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


Everything within the Land model (Soil Plant Atmosphere Module, Land Hydrology, etc)

Accounting for canopy structure improves hyperspectral radiative transfer and sun-induced chlorophyll fluorescence representations in a new generation Earth System model

Testing stomatal models at the stand level in deciduous angiosperm and evergreen gymnosperm forests using CliMA Land (v0.1)

On the impact of canopy model complexity on simulated carbon, water, and solar-induced chlorophyll fluorescence fluxes

The Importance of Hyperspectral Soil Albedo Information for Improving Earth System Model Projections

Zenodo (CERN European Organization for Nuclear Research)

Toward More Accurate Modeling of Canopy Radiative Transfer and Leaf Electron Transport in Land Surface Modeling

Journal of Advances in Modeling Earth Systems


Peptide-MHC I binding affinity prediction

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

MHCflurry: open-source class I MHC binding affinity prediction

MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing

Predicting Antigen Presentation—What Could We Learn From a Million Peptides?

Sparse-Input Neural Networks for High-dimensional Nonparametric Regression and Classification

DeepLigand: accurate prediction of MHC class I ligands using peptide embedding

An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer

Computational cancer neoantigen prediction: current status and recent advances

Characterization of SARS-CoV-2 viral diversity within and across hosts

Predicting Peptide-MHC Binding Affinities with Imputed Training Data


Build and train Lipschitz constrained networks: TensorFlow implementation of k-Lipschitz layers

Achieving robustness in classification using optimal transport with hinge regularization

White Paper Machine Learning in Certified Systems

Pay attention to your loss: understanding misconceptions about 1-Lipschitz neural networks

Existence, Stability and Scalability of Orthogonal Convolutional Neural Networks

Robust One-Class Classification with Signed Distance Function using 1-Lipschitz Neural Networks

DP-SGD Without Clipping: The Lipschitz Neural Network Way

The Rise of Open Science: Tracking the Evolution and Perceived Value of Data and Methods Link-Sharing Practices

On the explainable properties of 1-Lipschitz Neural Networks: An Optimal Transport Perspective


C++ header-only library with methods to efficiently encode/decode Morton codes in/from 2D/3D coordinates

Efficiently Generating Geometric Inhomogeneous and Hyperbolic Random Graphs

GLIN: A (G)eneric (L)earned (In)dexing Mechanism for Complex Geometries


QIIME 2 plugin supporting taxonomic classification

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

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

Geographical and Cultivar Features Differentiate Grape Microbiota in Northern Italy and Spain Vineyards

Experimental Inoculation of Coral Recruits With Marine Bacteria Indicates Scope for Microbiome Manipulation in Acropora tenuis and Platygyra daedalea

Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy)

Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling.

Effects of Zinc Pollution and Compost Amendment on the Root Microbiome of a Metal Tolerant Poplar Clone

Tibet plateau probiotic mitigates chromate toxicity in mice by alleviating oxidative stress in gut microbiota

Production of Naturally γ-Aminobutyric Acid-Enriched Cheese Using the Dairy Strains Streptococcus thermophilus 84C and Lactobacillus brevis DSM 32386

Optimizing taxonomic classification of marker gene amplicon sequences


A single molecule sequence assembler for genomes large and small.

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Fast and accurate de novo genome assembly from long uncorrected reads

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

Oxford Nanopore MinION Sequencing and Genome Assembly

基因组蛋白质组与生物信息学报

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm

Nanopore Sequencing Technology and Tools: Computational Analysis of the Current State, Bottlenecks, and Future Directions

Research in Computational Molecular Biology

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

Prevotella copri increases fat accumulation in pigs fed with formula diets


ezkl is an engine for doing inference for deep learning models and other computational graphs in a zk-snark (ZKML). Use it from Python, Javascript, or the command line.

