly runtime for transformer inference (Bert, Albert, GPT2, Decoders, etc) on CPU and GPU.

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

RoBERTa: A Robustly Optimized BERT Pretraining Approach

ALBERT: A Lite BERT for Self-supervised Learning of Language Representations

TurboTransformers: An Efficient GPU Serving System For Transformer Models

Scale-out Systolic Arrays


Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to  Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA

PROTAC-Design-Evaluator (PRODE): An Advanced Method for In-Silico PROTAC Design

Harnessing Protein-Ligand Interaction Fingerprints to Predict New Scaffolds of RIPK1 Inhibitors


Real-time Precise Point Positioning with a Xiaomi MI 8 Android Smartphone

RTK with the Assistance of an IMU-Based Pedestrian Navigation Algorithm for Smartphones

Ionosphere-Constrained Single-Frequency PPP with an Android Smartphone and Assessment of GNSS Observations


Python library to facilitate genome assembly, annotation, and comparative genomics

ALLMAPS: robust scaffold ordering based on multiple maps

A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

Analysis of the Coptis chinensis genome reveals the diversification of protoberberine-type alkaloids

Catalase (CAT) Gene Family in Rapeseed (Brassica napus L.): Genome-Wide Analysis, Identification, and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions

International journal of molecular sciences

Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly

The EccDNA Replicon: A Heritable, Extranuclear Vehicle That Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri.

Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions

De novo phased assembly of the Vitis riparia grape genome

A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]


DBpedia Spotlight is a tool for automatically annotating mentions of DBpedia resources in text.

Label Embedding for Zero-shot Fine-grained Named Entity Typing

International Conference on Computational Linguistics

Weakly-supervised Relation Extraction by Pattern-enhanced Embedding Learning

The Online Dissemination of Nature–Health Concepts: Lessons from Sentiment Analysis of Social Media Relating to “Nature-Deficit Disorder”

International journal of environmental research and public health

Automatic Synonym Discovery with Knowledge Bases

Semantic homophily in online communication: evidence from Twitter

OntoSeg: A Novel Approach to Text Segmentation Using Ontological Similarity

Combining Open Source Annotators for Entity Linking through Weighted Voting

Joint Conference on Lexical and Computational Semantics

A Context-Aware Conversational Agent in the Rehabilitation Domain

Supporting the Linked Data Life Cycle Using an Integrated Tool Stack

Linked Open Data -- Creating Knowledge Out of Interlinked Data

Building Enterprise Ready Applications Using Linked Open Data


TPRF: The Two-Particle Response Function tool box for TRIQS

Strongly Correlated Materials from a Numerical Renormalization Group Perspective: How the Fermi-Liquid State of Sr 2 RuO 4 Emerges

Magnetic response of Sr2RuO4: Quasi-local spin fluctuations due to Hund's coupling

Distinct spin and orbital dynamics in Sr_2RuO_4

Larmor precession in strongly correlated itinerant electron systems

Dual Bethe-Salpeter equation for the multiorbital lattice susceptibility within dynamical mean-field theory

Second-order phase transitions and divergent linear response in dynamical mean-field theory


Unofficial Parallel WaveGAN (+ MelGAN & Multi-band MelGAN & HiFi-GAN & StyleMelGAN) with Pytorch

FastSpeech 2: Fast and High-Quality End-to-End Text to Speech

WaveGrad: Estimating Gradients for Waveform Generation

A Survey on Neural Speech Synthesis

Recent Developments on ESPnet Toolkit Boosted by Conformer

Voice Transformer Network: Sequence-to-Sequence Voice Conversion Using Transformer with Text-to-Speech Pretraining

WaveFake: A Data Set to Facilitate Audio Deepfake Detection

ISTFTNET: Fast and Lightweight Mel-Spectrogram Vocoder Incorporating Inverse Short-Time Fourier Transform

Emotion Intensity and its Control for Emotional Voice Conversion

IEEE Transactions on Affective Computing

The 2020 ESPnet Update: New Features, Broadened Applications, Performance Improvements, and Future Plans

Audiodec: An Open-Source Streaming High-Fidelity Neural Audio Codec

IEEE International Conference on Acoustics, Speech, and Signal Processing


A Semi-Automated Machine Learning Pipeline. Developed by the Shiu Lab. Implemented using SciKit-Learn

Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots1[OPEN]

The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

Within- and cross-species predictions of plant specialized metabolism genes using transfer learning

Modeling alternative translation initiation sites in plants reveals evolutionarily conservedcis-regulatory codes in eukaryotes


Open source code for AlphaFold.

Highly accurate protein structure prediction with AlphaFold

Highly accurate protein structure prediction for the human proteome

Improved prediction of protein-protein interactions using AlphaFold2

Before and after AlphaFold2: An overview of protein structure prediction

How good are AlphaFold models for docking-based virtual screening?

Artificial intelligence for drug discovery: Resources, methods, and applications

xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning

AFsample: improving multimer prediction with AlphaFold using massive sampling

Unraveling the functional dark matter through global metagenomics


AI for Global Climate Cooperation: Modeling Global Climate Negotiations, Agreements, and Long-Term Cooperation in RICE-N. ai4climatecoop.org

WarpDrive: Extremely Fast End-to-End Deep Multi-Agent Reinforcement Learning on a GPU


Data package: conventional power plants


The OLD Gazebo Simulation repository.

The MRS UAV System: Pushing the Frontiers of Reproducible Research, Real-world Deployment, and Education with Autonomous Unmanned Aerial Vehicles

Journal of Intelligent and Robotic Systems

MRS Modular UAV Hardware Platforms for Supporting Research in Real-World Outdoor and Indoor Environments

International Conference on Unmanned Aircraft Systems

MRS Drone: A Modular Platform for Real-World Deployment of Aerial Multi-Robot Systems

New Era in Cultural Heritage Preservation: Cooperative Aerial Autonomy for Fast Digitalization of Difficult-to-Access Interiors of Historical Monuments


Automatic metrics for GEM tasks

Large Language Models Can Be Strong Differentially Private Learners

RAFT: Reward rAnked FineTuning for Generative Foundation Model Alignment

ExT5: Towards Extreme Multi-Task Scaling for Transfer Learning

MVP: Multi-task Supervised Pre-training for Natural Language Generation

Automatic Construction of Evaluation Suites for Natural Language Generation Datasets

BEAMetrics: A Benchmark for Language Generation Evaluation Evaluation

The Whole Truth and Nothing But the Truth: Faithful and Controllable Dialogue Response Generation with Dataflow Transduction and Constrained Decoding

ASPIRO: Any-shot Structured Parsing-error-Induced ReprOmpting for Consistent Data-to-Text Generation


Stellar Population Synthesis Modeling

PopSyCLE: A New Population Synthesis Code for Compact Object Microlensing Events

SPISEA: A Python-based Simple Stellar Population Synthesis Code for Star Clusters

Gravitational Microlensing Event Statistics for the Zwicky Transient Facility

Primordial Black Hole Dark Matter Simulations Using PopSyCLE


Creative Commons Attribution Share Alike 4.0 International

Open intercharge Protocol

Mobility in the Smart Grid: Roaming Protocols for EV Charging

An Overview of EV Roaming Protocols

Enabling EV Roaming Through Cascading WebSockets in OCPP 1.6

Journal Européen des Systèmes Automatisés


BirdNET analyzer for scientific audio data processing.

BirdNET: A deep learning solution for avian diversity monitoring

Global birdsong embeddings enable superior transfer learning for bioacoustic classification

Hearing to the Unseen: AudioMoth and BirdNET as a Cheap and Easy Method for Monitoring Cryptic Bird Species

Large-scale avian vocalization detection delivers reliable global biodiversity insights

Automated detection of gibbon calls from passive acoustic monitoring
  data using convolutional neural networks in the "torch for R" ecosystem

Correlation Clustering of Bird Sounds


Fast, general, and tested differentiable structured prediction in PyTorch

Fast and Accurate Neural CRF Constituency Parsing

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

Torch-Struct: Deep Structured Prediction Library

SynJax: Structured Probability Distributions for JAX


HTSeq is a Python library to facilitate processing and analysis of data from  high-throughput sequencing (HTS) experiments.

Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response

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

Genome-Scale CRISPR Knockout Screening Identifies BACH1 as a Key Regulator of Aflatoxin B1-Induced Oxidative Damage

Transcriptome-Guided Identification of Drugs for Repurposing to Treat Age-Related Hearing Loss

Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension

Deciphering the dynamic niches and regeneration-associated transcriptional program of motoneurons following peripheral nerve injury

Single cell qtSEQ: Cell-indexed quantitative and targeted RNA sequencing for sorted rare lymphocyte subpopulations

Sustained Stimulation of β2AR Inhibits Insulin Signaling in H9C2 Cardiomyoblast Cells Through the PKA-Dependent Signaling Pathway

Diabetes, metabolic syndrome and obesity : targets and therapy

Transcriptomic signatures associated with autoimmune thyroiditis in papillary thyroid carcinoma and cancer immunotherapy-induced thyroid dysfunction

Computational and structural biotechnology journal

Analysing high-throughput sequencing data in Python with HTSeq 2.0


Optimal Control for Switched Systems

Perceptive Locomotion Through Nonlinear Model-Predictive Control

Articulated Object Interaction in Unknown Scenes with Whole-Body Mobile Manipulation

Combining Learning-based Locomotion Policy with Model-based Manipulation for Legged Mobile Manipulators

Adaptive CLF-MPC With Application to Quadrupedal Robots

International Conference on Robotics and Automation

A Collision-Free MPC for Whole-Body Dynamic Locomotion and Manipulation

Offline motion libraries and online MPC for advanced mobility skills

The International Journal of Robotics Research

Versatile multicontact planning and control for legged loco-manipulation

N^2M^2: Learning Navigation for Arbitrary Mobile Manipulation Motions in Unseen and Dynamic Environments

Planar Bipedal Locomotion with Nonlinear Model Predictive Control: Online Gait Generation using Whole-Body Dynamics

Dadu-RBD: Robot Rigid Body Dynamics Accelerator with Multifunctional Pipelines


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

Programming Language Design and Implementation

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

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

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

Faster Secure Data Mining via Distributed Homomorphic Encryption

ScionFL: Efficient and Robust Secure Quantized Aggregation

Privacy and Integrity Preserving Computations with CRISP

FHEBench: Benchmarking Fully Homomorphic Encryption Schemes

MPC-Pipe: an Efficient Pipeline Scheme for Secure Multi-party Machine Learning Inference

A efficient and robust privacy-preserving framework for cross-device federated learning


Cedille, a dependently typed programming languages based on the Calculus of Dependent Lambda Eliminations

Elaborating Inductive Definitions and Course-of-Values Induction in Cedille.

