FedNLP: An Industry and Research Integrated Platform for Federated Learning in Natural Language Processing, Backed by FedML, Inc. The Previous Research Version is Accepted to NAACL 2022

FedNLP: Benchmarking Federated Learning Methods for Natural Language Processing Tasks

Federated Learning Meets Natural Language Processing: A Survey

Can Foundation Models Help Us Achieve Perfect Secrecy?

Federated Model Decomposition with Private Vocabulary for Text Classification

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


Survival package for R

B cells sustain inflammation and predict response to immune checkpoint blockade in human melanoma

The journal of investigative dermatology/Journal of investigative dermatology

Automated image analysis of NSCLC biopsies to predict response to anti-PD-L1 therapy

Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes

Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response

Survival analysis: Part II — applied clinical data analysis

Determinants of frailty development and progression using a multidimensional frailty index: Evidence from the English Longitudinal Study of Ageing

Integrative Tumor and Immune Cell Multi-omic Analyses Predict Response to Immune Checkpoint Blockade in Melanoma

When and where mortality occurs throughout the annual cycle changes with age in a migratory bird: individual vs population implications

Expressed fusion gene landscape and its impact in multiple myeloma

Unraveling the Host Plant Alternation of Cacopsylla pruni – Adults but Not Nymphs Can Survive on Conifers Due to Phloem/Xylem Composition


A simple method to perform semi-supervised learning with limited data.

FixMatch: Simplifying Semi-Supervised Learning with Consistency and Confidence

Dash: Semi-Supervised Learning with Dynamic Thresholding

Exponential Moving Average Normalization for Self-supervised and Semi-supervised Learning

Not All Unlabeled Data are Equal: Learning to Weight Data in Semi-supervised Learning

AlphaMatch: Improving Consistency for Semi-supervised Learning with Alpha-divergence

Enhancing MR Image Segmentation with Realistic Adversarial Data
  Augmentation

Distribution-Aware Semantics-Oriented Pseudo-label for Imbalanced Semi-Supervised Learning.

Credal Self-Supervised Learning

Building One-Shot Semi-Supervised (BOSS) Learning Up to Fully Supervised Performance

Fix-A-Step: Semi-supervised Learning from Uncurated Unlabeled Data


A Python library to capture the energy consumption of code snippets

Extreme compression of sentence-transformer ranker models: faster
  inference, longer battery life, and less storage on edge devices

Efficiency metrics for auditory neuromorphic spike encoding techniques using information theory

Energy-Efficient On-Board Radio Resource Management for Satellite Communications via Neuromorphic Computing


R package for the analysis of massive SNP arrays.

Efficient toolkit implementing best practices for principal component analysis of population genetic data

Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics

Optimal Linkage Disequilibrium Splitting

MUSSEL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups

bioRxiv : the preprint server for biology


Source code of FUMA GWAS web application

Functional mapping and annotation of genetic associations with FUMA

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

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

Independent Genomic Sources of Brain Structure and Function

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


Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Clinical and translational values of spatial transcriptomics

Signal transduction and targeted therapy

Spatial omics: Navigating to the golden era of cancer research

Cell type-specific inference of differential expression in spatial transcriptomics

Benchmarking and integration of methods for deconvoluting spatial transcriptomic data

Integrative analysis of spatial transcriptome with single-cell transcriptome and single-cell epigenome in mouse lungs after immunization


3D mesh stylization driven by a text input in PyTorch

LION: Latent Point Diffusion Models for 3D Shape Generation

Text2Mesh: Text-Driven Neural Stylization for Meshes

TexFusion: Synthesizing 3D Textures with Text-Guided Image Diffusion Models


Bagpipes is a state of the art code for generating realistic model galaxy spectra and fitting these to spectroscopic and photometric observations. Users should install with pip, not by cloning the repository.

Normal, dust-obscured galaxies in the epoch of reionization

Probing the Nature of High-redshift Weak Emission Line Quasars: A Young Quasar with a Starburst Host Galaxy

New Observational H(z) Data from Full-spectrum Fitting of Cosmic Chronometers in the LEGA-C Survey

The Astrophysical journal. Supplement series/Astrophysical journal. Supplement series

An Extremely Compact, Low-mass Galaxy on its Way to Quiescence at z = 5.2

Lightning: An X-Ray to Submillimeter Galaxy SED-fitting Code with Physically Motivated Stellar, Dust, and AGN Models

High dust content of a quiescent galaxy at z~2 revealed by deep ALMA
  observation


Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards

DeltaDelta Neural Networks for Lead Optimization of Small Molecule Potency

A Physics-Guided Neural Network for Predicting Protein–Ligand Binding Free Energy: From Host–Guest Systems to the PDBbind Database

Supercomputer Docking

Supercomputing frontiers and innovations

Predicting binding free energies: Frontiers and benchmarks (a perpetual review)


HiGHmed Data Sharing Framework funded by the German Federal Ministry of Education and Research (BMBF, grant ids: 01ZZ1802E and 01ZZ1802A)

Executing Distributed Healthcare and Research Processes - The HiGHmed Data Sharing Framework

Studies in health technology and informatics

A Federated Record Linkage Algorithm for Secure Medical Data Sharing

Feasibility Queries in Distributed Architectures – Concept and Implementation in HiGHmed

Data Sharing in Distributed Architectures – Concept and Implementation in HiGHmed


Post hoc inference via multiple testing

Post hoc inference via joint family-wise error rate control

Post hoc false positive control for structured hypotheses

Post hoc false positive control for spatially structured hypotheses

On agnostic post hoc approaches to false positive control


A Large-scale Chinese Short-Text Conversation Dataset and Chinese pre-training dialog models

The Curious Case of Neural Text Degeneration

Neural Responding Machine for Short-Text Conversation

TransferTransfo: A Transfer Learning Approach for Neural Network Based Conversational Agents

A Large-Scale Chinese Short-Text Conversation Dataset

Towards an Online Empathetic Chatbot with Emotion Causes

SIGIR '21 - PROCEEDINGS OF THE 44TH INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL

CPED: A Large-Scale Chinese Personalized and Emotional Dialogue Dataset for Conversational AI

Retrieve, Discriminate and Rewrite: A Simple and Effective Framework for Obtaining Affective Response in Retrieval-Based Chatbots

Findings of the Association for Computational Linguistics: EMNLP 2021

Prediction, Selection, and Generation: Exploration of Knowledge-Driven Conversation System

RealMedDial: A Real Telemedical Dialogue Dataset Collected from Online Chinese Short-Video Clips

International Conference on Computational Linguistics


NeuralTalk is a Python+numpy project for learning Multimodal Recurrent Neural Networks that describe images with sentences.

Show and Tell: A Neural Image Caption Generator

SCA-CNN: Spatial and Channel-wise Attention in Convolutional Networks for Image Captioning

Image Captioning with Semantic Attention

Knowing When to Look: Adaptive Attention via a Visual Sentinel for Image Captioning

A Shared Task on Multimodal Machine Translation and Crosslingual Image Description

Proceedings of the First Conference on Machine Translation: Volume 2,
          Shared Task Papers

Guiding Long-Short Term Memory for Image Caption Generation

Text-Guided Attention Model for Image Captioning

Cross-Lingual Image Caption Generation

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

Neural Image Caption Generation with Weighted Training and Reference

Unsupervised Visual Sense Disambiguation for Verbs using Multimodal Embeddings


A Comprehensive Exploration on WikiSQL with Table-Aware Word
  Contextualization

A Discrete Hard EM Approach for Weakly Supervised Question Answering

Structure-Grounded Pretraining for Text-to-SQL

North American Chapter of the Association for Computational Linguistics

An Imitation Game for Learning Semantic Parsers from User Interaction

Generating Semantically Valid Adversarial Questions for TableQA


Bag of Tricks and A Strong Baseline for Deep Person Re-identification

A Strong Baseline and Batch Normalization Neck for Deep Person Re-Identification

Multi-Domain Learning and Identity Mining for Vehicle Re-Identification

How important are faces for person re-identification?

Rethinking Person Re-Identification via Semantic-Based Pretraining

Improving Person Re-Identification with Temporal Constraints

Person re-identification: Implicitly defining the receptive fields of deep learning classification frameworks


GraftM - Rapid community profiles from metagenomes

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus

Differences in Ureolytic Bacterial Composition between the Rumen Digesta and Rumen Wall Based on ureC Gene Classification

Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity

Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes

Legume crop rotation suppressed nitrifying microbial community in a sugarcane cropping soil

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment


Patent analysis using the Google Patents Public Datasets on BigQuery

The Harvard USPTO Patent Dataset: A Large-Scale, Well-Structured, and
  Multi-Purpose Corpus of Patent Applications

Supervised Contrastive Learning for Interpretable Long-Form Document Matching

Supervised Contrastive Learning for Interpretable Long Document Comparison.

CinPatent: Datasets for Patent Classification


Fast and flexible Gaussian Process regression in Python

A rocky planet transiting a nearby low-mass star

juliet: a versatile modelling tool for transiting and non-transiting exoplanetary systems

Monthly notices of the Royal Astronomical Society

Extending the modeling of the anisotropic galaxy power spectrum to k = 0.4 hMpc−1

Journal of Cosmology and Astroparticle Physics

Constraints on the interacting vacuum-geodesic CDM scenario

An Ultra-short Period Rocky Super-Earth with a Secondary Eclipse and a Neptune-like Companion around K2-141

Warm terrestrial planet with half the mass of Venus transiting a nearby star

A precise optical transmission spectrum of the inflated exoplanet WASP-52b

Monthly Notices of the Royal Astronomical Society

Non-detection of HC11N towards TMC-1: constraining the chemistry of large carbon-chain molecules

The spectral energy distribution of powerful starburst galaxies - I. Modelling the radio continuum

Spin-Orbit Misalignments of Three Jovian Planets via Doppler Tomography


Official repo for consistency models.