Verifiable evaluations of machine learning models using zkSNARKs

Trust the Process: Zero-Knowledge Machine Learning to Enhance Trust in
  Generative AI Interactions

opp/ai: Optimistic Privacy-Preserving AI on Blockchain

Proof of Quality: A Costless Paradigm for Trustless Generative AI Model Inference on Blockchains


NeuroDebian packaging of SPM12 (official repo at https://github.com/spm)

fNIRS Optodes’ Location Decider (fOLD): a toolbox for probe arrangement guided by brain regions-of-interest

Blood-brain barrier imaging as a potential biomarker for bipolar disorder progression

Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and neurodegeneration: a prospective cross-sectional study


Official implementation of "Variable-Rate Deep Image Compression through Spatially-Adaptive Feature Transform", ICCV 2021

Recovering Realistic Texture in Image Super-resolution by Deep Spatial Feature Transform


S2VC: A Framework for Any-to-Any Voice Conversion with Self-Supervised Pretrained Representations

Robust universal neural vocoding

Retriever: Learning Content-Style Representation as a Token-Level Bipartite Graph

Identifying Source Speakers for Voice Conversion based Spoofing Attacks on Speaker Verification Systems

Toward Degradation-Robust Voice Conversion


Exploring Self-attention for Image Recognition, CVPR2020.

Involution: Inverting the Inherence of Convolution for Visual Recognition

Studying inductive biases in image classification task


Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer

scCODA is a Bayesian model for compositional single-cell data analysis

Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease


A WGS de novo assembler based on the FMD-index for large genomes

The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley


A PyTorch implementation of DenseNet.

Densely Connected Convolutional Networks

FreezeOut: Accelerate Training by Progressively Freezing Layers

To Ensemble or Not Ensemble: When does End-To-End Training Fail?

Automatic Data Augmentation by Learning the Deterministic Policy


Per-Pixel Classification is Not All You Need for Semantic Segmentation (NeurIPS 2021, spotlight)

Visual ChatGPT: Talking, Drawing and Editing with Visual Foundation Models

Panoptic SegFormer: Delving Deeper into Panoptic Segmentation with Transformers

DatasetDM: Synthesizing Data with Perception Annotations Using Diffusion Models

Guess What Moves: Unsupervised Video and Image Segmentation by Anticipating Motion

SAPA: Similarity-Aware Point Affiliation for Feature Upsampling


Unofficial reimplementation of ECAPA-TDNN for speaker recognition (EER=0.86 for Vox1_O when train only in Vox2)

SASV 2022: The First Spoofing-Aware Speaker Verification Challenge

SASV Challenge 2022: A Spoofing Aware Speaker Verification Challenge Evaluation Plan

HLT-NUS SUBMISSION FOR 2020 NIST Conversational Telephone Speech SRE

Baseline Systems for the First Spoofing-Aware Speaker Verification Challenge: Score and Embedding Fusion

Prompt-driven Target Speech Diarization

Self-Supervised Training of Speaker Encoder With Multi-Modal Diverse Positive Pairs

Unifying Cosine and PLDA Back-ends for Speaker Verification

USED: Universal Speaker Extraction and Diarization

A Comparison of Differential Performance Metrics for the Evaluation of Automatic Speaker Verification Fairness

Speaker-Aware Anti-Spoofing


pipeline for the analysis of small RNA data

Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis

Regional and subtype-dependent miRNA signatures in sporadic Creutzfeldt-Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis

Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements


Exclusively Dark (ExDARK) dataset which to the best of our knowledge, is the largest collection of low-light images taken in very low-light environments to twilight (i.e 10 different conditions) to-date with image class and object level annotations.

Getting to Know Low-light Images with The Exclusively Dark Dataset

Survey and Performance Analysis of Deep Learning Based Object Detection in Challenging Environments

Research on Improved YOLOv5 for Low-Light Environment Object Detection

A Novel Luminance-Based Algorithm for Classification of Semi-Dark Images

Exploiting Concepts of Instance Segmentation to Boost Detection in Challenging Environments


Rectified Rotary Position Embeddings

YaRN: Efficient Context Window Extension of Large Language Models

LLM Maybe LongLM: Self-Extend LLM Context Window Without Tuning

Transformers Can Achieve Length Generalization But Not Robustly

Training-Free Long-Context Scaling of Large Language Models

The What, Why, and How of Context Length Extension Techniques in Large Language Models -- A Detailed Survey

Hierarchical Context Merging: Better Long Context Understanding for
  Pre-trained LLMs