Efficient lambda encodings for Mendler-style coinductive types in Cedille


Monte Carlo eXtreme (MCX) - GPU-accelerated photon transport simulator

A hybrid mesh and voxel based Monte Carlo algorithm for accurate and efficient photon transport modeling in complex bio-tissues

MCDataset: a public reference dataset of Monte Carlo simulated quantities for multilayered and voxelated tissues computed by massively parallel PyXOpto Python package

Quantitative photoacoustic estimates of intervascular blood oxygenation differences using linear unmixing

Effects of atlas-based anatomy on modelled light transport in the neonatal head


DataComp: In search of the next generation of multimodal datasets

The Devil is in the Details: A Deep Dive into the Rabbit Hole of Data Filtering

Blind Baselines Beat Membership Inference Attacks for Foundation Models

Variance Alignment Score: A Simple But Tough-to-Beat Data Selection
  Method for Multimodal Contrastive Learning


A higher-level Neural Network library for microcontrollers.

A Comprehensive Review and a Taxonomy of Edge Machine Learning: Requirements, Paradigms, and Techniques

Echo State Networks for Estimating Exteroceptive Conditions From Proprioceptive States in Quadruped Robots

Evaluation of Convolution Primitives for Embedded Neural Networks on 32-bit Microcontrollers

Evaluation of Parameter-based Attacks against Embedded Neural Networks with Laser Injection


A PyTorch library for all things Reinforcement Learning (RL) for Combinatorial Optimization (CO)

Attention, Learn to Solve Routing Problems!

RL4CO: an Extensive Reinforcement Learning for Combinatorial Optimization Benchmark

Ant Colony Sampling with GFlowNets for Combinatorial Optimization

Enhancing Sample Efficiency in Black-box Combinatorial Optimization via Symmetric Replay Training

Ensembling Prioritized Hybrid Policies for Multi-agent Pathfinding

RouteFinder: Towards Foundation Models for Vehicle Routing Problems

Tackling Prevalent Conditions in Unsupervised Combinatorial Optimization: Cardinality, Minimum, Covering, and More


A toolkit for robot learning research.

RLBench: The Robot Learning Benchmark & Learning Environment

Transferring End-to-End Visuomotor Control from Simulation to Real World for a Multi-Stage Task

Task-Embedded Control Networks for Few-Shot Imitation Learning

PyRep: Bringing V-REP to Deep Robot Learning

Instruction-Following Agents with Multimodal Transformer


Framework-agnostic implementation for state-of-the-art saliency methods (XRAI, BlurIG, SmoothGrad, and more).

SmoothGrad: removing noise by adding noise

Toward Trustworthy AI Development: Mechanisms for Supporting Verifiable Claims

XRAI: Better Attributions Through Regions

A Survey of Deep Learning for Scientific Discovery

Guided Integrated Gradients: An Adaptive Path Method for Removing Noise

Attribution in Scale and Space

Detection of signs of disease in external photographs of the eyes via deep learning

Understanding Impacts of High-Order Loss Approximations and Features in Deep Learning Interpretation

Shared Interest: Measuring Human-AI Alignment to Identify Recurring Patterns in Model Behavior

A Primer on the Inner Workings of Transformer-based Language Models


This is an open-source implementation of the ITU P.808 standard for "Subjective evaluation of speech quality with a crowdsourcing approach" (see https://www.itu.int/rec/T-REC-P.808/en). It uses Amazon Mechanical Turk as the crowdsourcing platform. It includes implementations for Absolute Category Rating (ACR), Degradation Category Rating (DCR), and Comparison Category Rating (CCR).

The INTERSPEECH 2020 Deep Noise Suppression Challenge: Datasets, Subjective Testing Framework, and Challenge Results

Interspeech 2021 Deep Noise Suppression Challenge

The INTERSPEECH 2020 Deep Noise Suppression Challenge: Datasets, Subjective Speech Quality and Testing Framework

An Open source Implementation of ITU-T Recommendation P.808 with Validation

ICASSP 2021 Acoustic Echo Cancellation Challenge: Datasets, Testing Framework, and Results

ICASSP 2022 Acoustic Echo Cancellation Challenge

Subjective Evaluation of Noise Suppression Algorithms in Crowdsourcing

Crowdsourcing approach for subjective evaluation of echo impairment

Application of Just-Noticeable Difference in Quality as Environment Suitability Test for Crowdsourcing Speech Quality Assessment Task

Deep model with built-in cross-attention alignment for acoustic echo cancellation


Patator is a multi-purpose brute-forcer, with a modular design and a flexible usage.

Flow-Based Web Application Brute-Force Attack and Compromise Detection

Journal of Network and Systems Management

In Search of netUnicorn: A Data-Collection Platform to Develop Generalizable ML Models for Network Security Problems

Proceedings of the 2023 ACM SIGSAC Conference on Computer and Communications Security

netFound: Foundation Model for Network Security


Pipeline of tools to process raw fastq data and produce meaningful genomic data

Single-cell derived tumor organoids display diversity in HLA class I peptide presentation

Precancerous liver diseases do not cause increased mutagenesis in liver stem cells

Zenodo (CERN European Organization for Nuclear Research)

Rapid identification of genomic structural variations with nanopore sequencing enables blood-based cancer monitoring


Synthesizer - a code for creating synthetic astrophysical observables

First Light and Reionization Epoch Simulations (flares) - XIV. The Balmer/4000 Å breaks of distant galaxies


A Toolbox for Adversarial Robustness Research

Reliable evaluation of adversarial robustness with an ensemble of diverse parameter-free attacks

EAD: Elastic-Net Attacks to Deep Neural Networks via Adversarial Examples

advertorch v0.1: An Adversarial Robustness Toolbox based on PyTorch

Foolbox Native: Fast adversarial attacks to benchmark the robustness of machine learning models in PyTorch, TensorFlow, and JAX

Adversarial Examples on Object Recognition: A Comprehensive Survey

Composite Adversarial Attacks

SpoC: Spoofing Camera Fingerprints

MALI: A memory efficient and reverse accurate integrator for Neural ODEs

Scattering Model Guided Adversarial Examples for SAR Target Recognition: Attack and Defense

DISCO: Adversarial Defense with Local Implicit Functions


Awful AI is a curated list to track current scary usages of AI - hoping to raise awareness

Toward Trustworthy AI Development: Mechanisms for Supporting Verifiable Claims

Social Network Structure as a Predictor of Social Behavior: The Case of Protest in the 2016 US Presidential Election

The AI Incident Database as an Educational Tool to Raise Awareness of AI Harms: A Classroom Exploration of Efficacy, Limitations, & Future Improvements

Prioritizing Policies for Furthering Responsible Artificial Intelligence in the United States


Linear framework to combine tractography and tissue micro-structure estimation with diffusion MRI

Microstructure Informed Tractography: Pitfalls and Open Challenges

Resolving bundle-specific intra-axonal T2 values within a voxel using diffusion-relaxation tract-based estimation

Plis de passage in the superior temporal sulcus: Morphology and local connectivity

Fiber up‐sampling and quality assessment of tractograms – towards quantitative brain connectivity

The human brain connectome weighted by the myelin content and total intra-axonal cross-sectional area of white matter tracts

Incorporating outlier information into diffusion-weighted MRI modeling for robust microstructural imaging and structural brain connectivity analyses

Evaluation of tractogram filtering methods using human-like connectome phantoms


Automated reaction pathway search for gas-phase molecules

KinBot: Automated stationary point search on potential energy surfaces

Unimolecular Reaction Pathways of a γ-Ketohydroperoxide from Combined Application of Automated Reaction Discovery Methods

Journal of the American Chemical Society

Adventures on the C3H5O potential energy surface: OH+propyne, OH+allene and related reactions

Pressure-Dependent Competition among Reaction Pathways from First- and Second-O2 Additions in the Low-Temperature Oxidation of Tetrahydrofuran

Influence of oxygenation in cyclic hydrocarbons on chain-termination reactions from R + O2: tetrahydropyran and cyclohexane

Decomposition and isomerization of 1-pentanol radicals and the pyrolysis of 1-pentanol

Quantitative Detection of Products and Radical Intermediates in Low-Temperature Oxidation of Cyclopentane.

Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane.

A Combined Experimental and Theoretical Study of the Reaction OH + 2-Butene in the 400-800 K Temperature Range.

A New Pathway for Intersystem Crossing: Unexpected Products in the O(3P) + Cyclopentene Reaction.