Consistency Models

One-step Diffusion with Distribution Matching Distillation

A Geometric Perspective on Diffusion Models


Aave Protocol Version 1.0 - Decentralized Lending Pools

Quantifying Blockchain Extractable Value: How dark is the forest?

Attacking the DeFi Ecosystem with Flash Loans for Fun and Profit

The Decentralized Financial Crisis

On the Just-In-Time Discovery of Profit-Generating Transactions in DeFi Protocols

An Empirical Study of DeFi Liquidations: Incentives, Risks, and Instabilities

SoK: Lending Pools in Decentralized Finance

CeFi vs. DeFi -- Comparing Centralized to Decentralized Finance

SoK: Decentralized Finance (DeFi) Attacks

Flashot: A Snapshot of Flash Loan Attack on DeFi Ecosystem

Perpetual Contract NFT as Collateral for DeFi Composability


Genome-wide Efficient Mixed Model Association

Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies

rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study

基因组蛋白质组与生物信息学报

A genome-wide association study finds genetic variants associated with neck or shoulder pain in UK Biobank

New insights into the associations among feed efficiency, metabolizable efficiency traits and related QTL regions in broiler chickens

Genome-wide association study meta-analysis of suicide death and suicidal behavior

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers

Genome-Wide Association Study of Starch Properties in Local Thai Rice

Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community


A machine learning tool for fishing entities

Covid-on-the-Web: Knowledge Graph and Services to Advance COVID-19 Research

How can voting mechanisms improve the robustness and generalizability of toponym disambiguation?

Covid-on-the-Web: Exploring the COVID-19 scientific literature through visualization of linked data from entity and argument mining

The Kairntech Sherpa – An ML Platform and API for the Enrichment of (not only) Scientific Content

Annotating Entities with Fine-Grained Types in Austrian Court Decisions

Extending electronic medical records vector models with knowledge graphs to improve hospitalization prediction


The open source toolbox for reproducible diffusion MRI-based microstructure estimation

Challenges for biophysical modeling of microstructure

Numerical modeling of the effects of beach slope on water-table fluctuation in the unconfined aquifer of Donghai Island, China

Changes in white matter microstructure following serial ketamine infusions in treatment resistant depression

Diffusion-weighted MR spectroscopy: consensus, recommendations and
  resources from acquisition to modelling

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

Evaluating NODDI‐based biomarkers of Alzheimer’s disease


Bayes Net Toolbox for Matlab

Causality-based Feature Selection: Methods and Evaluations

Exact Inference Techniques for the Analysis of Bayesian Attack Graphs

Efficient Attack Graph Analysis through Approximate Inference

BARD: A Structured Technique for Group Elicitation of Bayesian Networks to Support Analytic Reasoning

Risk analysis : an official publication of the Society for Risk Analysis

Cause vs. effect in context-sensitive prediction of business process instances

A Review on Algorithms for Constraint-based Causal Discovery

An Investigation into Unsafe Behaviors and Traffic Accidents Involving Unlicensed Drivers: A Perspective for Alignment Measurement

International journal of environmental research and public health

A Recursive Markov Boundary-Based Approach to Causal Structure Learning

Causality-Aided Falsification

Pedestrians’ Injury Severity in Traffic Accidents in Spain: A Pedestrian Actions Approach


A Very Low-Bitrate Codec for Speech Compression

Efficient Neural Audio Synthesis

SoundStream: An End-to-End Neural Audio Codec

High Fidelity Neural Audio Compression

Wavenet based low rate speech coding

Generative Speech Coding with Predictive Variance Regularization

End-to-End Neural Speech Coding for Real-Time Communications

Latent-Domain Predictive Neural Speech Coding

CQNV: A combination of coarsely quantized bitstream and neural vocoder
  for low rate speech coding

An Intra-BRNN and GB-RVQ Based END-TO-END Neural Audio Codec

Handling Background Noise in Neural Speech Generation


NCCL Tests

Evaluating Modern GPU Interconnect: PCIe, NVLink, NV-SLI, NVSwitch and GPUDirect

IEEE transactions on parallel and distributed systems

Daydream: Accurately Estimating the Efficacy of Optimizations for DNN Training

Performance Analysis of Deep Learning Workloads on Leading-edge Systems

Multi-node Bert-pretraining: Cost-efficient Approach

Efficient Direct-Connect Topologies for Collective Communications

Srifty: Swift and Thrifty Distributed Training on the Cloud

A Hardware Evaluation Framework for Large Language Model Inference

DeAR: Accelerating Distributed Deep Learning with Fine-Grained All-Reduce Pipelining

Using machine learning to model the training scalability of convolutional neural networks on clusters of GPUs


Distributed deep learning on Hadoop and Spark clusters.

BigDL: A Distributed Deep Learning Framework for Big Data

Scalable Deep Learning on Distributed Infrastructures: Challenges, Techniques and Tools

GossipGraD: Scalable Deep Learning using Gossip Communication based Asynchronous Gradient Descent.

Scanner: Efficient Video Analysis at Scale

A Survey on Spark Ecosystem: Big Data Processing Infrastructure, Machine Learning, and Applications

DeepSpark: A Spark-Based Distributed Deep Learning Framework for Commodity Clusters

What does fault tolerant Deep Learning need from MPI?

Barista - a Graphical Tool for Designing and Training Deep Neural Networks


Open-Source Large Vocabulary Continuous Speech Recognition Engine

Neuro-SERKET: Development of Integrative Cognitive System Through the Composition of Deep Probabilistic Generative Models

Robust Understanding of Robot-Directed Speech Commands Using Sequence to Sequence With Noise Injection

Information Navigation System with Discovering User Interests

Annual Meeting of the Special Interest Group on Discourse and Dialogue

Double Articulation Analyzer With Prosody for Unsupervised Word and Phone Discovery


Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

Fast and accurate de novo genome assembly from long uncorrected reads

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

Research in Computational Molecular Biology

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus

Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development

Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics

De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology

Computational and structural biotechnology journal

Transmission of Similar Mcr-1 Carrying Plasmids among Different Escherichia coli Lineages Isolated from Livestock and the Farmer

Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production


nuScenes: A multimodal dataset for autonomous driving

Scalability in Perception for Autonomous Driving: Waymo Open Dataset

Center-based 3D Object Detection and Tracking

Multimodal Virtual Point 3D Detection

VISTA: Boosting 3D Object Detection via Dual Cross-VIew SpaTial Attention

Robo3D: Towards Robust and Reliable 3D Perception against Corruptions

It's All Around You: Range-Guided Cylindrical Network for 3D Object Detection

FP8 versus INT8 for efficient deep learning inference

CenterAtt: Fast 2-stage Center Attention Network

PAI3D: Painting Adaptive Instance-Prior for 3D Object Detection


RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

Methods to study splicing from high-throughput RNA Sequencing data

SPLICEOSOMAL PRE-MRNA SPLICING: METHODS AND PROTOCOLS

The Transcription Factor bZIP60 Links the Unfolded Protein Response to the Heat Stress Response in Maize.

Gasdermin D inhibition confers antineutrophil-mediated cardioprotection in acute myocardial infarction

The Journal of clinical investigation/The journal of clinical investigation

A simple guide to de novo transcriptome assembly and annotation

Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders

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

Mitochondrial Ca2+ Overload Leads to Mitochondrial Oxidative Stress and Delayed Meiotic Resumption in Mouse Oocytes

Frontiers in cell and developmental biology

Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity

Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme

Transcriptomic Profiling and Physiological Responses of Halophyte Kochia sieversiana Provide Insights into Salt Tolerance


Longformer: The Long-Document Transformer

Fake news detection based on news content and social contexts: a transformer-based approach

International journal of data science and analytics

DocNLI: A Large-scale Dataset for Document-level Natural Language Inference

Globalizing BERT-based Transformer Architectures for Long Document Summarization

Conference of the European Chapter of the Association for Computational Linguistics

MultiHiertt: Numerical Reasoning over Multi Hierarchical Tabular and Textual Data

Revisiting Transformer-based Models for Long Document Classification

An Exploratory Study on Long Dialogue Summarization: What Works and What's Next

Document Classification for COVID-19 Literature

"Let Your Characters Tell Their Story": A Dataset for Character-Centric Narrative Understanding

RoR: Read-over-Read for Long Document Machine Reading Comprehension


FCOS: Fully Convolutional One-Stage Object Detection (ICCV'19)

Spatial Attention Fusion for Obstacle Detection Using MmWave Radar and Vision Sensor

EAGLE: Large-scale Vehicle Detection Dataset in Real-World Scenarios
  using Aerial Imagery

Persistent Animal Identification Leveraging Non-Visual Markers


Transcript assembly and quantification for RNA-Seq

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise

Improved transcriptome assembly using a hybrid of long and short reads with StringTie

Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease

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

bioRxiv : the preprint server for biology

Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment

Mutant U2AF1-induced alternative splicing of H2afy (macroH2A1) regulates B-lymphopoiesis in mice

Efficacy of pembrolizumab and comprehensive CD274/PD-L1 profiles in patients previously treated with chemoradiation therapy as radical treatment in bladder cancer

Chemerin Impact on Alternative mRNA Transcription in the Porcine Luteal Cells


Connect suppliers, distributors and consumers to trade local produce.