Ada-LEval: Evaluating long-context LLMs with length-adaptable benchmarks

LongAgent: Scaling Language Models to 128k Context through Multi-Agent
  Collaboration

Extending LLMs' Context Window with 100 Samples

LongHeads: Multi-Head Attention is Secretly a Long Context Processor


R script for the covid balf data analysis

Mapping single-cell data to reference atlases by transfer learning

scCODA is a Bayesian model for compositional single-cell data analysis

Synthetic lethality-based prediction of anti-SARS-CoV-2 targets

Expression profiles of respiratory V-ATPase and calprotectin in SARS-CoV-2 infection


FLOPs calculator with tf.profiler for neural network architecture written in tensorflow 2.2+ (tf.keras)

Trustworthy Privacy-Preserving Hierarchical Ensemble and Federated Learning in Healthcare 4.0 With Blockchain

IEEE Transactions on Industrial Informatics

Energy Efficiency of Training Neural Network Architectures: An Empirical Study

Patching Weak Convolutional Neural Network Models through Modularization and Composition

Contrastive encoder pre-training-based clustered federated learning for heterogeneous data

Neural networks : the official journal of the International Neural Network Society

A Safe Genetic Algorithm Approach for Energy Efficient Federated Learning in Wireless Communication Networks

A Safe Deep Reinforcement Learning Approach for Energy Efficient Federated Learning in Wireless Communication Networks

Reusing Convolutional Neural Network Models through Modularization and Composition


Official Implementation for the ICML2022 paper "Directed Acyclic Transformer for Non-Autoregressive Machine Translation"

A Survey on Non-Autoregressive Generation for Neural Machine Translation and Beyond

Viterbi Decoding of Directed Acyclic Transformer for Non-Autoregressive Machine Translation

Directed Acyclic Transformer Pre-training for High-quality Non-autoregressive Text Generation


MobileNetV3 in pytorch and ImageNet pretrained models

Searching for MobileNetV3

Mitigating dataset harms requires stewardship: Lessons from 1000 papers

A Fine-Tuned CatBoost-Based Speech Disorder Detection Model


Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish

ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes

High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes

Evolutionary history of two evergreen Rhododendron species as revealed by chromosome-level genome assembly

Comparative genomics reveals putative evidence for high-elevation adaptation in the American pika (Ochotona princeps)


YAMP: Yet Another Metagenomic Pipeline

YAMP: a containerized workflow enabling reproducibility in metagenomics research

YAMP: a framework enabling reproducibility in metagenomics research


Scene Text Visual Question Answering

Hierarchical multimodal transformers for Multi-Page DocVQA

Document Understanding Dataset and Evaluation (DUDE)


Computing water flow through complex landscapes – Part 1: Incorporating depressions in flow routing using FlowFill

Computing water flow through complex landscapes, Part 2: Finding hierarchies in depressions and morphological segmentations

Computing water flow through complex landscapes, Part 3: Fill-Spill-Merge: Flow routing in depression hierarchies


Code for Which Tasks Should Be Learned Together in Multi-task Learning?

Efficiently Identifying Task Groupings for Multi-Task Learning

Measuring and Harnessing Transference in Multi-Task Learning

Smart Multi-tenant Federated Learning


Deep Biaffine Attention for Neural Dependency Parsing

Universal Dependencies Parsing for Colloquial Singaporean English

Supervised Treebank Conversion: Data and Approaches

PROCEEDINGS OF THE 56TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS (ACL), VOL 1


Modular reinforcement learning library (on PyTorch and JAX) with support for NVIDIA Isaac Gym, Omniverse Isaac Gym and Isaac Lab

Proximal Policy Optimization Algorithms

Continuous control with deep reinforcement learning

Playing Atari with Deep Reinforcement Learning

Asynchronous Methods for Deep Reinforcement Learning

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

Trust Region Policy Optimization

Addressing Function Approximation Error in Actor-Critic Methods

DeepMind Control Suite

Isaac Gym: High Performance GPU-Based Physics Simulation For Robot Learning

skrl: Modular and Flexible Library for Reinforcement Learning


A fast python-based RM synthesis and RM CLEAN application and library

Faraday tomography of the local interstellar medium with LOFAR: Galactic foregrounds towards IC 342