BERT score for text generation

BERTScore: Evaluating Text Generation with BERT

BLEURT: Learning Robust Metrics for Text Generation

Automated Concatenation of Embeddings for Structured Prediction

BRIO: Bringing Order to Abstractive Summarization

DiffuSeq: Sequence to Sequence Text Generation with Diffusion Models

TRUE: Re-evaluating Factual Consistency Evaluation

Automatic Machine Translation Evaluation in Many Languages via Zero-Shot Paraphrasing

CM3: A Causal Masked Multimodal Model of the Internet

AlignScore: Evaluating Factual Consistency with A Unified Alignment Function

Like hiking? You probably enjoy nature: Persona-grounded Dialog with Commonsense Expansions


A machine learning toolkit for log parsing [ICSE'19, DSN'16]

Tools and Benchmarks for Automated Log Parsing

Log-based Anomaly Detection Without Log Parsing

Log-based Anomaly Detection with Deep Learning: How Far Are We?

Proceedings of the 44th International Conference on Software Engineering

Self-Supervised Log Parsing

UniParser: A Unified Log Parser for Heterogeneous Log Data

Multi-Scale One-Class Recurrent Neural Networks for Discrete Event Sequence Anomaly Detection

Log Parsing with Prompt-based Few-shot Learning

Log Parsing: How Far Can ChatGPT Go?

A Directed Acyclic Graph Approach to Online Log Parsing

A Comprehensive Survey of Logging in Software: From Logging Statements Automation to Log Mining and Analysis


High-quality Nanopore-only genome polisher

Comparison of De Novo Assembly Strategies for Bacterial Genomes

International journal of molecular sciences

The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS

Insight into the Mechanisms of Carbapenem Resistance in Klebsiella pneumoniae: A Study on IS26 Integrons, Beta-Lactamases, Porin Modifications, and Plasmidome Analysis

Integrative and Conjugative Elements and Prophage DNA as Carriers of Resistance Genes in Erysipelothrix rhusiopathiae Strains from Domestic Geese in Poland

International Journal of Molecular Sciences


WashU Epigenome Browser

WashU Epigenome Browser update 2022

The qBED track: a novel genome browser visualization for point processes

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser


MITIE: library and tools for information extraction

A Survey on Deep Learning Toolkits and Libraries for Intelligent User Interfaces

Adaptive Geoparsing Method for Toponym Recognition and Resolution in Unstructured Text

GeoAnnotator: A Collaborative Semi-Automatic Platform for Constructing Geo-Annotated Text Corpora

ISPRS International Journal of Geo-Information

Incorporating Trustiness and Collective Synonym/Contrastive Evidence into Taxonomy Construction

Empirical Methods in Natural Language Processing

Query Interpretations from Entity-Linked Segmentations

Antibody Exchange: Information Extraction of Biological Antibody Donation and a Web-Portal to Find Donors and Seekers

International Conference on Data Technologies and Applications

Utilisation des relations d'une base de connaissances pour la désambigud'entités nommées (Using the Relations of a Knowledge Base to Improve Entity Linking )

NLU-Co at SemEval-2020 Task 5: NLU/SVM Based Model Apply Tocharacterise and Extract Counterfactual Items on Raw Data

International Workshop on Semantic Evaluation

Bio-Resource Exchange: Study of Prevalence of Antibody Donation and Development of a Web Portal to Facilitate it


Official repository for Semantic Web for Earth and Environmental Terminology (SWEET) Ontologies

Ontology engineering methodologies for the evolution of living and reused ontologies: status, trends, findings and recommendations

Artificial intelligence in space


Find dates inside text using Python and get back datetime objects

Looking Beyond IoCs: Automatically Extracting Attack Patterns from External CTI

An Empirical Study on Code Comment Completion

Unsupervised Key Event Detection from Massive Text Corpora

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

htmldate: A Python package to extract publication dates from web pages

Unsupervised Evaluation of Code LLMs with Round-Trip Correctness


Who Are You? Bayesian Prediction of Racial Category Using Surname and Geolocation

Racial and Gender Disparities among Evicted Americans

Addressing census data problems in race imputation via fully Bayesian Improved Surname Geocoding and name supplements

At‐Large Elections and Minority Representation in Local Government

Enhancing Race and Ethnicity using Bayesian Imputation in an All Payer Claims Database


ALBERT: A Lite BERT for Self-supervised Learning of Language Representations

Pre-trained models for natural language processing: A survey

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing

A Survey on Text Classification: From Shallow to Deep Learning

A Comprehensive Survey of AI-Generated Content (AIGC): A History of Generative AI from GAN to ChatGPT

CLUE: A Chinese Language Understanding Evaluation Benchmark

Token-Aware Virtual Adversarial Training in Natural Language Understanding

Deep Learning-Based Natural Language Processing for Screening Psychiatric Patients

How to decay your learning rate

Event Clustering within News Articles


The open-sourced Python toolbox for backdoor attacks and defenses.

Black-Box Dataset Ownership Verification via Backdoor Watermarking

BackdoorBox: A Python Toolbox for Backdoor Learning

Domain Watermark: Effective and Harmless Dataset Copyright Protection is Closed at Hand

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

Defending Against Backdoor Attacks by Layer-wise Feature Analysis

Nearest is Not Dearest: Towards Practical Defense against
  Quantization-conditioned Backdoor Attacks

IBD-PSC: Input-level Backdoor Detection via Parameter-oriented Scaling
  Consistency

Poisoning-Based Backdoor Attacks in Computer Vision

Proceedings of the AAAI Conference on Artificial Intelligence


IEEE 802.11 a/g/p Transceiver

Fair Coexistence of Scheduled and Random Access Wireless Networks: Unlicensed LTE/WiFi

Colosseum as a Digital Twin: Bridging Real-World Experimentation and Wireless Network Emulation

Channel Measurement and Feasibility Test for Wireless Avionics Intra-Communications

Transparent and Tamper-Proof Event Ordering in the Internet of Things Platforms


A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations

Computational cancer neoantigen prediction: current status and recent advances

ProTECT—Prediction of T-Cell Epitopes for Cancer Therapy


Monte Carlo Simulation propagating charged Leptons through Media as C++ Library

PROPOSAL: A library to propagate leptons and high energy photons

A C++ Cherenkov photons simulation in CORSIKA 8

The effect of improved high-energy muon cross-sections

Improvements in charged lepton and photon propagation for the software PROPOSAL


✨Fast Coreference Resolution in spaCy with Neural Networks

Visual Coreference Resolution in Visual Dialog using Neural Module Networks

Language Models are Open Knowledge Graphs

Using Local Knowledge Graph Construction to Scale Seq2Seq Models to Multi-Document Inputs

Advancing the State of the Art in Open Domain Dialog Systems through the Alexa Prize

EXTRACTOR: Extracting Attack Behavior from Threat Reports

Document-level Neural MT: A Systematic Comparison

HAL (Le Centre pour la Communication Scientifique Directe)

BiasFinder: Metamorphic Test Generation to Uncover Bias for Sentiment Analysis Systems

Interpreting Language Models with Contrastive Explanations

Semantic Representation for Dialogue Modeling

Repurposing Entailment for Multi-Hop Question Answering Tasks


AMPtorch: Atomistic Machine Learning Package (AMP) - PyTorch

Enabling robust offline active learning for machine learning potentials using simple physics-based priors

Machine Learning: Science and Technology

Robust and scalable uncertainty estimation with conformal prediction for machine-learned interatomic potentials

A Universal Framework for Featurization of Atomistic Systems

Machine Learning Diffusion Monte Carlo Forces

GMP-Featurizer: A parallelized Python package for efficiently computing the Gaussian Multipole features of atomic systems


A Julia/JuMP Package for Gas Network Optimization

Operation of Natural Gas Pipeline Networks With Storage Under Transient Flow Conditions

IEEE Transactions on Control Systems Technology

Graph-Based Modeling and Decomposition of Energy Infrastructures

Robust Gas Pipeline Network Expansion Planning to Support Power System Reliability

Demand Response Analogues for Residential Loads in Natural Gas Networks

Natural gas maximal load delivery for multi-contingency analysis


Repository for the Human Disease Ontology.

Human Disease Ontology 2018 update: classification, content and workflow expansion

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

Disease Ontology: improving and unifying disease annotations across species

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction

A platform for oncogenomic reporting and interpretation

Identification of clinical disease trajectories in neurodegenerative disorders with natural language processing

Assessing resource use: a case study with the Human Disease Ontology

Database : the journal of biological databases and curation


MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

DrImpute: imputing dropout events in single cell RNA sequencing data

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data

K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data

Targeting TMEM176B Enhances Antitumor Immunity and Augments the Efficacy of Immune Checkpoint Blockers by Unleashing Inflammasome Activation

netSmooth: Network-smoothing based imputation for single cell RNA-seq

A universal deep neural network for in-depth cleaning of single-cell RNA-Seq data

Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction

Molecular Cross-Validation for Single-Cell RNA-seq

Interferon-stimulated neutrophils as a predictor of immunotherapy response

scRNA‐seq data analysis method to improve analysis performance


Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector

A maternal germline mutator phenotype in a family affected by heritable colorectal cancer

medRxiv : the preprint server for health sciences


LLM-jp: A Cross-organizational Project for the Research and Development
  of Fully Open Japanese LLMs

Building a Large Japanese Web Corpus for Large Language Models

Analyzing Social Biases in Japanese Large Language Models


Barnes-Hut t-SNE

A method for the generation of human stem cell-derived alpha cells

Ventricular-Subventricular Zone Contact by Glioblastoma is Not Associated with Molecular Signatures in Bulk Tumor Data

Self-Supervised Learning from Web Data for Multimodal Retrieval

RETRACTED ARTICLE: AKT3-mediated IWS1 phosphorylation promotes the proliferation of EGFR-mutant lung adenocarcinomas through cell cycle-regulated U2AF2 RNA splicing

The Stars of the HETDEX Survey. I. Radial Velocities and Metal-poor Stars from Low-resolution Stellar Spectra

PixelSNE: Visualizing Fast with Just Enough Precision via Pixel-Aligned Stochastic Neighbor Embedding

Stochastic Cluster Embedding

T-SNE Is Not Optimized to Reveal Clusters in Data

SG-t-SNE-Π: Swift Neighbor Embedding of Sparse Stochastic Graphs


Lora beYond Conventional methods, Other Rank adaptation Implementations for Stable diffusion.