CaMa-Flood_v4 development master

Assimilation of transformed water surface elevation to improve river discharge estimation in a continental-scale river


(ෆ`꒳´ෆ) A Survey on Text-to-Image Generation/Synthesis.

To Create What You Tell: Generating Videos from Captions

A survey and taxonomy of adversarial neural networks for text‐to‐image synthesis

CPGAN: Content-Parsing Generative Adversarial Networks for Text-to-Image Synthesis

Unifying Multimodal Transformer for Bi-directional Image and Text Generation

Text-to-image Synthesis via Symmetrical Distillation Networks

Cycle-Consistent Inverse GAN for Text-to-Image Synthesis

Multi-caption Text-to-Face Synthesis: Dataset and Algorithm

Proceedings of the 29th ACM International Conference on Multimedia

End-to-End Text-to-Image Synthesis with Spatial Constrains

ACM transactions on intelligent systems and technology

Generative Adversarial Network for Text-to-Face Synthesis and Manipulation

R-GAN: Exploring Human-like Way for Reasonable Text-to-Image Synthesis via Generative Adversarial Networks


A graph-based approach to diploid genome assembly

A haplotype-aware de novo assembly of related individuals using pedigree sequence graph

A haplotype-aware de novo assembly of related individuals using pedigree graph


Decision Intelligence Platform for Autonomous Driving simulation.

SafeBench: A Benchmarking Platform for Safety Evaluation of Autonomous
  Vehicles

Learning to Drive by Watching YouTube Videos: Action-Conditioned Contrastive Policy Pretraining

ScenarioNet: Open-Source Platform for Large-Scale Traffic Scenario
  Simulation and Modeling


A kernel-density-based, embarrassingly parallel ensemble sampler

Data Analysis Recipes: Using Markov Chain Monte Carlo

The Astrophysical journal. Supplement series/Astrophysical journal. Supplement series

emcee v3: A Python ensemble sampling toolkit for affine-invariant MCMC

Inferring probabilistic stellar rotation periods using Gaussian processes

GW190521 May Be an Intermediate-mass Ratio Inspiral

Forecasts for detecting the gravitational-wave memory effect with Advanced LIGO and Virgo

Parameter estimation with gravitational waves

Hierarchical Inference of Binary Neutron Star Mass Distribution and Equation of State with Gravitational Waves

Ensemble slice sampling

Colmena: Scalable Machine-Learning-Based Steering of Ensemble Simulations for High Performance Computing

Observing the circumgalactic medium of simulated galaxies through synthetic absorption spectra

Monthly notices of the Royal Astronomical Society


An easy-to-use Japanese Text Processing tool, which makes it possible to switch tokenizers with small changes of code.

fugashi, a Tool for Tokenizing Japanese in Python

Finding the Right Recipe for Low Resource Domain Adaptation in Neural
  Machine Translation

Japanese SimCSE Technical Report


An "R" package for automatic download and preprocessing of MODIS Land Products Time Series

Could climate trends disrupt the contact rates between Ixodes ricinus (Acari, Ixodidae) and the reservoirs of Borrelia burgdorferi s.l.?

RGISTools: Downloading, Customizing, and Processing Time Series of
  Remote Sensing Data in R


⛔ DEPRECATED <Python Framework for Reproducible Deep Learning Experiments>

DeepDIVA: A Highly-Functional Python Framework for Reproducible Experiments

Offline Signature Verification by Combining Graph Edit Distance and Triplet Networks

STRUCTURAL, SYNTACTIC, AND STATISTICAL PATTERN RECOGNITION, S+SSPR 2018

Are You Tampering With My Data?


Multi-Objective Reinforcement Learning algorithms implementations.

A Generalized Algorithm for Multi-Objective Reinforcement Learning and Policy Adaptation

Multi-Objective Deep Reinforcement Learning

Prediction-Guided Multi-Objective Reinforcement Learning for Continuous Robot Control

International Conference on Machine Learning

Sample-Efficient Multi-Objective Learning via Generalized Policy
  Improvement Prioritization

Pareto Conditioned Networks

A Toolkit for Reliable Benchmarking and Research in Multi-Objective Reinforcement Learning

Hyperparameter Optimization for Multi-Objective Reinforcement Learning


Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

NanoPack: visualizing and processing long-read sequencing data

Computational methods for 16S metabarcoding studies using Nanopore sequencing data

Comprehensive Pathogen Identification, Antibiotic Resistance, and Virulence Genes Prediction Directly From Simulated Blood Samples and Positive Blood Cultures by Nanopore Metagenomic Sequencing

Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii


Cingulata (pronounced "tchingulata") is a compiler toolchain and RTE for running C++ programs over encrypted data by means of fully homomorphic encryption techniques.

Homomorphic Encryption for Machine Learning in Medicine and Bioinformatics

EVA: An Encrypted Vector Arithmetic Language and Compiler for Efficient Homomorphic Computation

Programming Language Design and Implementation

CPU and GPU Accelerated Fully Homomorphic Encryption

KONFIDO: An OpenNCP-Based Secure eHealth Data Exchange System

SECURITY IN COMPUTER AND INFORMATION SCIENCES, EURO-CYBERSEC 2018

CHET: Compiler and Runtime for Homomorphic Evaluation of Tensor Programs


High-quality single-file implementations of SOTA Offline and Offline-to-Online RL algorithms: AWAC, BC, CQL, DT, EDAC, IQL, SAC-N, TD3+BC, LB-SAC, SPOT, Cal-QL, ReBRAC

CORL: Research-oriented Deep Offline Reinforcement Learning Library

Synthetic Experience Replay

Diffusion Model is an Effective Planner and Data Synthesizer for
  Multi-Task Reinforcement Learning

Improving Offline-to-Online Reinforcement Learning with Q-Ensembles

Sequence Modeling is a Robust Contender for Offline Reinforcement
  Learning

Cross-Domain Policy Adaptation via Value-Guided Data Filtering

Towards Robust Offline-to-Online Reinforcement Learning via Uncertainty
  and Smoothness

Counterfactual Conservative Q Learning for Offline Multi-agent
  Reinforcement Learning


A Python interface for reinforcement learning environments

Magnetic control of tokamak plasmas through deep reinforcement learning

dm_control: Software and Tasks for Continuous Control

AndroidEnv: A Reinforcement Learning Platform for Android

Using Unity to Help Solve Intelligence

Learning Robust Real-Time Cultural Transmission without Human Data


Universal Proposition Banks for Multilingual Semantic Role Labeling

Cross-Lingual Transfer of Semantic Roles: From Raw Text to Semantic Roles

Towards Deep Universal Dependencies

Proceedings of the Fifth International Conference on Dependency Linguistics (Depling, SyntaxFest 2019)

Improved Semantic Role Labeling using Parameterized Neighborhood Memory
  Adaptation

Abstract meaning representation of Turkish

Making a Semantic Event-type Ontology Multilingual

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION

Construct a Sense-Frame Aligned Predicate Lexicon for Chinese AMR Corpus

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


Diffprivlib: The IBM Differential Privacy Library

Differentially private random decision forests using smooth sensitivity

Differentially Private Synthetic Data: Applied Evaluations and Enhancements

Exploring Design and Governance Challenges in the Development of Privacy-Preserving Computation

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

Are We There Yet? Timing and Floating-Point Attacks on Differential Privacy Systems

Secure Random Sampling in Differential Privacy

Widespread Underestimation of Sensitivity in Differentially Private Libraries and How to Fix It

Training Differentially Private Models with Secure Multiparty
  Computation

An Analysis of the Deployment of Models Trained on Private Tabular Synthetic Data: Unexpected Surprises

GRAIMATTER Green Paper: Recommendations for disclosure control of
  trained Machine Learning (ML) models from Trusted Research Environments
  (TREs)


A lightweight, scalable, and general framework for visual question answering research

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

VQA-MHUG: A Gaze Dataset to Study Multimodal Neural Attention in Visual Question Answering

Multimodal Integration of Human-Like Attention in Visual Question Answering

Estimating semantic structure for the VQA answer space

What's Different between Visual Question Answering for Machine
  "Understanding" Versus for Accessibility?


Ambiguity of Uppercase vs Lowercase in RFC 2119 Key Words

Sender Policy Framework (SPF) for Authorizing Use of Domains in Email, Version 1

Domain-based Message Authentication, Reporting, and Conformance (DMARC)

The Authenticated Received Chain (ARC) Protocol


Randomized Dimension Reduction Library

Sparse Principal Component Analysis via Variable Projection

Randomized Dynamic Mode Decomposition

SIAM journal on applied dynamical systems

Randomized nonnegative matrix factorization

Semi-supervised Embedding Learning for High-dimensional Bayesian Optimization.