New constraints on the magnetization of the cosmic web using LOFAR Faraday rotation observations

Monthly Notices of the Royal Astronomical Society

Magnetism Science with the Square Kilometre Array

The intergalactic magnetic field probed by a giant radio galaxy

Dissecting nonthermal emission in the complex multiple-merger galaxy cluster Abell 2744: Radio and X-ray analysis

Particle re-acceleration and Faraday-complex structures in the RXC J1314.4-2515 galaxy cluster

Monthly notices of the Royal Astronomical Society

Polarized point sources in the LOFAR Two-meter Sky Survey: A preliminary catalog

MeerKAT view of the diffuse radio sources in Abell 3667 and their interactions with the thermal plasma

Diffuse polarized emission in the LOFAR Two-meter Sky Survey

The LOFAR view of intergalactic magnetic fields with giant radio galaxies


A codebase & model zoo for pretrained backbone based on MegEngine.

Deep Residual Learning for Image Recognition

Very Deep Convolutional Networks for Large-Scale Image Recognition

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

MobileNetV2: Inverted Residuals and Linear Bottlenecks

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks

ShuffleNet V2: Practical Guidelines for Efficient CNN Architecture Design

Deep High-Resolution Representation Learning for Visual Recognition

RepVGG: Making VGG-style ConvNets Great Again

Designing Network Design Spaces


Software for the visualization of sequence-function relationships

Logomaker: beautiful sequence logos in Python

Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents

DeepSecE: A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in Gram-Negative Bacteria


Code for TMI 2018 "Joint Optic Disc and Cup Segmentation Based on Multi-label Deep Network and Polar Transformation"

CE-Net: Context Encoder Network for 2D Medical Image Segmentation

Joint Optic Disc and Cup Segmentation Based on Multi-Label Deep Network and Polar Transformation

Mixed-Supervised Dual-Network for Medical Image Segmentation

Disc-Aware Ensemble Network for Glaucoma Screening From Fundus Image


Code for "Learning to summarize from human feedback"

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

Dataset Reset Policy Optimization for RLHF

DecipherPref: Analyzing Influential Factors in Human Preference Judgments via GPT-4

The Importance of Online Data: Understanding Preference Fine-tuning via Coverage

Self-Improving Robust Preference Optimization

Contrastive Policy Gradient: Aligning LLMs on sequence-level scores in a
  supervised-friendly fashion


Semi-supervised Medical Image Segmentation through Dual-task Consistency

Uncertainty-aware Self-ensembling Model for Semi-supervised 3D Left Atrium Segmentation

Semi-Supervised Semantic Segmentation with Cross-Consistency Training

Shape-aware Semi-supervised 3D Semantic Segmentation for Medical Images

Medical Image Computing and Computer-Assisted Intervention

Semi-supervised Left Atrium Segmentation with Mutual Consistency Training

Local and Global Structure-Aware Entropy Regularized Mean Teacher Model for 3D Left Atrium Segmentation


Data augmentation for NLP, presented at EMNLP 2019

EDA: Easy Data Augmentation Techniques for Boosting Performance on Text Classification Tasks

A Survey of Data Augmentation Approaches for NLP

Generative Data Augmentation for Commonsense Reasoning

Discriminative Nearest Neighbor Few-Shot Intent Detection by Transferring Natural Language Inference

PromDA: Prompt-based Data Augmentation for Low-Resource NLU Tasks

FlipDA: Effective and Robust Data Augmentation for Few-Shot Learning

Tell Me How to Ask Again: Question Data Augmentation with Controllable Rewriting in Continuous Space

A little goes a long way: Improving toxic language classification despite data scarcity

Consistency Training with Virtual Adversarial Discrete Perturbation

Causal Intervention Improves Implicit Sentiment Analysis


Repository for Frequency Word List Generator and processed files

Defending Pre-trained Language Models from Adversarial Word Substitution Without Performance Sacrifice

Frequency, Informativity and Word Length: Insights from Typologically Diverse Corpora