Few-Shot Parameter-Efficient Fine-Tuning is Better and Cheaper than In-Context Learning

DyLoRA: Parameter Efficient Tuning of Pre-trained Models using Dynamic Search-Free Low-Rank Adaptation

FedPara: Low-Rank Hadamard Product for Communication-Efficient Federated Learning

Navigating Text-To-Image Customization: From LyCORIS Fine-Tuning to Model Evaluation

Parameter-Efficient Orthogonal Finetuning via Butterfly Factorization

Controllable Generation with Text-to-Image Diffusion Models: A Survey

Large Convolutional Model Tuning via Filter Subspace


A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Loop extrusion as a mechanism for formation of DNA damage repair foci

Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

Cohesin residency determines chromatin loop patterns

Chloranthus genome provides insights into the early diversification of angiosperms


Dynamic analysis framework for JavaScript

Towards Runtime Monitoring of Node.js and Its Application to the Internet of Things

Gelato: Feedback-driven and Guided Security Analysis of Client-side Web Applications

Automatic Root Cause Quantification for Missing Edges in JavaScript Call Graphs (Extended Version)


InternLM-XComposer-2.5: A Versatile Large Vision Language Model Supporting Long-Contextual Input and Output

Compositional Semantic Parsing on Semi-Structured Tables

ShareGPT4V: Improving Large Multi-Modal Models with Better Captions

InternLM-XComposer: A Vision-Language Large Model for Advanced Text-image Comprehension and Composition

InternLM-XComposer2: Mastering Free-form Text-Image Composition and
  Comprehension in Vision-Language Large Model

InternLM-XComposer2-4KHD: A Pioneering Large Vision-Language Model
  Handling Resolutions from 336 Pixels to 4K HD

DualFocus: Integrating Macro and Micro Perspectives in Multi-modal Large
  Language Models


Dataflow QNN inference accelerator examples on FPGAs

BinaryCoP: Binary Neural Network-based COVID-19 Face-Mask Wear and Positioning Predictor on Edge Devices

SAMO: Optimised Mapping of Convolutional Neural Networks to Streaming Architectures

Pentimento: Data Remanence in Cloud FPGAs


VVenC, the Fraunhofer Versatile Video Encoder

Developments in International Video Coding Standardization After AVC, With an Overview of Versatile Video Coding (VVC)

Versatile Video Coding Standard: A Review From Coding Tools to Consumers Deployment

Energy Efficient Video Decoding for VVC Using a Greedy Strategy-Based Design Space Exploration

IEEE Transactions on Circuits and Systems for Video Technology

A Complete End-To-End Open Source Toolchain for the Versatile Video Coding (VVC) Standard

Open GOP Resolution Switching in HTTP Adaptive Streaming with VVC

Optimized Decoding-Energy-Aware Encoding in Practical VVC Implementations

The Bjøntegaard Bible Why Your Way of Comparing Video Codecs May Be Wrong

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

All-Intra Rate Control Using Low Complexity Video Features for Versatile Video Coding

VVC Subpicture-Based Frame Packing for MPEG Immersive Video

Advanced Design Space Exploration for Joint Energy and Quality Optimization for VVC


This is the top-level project for the PULP Platform. It instantiates a PULP open-source system with a PULP SoC (microcontroller) domain accelerated by a PULP cluster with 8 cores.

An IoT Endpoint System-on-Chip for Secure and Energy-Efficient Near-Sensor Analytics

Enabling mixed-precision quantized neural networks in extreme-edge devices

A Low-Power Transprecision Floating-Point Cluster for Efficient Near-Sensor Data Analytics

Marsellus: A Heterogeneous RISC-V AI-IoT End-Node SoC with 2-to-8b DNN Acceleration and 30%-Boost Adaptive Body Biasing


Official DeiT repository

Training data-efficient image transformers & distillation through attention

Going deeper with Image Transformers

ConViT: Improving Vision Transformers with Soft Convolutional Inductive Biases

ResMLP: Feedforward networks for image classification with data-efficient training

Focal Self-attention for Local-Global Interactions in Vision Transformers

DeiT III: Revenge of the ViT

A-ViT: Adaptive Tokens for Efficient Vision Transformer

Is synthetic data from generative models ready for image recognition?

Task-Oriented Multi-User Semantic Communications

Not All Images are Worth 16x16 Words: Dynamic Transformers for Efficient Image Recognition


Google's differential privacy libraries.

Google COVID-19 Community Mobility Reports: Anonymization Process Description (version 1.1)

How to DP-fy ML: A Practical Guide to Machine Learning with Differential Privacy

LinkedIn's Audience Engagements API

Privacy in targeted advertising: A survey

Composition of Differential Privacy & Privacy Amplification by Subsampling

Connect the Dots: Tighter Discrete Approximations of Privacy Loss Distributions

Multi-Epoch Matrix Factorization Mechanisms for Private Machine Learning

FriendlyCore: Practical Differentially Private Aggregation

Google COVID-19 Search Trends Symptoms Dataset: Anonymization Process Description (version 1.0)

Challenges towards the Next Frontier in Privacy


Digital Design with Chisel

Open-Source Verification with Chisel and Scala

Deep Learning Accelerators’ Configuration Space Exploration Effect on Performance and Resource Utilization: A Gemmini Case Study


Python package for information theory.

Measuring Multivariate Redundant Information with Pointwise Common Change in Surprisal

Multivariate Dependence Beyond Shannon Information

dit: a Python package for discrete information theory

Unique Information via Dependency Constraints

The Partial Entropy Decomposition: Decomposing multivariate entropy and mutual information via pointwise common surprisal

BROJA-2PID: A Robust Estimator for Bivariate Partial Information Decomposition

Computing the Unique Information

International Symposium on Information Theory

Inter-scale information flow as a surrogate for downward causation that maintains spiral waves

Chaos An Interdisciplinary Journal of Nonlinear Science

Contextual Modulation in Mammalian Neocortex is Asymmetric

The Value of Information When Deciding What to Learn


A list of backdoor learning resources

Backdoor Learning: A Survey

Februus: Input Purification Defense Against Trojan Attacks on Deep Neural Network Systems

Composite Backdoor Attack for Deep Neural Network by Mixing Existing Benign Features

Conference on Computer and Communications Security

Backdoor Attacks and Countermeasures on Deep Learning: A Comprehensive Review

BadNL: Backdoor Attacks against NLP Models with Semantic-preserving Improvements

Disabling Backdoor and Identifying Poison Data by using Knowledge Distillation in Backdoor Attacks on Deep Neural Networks

Proceedings of the 13th ACM Workshop on Artificial Intelligence and Security

BlindNet backdoor: Attack on deep neural network using blind watermark

Backdoors hidden in facial features: a novel invisible backdoor attack against face recognition systems

Peer-to-Peer Networking and Applications

Anti-Distillation Backdoor Attacks: Backdoors Can Really Survive in Knowledge Distillation

PROCEEDINGS OF THE 29TH ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA, MM 2021

Backdoor Attacks on Image Classification Models in Deep Neural Networks


CFE is a conceptual rainfall-runoff model with an implementation of the Basic Model Interface.

Comprehensive Analysis of the NOAA National Water Model: A Call for Heterogeneous Formulations and Diagnostic Model Selection

Journal of Geophysical Research: Atmospheres


R package for analysis and visualisation of biological signals in weather radar data

High-Resolution Spatial Distribution of Bird Movements Estimated from a Weather Radar Network


June is a framework for agent based modelling in an epidemiological and geographical context.

June: open-source individual-based epidemiology simulation

Bayesian emulation and history matching of JUNE

A Mixed-Method Approach to Determining Contact Matrices in the Cox's Bazar Refugee Settlement


Hardware-agnostic Framework for Large-scale Knowledge Graph Embeddings

Complex Query Answering with Neural Link Predictors

Hardware-agnostic Computation for Large-scale Knowledge Graph Embeddings

Kronecker Decomposition for Knowledge Graph Embeddings

Clifford Embeddings - A Generalized Approach for Embedding in Normed Algebras

Machine Learning and Knowledge Discovery in Databases: Research Track


Microbiome Projects from the Department of Genetics and Department of Gastroenterology and Hepatology , University Medical Centre Groningen

Stability of the human gut virome and effect of gluten-free diet.

Genetic, parental and lifestyle factors influence telomere length

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease

Unraveling interindividual variation of trimethylamine N‐oxide and its precursors at the population level


Official git repo for iodine dns tunnel

Entropy-based Prediction of Network Protocols in the Forensic Analysis of DNS Tunnels

Summary of DNS Over HTTPS Abuse

Evaluation of Apache Spot's machine learning capabilities in an SDN/NFV enabled environment

Zenodo (CERN European Organization for Nuclear Research)

IoT Multi-Vector Cyberattack Detection Based on Machine Learning Algorithms: Traffic Features Analysis, Experiments, and Efficiency


Make human motion capture easier.