Scalable diagnostics for global atmospheric chemistry using Ristretto library (version 1.0)


Large category of modules over monads on top of UniMaths and Display category

High-level signatures and initial semantics

Modular specification of monads through higher-order presentations

Signatures and models for syntax and operational semantics in the presence of variable binding


ATHENA: Advanced Techniques for High dimensional parameter spaces to Enhance Numerical Analysis

A Supervised Learning Approach Involving Active Subspaces for an Efficient Genetic Algorithm in High-Dimensional Optimization Problems

Enhancing CFD predictions in shape design problems by model and parameter space reduction

Advanced modeling and simulation in engineering sciences

Hull Shape Design Optimization with Parameter Space and Model Reductions, and Self-Learning Mesh Morphing

Journal of marine science and engineering

A multifidelity approach coupling parameter space reduction and nonintrusive POD with application to structural optimization of passenger ship hulls

Multi‐fidelity data fusion through parameter space reduction with applications to automotive engineering

A local approach to parameter space reduction for regression and
  classification tasks

Multi‐fidelity data fusion for the approximation of scalar functions with low intrinsic dimensionality through active subspaces

Proceedings in applied mathematics and mechanics

Level set learning with pseudo-reversible neural networks for nonlinear
  dimension reduction in function approximation


Build Graph Nets in Tensorflow

Learning to Simulate Complex Physics with Graph Networks

Graph Neural Network for Traffic Forecasting: A Survey

Computing Graph Neural Networks: A Survey from Algorithms to Accelerators

A Survey of Deep Learning for Scientific Discovery

Accelerated Charged Particle Tracking with Graph Neural Networks on FPGAs

Graph Neural Networks for Particle Tracking and Reconstruction

Learning to Manipulate Object Collections Using Grounded State Representations

Graph Neural Networks: Methods, Applications, and Opportunities

GRANITE: A Graph Neural Network Model for Basic Block Throughput Estimation

Simulating Liquids with Graph Networks


FarmVibes.AI: Multi-Modal GeoSpatial ML Models for Agriculture and Sustainability

Seeing Through Clouds in Satellite Images

RAG vs Fine-tuning: Pipelines, Tradeoffs, and a Case Study on
  Agriculture

GPT-4 as an Agronomist Assistant? Answering Agriculture Exams Using Large Language Models


中文LLaMA-2 & Alpaca-2大模型二期项目 + 64K超长上下文模型 (Chinese LLaMA-2 & Alpaca-2 LLMs with 64K long context models)

Extending Context Window of Large Language Models via Positional
  Interpolation

Efficient and Effective Text Encoding for Chinese LLaMA and Alpaca

YaRN: Efficient Context Window Extension of Large Language Models

DISC-LawLLM: Fine-tuning Large Language Models for Intelligent Legal
  Services

Retrieve-Rewrite-Answer: A KG-to-Text Enhanced LLMs Framework for
  Knowledge Graph Question Answering

Conversational Recommender System and Large Language Model Are Made for Each Other in E-commerce Pre-sales Dialogue

TencentLLMEval: A Hierarchical Evaluation of Real-World Capabilities for
  Human-Aligned LLMs


Document Image Binarization

A selectional auto-encoder approach for document image binarization

Mixed Model OCR Training on Historical Latin Script for Out-of-the-Box Recognition and Finetuning

Open Source Handwritten Text Recognition on Medieval Manuscripts using
  Mixed Models and Document-Specific Finetuning


C++ implementation of a fast hash map and hash set using robin hood hashing

Benchmarking Learned Indexes

PSF-LO: Parameterized Semantic Features Based Lidar Odometry

Dynamic Path-Decomposed Tries

LSI: A Learned Secondary Index Structure

GraphTango: A Hybrid Representation Format for Efficient Streaming Graph
  Updates and Analysis

Mallob: Scalable SAT Solving On Demand With Decentralized Job Scheduling

Design of a Resilient, High-Throughput, Persistent Storage System for the ATLAS Phase-II DAQ System


Generating bash command from natural language https://arxiv.org/abs/1802.08979

Neural Machine Translation by Jointly Learning to Align and Translate

Incorporating Copying Mechanism in Sequence-to-Sequence Learning

NL2Bash: A Corpus and Semantic Parser for Natural Language Interface to the Linux Operating System

Neural Machine Translation for Code Generation


Official PyTorch implementation of Dreaming to Distill: Data-free Knowledge Transfer via DeepInversion (CVPR 2020)

Do Gradient Inversion Attacks Make Federated Learning Unsafe?

Decompiling x86 Deep Neural Network Executables

Zero-Shot Learning Of A Conditional Generative Adversarial Network For Data-Free Network Quantization


Open Source Photometric classification https://supernnova.readthedocs.io

SuperNNova: an open-source framework for Bayesian, neural network-based supernova classification

Monthly Notices of the Royal Astronomical Society

Exempla Gratis (E.G.): Code Examples for Free

The Dark Energy Survey supernova program: cosmological biases from supernova photometric classification


Python interface to Metview meteorological workstation and batch system


Open-source implementation of Google Vizier for hyper parameters tuning

Google Vizier: A Service for Black-Box Optimization

Hyper-Parameter Optimization: A Review of Algorithms and Applications

Benchmark and Survey of Automated Machine Learning Frameworks

Efficient Deep Learning: A Survey on Making Deep Learning Models Smaller, Faster, and Better

AutoML to Date and Beyond: Challenges and Opportunities

Survey on Automated Machine Learning.

Open Source Vizier: Distributed Infrastructure and API for Reliable and
  Flexible Blackbox Optimization

Auptimizer - an Extensible, Open-Source Framework for Hyperparameter Tuning

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


A simple and highly efficient RTS-game-inspired environment for reinforcement learning (formerly Gym-MicroRTS)

Gym-µRTS: Toward Affordable Full Game Real-time Strategy Games Research with Deep Reinforcement Learning

Action Guidance: Getting the Best of Sparse Rewards and Shaped Rewards for Real-time Strategy Games

Comparing Observation and Action Representations for Deep Reinforcement Learning in MicroRTS.

Transformers as Policies for Variable Action Environments


A toolbox for working with Allen Human Brain Atlas microarray expression data

Standardizing workflows in imaging transcriptomics with the abagen toolbox

Differences in subcortico-cortical interactions identified from connectome and microcircuit models in autism

An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization

Brain atrophy progression in Parkinson’s disease is shaped by connectivity and local vulnerability

Connectivity alterations in autism reflect functional idiosyncrasy

Regional Radiomics Similarity Networks Reveal Distinct Subtypes and Abnormality Patterns in Mild Cognitive Impairment

A dynamic gradient architecture generates brain activity states

Structural Features of the Human Connectome That Facilitate the Switching of Brain Dynamics via Noradrenergic Neuromodulation

Revealing the neurobiology underlying interpersonal neural synchronization with multimodal data fusion

Relationship between cerebrospinal fluid neurodegeneration biomarkers and temporal brain atrophy in cognitively healthy older adults


Long read based human genomic structural variation detection with cuteSV

Long-read-based human genomic structural variation detection with cuteSV

Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology

Regenotyping structural variants through an accurate force-calling method

Structural Variant Detection from Long-Read Sequencing Data with cuteSV.

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


An open source, embedded, high performance g-code-parser and CNC milling controller written in optimized C that will run on a straight Arduino

Intrinsic motivation and episodic memories for robot exploration of high-dimensional sensory spaces

Opportunities for Robotic Systems and Automation in Cotton Production

Ecology of fear in highly invasive fish revealed by robots

Recent Developments Regarding Painting Robots for Research in Automatic Painting, Artificial Creativity, and Machine Learning

Design and Implementation of an Urban Farming Robot

Opportunistic and Location-Based Collaboration Architecture among Mobile Assets and Fixed Manufacturing Processes

How particle shape affects granular segregation in industrial and geophysical flows

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

Concept for a precise academic Gripper


machine learning with logical rules in Python

Computer-Assisted Creation of Boolean Search Rules for Text Classification in the Legal Domain

Counterfactual Phenotyping with Censored Time-to-Events

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

NetRCA: An Effective Network Fault Cause Localization Algorithm

Computing Rule-Based Explanations of Machine Learning Classifiers using
  Knowledge Graphs

Rule-based Out-Of-Distribution Detection

Shapley-based Explainable AI for Clustering Applications in Fault
  Diagnosis and Prognosis

Intelligent Tools to Monitor, Control and Predict Wastewater Reclamation and Reuse


BEELINE: evaluation of algorithms for gene regulatory network inference

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG

Inferring Gene Regulatory Networks From Single-Cell Transcriptomic Data Using Bidirectional RNN


:angel: Morph faces with Python, Numpy, Scipy

Deep Face Representations for Differential Morphing Attack Detection

One-shot Face Reenactment

Face morph detection for unknown morphing algorithms and image sources: a multi-scale block local binary pattern fusion approach

Mapping the perception-space of facial expressions in the era of face masks

Deep Composite Face Image Attacks: Generation, Vulnerability and Detection


Easily share permanent links to ChatGPT conversations with your friends

A Survey of Large Language Models

MiniGPT-4: Enhancing Vision-Language Understanding with Advanced Large
  Language Models

MiniGPT-v2: large language model as a unified interface for
  vision-language multi-task learning

Deductive Verification of Chain-of-Thought Reasoning

LLaSM: Large Language and Speech Model

The Shifted and The Overlooked: A Task-oriented Investigation of User-GPT Interactions


LexNLP by LexPredict

LexNLP: Natural Language Processing and Information Extraction For Legal and Regulatory Texts

Extracting Outcomes from Appellate Decisions in US State Courts

The Case for a Linked Data Research Engine for Legal Scholars

eyecite: A tool for parsing legal citations

CaseGNN: Graph Neural Networks for Legal Case Retrieval with
  Text-Attributed Graphs


Data and analysis for NA12878 genome on nanopore

Nanopore sequencing and assembly of a human genome with ultra-long reads

Nanopore native RNA sequencing of a human poly(A) transcriptome

RNA modifications detection by comparative Nanopore direct RNA sequencing

Beyond mass spectrometry, the next step in proteomics

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

Profiling the genome-wide landscape of tandem repeat expansions

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification

DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation

The RNA Atlas expands the catalog of human non-coding RNAs

Zenodo (CERN European Organization for Nuclear Research)

Interrogating the “unsequenceable” genomic trinucleotide repeat disorders by long-read sequencing


Decoder, aligner, and model optimizer for statistical machine translation and other structured prediction models based on (mostly) context-free formalisms