Expectations over Unspoken Alternatives Predict Pragmatic Inferences

SHIKEBLCU at SemEval-2020 Task 2: An External Knowledge-enhanced Matrix for Multilingual and Cross-Lingual Lexical Entailment

International Workshop on Semantic Evaluation

Incremental Improvement of a Question Answering System by Re-ranking Answer Candidates using Machine Learning

Analyze the Usage of Legal Definitions in Indonesian Regulation Using Text Mining Case Study: Treasury and Budget Law

An automated approach to mitigate transcription errors in braille texts for the Portuguese language

Exploring Probabilistic Soft Logic as a framework for integrating top-down and bottom-up processing of language in a task context

Enhancing Pre-trained Language Model with Lexical Simplification


SAFE: Self-Attentive Function Embeddings for binary similarity

SAFE: Self-Attentive Function Embeddings for Binary Similarity

Semantic-aware Binary Code Representation with BERT

XFL: Naming Functions in Binaries with Extreme Multi-label Learning

UniASM: Binary Code Similarity Detection without Fine-tuning

FuncFooler: A Practical Black-box Attack Against Learning-based Binary Code Similarity Detection Methods


C# client for General Bikeshare Feed Specification (GBFS)


Learn interpretable computational phenotyping models from k-merized genomic data

Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons

Interpretable genotype-to-phenotype classifiers with performance guarantees

Evaluation of Machine Learning Models for Predicting Antimicrobial Resistance of Actinobacillus pleuropneumoniae From Whole Genome Sequences

Large scale modeling of antimicrobial resistance with interpretable classifiers


ConceptNet 5.5: An Open Multilingual Graph of General Knowledge

TechNet: Technology semantic network based on patent data

ConceptNet at SemEval-2017 Task 2: Extending Word Embeddings with Multilingual Relational Knowledge

Meeting of the Association for Computational Linguistics

An Ensemble Method to Produce High-Quality Word Embeddings (2016)

XL-AMR: Enabling Cross-Lingual AMR Parsing with Transfer Learning Techniques

PROCEEDINGS OF THE 2020 CONFERENCE ON EMPIRICAL METHODS IN NATURAL LANGUAGE PROCESSING (EMNLP)

Enhance word representation for out-of-vocabulary on Ubuntu dialogue corpus

Comparative Analysis of Word Embeddings for Capturing Word Similarities

Cross-lingual Document Retrieval using Regularized Wasserstein Distance

Can Pre-trained Language Models Understand Chinese Humor?

A Study on Efficiency, Accuracy and Document Structure for Answer Sentence Selection


A CLI tool/python module for generating images from text using guided diffusion and CLIP from OpenAI.

Diffusion Models Beat GANs on Image Synthesis

Design Guidelines for Prompt Engineering Text-to-Image Generative Models

Diffusion-based Image Translation using Disentangled Style and Content Representation

3DALL-E: Integrating Text-to-Image AI in 3D Design Workflows

Opal: Multimodal Image Generation for News Illustration


Evaluation of CNN-based Automatic Music Tagging Models

Semi-supervised Music Tagging Transformer

MusCaps: Generating Captions for Music Audio

Emotion Embedding Spaces for Matching Music to Stories

A Benchmarking Initiative for Audio-Domain Music Generation Using the Freesound Loop Dataset

Auxiliary self-supervision to metric learning for music similarity-based retrieval and auto-tagging


Trust Region Policy Optimization with TensorFlow and OpenAI Gym

Trust Region Policy Optimization

High-Dimensional Continuous Control Using Generalized Advantage Estimation

Emergence of Locomotion Behaviours in Rich Environments

Autonomous Six-Degree-of-Freedom Spacecraft Docking Maneuvers via Reinforcement Learning

Foresee then Evaluate: Decomposing Value Estimation with Latent Future Prediction

Intelligent Trainer for Model-Based Reinforcement Learning


McLuster - a tool to make a star cluster

Formation of massive black holes in galactic nuclei: runaway tidal encounters

TIDAL STREAM MORPHOLOGY AS AN INDICATOR OF DARK MATTER HALO GEOMETRY: THE CASE OF PALOMAR 5

Complete ejection of OB stars from very young star clusters and the formation of multiple populations