Neural Body: Implicit Neural Representations with Structured Latent Codes for Novel View Synthesis of Dynamic Humans

Fast and Robust Multi-Person 3D Pose Estimation from Multiple Views

Neural Actor: Neural Free-view Synthesis of Human Actors with Pose Control

Neural Human Performer: Learning Generalizable Radiance Fields for Human Performance Rendering

Structured Local Radiance Fields for Human Avatar Modeling

Reconstructing 3D Human Pose by Watching Humans in the Mirror

Motion Capture from Internet Videos

AvatarCap: Animatable Avatar Conditioned Monocular Human Volumetric Capture

Dynamic Multi-Person Mesh Recovery From Uncalibrated Multi-View Cameras

Novel View Synthesis of Human Interactions from Sparse Multi-view Videos

Special Interest Group on Computer Graphics and Interactive Techniques Conference Proceedings


Animal Part Tracker

Cortical pattern generation during dexterous movement is input-driven

State-dependent decoupling of sensory and motor circuits underlies behavioral flexibility in Drosophila

Disrupting cortico-cerebellar communication impairs dexterity

A persistent behavioral state enables sustained predation of humans by mosquitoes

Dynamics of the Cortico-Cerebellar Loop Fine-Tune Dexterous Movement


Multi-layer Recurrent Neural Networks (LSTM, GRU, RNN) for character-level language models in Torch

Generating Sequences With Recurrent Neural Networks

AdaComp : Adaptive Residual Gradient Compression for Data-Parallel Distributed Training

Music transcription modelling and composition using deep learning

Recurrent Neural Networks Hardware Implementation on FPGA

SYSTRAN's Pure Neural Machine Translation Systems

Teaching Arithmetic to Small Transformers

Deep Learning At Scale and At Ease

Confidence through Attention

Learning to Capitalize with Character-Level Recurrent Neural Networks: An Empirical Study

Empirical Methods in Natural Language Processing

Optimizing seed inputs in fuzzing with machine learning


Flatiron Institute Fast Multipole Libraries --- This codebase is a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine.

Randomized Compression of Rank-Structured Matrices Accelerated with Graph Coloring

A fast boundary integral method for high-order multiscale mesh generation

A Dual-space Multilevel Kernel-splitting Framework for Discrete and Continuous Convolution

FMM-Accelerated Solvers for the Laplace–Beltrami Problem on Complex Surfaces in Three Dimensions

Modeling transcranial magnetic stimulation coil with magnetic cores

Debye source representations for type-I superconductors, I

3D Interface Models for Rayleigh-Taylor Problems

Near-optimal hierarchical matrix approximation from matrix-vector
  products

Example of Steady-State Electric-Current Modeling of a Complicated Cellular Topology with Boundary Element Fast Multipole Method


R interface to the ANTs biomedical image processing library

Recommendations for Processing Head CT Data

ENIGMA brain injury: Framework, challenges, and opportunities

Multivariate MR Biomarkers Better Predict Cognitive Dysfunction in Mouse Models of Alzheimers Disease

Interpretable, similarity-driven multi-view embeddings from high-dimensional biomedical data

Clinical, Technical, and MRI Features Associated with Patients' Outcome at 3 Months and 2 Years following Prostate Artery Embolization: Is There an Added Value of Radiomics?

Testing the accuracy of 3D automatic landmarking via genome-wide association studies

Distal neuropathic pain in HIV is associated with functional connectivity patterns in default mode and salience networks

Frontiers in pain research (Lausanne, Switzerland)


A Static Analysis Tool for Detecting Security Vulnerabilities in Python Web Applications

Adversarial Machine Learning -- Industry Perspectives

Towards Measuring Supply Chain Attacks on Package Managers for Interpreted Languages

Measuring and Preventing Supply Chain Attacks on Package Managers.

DeVAIC: A Tool for Security Assessment of AI-generated Code


CodeBERT

CodeBERT: A Pre-Trained Model for Programming and Natural Languages

CodeSearchNet Challenge: Evaluating the State of Semantic Code Search

GraphCodeBERT: Pre-training Code Representations with Data Flow

UniXcoder: Unified Cross-Modal Pre-training for Code Representation

A Comprehensive Survey of AI-Generated Content (AIGC): A History of Generative AI from GAN to ChatGPT

Automating Code Review Activities by Large-Scale Pre-training

CoSQA: 20,000+ Web Queries for Code Search and Question Answering

CodeTrans: Towards Cracking the Language of Silicon's Code Through Self-Supervised Deep Learning and High Performance Computing

Multilingual training for Software Engineering

A Search-Based Testing Framework for Deep Neural Networks of Source Code Embedding


PromptKG Family: a Gallery of Prompt Learning & KG-related research works, toolkits, and paper-list.

From Discrimination to Generation: Knowledge Graph Completion with Generative Transformer

Decoupling Knowledge from Memorization: Retrieval-augmented Prompt Learning

Relation Extraction as Open-book Examination: Retrieval-enhanced Prompt Tuning

Proceedings of the 45th International ACM SIGIR Conference on Research and Development in Information Retrieval

Editing Language Model-based Knowledge Graph Embeddings

Contrastive Demonstration Tuning for Pre-trained Language Models

LambdaKG: A Library for Pre-trained Language Model-Based Knowledge Graph Embeddings

Commonsense Knowledge Salience Evaluation with a Benchmark Dataset in E-commerce


A benchmark environment for fully cooperative human-AI performance.

On the Utility of Learning about Humans for Human-AI Coordination

Heterogeneous Multi-agent Zero-Shot Coordination by Coevolution

A Hierarchical Approach to Population Training for Human-AI Collaboration

Quantifying Zero-shot Coordination Capability with Behavior Preferring Partners

Select to Perfect: Imitating desired behavior from large multi-agent data

Explaining the Behaviour of Reinforcement Learning Agents in a Multi-Agent Cooperative Environment Using Policy Graphs


MCP-Reborn is an MCP (Mod Coder Pack) for Minecraft for making modded clients and researching its code. (1.13-1.20.1)

Video PreTraining (VPT): Learning to Act by Watching Unlabeled Online Videos

JARVIS-1: Open-World Multi-task Agents with Memory-Augmented Multimodal Language Models

GROOT: Learning to Follow Instructions by Watching Gameplay Videos


Start-to-end photon experiment simulation platform

SIMEX: Simulation of Experiments at Advanced Light Sources

Simulations of future particle accelerators: issues and mitigations

Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN


Platform for Situated Intelligence

AffectiveSpotlight: Facilitating the Communication of Affective Responses from Audience Members during Online Presentations

Proceedings of the 2021 CHI Conference on Human Factors in Computing Systems

Platform for Situated Intelligence

EMISSOR: A platform for capturing multimodal interactions as Episodic Memories and Interpretations with Situated Scenario-based Ontological References

Can Foundation Models Watch, Talk and Guide You Step by Step to Make a Cake?

Accelerating the Development of Multimodal, Integrative-AI Systems with Platform for Situated Intelligence


LabStreamingLayer super repository comprising submodules for LSL and associated apps.

Validating Deep Neural Networks for Online Decoding of Motor Imagery Movements from EEG Signals

Detecting and Quantifying Mind Wandering during Simulated Driving

Walking through Architectural Spaces: The Impact of Interior Forms on Human Brain Dynamics

Understanding Minds in Real-World Environments: Toward a Mobile Cognition Approach

A Riemannian Modification of Artifact Subspace Reconstruction for EEG Artifact Handling

Breeze: Sharing Biofeedback Through Wearable Technologies

PROCEEDINGS OF THE 2018 CHI CONFERENCE ON HUMAN FACTORS IN COMPUTING SYSTEMS (CHI 2018)

Optical imaging and spectroscopy for the study of the human brain: status report

Real-time synthesis of imagined speech processes from minimally invasive recordings of neural activity

Decoding Movement From Electrocorticographic Activity: A Review

Mobile Brain/Body Imaging (MoBI) of Physical Interaction with Dynamically Moving Objects


Wildfire Predictive Services to support decision making in prevention, preparedness, response and recovery


Use DNN to study the brain and use brain measurement to evaluate DNN

DNNBrain: A Unifying Toolbox for Mapping Deep Neural Networks and Brains

Semantic Relatedness Emerges in Deep Convolutional Neural Networks Designed for Object Recognition

Hierarchical Sparse Coding of Objects in Deep Convolutional Neural Networks

An overview of open source Deep Learning-based libraries for Neuroscience


Wind Energy with Integrated Servo-controls Toolset

Land-based wind turbines with flexible rail transportable blades – Part I: Conceptual design and aeroservoelastic performance


GeoClimate: a Geospatial processing toolbox for environmental and climate studies


Code and tutorials to visualise your data that is both beautiful *and* statistically valid

Raincloud plots: a multi-platform tool for robust data visualization

A multi-site, multi-disorder resting-state magnetic resonance image database

High-resolution dietary reconstruction of victims of the 79 CE Vesuvius eruption at Herculaneum by compound-specific isotope analysis

Good scientific practice in EEG and MEG research: Progress and perspectives

The effects of multi-echo fMRI combination and rapid T-2*-mapping on offline and real-time BOLD sensitivity

rt-me-fMRI: A task and resting state dataset for real-time, multi-echo fMRI methods development and validation

A dynamic link between respiration and arousal

Sequential Finger-tapping Learning Mediated by the Primary Motor Cortex and Fronto-parietal Network: A Combined MRI-MRS Study


The Push programming language and the PushGP genetic programming system implemented in Clojure.