Multilingual Distributed Representations without Word Alignment

Modeling Source Syntax for Neural Machine Translation

Multimodal Pivots for Image Caption Translation

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

Joint Feature Selection in Distributed Stochastic Learning for Large-Scale Discriminative Training in SMT

Meeting of the Association for Computational Linguistics

Prompsit’s submission to WMT 2018 Parallel Corpus Filtering shared task

Proceedings of the Third Conference on Machine Translation: Shared Task Papers

Attention Focusing for Neural Machine Translation by Bridging Source and Target Embeddings

Real Time Adaptive Machine Translation for Post-Editing with cdec and TransCenter

Conference of the European Chapter of the Association for Computational Linguistics

Beyond Bilingual: Multi-sense Word Embeddings using Multilingual Context

Boosting Cross-Language Retrieval by Learning Bilingual Phrase Associations from Relevance Rankings

Empirical Methods in Natural Language Processing

Response-based Learning for Grounded Machine Translation

PROCEEDINGS OF THE 52ND ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS, VOL 1


Code for a multi-agent particle environment used in the paper "Multi-Agent Actor-Critic for Mixed Cooperative-Competitive Environments"

Actor-Attention-Critic for Multi-Agent Reinforcement Learning

Learning Transferable Cooperative Behavior in Multi-Agent Teams

Learning Implicit Credit Assignment for Cooperative Multi-Agent Reinforcement Learning

Feudal Multi-Agent Hierarchies for Cooperative Reinforcement Learning

Learning Structured Communication for Multi-agent Reinforcement Learning

Delay-Aware Multi-Agent Reinforcement Learning for Cooperative and Competitive Environments

Plan Better Amid Conservatism: Offline Multi-Agent Reinforcement Learning with Actor Rectification

Continuously Discovering Novel Strategies via Reward-Switching Policy Optimization

GCS: Graph-based Coordination Strategy for Multi-Agent Reinforcement
  Learning


cytofkit: an integrated flow/mass cytometry data analysis pipeline

High-Dimensional Single-Cell Quantitative Profiling of Skeletal Muscle Cell Population Dynamics during Regeneration

Granzyme B PET Imaging of Combined Chemotherapy and Immune Checkpoint Inhibitor Therapy in Colon Cancer

Imaging Kv1.3 Expressing Memory T Cells as a Marker of Immunotherapy Response

Inflammatory bone marrow signaling in pediatric acute myeloid leukemia distinguishes patients with poor outcomes

Using ICLite for deconvolution of bulk transcriptional data from mixed cell populations


Anomaly Detection with R

A review on outlier/anomaly detection in time series data

Evaluating Real-Time Anomaly Detection Algorithms -- The Numenta Anomaly Benchmark

International Conference on Machine Learning and Applications

Automatic Anomaly Detection in the Cloud Via Statistical Learning

Population mobility reductions associated with travel restrictions during the Ebola epidemic in Sierra Leone: use of mobile phone data

The Building Data Genome Project 2, energy meter data from the ASHRAE Great Energy Predictor III competition

RobustTAD: Robust Time Series Anomaly Detection via Decomposition and Convolutional Neural Networks

Unsupervised Anomaly Detection Approach for Time-Series in Multi-Domains Using Deep Reconstruction Error

ReRe: A Lightweight Real-Time Ready-to-Go Anomaly Detection Approach for Time Series

Computer Software and Applications Conference

RePAD: Real-time Proactive Anomaly Detection for Time Series

Precision and Recall for Range-Based Anomaly Detection


Clonal expansion and activation of tissue-resident memory-like TH17 cells expressing GM-CSF in the lungs of patients with severe COVID-19

Characterizing dedifferentiation of thyroid cancer by integrated analysis

CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes

Single-Cell Transcriptomics Reveals the Complexity of the Tumor Microenvironment of Treatment-Naive Osteosarcoma

The developing mouse coronal suture at single-cell resolution

Single-Cell Transcriptional Survey of Ileal-Anal Pouch Immune Cells From Ulcerative Colitis Patients

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

Macrophages orchestrate the expansion of a proangiogenic perivascular niche during cancer progression

Human Bone Marrow Organoids for Disease Modeling, Discovery, and Validation of Therapeutic Targets in Hematologic Malignancies

Single-cell RNA sequencing reveals spatiotemporal heterogeneity and malignant progression in pancreatic neuroendocrine tumor

International journal of biological sciences


Deep Learning in Javascript. Train Convolutional Neural Networks (or ordinary ones) in your browser.

SimpleDS: A Simple Deep Reinforcement Learning Dialogue System

Deep-Spying: Spying using Smartwatch and Deep Learning

Bootstrapping incremental dialogue systems: using linguistic knowledge to learn from minimal data

CrossCheck: Rapid, Reproducible, and Interpretable Model Evaluation

Front-end deep learning web apps development and deployment: a review

Applied intelligence (Dordrecht, Netherlands)

Fabrik: An Online Collaborative Neural Network Editor

Using Open-Source Software for Business, Urban, and Other Applications of Deep Neural Networks, Machine Learning, and Data Analytics Tools

International journal of artificial intelligence and machine learning


Software interfaces for interacting with brain atlases - Python client

Brain simulation as a cloud service: The Virtual Brain on EBRAINS

Cytoarchitectonic Maps of the Human Metathalamus in 3D Space

Cytoarchitecture, intersubject variability, and 3D mapping of four new areas of the human anterior prefrontal cortex


Nvidia Semantic Segmentation monorepo

PointPainting: Sequential Fusion for 3D Object Detection

Improving Semantic Segmentation via Video Propagation and Label Relaxation

Hierarchical Multi-Scale Attention for Semantic Segmentation

DeepFusion: Lidar-Camera Deep Fusion for Multi-Modal 3D Object Detection

PandaSet: Advanced Sensor Suite Dataset for Autonomous Driving

SemSegMap – 3D Segment-based Semantic Localization

Simple and Efficient Architectures for Semantic Segmentation

Contour-Aware Equipotential Learning for Semantic Segmentation

Vision-Based Large-scale 3D Semantic Mapping for Autonomous Driving Applications

Probing Contextual Diversity for Dense Out-of-Distribution Detection


mean Average Precision - This code evaluates the performance of your neural net for object recognition.

Scenic: A Language for Scenario Specification and Data Generation

An Asphalt Damage Dataset and Detection System Based on RetinaNet for Road Conditions Assessment

Retinopathy of Prematurity Stage Diagnosis Using Object Segmentation and Convolutional Neural Networks

New Dark Area Sensitive Tone Mapping for Deep Learning Based Traffic Sign Recognition

Detection of Waste Containers Using Computer Vision

Computational classification of animals for a highway detection system

Brazilian Journal of Veterinary Research and Animal Science

Ensembling object detectors for image and video data analysis

Sistem Pendeteksi Genus Gulma Pada Tanaman Jagung Menggunakan Algoritme Single Shot Detector

Robust In-Plane Structures Oscillation Monitoring by Terrestrial Photogrammetry


Neural network visualization toolkit for keras

iNNvestigate neural networks!

Predicting EGFR mutation status in lung adenocarcinoma on computed tomography image using deep learning

Big-Data Science in Porous Materials: Materials Genomics and Machine Learning

DeepCOVID-XR: An Artificial Intelligence Algorithm to Detect COVID-19 on Chest Radiographs Trained and Tested on a Large U.S. Clinical Data Set.

Training confounder-free deep learning models for medical applications

Training deep neural networks for binary communication with the Whetstone method

Real-time pollen monitoring using digital holography

Convolutional Neural Networks for Neuroimaging in Parkinson's Disease: Is Preprocessing Needed?

A deep learning approach to programmable RNA switches

Ensemble Deep Learning on Large, Mixed-Site fMRI Datasets in Autism and Other Tasks


Interactively explore metagenomes and more from a web browser.

Engineering of CRISPR-Cas12b for human genome editing

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination

Computational methods for 16S metabarcoding studies using Nanopore sequencing data

Computational and structural biotechnology journal

Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens

A benchmark dataset of herbarium specimen images with label data

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits

Does Organic Farming Increase Raspberry Quality, Aroma and Beneficial Bacterial Biodiversity?

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests


Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.

Lateral Gene Transfer from the Dead

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

Buxus and Tetracentron genomes help resolve eudicot genome history

MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers

Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis


The quasiparticle self-consistent GW method  in the PMT method (LAPW+LMTO+Lo).

Research Update: Relativistic origin of slow electron-hole recombination in hybrid halide perovskite solar cells

Model Construction and a Possibility of Cupratelike Pairing in a New d9 Nickelate Superconductor (Nd,Sr)NiO<…

Microscopic understanding of magnetic interactions in bilayer CrI 3

Questaal: A package of electronic structure methods based on the linear muffin-tin orbital technique

Accurate energy bands calculated by the hybrid quasiparticle self-consistent GW method implemented in the ecalj package

Direct theoretical evidence for weaker correlations in electron-doped and Hg-based hole-doped cuprates

Effect of ladder diagrams on optical absorption spectra in a quasiparticle self-consistent GW framework

Research Portal (Queen's University Belfast)

Dynamic symmetry breaking and spin splitting in metal halide perovskites

Self-energies in itinerant magnets: A focus on Fe and Ni

Reliability and applicability of magnetic-force linear response theory: Numerical parameters, predictability, and orbital resolution


Implementation of Ogata's (2005) method for Hankel transforms.