Direct N-body simulations of globular clusters - II. Palomar 4

Exploding Satellites - The Tidal Debris of the Ultra-Faint Dwarf Galaxy Hercules

Direct N-body simulations of globular clusters – III. Palomar 4 on an eccentric orbit

The effect of primordial mass segregation on the size scale of globular clusters

A Monte Carlo study of early gas expulsion and evolution of star clusters: new simulations with the MOCCA code in the amuse framework

mocca: dynamics and evolution of single and binary stars of multiple stellar populations in tidally filling and underfilling globular star clusters


Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake

dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology

Soil Texture, Sampling Depth and Root Hairs Shape the Structure of ACC Deaminase Bacterial Community Composition in Maize Rhizosphere

Effects of Tree Composition and Soil Depth on Structure and Functionality of Belowground Microbial Communities in Temperate European Forests

Water Deficit History Selects Plant Beneficial Soil Bacteria Differently Under Conventional and Organic Farming


BIOMASS Product Algorithm Laboratory


Processing pipeline for GLEAM-X

Murchison Widefield Array rapid-response observations of the short GRB 180805A

Publications of the Astronomical Society of Australia

Early-time searches for coherent radio emission from short GRBs with the Murchison Widefield Array

A census of compact sources at 162 MHz: First data release from the MWA Phase II IPS Survey

System equivalent flux density of a low-frequency polarimetric phased array interferometer


Optical ray tracing for luminescent materials and spectral converter photovoltaic devices

Luminescent solar concentrators with fiber geometry

Development of an Off‐Grid Solar‐Powered Autonomous Chemical Mini‐Plant for Producing Fine Chemicals

An Open-Source Monte Carlo Ray-Tracing Simulation Tool for Luminescent Solar Concentrators with Validation Studies Employing Scattering Phosphor Films

Numerical Method for Calculation of Power Conversion Efficiency and Colorimetrics of Rectangular Luminescent Solar Concentrators

Ray trace modeling to characterize efficiency of unconventional luminescent solar concentrator geometries


List of papers, code and experiments using deep learning for time series forecasting

Statistical and Machine Learning forecasting methods: Concerns and ways forward

Traffic transformer: Capturing the continuity and periodicity of time series for traffic forecasting

DSANet: Dual Self-Attention Network for Multivariate Time Series Forecasting

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

Attention based Multi-Modal New Product Sales Time-series Forecasting

Forecasting Big Time Series: Theory and Practice

WWW'20: COMPANION PROCEEDINGS OF THE WEB CONFERENCE 2020

Forecasting the Evolution of Hydropower Generation

Forecasting Multivariate Time-Series Data Using LSTM and Mini-Batches

Lecture notes on data engineering and communications technologies

Resilient Neural Forecasting Systems

Deep State-Space Generative Model For Correlated Time-to-Event Predictions

Augmented Out-of-Sample Comparison Method for Time Series Forecasting Techniques


P4 Applications WG repo

PINT: Probabilistic In-band Network Telemetry

Efficient Measurement on Programmable Switches Using Probabilistic Recirculation

International Conference on Network Protocols

Zero-CPU Collection with Direct Telemetry Access

Application Layer Packet Processing Using PISA Switches

Direct Telemetry Access

DUNE: Improving Accuracy for Sketch-INT Network Measurement Systems

Tracking the QUIC spin bit on Tofino

Proceedings of the 2021 Workshop on Evolution, Performance and Interoperability of QUIC

RackBlox: A Software-Defined Rack-Scale Storage System with Network-Storage Co-Design

Symposium on Operating Systems Principles


Statistical fine-mapping pipeline in FinnGen

FinnGen: Unique genetic insights from combining isolated population and national health register data

Insights from complex trait fine-mapping across diverse populations

Genetic Risk Factors Associated With Preeclampsia and Hypertensive Disorders of Pregnancy

Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics


A survey of known lower bounds in arithmetic circuits.