Problem-solving benefits of down-sampled lexicase selection

Lexicase Selection of Specialists

Comparing and Combining Lexicase Selection and Novelty Search

Lexicase selection at scale

Proceedings of the Genetic and Evolutionary Computation Conference Companion

Stochastic synthesis of recursive functions made easy with bananas, lenses, envelopes and barbed wire

Genetic Programming and Evolvable Machines

Population Diversity Leads to Short Running Times of Lexicase Selection

Optimizing LLVM Pass Sequences with Shackleton: A Linear Genetic Programming Framework


MONAI Generative Models makes it easy to train, evaluate, and deploy generative models and related applications

Generative AI for Medical Imaging: extending the MONAI Framework

Generating Realistic Brain MRIs via a Conditional Diffusion Probabilistic Model


BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

bioRxiv : the preprint server for biology

Twelve quick steps for genome assembly and annotation in the classroom

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)

Foster thy young: enhanced prediction of orphan genes in assembled genomes

Genomic and Metabolomic Analyses of the Medicinal Fungus Inonotus hispidus for Its Metabolite’s Biosynthesis and Medicinal Application

Illumina and PacBio DNA sequencing data, de novo assembly and annotation of the genome of Aurantiochytrium limacinum strain CCAP_4062/1

Defining the ‘HoneySweet’ insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica)

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

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


A collection of tools for painting super-resolution images

Single-molecule localization microscopy

Simultaneous orientation and 3D localization microscopy with a Vortex point spread function

Rapid and efficient C-terminal labeling of nanobodies for DNA-PAINT

Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard

Toward Absolute Molecular Numbers in DNA-PAINT

Super-resolved visualization of single DNA-based tension sensors in cell adhesion

Quantification of Strand Accessibility in Biostable DNA Origami with Single-Staple Resolution

nanoTRON: a Picasso module for MLP-based classification of super-resolution data

Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus

Super-resolution imaging and quantitative analysis of microtubule arrays in model neurons show that epothilone D increases the density but decreases the length and straightness of microtubules in axon-like processes


Library for Digital Pathology Image Processing

HistoCartography: A Toolkit for Graph Analytics in Digital Pathology

AI slipping on tiles: data leakage in digital pathology

Development and Validation of a Machine Learning Model for Detection and Classification of Tertiary Lymphoid Structures in Gastrointestinal Cancers

Quantification of the Immune Content in Neuroblastoma: Deep Learning and Topological Data Analysis in Digital Pathology

International journal of molecular sciences

Interpretable histopathology-based prediction of disease relevant features in Inflammatory Bowel Disease biopsies using weakly-supervised deep learning

Development and interpretation of a pathomics-driven ensemble model for predicting the response to immunotherapy in gastric cancer


Hydrological modeling


PyTorch implementation of the U-Net for image semantic segmentation with high quality images

U-Net: Convolutional Networks for Biomedical Image Segmentation

Mixed Precision Training

Convolutional Neural Networks for Image-Based High-Throughput Plant Phenotyping: A Review

ADN: Artifact Disentanglement Network for Unsupervised Metal Artifact Reduction

Noise2Inverse: Self-Supervised Deep Convolutional Denoising for Tomography

CaDIS: Cataract Dataset for Image Segmentation

Do Neural Optimal Transport Solvers Work? A Continuous Wasserstein-2 Benchmark

Neural Optimal Transport

Segmentation of dental cone-beam CT scans affected by metal artifacts using a mixed-scale dense convolutional neural network

Generative Modeling with Optimal Transport Maps


brozzler - distributed browser-based web crawler

The Memento Tracer Framework: Balancing Quality and Scalability for Web Archiving

Discovering Scholarly Orphans Using ORCID

Supporting Web Archiving via Web Packaging

Exploring the Intersections of Web Science and Accessibility


A cool place to store your Hi-C

HiGlass: web-based visual exploration and analysis of genome interaction maps

Cooler: scalable storage for Hi-C data and other genomically-labeled arrays

A mechanism of cohesin‐dependent loop extrusion organizes zygotic genome architecture

Molecular basis of CTCF binding polarity in genome folding

SMC complexes differentially compact mitotic chromosomes according to genomic context

Conformation of sister chromatids in the replicated human genome

Cohesin residency determines chromatin loop patterns

Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

BRD2 compartmentalizes the accessible genome


A repository for storing models that have been inter-converted between various frameworks. Supported frameworks are TensorFlow, PyTorch, ONNX, OpenVINO, TFJS, TFTRT, TensorFlowLite (Float32/16/INT8), EdgeTPU, CoreML.

EfficientDeRain: Learning Pixel-wise Dilation Filtering for High-Efficiency Single-Image Deraining

YOLOPv2: Better, Faster, Stronger for Panoptic Driving Perception

Fully Convolutional Line Parsing

PTMTorrent: A Dataset for Mining Open-source Pre-trained Model Packages


NumPy & SciPy for GPU

ChainerCV: a Library for Deep Learning in Computer Vision

On Distribution Shift in Learning-based Bug Detectors

Long-Range Nonequilibrium Coherent Tunneling Induced by Fractional Vibronic Resonances.

Iterative static field map estimation for off‐resonance correction in non‐Cartesian susceptibility weighted imaging

Changes from the Trenches: Should We Automate Them?

AMReX and pyAMReX: Looking Beyond ECP

2D Simplified Wildfire Spreading Model in Python: From NumPy to CuPy

Accelerating Spectroscopic Data Processing Using Python and GPUs on NERSC Supercomputers

Proceedings of the Python in Science Conferences


Scalable datastore for metrics, events, and real-time analytics

Is your clock-face cozie? A smartwatch methodology for the in-situ collection of occupant comfort data

A wearable IoT aldehyde sensor for pediatric asthma research and management

An Empirical Analysis of UI-based Flaky Tests

Effectively Testing System Configurations of Critical IoT Analytics Pipelines

NagareDB: A Resource-Efficient Document-Oriented Time-Series Database

International Conference on Data Technologies and Applications

Magpie: Automatically Tuning Static Parameters for Distributed File Systems using Deep Reinforcement Learning

AVUBDI: A Versatile Usable Big Data Infrastructure and Its Monitoring Approaches for Process Industry


The SkyLLH framework is an open-source Python3-based package licensed under the GPLv3 license. It provides a modular framework for implementing custom likelihood functions and executing log-likelihood ratio hypothesis tests. The idea is to provide a class structure tied to the mathematical objects of the likelihood functions.

SkyLLH -- A generalized Python-based tool for log-likelihood analyses in multi-messenger astronomy

The Spectra of IceCube Neutrino (SIN) candidate sources -- IV. Spectral energy distributions and multi-wavelength variability

The SkyLLH framework for IceCube point-source search

Fitting neutrino flares: Applying expectation maximization on neutrino data


Easy-to-use glTF 2.0-compliant OpenGL renderer for visualization of 3D scenes.

Habitat 2.0: Training Home Assistants to Rearrange their Habitat

ACRONYM: A Large-Scale Grasp Dataset Based on Simulation

TACTO: A Fast, Flexible, and Open-Source Simulator for High-Resolution Vision-Based Tactile Sensors

Tactile Object Pose Estimation from the First Touch with Geometric Contact Rendering

ImFace: A Nonlinear 3D Morphable Face Model with Implicit Neural Representations

Let's Face It: Probabilistic Multi-modal Interlocutor-aware Generation of Facial Gestures in Dyadic Settings

Proceedings of the 20th ACM International Conference on Intelligent Virtual Agents

ShapeMap 3-D: Efficient shape mapping through dense touch and vision

Tac2Pose: Tactile Object Pose Estimation from the First Touch

NIFTY: Neural Object Interaction Fields for Guided Human Motion Synthesis

Active 3D Shape Reconstruction from Vision and Touch


Julia interface for Reading from the Earth System Datacube


C++ library for zkSNARKs

Advances and Open Problems in Federated Learning

Untangling Blockchain: A Data Processing View of Blockchain Systems

A blockchain-based scheme for privacy-preserving and secure sharing of medical data

DECO: Liberating Web Data Using Decentralized Oracles for TLS

Conference on Computer and Communications Security

zkBridge: Trustless Cross-chain Bridges Made Practical

VeriML: Enabling Integrity Assurances and Fair Payments for Machine Learning as a Service

Non-Interactive Zero-Knowledge for Blockchain: A Survey

ZETH: On Integrating Zerocash on Ethereum

SEAL: A Strategy-Proof and Privacy-Preserving UAV Computation Offloading Framework

ZKlaims: Privacy-preserving Attribute-based Credentials using Non-interactive Zero-knowledge Techniques

PROCEEDINGS OF THE 16TH INTERNATIONAL JOINT CONFERENCE ON E-BUSINESS AND TELECOMMUNICATIONS, VOL 2: SECRYPT


Simulation framework

An Efficient Algorithm for Power Dominating Set


General technology for enabling AI capabilities w/ LLMs and MLLMs

Automatic Prompt Optimization with "Gradient Descent" and Beam Search

Optimizing Prompts for Text-to-Image Generation

Why Can GPT Learn In-Context? Language Models Implicitly Perform Gradient Descent as Meta-Optimizers

Adapting Large Language Models via Reading Comprehension

Knowledge Distillation of Large Language Models

Structured Prompting: Scaling In-Context Learning to 1,000 Examples

UPRISE: Universal Prompt Retrieval for Improving Zero-Shot Evaluation

Inference with Reference: Lossless Acceleration of Large Language Models

Learning to Retrieve In-Context Examples for Large Language Models

Large Language Model for Science: A Study on P vs. NP


Tool Learning for Big Models, Open-Source Solutions of ChatGPT-Plugins

Tool Learning with Foundation Models

Data-Copilot: Bridging Billions of Data and Humans with Autonomous Workflow

Agent-Pro: Learning to Evolve via Policy-Level Reflection and
  Optimization

A Review of Large Language Models and Autonomous Agents in Chemistry

LLMs in the Imaginarium: Tool Learning through Simulated Trial and Error


Shifter - Linux Containers for HPC

Shifter: Containers for HPC

Containers for Portable, Productive, and Performant Scientific Computing

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

Observability and chaos engineering on system calls for containerized applications in Docker

CMS use of allocation based HPC resources


Karate Club: An API Oriented Open-source Python Framework for Unsupervised Learning on Graphs (CIKM 2020)

node2vec: Scalable Feature Learning for Networks

DeepWalk: Online Learning of Social Representations

PROCEEDINGS OF THE 20TH ACM SIGKDD INTERNATIONAL CONFERENCE ON KNOWLEDGE DISCOVERY AND DATA MINING (KDD'14)