What is the Price of Abandoning Dark Matter? Cosmological Constraints on Alternative Gravity Theories

TheHaloMod: An online calculator for the halo model

hankel: A Python library for performing simple and accurate Hankel transformations

Probing delayed-end reionization histories with the 21-cm LAE cross-power spectrum

Monthly Notices of the Royal Astronomical Society

Cosmic flexion


Work with PBRT v4

Neural Network Generalization: The Impact of Camera Parameters

Soft Prototyping Camera Designs for Car Detection Based on a Convolutional Neural Network

A computational observer model of spatial contrast sensitivity: Effects of photocurrent encoding, fixational eye movements, and inference engine

Software-Defined Imaging: A Survey

Simulations of fluorescence imaging in the oral cavity

Accurate smartphone camera simulation using 3D scenes


CBE Thermal Comfort Tool for ASHRAE-55

comf: An R Package for Thermal Comfort Studies


List of major cities of the world as a datapackage

Global Syntactic Variation in Seven Languages: Toward a Computational Dialectology

Mapping Languages and Demographics with Georeferenced Corpora

Towards Sentence Level Inference Attack Against Pre-trained Language Models

Proceedings on Privacy Enhancing Technologies


DeepSphere: a graph-based spherical CNN (PyTorch)

DeepSphere: a graph-based spherical CNN

Neural simulation-based inference approach for characterizing the Galactic Center γ -ray excess

DeepSphere: towards an equivariant graph-based spherical CNN

Inferring dark matter substructure with astrometric lensing beyond the power spectrum


Meta-pipeline to identify transposable element insertions using next generation sequencing data

On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

Nuclear Ccr4-Not mediates the degradation of telomeric and transposon transcripts at chromatin in the Drosophila germline

Genomic analysis of P elements in natural populations of Drosophila melanogaster

Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast

bioRxiv : the preprint server for biology


Tools for interacting with NOIRLab's Astro Data Lab.

The Dark Energy Survey Data Release 2

The Astrophysical journal. Supplement series/Astrophysical journal. Supplement series

An empirical model of the Gaia DR3 selection function

Deep Synoptic Array Science: A Massive Elliptical Host Among Two Galaxy-cluster Fast Radio Bursts

Linking Extragalactic Transients and Their Host Galaxy Properties: Transient Sample, Multiwavelength Host Identification, and Database Construction

Jupyter-Enabled Astrophysical Analysis Using Data-Proximate Computing Platforms

Deep drilling in the time domain with DECam: survey characterization


A GPipe implementation in PyTorch

GPipe: Efficient Training of Giant Neural Networks using Pipeline Parallelism

torchgpipe: On-the-fly Pipeline Parallelism for Training Giant Models

Micro Batch Streaming: Allowing the Training of DNN Models to Use a
  large Batch Size in Memory Constrained Environments

A Survey and Empirical Evaluation of Parallel Deep Learning Frameworks


Create and maintain phylogenetic "reference packages" of biological sequences.

Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections

Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project

Mercury methylating microbial communities of boreal forest soils

An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees

IEEE/ACM transactions on computational biology and bioinformatics

metaXplor: an interactive viral and microbial metagenomic data manager

Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities

BATCH-SCAMPP: Scaling phylogenetic placement methods to place many sequences


Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109

Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation

Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling

An Empirical Evaluation of Generic Convolutional and Recurrent Networks for Sequence Modeling

Yet Another ICU Benchmark: A Flexible Multi-Center Framework for
  Clinical ML


Repository for mini-projects in the Data science for Sustainable development project


:rainbow: :camera: Gradient-weighted Class Activation Mapping (Grad-CAM) Demo

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

International journal of computer vision

Survey of Explainable AI Techniques in Healthcare

Explainable, Domain-Adaptive, and Federated Artificial Intelligence in Medicine


A novel approach for synthesizing tabular data using pretrained large language models

Language Models are Realistic Tabular Data Generators

Mixed-Type Tabular Data Synthesis with Score-based Diffusion in Latent
  Space

CuTS: Customizable Tabular Synthetic Data Generation


Package to calculate several thermal comfort indices (e.g. PMV, PPD, SET, adaptive) and convert physical variables.


Pyro models of SARS-CoV-2 variants

Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness

medRxiv : the preprint server for health sciences

Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection

Early warning of emerging infectious diseases based on multimodal data


Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.


SIDH Library is a fast and portable software library that implements state-of-the-art supersingular isogeny cryptographic schemes. The chosen parameters aim to provide security against attackers running a large-scale quantum computer, and security against classical algorithms.

SIDH on ARM: Faster Modular Multiplications for Faster Post-Quantum Supersingular Isogeny Key Exchange

IACR transactions on cryptographic hardware and embedded systems

Supersingular Curves You Can Trust

New Techniques for SIDH-based NIKE

Cold Boot Attacks on the Supersingular Isogeny Key Encapsulation (SIKE) Mechanism

Faulty isogenies: a new kind of leakage

An Alternative Approach for Computing Discrete Logarithms in Compressed SIDH.


A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

LocusZoom.js: interactive and embeddable visualization of genetic association study results

ZEAMAP, a Comprehensive Database Adapted to the Maize Multi-Omics Era

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

Exploring various polygenic risk scores for skin cancer in the phenomes of the Michigan genomics initiative and the UK Biobank with a visual catalog: PRSWeb


An R Framework for Climate Data Access and Post-processing

Configuration and intercomparison of deep learning neural models for statistical downscaling

Testing bias adjustment methods for regional climate change applications under observational uncertainty and resolution mismatch

CLIMBra - Climate Change Dataset for Brazil

Anthropogenic climate change impacts exacerbate summer forest fires in California

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

Simulating thermal dynamics of the largest lake in the Caucasus region: The mountain Lake Sevan


Another Gtf/Gff Analysis Toolkit

A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma

A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state

The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders

Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss

Barcoded RH-seq illuminates the complex genetic basis of yeast thermotolerance

Homozygosity at its Limit: Inbreeding Depression in Wild Arabidopsis arenosa Populations

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata

The genome sequence ofHirschfeldia incana, a species with high photosynthetic light-use efficiency

A first draft genome of holm oak (Quercus ilex subsp. ballota), the most representative species of the Mediterranean forest and the Spanish agrosylvopastoral ecosystem “dehesa”


Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

Molecular Epidemiology and Colistin Resistant Mechanism of mcr-Positive and mcr-Negative Clinical Isolated Escherichia coli

Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS26 Transposon in a Unique Chromosomal Location

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism

Clonal spread of Escherichia coli O101:H9-ST10 and O101:H9-ST167 strains carrying fosA3 and blaCTX-M-14 among diarrheal calves in a Chinese farm, with Australian Chroicocephalus as the possible origin of E. coli O101:H9-ST10

Horizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania

Global Phylogeny and F Virulence Plasmid Carriage in Pandemic Escherichia coli ST1193

Infection of Cronobacter sakazakii ST1 Producing SHV-12 in a Premature Infant Born from Triplet Pregnancy

Complete Genome Sequencing of Leptospira interrogans Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes

Genome-Based Epidemiologic Analysis of VIM/IMP Carbapenemase-Producing Enterobacter spp., Poland.


Sentinel-2 for Agriculture (Sen2Agri) is a software system processing high resolution satellite images for agricultural purposes funded by ESA (European Space Agency). Please register on the Sen2Agri webpage for Sen2Agri system updates and information.


AcademiCodec: An Open Source Audio Codec Model for Academic Research

InstructTTS: Modelling Expressive TTS in Discrete Latent Space with
  Natural Language Style Prompt

HiFi-Codec: Group-residual Vector quantization for High Fidelity Audio
  Codec

Fewer-token Neural Speech Codec with Time-invariant Codes

Efficient Parallel Audio Generation using Group Masked Language Modeling


Energy performance and Carbon emissions Assessment and Monitoring tool (Lluís Bosch, Lluís Corominas, IWA, Wacclim project, GIZ)


Find, circularise and annotate mitogenome from PacBio assemblies

MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

marcelauliano/MitoHiFi: mitohifi_v2.0

Semi-automated assembly of high-quality diploid human reference genomes

Inferring microbiota functions from taxonomic genes: a review

The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting

A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii

The genome sequence of the blue-rayed limpet, Patella pellucida Linnaeus, 1758

A draft reference genome of the red abalone, Haliotis rufescens, for conservation genomics


FIELDimageR: A R package to analyze orthomosaic images from agricultural field trials. This package is a compilation of functions to analyze pos-mosaicking images from research fields, and allows to: crop the image; remove soil effect; build vegetation indices; rotate the image; build the plot shapefile; extract information for each plot; and evaluate stand count, canopy percentage, and plant height.

FIELDimageR: An R package to analyze orthomosaic images from agricultural field trials


An Efficient, Scalable and Optimized Python Framework for Deep Forest (2021.2.1)

SDTR: Soft Decision Tree Regressor for Tabular Data

Detecting Blood Methylation Signatures in Response to Childhood Cancer Radiotherapy via Machine Learning Methods

Characterization of spleen and lymph node cell types via CITE-seq and machine learning methods


[ECCV 2022] ByteTrack: Multi-Object Tracking by Associating Every Detection Box

Detection Recovery in Online Multi-Object Tracking with Sparse Graph Tracker

LettuceTrack: Detection and tracking of lettuce for robotic precision spray in agriculture

Continuous Human Action Recognition for Human-machine Interaction: A Review

LettuceMOT: A dataset of lettuce detection and tracking with re-identification of re-occurred plants for agricultural robots

Bag of Tricks for Domain Adaptive Multi-Object Tracking


CoLight: Learning Network-level Cooperation for Traffic Signal Control

PROCEEDINGS OF THE 28TH ACM INTERNATIONAL CONFERENCE ON INFORMATION & KNOWLEDGE MANAGEMENT (CIKM '19)

CityFlow: A Multi-Agent Reinforcement Learning Environment for Large Scale City Traffic Scenario

WEB CONFERENCE 2019: PROCEEDINGS OF THE WORLD WIDE WEB CONFERENCE (WWW 2019)

GeneraLight: Improving Environment Generalization of Traffic Signal Control via Meta Reinforcement Learning

International Conference on Information and Knowledge Management

PlanLight: Learning to Optimize Traffic Signal Control With Planning and Iterative Policy Improvement


An extension of xarray for climate data analysis on structured grids.


GNU Radio blocks for receiving LoRa modulated radio messages using SDR

LoRaWAN Physical Layer-Based Attacks and Countermeasures, A Review

Attack-Aware Synchronization-Free Data Timestamping in LoRaWAN

Testbed for LoRaWAN Security: Design and Validation through Man-in-the-Middle Attacks Study

Attack-Aware Data Timestamping in Low-Power Synchronization-Free LoRaWAN

Development and Testing of a Real-Time LoRawan Sniffer Based on GNU-Radio

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


Chinese version of CLIP which achieves Chinese cross-modal retrieval and representation generation.

AutoAugment: Learning Augmentation Policies from Data

Chinese CLIP: Contrastive Vision-Language Pretraining in Chinese

GlyphDraw: Seamlessly Rendering Text with Intricate Spatial Structures
  in Text-to-Image Generation


Strelka2 germline and somatic small variant caller

Strelka2: fast and accurate calling of germline and somatic variants

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Curated variation benchmarks for challenging medically relevant autosomal genes

Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival

The clonal evolution of metastatic colorectal cancer

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

Strelka2: Fast and accurate variant calling for clinical sequencing applications

Low-burden TP53 mutations in CLL: clinical impact and clonal evolution within the context of different treatment options

Analysis pipelines for cancer genome sequencing in mice


The GitHub repository for the paper "Informer" accepted by AAAI 2021.

Informer: Beyond Efficient Transformer for Long Sequence Time-Series Forecasting

TS2Vec: Towards Universal Representation of Time Series

TCCT: Tightly-coupled convolutional transformer on time series forecasting

PromptCast: A New Prompt-based Learning Paradigm for Time Series
  Forecasting

Ti-MAE: Self-Supervised Masked Time Series Autoencoders

The Capacity and Robustness Trade-off: Revisiting the Channel
  Independent Strategy for Multivariate Time Series Forecasting

A Survey on Time-Series Pre-Trained Models

Dish-TS: A General Paradigm for Alleviating Distribution Shift in Time Series Forecasting

Online Metro Origin-Destination Prediction via Heterogeneous Information Aggregation

What is Next when Sequential Prediction Meets Implicitly Hard Interaction?

PROCEEDINGS OF THE 30TH ACM INTERNATIONAL CONFERENCE ON INFORMATION & KNOWLEDGE MANAGEMENT, CIKM 2021


AMR-to-text Generation with Synchronous Node Replacement Grammar

Creation of a Balanced State-of-the-Art Multilayer Corpus for NLU

PROCEEDINGS OF THE ELEVENTH INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION (LREC 2018)

Augmenting Abstract Meaning Representation for Human-Robot Dialogue

Proceedings of the First International Workshop on Designing Meaning Representations

A Human Evaluation of AMR-to-English Generation Systems

Abstract Syntax as Interlingua: Scaling Up the Grammatical Framework from Controlled Languages to Robust Pipelines

Meeting of the Association for Computational Linguistics

Adposition and Case Supersenses v2.6: Guidelines for English

Spanish Abstract Meaning Representation: Annotation of a General Corpus

Abstract meaning representation of Turkish

Semantic-Based Opinion Summarization

Recent Advances in Natural Language Processing

Intensionalizing Abstract Meaning Representations: Non-Veridicality and Scope


Deformable Convolutional Networks

R-FCN: Object Detection via Region-based Fully Convolutional Networks

Deformable Convolutional Networks

DOTA: A Large-scale Dataset for Object Detection in Aerial Images

Deformable ConvNets v2: More Deformable, Better Results

Simple Baselines for Human Pose Estimation and Tracking

MVOR: A Multi-view RGB-D Operating Room Dataset for 2D and 3D Human Pose Estimation

EAGLE: Large-scale Vehicle Detection Dataset in Real-World Scenarios
  using Aerial Imagery

Towards Interpretable R-CNN by Unfolding Latent Structures

Adaptive Precision Training: Quantify Back Propagation in Neural Networks with Fixed-point Numbers


In-Medium Similarity Renormalization Group software for nuclear structure calculations. Written in C++, with Python bindings.

Ab initio predictions link the neutron skin of 208Pb to nuclear forces

Converged ab initio calculations of heavy nuclei

Ab initio multishell valence-space Hamiltonians and the island of inversion

Probing chiral interactions up to next-to-next-to-next-to-leading order in medium-mass nuclei

In-medium similarity renormalization group with three-body operators

Systematics of E2 strength in the sd shell with the valence-space in-medium similarity renormalization group

Mass measurements of 99–101In challenge ab initio nuclear theory of the nuclide 100Sn

Natural orbitals for many-body expansion methods

Precision Mass Measurements of Neutron-Rich Scandium Isotopes Refine the Evolution of N=32 and N=34 Shell Closures

Nuclear Forces for Precision Nuclear Physics: A Collection of Perspectives

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)


Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.

Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia

Sequencing of animal viruses: quality data assurance for NGS bioinformatics

Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation

The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency.

The Plant journal : for cell and molecular biology

Reference Genome Sequences of the Oriental Armyworm, Mythimna separata (Lepidoptera: Noctuidae)


CLASSLA Fork of the Official Stanford NLP Python Library for Many Human Languages

The CLASSLA-StanfordNLP model for lemmatisation of non-standard Croatian 1.1

Multilingual Named Entity Recognition and Matching Using BERT and Dedupe for Slavic Languages

Workshop on Balto-Slavic Natural Language Processing

Introducing the CURLICAT Corpora: Seven-language Domain Specific Annotated Corpora from Curated Sources

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION

CLASSLA-Stanza: The Next Step for Linguistic Processing of South Slavic
  Languages

The CLASSLA-StanfordNLP model for UD dependency parsing of standard Slovenian

The CLASSLA-StanfordNLP model for named entity recognition of standard Croatian 1.0


Source code of the catalogue browser java application.

Reporting data on pesticide residues in food and feed according to Regulation (EC) No 396/2005 (2017 data collection)

EFSA journal. European Food Safety Authority

Reporting data on pesticide residues in food and feed according to Regulation (EC) No 396/2005 (2018 data collection)

Evaluation of Dietary Intake and Anthropometric Status in 1–9-Year-Old Children Living in Serbia: National Food Consumption Survey according to the EU Menu Methodology


MCFOST radiative transfer code

A likely flyby of binary protostar Z CMa caught in action

On the rise times in FU Orionis events

Monthly Notices of the Royal Astronomical Society: Letters

Sustained FU Orionis-type outbursts from colliding discs in stellar flybys

A kinematic excess in the annular gap and gas depleted cavity in the
  disc around HD 169142

Morphology of the gas-rich debris disk around HD 121617 with SPHERE
  observations in polarized light

Spectroscopic and interferometric signatures of magnetospheric accretion in young stars

Kinematic Structures in Planet-Forming Disks


An extension of LPeg that supports labeled failures

Syntax Error Recovery in Parsing Expression Grammars

Error Reporting in Parsing Expression Grammars

Automatic Syntax Error Reporting and Recovery in Parsing Expression Grammars

Error recovery in parsing expression grammars through labeled failures and its implementation based on a parsing machine

Journal of visual languages and computing


A pixel classification based multiplexed image segmentation pipeline

Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions

Zenodo (CERN European Organization for Nuclear Research)

Breast tumor microenvironment structures are associated with genomic features and clinical outcome

Deep spatial profiling of COVID19 brains reveals neuroinflammation by compartmentalized local immune cell interactions and targets for intervention

PDL1 shapes the classical Hodgkin lymphoma microenvironment without inducing T-cell exhaustion

Characterisation of tumour immune microenvironment remodelling following oncogene inhibition in preclinical studies using an optimised imaging mass cytometry workflow

Acquired resistance to anti-PD1 therapy in patients with NSCLC associates with immunosuppressive T cell phenotype

Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of oesophagael adenocarcinoma


Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group

Nanopore sequencing and assembly of a human genome with ultra-long reads

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

Research in Computational Molecular Biology

Real-time mapping of nanopore raw signals

De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads

Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

NanoReviser: An Error-Correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm

Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding

Finite-State Semi-Markov Channels for Nanopore Sequencing

Sigmoni: classification of nanopore signal with a compressed pangenome index

bioRxiv : the preprint server for biology

Basecalling Using Joint Raw and Event Nanopore Data Sequence-to-Sequence Processing


A toolkit for single-cell immune profiling

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

Unravelling the role of immune cells and FN1 in the recurrence and therapeutic process of skull base chordoma

T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps


A novel machine learning pipeline to analyse spatial transcriptomics data

stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues

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

Deep Learning in Single-Cell Analysis

Combining single-cell sequencing and spatial transcriptome sequencing to identify exosome-related features of glioblastoma and constructing a prognostic model to identify BARD1 as a potential therapeutic target for GBM patients


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


A home for ethereum smart contracts.