GraRep: Learning Graph Representations with Global Structural Information

International Conference on Information and Knowledge Management

Asymmetric Transitivity Preserving Graph Embedding

Network Representation Learning with Rich Text Information

PROCEEDINGS OF THE TWENTY-FOURTH INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE (IJCAI)

Community Preserving Network Embedding

THIRTY-FIRST AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE

Network Embedding as Matrix Factorization: Unifying DeepWalk, LINE, PTE, and node2vec

Overlapping community detection at scale: a nonnegative matrix factorization approach

Multi-scale Attributed Node Embedding

graph2vec: Learning Distributed Representations of Graphs


Collaborative editing in any app

Real Differences between OT and CRDT in Correctness and Complexity for Consistency Maintenance in Co-Editors

Proceedings of the ACM on Human-Computer Interaction

Real Differences between OT and CRDT under a General Transformation Framework for Consistency Maintenance in Co-Editors

Real Differences between OT and CRDT in Building Co-Editing Systems and Real World Applications

Real Differences between OT and CRDT for Co-Editors


A differentiable PDE solving framework for machine learning

Solver-in-the-Loop: Learning from Differentiable Physics to Interact with Iterative PDE-Solvers

Message Passing Neural PDE Solvers

Learning to Control PDEs with Differentiable Physics

Physics-based Deep Learning

Towards Multi-spatiotemporal-scale Generalized PDE Modeling

Clifford Neural Layers for PDE Modeling

Meta-Learning Dynamics Forecasting Using Task Inference

Learning to Accelerate Partial Differential Equations via Latent Global Evolution

Geometric Clifford Algebra Networks

MAgNet: Mesh Agnostic Neural PDE Solver


This repository contains data on Coronavirus Disease 2019 (COVID-19) in New York City (NYC), from the NYC Department of Health and Mental Hygiene.

Characteristics Associated With Out-of-Hospital Cardiac Arrests and Resuscitations During the Novel Coronavirus Disease 2019 Pandemic in New York City

Spatial Inequities in COVID-19 Testing, Positivity, Confirmed Cases, and Mortality in 3 U.S. Cities

Oscillations in U.S. COVID-19 Incidence and Mortality Data Reflect Diagnostic and Reporting Factors

Dynamics of COVID-19 under social distancing measures are driven by transmission network structure

medRxiv : the preprint server for health sciences

Exposure density and neighborhood disparities in COVID-19 infection risk

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

Estimating SARS-CoV-2 infections from deaths, confirmed cases, tests, and random surveys

Differential COVID-19 case positivity in New York City neighborhoods: socioeconomic factors and mobility

Forecasting the Spread of COVID-19 under Different Reopening Strategies

Time-dependent heterogeneity leads to transient suppression of the COVID-19 epidemic, not herd immunity

Visualizing the invisible: The effect of asymptomatic transmission on the outbreak dynamics of COVID-19


TAPAS - Translational Algorithms for Psychiatry-Advancing Science

The effects of multi-echo fMRI combination and rapid T-2*-mapping on offline and real-time BOLD sensitivity

Altered Perception of Environmental Volatility During Social Learning in Emerging Psychosis

Evidence for Reduced Sensory Precision and Increased Reliance on Priors in Hallucination-Prone Individuals in a General Population Sample

rt-me-fMRI: A task and resting state dataset for real-time, multi-echo fMRI methods development and validation

Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN


Ewasm Design Overview and Specification

A Blockchain Platform for User Data Sharing Ensuring User Control and Incentives

User Data Sharing Frameworks: A Blockchain-Based Incentive Solution

An Empirical Study Into the Success of Listed Smart Contracts in Ethereum

A Survey on EOSIO Systems Security: Vulnerability, Attack, and Mitigation


Artificial Intelligence Research for Science (AIRS)

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Periodic Graph Transformers for Crystal Material Property Prediction

Group Equivariant Fourier Neural Operators for Partial Differential Equations

Efficient Approximations of Complete Interatomic Potentials for Crystal Property Prediction

A Latent Diffusion Model for Protein Structure Generation

Efficient and Equivariant Graph Networks for Predicting Quantum Hamiltonian

QH9: A Quantum Hamiltonian Prediction Benchmark for QM9 Molecules

Complete and Efficient Graph Transformers for Crystal Material Property
  Prediction

Towards Symmetry-Aware Generation of Periodic Materials

Crystalformer: Infinitely Connected Attention for Periodic Structure
  Encoding


A microbenchmark support library

The Double Sphere Camera Model

The valuation of currency options by fractional Brownian motion

Guidelines for Experimental Algorithmics: A Case Study in Network Analysis

ArborX: A Performance Portable Geometric Search Library

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

Software-based data acquisition and processing for neutron detectors at European Spallation Source—early experience from four detector designs

Testing Very Large Database Management Systems: The Case of SAP HANA

Benanza: Automatic μBenchmark Generation to Compute "Lower-bound" Latency and Inform Optimizations of Deep Learning Models on GPUs

International Parallel and Distributed Processing Symposium

Polylidar3D -- Fast Polygon Extraction from 3D Data

Distributed and parallel sparse convex optimization for radio interferometry with PURIFY


Kubernetes community content

Foggy: A Platform for Workload Orchestration in a Fog Computing Environment

IEEE International Conference on Cloud Computing Technology and Science

A Comprehensive Feature Comparison Study of Open-Source Container Orchestration Frameworks

The Schulze Method of Voting

Computing Without Borders: The Way Towards Liquid Computing

Architecture Integration of 5G Networks and Time-Sensitive Networking with Edge Computing for Smart Manufacturing

Kubernetes Autoscaling: YoYo Attack Vulnerability and Mitigation

International Conference on Cloud Computing and Services Science

Managing Feature Compatibility in Kubernetes: Vendor Comparison and Analysis

An empirical study of vulnerabilities in edge frameworks to support security testing improvement

Zenodo (CERN European Organization for Nuclear Research)

Collective Autoscaling for Cloud Microservices

Multitenant Containers as a Service (CaaS) for Clouds and Edge Clouds


AQT: Accurate Quantized Training

Efficiently Scaling Transformer Inference

PokeBNN: A Binary Pursuit of Lightweight Accuracy

4-bit Conformer with Native Quantization Aware Training for Speech Recognition

Pareto-Optimal Quantized ResNet Is Mostly 4-bit

Binarized Neural Machine Translation


Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Journal of computational biology : a journal of computational molecular cell biology

fastp: an ultra-fast all-in-one FASTQ preprocessor

Minimap2: pairwise alignment for nucleotide sequences

Near-optimal probabilistic RNA-seq quantification

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

QUAST: quality assessment tool for genome assemblies

Twelve years of SAMtools and BCFtools

The Ensembl Variant Effect Predictor

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

MultiQC: summarize analysis results for multiple tools and samples in a single report


Utility functions for FACETS

Mapping molecular subtype specific alterations in breast cancer brain metastases identifies clinically relevant vulnerabilities

Pilot study of bempegaldesleukin in combination with nivolumab in patients with metastatic sarcoma

Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer

Clinical and Molecular Features of Long-term Response to Immune Checkpoint Inhibitors in Patients with Advanced Non–Small Cell Lung Cancer

Clinical cancer research : an official journal of the American Association for Cancer Research


Build, customize and control you own LLMs. From data pre-processing to fine-tuning, xTuring provides an easy way to personalize open-source LLMs. Join our discord community: https://discord.gg/TgHXuSJEk6

Learning to Filter Context for Retrieval-Augmented Generation

LLaMA-Reviewer: Advancing Code Review Automation with Large Language Models through Parameter-Efficient Fine-Tuning

INT2.1: Towards Fine-Tunable Quantized Large Language Models with Error Correction through Low-Rank Adaptation

PST-Bench: Tracing and Benchmarking the Source of Publications

Examining User-Friendly and Open-Sourced Large GPT Models: A Survey on Language, Multimodal, and Scientific GPT Models

LimGen: Probing the LLMs for Generating Suggestive Limitations of Research Papers


Benchmarking Deep Learning operations on different hardware

Mixed Precision Training

MLPerf Inference Benchmark

Benchmarking TPU, GPU, and CPU Platforms for Deep Learning

Sparse GPU Kernels for Deep Learning

PREMA: A Predictive Multi-task Scheduling Algorithm For Preemptible Neural Processing Units

Deep Learning at 15PF: Supervised and Semi-Supervised Classification for Scientific Data

CoSA: Scheduling by Constrained Optimization for Spatial Accelerators

TBD: Benchmarking and Analyzing Deep Neural Network Training

Beyond Human-Level Accuracy: Computational Challenges in Deep Learning

Beyond the Memory Wall: A Case for Memory-centric HPC System for Deep Learning


Astropy package for region handling

astroquery: An Astronomical Web-Querying Package in Python

SRG/eROSITA and XMM-Newton observations of Vela Jr

G189.6+03.3: The first complete X-ray view provided by SRG/eROSITA

Searching for X-ray counterparts of degree-wide TeV halos around middle-aged pulsars with SRG/eROSITA


A Large Quadcopter Swarm

Swarm Robotic Behaviors and Current Applications

A Fleet of Miniature Cars for Experiments in Cooperative Driving

Distributed Planning for Serving Cooperative Tasks with Time Windows: A Game Theoretic Approach

Decision-Making Among Bounded Rational Agents

M-SET: Multi-Drone Swarm Intelligence Experimentation with Collision
  Avoidance Realism


Add-On to NGSolve for unfitted finite element discretizations (XFEM, CutFEM, TraceFEM, etc...)