Elysium: Context-Aware Bytecode-Level Patching to Automatically Heal Vulnerable Smart Contracts


Genetic neural architecture search with Keras

Scaling tree-based automated machine learning to biomedical big data with a feature set selector

Automated Machine Learning: State-of-The-Art and Open Challenges

Monarch Butterfly Optimization Based Convolutional Neural Network Design

Evolutionary Design of Convolutional Neural Networks for Human Activity Recognition in Sensor-Rich Environments

Resource Usage and Performance Trade-offs for Machine Learning Models in Smart Environments

Neural Architecture Search for 1D CNNs—Different Approaches Tests and Measurements

MONCAE: Multi-Objective Neuroevolution of Convolutional Autoencoders


A simple toolkit for reading and manipulating beams from astrophysical radio spectral data cubes.

The Rapid ASKAP Continuum Survey I: Design and first results

Publications of the Astronomical Society of Australia/Publications Astronomical Society of Australia

CMZoom: Survey Overview and First Data Release

The Astrophysical journal. Supplement series/Astrophysical journal. Supplement series

ALMA-IMF. VII. First release of the full spectral line cubes: Core
  kinematics traced by DCN J=(3-2)


Feature as a Counter Parser for Networkmetrics

Towards a Reliable Comparison and Evaluation of Network Intrusion Detection Systems Based on Machine Learning Approaches

Multivariate Big Data Analysis for intrusion detection: 5 steps from the haystack to the needle

Multivariate Statistical Network Monitoring–Sensor: An effective tool for real-time monitoring and anomaly detection in complex networks and systems

International journal of distributed sensor networks

Leveraging a Probabilistic PCA Model to Understand the Multivariate Statistical Network Monitoring Framework for Network Security Anomaly Detection

Methodology for Collecting a Training Dataset for an Intrusion Detection Model

Труды Института системного программирования РАН


A python extension for quick access to bigWig and bigBed files

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

基因组蛋白质组与生物信息学报

Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans

Epiviz File Server: Query, transform and interactively explore data from indexed genomic files

The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart

Cohesin mediated loop extrusion from active enhancers form chromatin jets in C. elegans

Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization

DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks


Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models

Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics


DoubleML - Double Machine Learning in Python

Double/Debiased Machine Learning for Treatment and Causal Parameters

DoubleML -- An Object-Oriented Implementation of Double Machine Learning
  in R

Distributed Double Machine Learning with a Serverless Architecture

International Conference on Performance Engineering


A collection of scripts to assist in the retrieval of data from the ENA Browser

The European Nucleotide Archive in 2021

Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia

Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

mBodyMap: a curated database for microbes across human body and their associations with health and diseases

Discovery of the Pseudomonas Polyyne Protegencin by a Phylogeny-Guided Study of Polyyne Biosynthetic Gene Cluster Diversity

Bamboozle: A bioinformatic tool for identification and quantification of intraspecific barcodes

Mr.Vc v2: An updated version of database with increased data of transcriptome and experimental validated interactions


B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation

Likelihood-Based Inference of B Cell Clonal Families

Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation

Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data

Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage

Tracing Antibody Repertoire Evolution by Systems Phylogeny

Using B cell receptor lineage structures to predict affinity

Diversity and Function of Maternal HIV-1-Specific Antibodies at the Time of Vertical Transmission

Inference of B cell clonal families using heavy/light chain pairing information

Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection


CAMISIM: Simulating metagenomes and microbial communities

CAMISIM: simulating metagenomes and microbial communities

Terabase-scale metagenome coassembly with MetaHipMer

MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities


Paddle Large Scale Classification Tools，supports ArcFace, CosFace, PartialFC, Data Parallel + Model Parallel. Model includes ResNet, ViT, Swin, DeiT, CaiT, FaceViT, MoCo, MAE, ConvMAE, CAE.

An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

Training data-efficient image transformers & distillation through attention

CosFace: Large Margin Cosine Loss for Deep Face Recognition

Context Autoencoder for Self-Supervised Representation Learning

Partial FC: Training 10 Million Identities on a Single Machine

Token Merging: Your ViT But Faster

ConvMAE: Masked Convolution Meets Masked Autoencoders


BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data

BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq

BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing

Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data


An efficient index for the colored, compacted, de Bruijn graph

A space and time-efficient index for the compacted colored de Bruijn graph

Puffaligner: An Efficient and Accurate Aligner Based on the Pufferfish Index


Flood Risk modelling toolbox for Canada


feature extraction from speech signals

Modulation spectral features for speech emotion recognition using deep neural networks

Multilingual evaluation of interpretable biomarkers to represent language and speech patterns in Parkinson's disease

Early detection of Parkinson’s disease from multiple signal speech: Based on Mandarin language dataset


The TinyLlama project is an open endeavor to pretrain a 1.1B Llama model on 3 trillion tokens.

Pythia: A Suite for Analyzing Large Language Models Across Training and
  Scaling

TinyLlama: An Open-Source Small Language Model


hyperspectral galaxy modeling and deblending

scarlet: Source separation in multi-band images by Constrained Matrix Factorization

Strong lensing in UNIONS: Toward a pipeline from discovery to modeling

Block-simultaneous direction method of multipliers: a proximal primal-dual splitting algorithm for nonconvex problems with multiple constraints

Metadetection Weak Lensing for the Vera C. Rubin Observatory

Joint survey processing: combined resampling and convolution for galaxy modelling and deblending


TimerOne Library with optimization and expanded hardware support

Fabricating a Portable ECG Device Using AD823X Analog Front-End Microchips and Open-Source Development Validation

Portable ECG System Design Using the AD8232 Microchip and Open-Source Platform

The 6th International Electronic Conference on Sensors and Applications

Development of an open hardware bioreactor for optimized cardiac cell culture integrating programmable mechanical and electrical stimulations


all kinds of text classification models and more with deep learning

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

Neural Machine Translation by Jointly Learning to Align and Translate

Bag of Tricks for Efficient Text Classification

A Sensitivity Analysis of (and Practitioners' Guide to) Convolutional Neural Networks for Sentence Classification

FRAGE: Frequency-Agnostic Word Representation

Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation

ML-Bench: Large Language Models Leverage Open-source Libraries for
  Machine Learning Tasks


Miscellaneous collection of Python and R scripts for processing Iso-Seq data

De novo assembly of the cattle reference genome with single-molecule sequencing

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

The chromosome-scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis

Single-cell RNA-seq analysis of mouse preimplantation embryos by third-generation sequencing

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe

ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms


Dingo: Deep inference for gravitational-wave observations

Real-time gravitational-wave science with neural posterior estimation

Neural Importance Sampling for Rapid and Reliable Gravitational-Wave Inference

Group equivariant neural posterior estimation

Flow Matching for Scalable Simulation-Based Inference


Structural variation caller using third generation sequencing

Accurate detection of complex structural variations using single molecule sequencing

SVIM: structural variant identification using mapped long reads

Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer

A pipeline for complete characterization of complex germline rearrangements from long DNA reads

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle

Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv

Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

Correction of a Factor VIII genomic inversion with designer-recombinases

Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology


Pointcept: a codebase for point cloud perception research. Latest works: PTv3 (CVPR'24 Oral), PPT (CVPR'24), OA-CNNs (CVPR'24), MSC (CVPR'23)

4D Spatio-Temporal ConvNets: Minkowski Convolutional Neural Networks

Point Transformer

Searching Efficient 3D Architectures with Sparse Point-Voxel Convolution

PointContrast: Unsupervised Pre-training for 3D Point Cloud Understanding

PointGroup: Dual-Set Point Grouping for 3D Instance Segmentation

Exploring Data-Efficient 3D Scene Understanding with Contrastive Scene Contexts

Stratified Transformer for 3D Point Cloud Segmentation

Mix3D: Out-of-Context Data Augmentation for 3D Scenes

Point Transformer V2: Grouped Vector Attention and Partition-based
  Pooling

Swin3D: A Pretrained Transformer Backbone for 3D Indoor Scene
  Understanding


Creative Commons Attribution Share Alike 4.0 International

The Mobile Application Security Testing Guide (MASTG) is a comprehensive manual for mobile app security testing and reverse engineering. It describes the technical processes for verifying the controls listed in the OWASP Mobile Application Security Verification Standard (MASVS).

An Empirical Assessment of Global COVID-19 Contact Tracing Applications

A scalable, secure, and interoperable platform for deep data-driven health management

You Shall not Repackage! Demystifying Anti-Repackaging on Android

A First Look at On-device Models in iOS Apps

Secure cloud-based mobile apps: attack taxonomy, requirements, mechanisms, tests and automation

International journal of information security


Code used for evaluation and baselines in the PAN shared tasks.

Siamese Networks for Large-Scale Author Identification

SemEval-2023 Task 5: Clickbait Spoiling

Proceedings of the The 17th International Workshop on Semantic Evaluation (SemEval-2023)

ARC-NLP at PAN 2023: Transition-Focused Natural Language Inference for
  Writing Style Detection

ARC-NLP at PAN 2023: Hierarchical Long Text Classification for Trigger
  Detection

Improving Long-Text Authorship Verification via Model Selection and Data Tuning

Proceedings of the 7th Joint SIGHUM Workshop on Computational Linguistics for Cultural Heritage, Social Sciences, Humanities and Literature


Environment Data Model


Tools for multi-label classification problems.

On Data Augmentation for Extreme Multi-label Classification

A Survey on Extreme Multi-label Learning


SLING - A natural language frame semantics parser

Entities as Experts: Sparse Memory Access with Entity Supervision

A task in a suit and a tie: paraphrase generation with semantic augmentation

SLING: A framework for frame semantic parsing

DEEP: DEnoising Entity Pre-training for Neural Machine Translation

Cross-Lingual Fine-Grained Entity Typing