Projection-based reduced order models for a cut finite element method in parametrized domains

Falling balls in a viscous fluid with contact: Comparing numerical simulations with experimental data

A reduced order model for a stable embedded boundary parametrized Cahn-Hilliard phase-field system based on cut finite elements

High-order space–time finite element methods for the Poisson–Nernst–Planck equations: Positivity and unconditional energy stability

A Reduced Order Cut Finite Element method for geometrically parametrized steady and unsteady Navier–Stokes problems

Random geometries for optimal control PDE problems based on fictitious domain FEMs and cut elements

An Unfitted Finite Element Method for Two-Phase Stokes Problems with Slip Between Phases

Equal Higher Order Analysis of an Unfitted Discontinuous Galerkin Method for Stokes Flow Systems


Explore correlations in R

Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes

Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders

Environmental Impacts of Cement Production: A Statistical Analysis

Genetic gains in tropical maize hybrids across moisture regimes with multi-trait-based index selection

Duplication and Specialization of NUDX1 in Rosaceae Led to Geraniol Production in Rose Petals

Key traits and genes associate with salinity tolerance independent from vigor in cultivated sunflower (Helianthus annuus L.)

Diverse and mobile:eccDNA‐based identification of carrot low‐copy‐numberLTRretrotransposons active in callus cultures

The Plant journal : for cell and molecular biology

Development and Assessment of a Body Condition Score Scheme for European Bison (Bison bonasus)

Animals : an open access journal from MDPI


API & Webapp to answer questions about COVID-19. Using NLP (Question Answering) and trusted data sources.

COVID-QA: A Question Answering Dataset for COVID-19

Inexpensive Domain Adaptation of Pretrained Language Models: Case Studies on Biomedical NER and Covid-19 QA

What Are People Asking About COVID-19? A Question Classification Dataset

Collecting Verified COVID-19 Question Answer Pairs

Empirical Methods in Natural Language Processing

End-to-End QA on COVID-19: Domain Adaptation with Synthetic Training

An Empirical Study of Bugs in COVID-19 Software Projects

Journal of Software Engineering Research and Development

A COVID-19 Search Engine (CO-SE) with Transformer-based Architecture

An Approach to Ensure Fairness in News Articles


The Pharmacogenomic Clinical Annotation Tool

Pharmacogenetics at scale: An analysis of the UK Biobank

Pharmacogenomics Clinical Annotation Tool (PharmCAT)

PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation

Genetic Variation among Pharmacogenes in the Sardinian Population

International journal of molecular sciences

Using the PharmCAT tool for Pharmacogenetic clinical decision support


Semi-supervised learning for peptide identification from shotgun proteomics datasets

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

A framework for quality control in quantitative proteomics

bioRxiv : the preprint server for biology

RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein–RNA Cross-Linking/Mass Spectrometry Data


AIConfig is a config-based framework to build generative AI applications.

Chain-of-Thought Prompting Elicits Reasoning in Large Language Models

Self-Consistency Improves Chain of Thought Reasoning in Language Models

Automatic Chain of Thought Prompting in Large Language Models

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

Automatic Prompt Optimization with "Gradient Descent" and Beam Search

Llama Guard: LLM-based Input-Output Safeguard for Human-AI Conversations

Towards Understanding Chain-of-Thought Prompting: An Empirical Study of What Matters

Promptbreeder: Self-Referential Self-Improvement Via Prompt Evolution

Optimizing Prompts for Text-to-Image Generation

A Comprehensive Survey of Hallucination Mitigation Techniques in Large Language Models


Cyber Threat Intelligence Repository expressed in STIX 2.0

Automated Retrieval of ATT&CK Tactics and Techniques for Cyber Threat Reports

Game-Theoretic Decision Support for Cyber Forensic Investigations

Enhancing the STIX Representation of MITRE ATT&CK for Group Filtering and Technique Prioritization

Principled Data-Driven Decision Support for Cyber-Forensic Investigations

A Machine Learning based Empirical Evaluation of Cyber Threat Actors High Level Attack Patterns over Low level Attack Patterns in Attributing Attacks

Mining Temporal Attack Patterns from Cyberthreat Intelligence Reports


Smart contracts which are formally verified

A theory of Automated Market Makers in DeFi

(In)Stability for the Blockchain: Deleveraging Spirals and Stablecoin Attacks

End-to-End Formal Verification of Ethereum 2.0 Deposit Smart Contract

Deductive Verification of Smart Contracts with Dafny

Verification of the Incremental Merkle Tree Algorithm with Dafny

How Does Naming Affect LLMs on Code Analysis Tasks?

User Experience with Language-Independent Formal Verification

Expiring Assets in Automated Market Makers


Python wrapper for MFEM

Learning robust marking policies for adaptive mesh refinement

Dynamical low-rank approximation of the Vlasov-Poisson equation with piecewise linear spatial boundary

Constrained Local Approximate Ideal Restriction for Advection-Diffusion Problems

DynAMO: Multi-agent reinforcement learning for dynamic anticipatory mesh optimization with applications to hyperbolic conservation laws


TensorFlow Neural Machine Translation Tutorial

To prune, or not to prune: exploring the efficacy of pruning for model compression

QANet: Combining Local Convolution with Global Self-Attention for Reading Comprehension

Deep Learning Scaling is Predictable, Empirically

The Best of Both Worlds: Combining Recent Advances in Neural Machine Translation

Sequence-to-Sequence Prediction of Vehicle Trajectory via LSTM Encoder-Decoder Architecture

Differentiable Product Quantization for End-to-End Embedding Compression

Semi-Supervised Sequence Modeling with Cross-View Training

"Found in Translation": Predicting Outcomes of Complex Organic Chemistry Reactions using Neural Sequence-to-Sequence Models

Comparing Rewinding and Fine-tuning in Neural Network Pruning

emrQA: A Large Corpus for Question Answering on Electronic Medical Records


Visualization and analysis software for Hi-C data -

Telomere-to-telomere assembly of a complete human X chromosome

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000

Loop extrusion as a mechanism for formation of DNA damage repair foci

Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution

Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy

The genome of Medicago polymorpha provides insights into its edibility and nutritional value as a vegetable and forage legume

Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons

The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum)

The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case


Coq is a formal proof management system. It provides a formal language to write mathematical definitions, executable algorithms and theorems together with an environment for semi-interactive development of machine-checked proofs.

Coq Coq correct! verification of type checking and erasure for Coq, in Coq

Proceedings of the ACM on Programming Languages

QED at Large: A Survey of Engineering of Formally Verified Software

Foundations and Trends® in Programming Languages

Mtac2: Typed Tactics for Backward Reasoning in Coq

The Marriage of Univalence and Parametricity

Beyond Notations: Hygienic Macro Expansion for Theorem Proving Languages

Validating Mathematical Structures

Zippy LL(1) parsing with derivatives

Complete Bidirectional Typing for the Calculus of Inductive Constructions

Computable analysis and notions of continuity in Coq

The Trusted Computing Base of the CompCert Verified Compiler


A python binding for crfsuite

Negation Scope Detection for Twitter Sentiment Analysis

Automatically Tagging Constructions of Causation and Their Slot-Fillers

Transactions of the Association for Computational Linguistics

Toward a Standardized and More Accurate Indonesian Part-of-Speech Tagging

nala: text mining natural language mutation mentions

Sentence-Level Resampling for Named Entity Recognition

Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies

Beyond Query-Oriented Highlighting: Investigating the Effect of Snippet Text Highlighting in Search User Behavior

Computational intelligence and neuroscience

CMNEROne at SemEval-2022 Task 11: Code-Mixed Named Entity Recognition by leveraging multilingual data

AI pptX: Robust Continuous Learning for Document Generation with AI Insights.


MathChat: Converse to Tackle Challenging Math Problems with LLM Agents

Cost-Effective Hyperparameter Optimization for Large Language Model Generation Inference

StateFlow: Enhancing LLM Task-Solving through State-Driven Workflows

Training Language Model Agents without Modifying Language Models


Brain Modeling Toolkit

Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0

BioNet: A Python interface to NEURON for modeling large-scale networks

Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits

Reproducible Neural Network Simulations: Statistical Methods for Model Validation on the Level of Network Activity Data


Expression Atlas

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

Expression Atlas: gene and protein expression across multiple studies and organisms

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

β2 Integrins As Regulators of Dendritic Cell, Monocyte, and Macrophage Function


A large-scale dataset of both raw MRI measurements and clinical MRI images.

fastMRI: An Open Dataset and Benchmarks for Accelerated MRI

fastMRI: A Publicly Available Raw k-Space and DICOM Dataset of Knee Images for Accelerated MR Image Reconstruction Using Machine Learning

Score-based diffusion models for accelerated MRI

End-to-End Variational Networks for Accelerated MRI Reconstruction

Results of the 2020 fastMRI Challenge for Machine Learning MR Image Reconstruction

Robust Compressed Sensing MRI with Deep Generative Priors

Advancing machine learning for MR image reconstruction with an open competition: Overview of the 2019 fastMRI challenge

Using Deep Learning to Accelerate Knee MRI at 3 T: Results of an Interchangeability Study

GrappaNet: Combining Parallel Imaging with Deep Learning for Multi-Coil MRI Reconstruction

Accelerated MRI with Un-trained Neural Networks


COSMIC (Compact Object Synthesis and Monte Carlo Investigation Code)

COSMIC Variance in Binary Population Synthesis

A Census of Blue Stragglers in Gaia DR2 Open Clusters as a Test of Population Synthesis and Mass Transfer Physics

Observational signatures of the black hole mass distribution in the galactic center

Journal of Cosmology and Astroparticle Physics

Detectability of gravitational waves from a population of inspiralling black holes in Milky Way-mass galaxies

Monthly notices of the Royal Astronomical Society

Understanding the progenitor formation galaxies of merging binary black holes

Mapping progenitors of binary black holes and neutron stars with binary population synthesis


A platform for collecting and disseminating data for the Sustainable Development Goal global indicators.