On the complexity of partial derivatives

On Algebraic Branching Programs of Small Width

Succinct Hitting Sets and Barriers to Proving Algebraic Circuits Lower Bounds

An exponential lower bound for homogeneous depth-5 circuits over finite fields

Unbalancing Sets and An Almost Quadratic Lower Bound for Syntactically Multilinear Arithmetic Circuits

Geometric complexity theory and matrix powering

A Near-Optimal Depth-Hierarchy Theorem for Small-Depth Multilinear Circuits

The Chasm at Depth Four, and Tensor Rank : Old results, new insights

Ideals, determinants, and straightening: proving and using lower bounds for polynomial ideals

On geometric complexity theory: Multiplicity obstructions are stronger than occurrence obstructions


OpenXAI : Towards a Transparent Evaluation of Model Explanations

OpenXAI: Towards a Transparent Evaluation of Model Explanations

Analyzing Explainer Robustness via Probabilistic Lipschitzness of Prediction Functions

InterpretCC: Conditional Computation for Inherently Interpretable Neural
  Networks

Uncovering Unique Concept Vectors through Latent Space Decomposition


ML has an impact on the climate. But not all models are born equal. Compute your model's emissions with our calculator and add the results to your paper with our generated latex template

Quantifying the Carbon Emissions of Machine Learning


Transportation Networks for Research

Graph-based Semi-Supervised & Active Learning for Edge Flows

Residual Correlation in Graph Neural Network Regression

HodgeNet: Graph Neural Networks for Edge Data

Computing Dynamic User Equilibria on Large-Scale Networks with Software Implementation

A many-to-many assignment game and stable outcome algorithm to evaluate collaborative mobility-as-a-service platforms

Multi-objective minmax robust combinatorial optimization with cardinality-constrained uncertainty

A Stochastic Multiagent Optimization Framework for Interdependent Transportation and Power System Analyses

A Risk-Averse Shelter Location and Evacuation Routing Assignment Problem in an Uncertain Environment

International journal of environmental research and public health

In Congestion Games, Taxes Achieve Optimal Approximation

Evacuation route planning for alternative fuel vehicles


PaddleSpatial is an open-source spatial-temporal computing tool based on PaddlePaddle.

Generative Time Series Forecasting with Diffusion, Denoise, and Disentanglement

SDWPF: A Dataset for Spatial Dynamic Wind Power Forecasting Challenge at KDD Cup 2022

Towards Long-Term Time-Series Forecasting: Feature, Pattern, and Distribution

The Rise of Diffusion Models in Time-Series Forecasting

Multi-Temporal Relationship Inference in Urban Areas

Spatial Heterophily Aware Graph Neural Networks

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

SDWPF: A Dataset for Spatial Dynamic Wind Power Forecasting over a Large Turbine Array


Python package for the evaluation of odometry and SLAM

Kimera: an Open-Source Library for Real-Time Metric-Semantic Localization and Mapping

KITTI-360: A Novel Dataset and Benchmarks for Urban Scene Understanding in 2D and 3D

Towards High-Performance Solid-State-LiDAR-Inertial Odometry and Mapping

International Conference on Robotics and Automation

Recurrent Neural Network for (Un-)Supervised Learning of Monocular Video Visual Odometry and Depth

LAMP: Large-Scale Autonomous Mapping and Positioning for Exploration of Perceptually-Degraded Subterranean Environments

Super Odometry: IMU-centric LiDAR-Visual-Inertial Estimator for Challenging Environments

M2DGR: A Multi-sensor and Multi-scenario SLAM Dataset for Ground Robots

LOCUS: A Multi-Sensor Lidar-Centric Solution for High-Precision Odometry and 3D Mapping in Real-Time

A Review of Visual-Inertial Simultaneous Localization and Mapping from Filtering-Based and Optimization-Based Perspectives

Visual and Visual-Inertial SLAM: State of the Art, Classification, and Experimental Benchmarking

Zenodo (CERN European Organization for Nuclear Research)


Cytometry dATa anALYsis Tools

Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine

Neurocognitive and hypokinetic movement disorder with features of parkinsonism after BCMA-targeting CAR-T cell therapy

Impaired function and delayed regeneration of dendritic cells in COVID-19

Longitudinal liver sampling in patients with chronic hepatitis B starting antiviral therapy reveals hepatotoxic CD8+ T cells

Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets

Developing Human Skin Contains Lymphocytes Demonstrating a Memory Signature

High-dimensional profiling reveals Tc17 cell enrichment in active Crohn’s disease and identifies a potentially targetable signature

Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

Characterization of the Impact of Daclizumab Beta on Circulating Natural Killer Cells by Mass Cytometry

Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients

Frontiers in cellular and infection microbiology


Library for Low-Frequency

The LOFAR LBA Sky Survey: I. Survey description and preliminary data release

Magnetic fields and relativistic electrons fill entire galaxy cluster

Galaxy clusters enveloped by vast volumes of relativistic electrons

The LOFAR LBA Sky Survey II. First data release

The LOFAR LBA Sky Survey: Deep Fields I. The Boötes Field

Particle re-acceleration and diffuse radio sources in the galaxy cluster Abell 1550

ViCTORIA project: The LOFAR HBA Virgo Cluster Survey

Low-frequency radio observations of recurrent nova RS Ophiuchi with MeerKAT and LOFAR

Into the depths: Unveiling ELAIS-N1 with LOFAR’s deepest sub-arcsecond wide-field images


Xplique is a Neural Networks Explainability Toolbox

Explainable AI for Bioinformatics: Methods, Tools, and Applications

Xplique: A Deep Learning Explainability Toolbox

Unlocking Feature Visualization for Deeper Networks with MAgnitude Constrained Optimization

Less is More: Fewer Interpretable Region via Submodular Subset Selection


Python package for extracting representations from state-of-the-art computer vision models

Harmonizing the object recognition strategies of deep neural networks with humans

THINGSvision: A Python Toolbox for Streamlining the Extraction of Activations From Deep Neural Networks

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

Fine-grained knowledge about manipulable objects is well-predicted by CLIP


General purpose framework to run CMS experiment workflows on HDFS/Spark platform

The CMS monitoring infrastructure and applications

Exploiting Apache Spark platform for CMS computing analytics

The evolution of the CMS monitoring infrastructure

Big data solutions for CMS computing monitoring and analytics


Official data on the COVID-19 epidemic in Malaysia. Powered by CPRC, CPRC Hospital System, MKAK, and MySejahtera.

Risk of serious adverse events after the BNT162b2, CoronaVac, and ChAdOx1 vaccines in Malaysia: A self-controlled case series study

The Prevalence and Work-Related Factors of Burnout Among Public Health Workforce During the COVID-19 Pandemic

Journal of occupational and environmental medicine

Incidence, Prevalence, and Sources of COVID-19 Infection among Healthcare Workers in Hospitals in Malaysia

Assessment of Heterologous and Homologous Boosting With Inactivated COVID-19 Vaccine at 3 Months Compared With Homologous Boosting of BNT162b2 at 6 Months

Characterisation of COVID-19 deaths by vaccination types and status in Malaysia between February and September 2021

The Lancet regional health. Western Pacific

Estimating the COVID-19 mortality burden over two full years of the pandemic in Malaysia

Investigating Linkages Between Spatiotemporal Patterns of the COVID-19 Delta Variant and Public Health Interventions in Southeast Asia: Prospective Space-Time Scan Statistical Analysis Method

Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: From alpha to Omicron

A network analysis and support vector regression approaches for visualising and predicting the COVID-19 outbreak in Malaysia

Myocarditis/pericarditis following vaccination with BNT162b2, CoronaVac, and ChAdOx1 among adolescent and adult in Malaysia


Finite DIfference microMAGnetic code, based on Python, Cython and C

Binding a hopfion in a chiral magnet nanodisk

Driving magnetic skyrmions with microwave fields

Magnon-Driven Domain-Wall Motion with the Dzyaloshinskii-Moriya Interaction

Micromagnetics and spintronics: models and numerical methods

Tomorrow’s micromagnetic simulations

Microwave-induced dynamic switching of magnetic skyrmion cores in nanodots

Nanoscale magnetic skyrmions and target states in confined geometries

Fidimag – A Finite Difference Atomistic and Micromagnetic Simulation Package

Proposal for a micromagnetic standard problem for materials with Dzyaloshinskii-Moriya interaction

User interfaces for computational science: A domain specific language for OOMMF embedded in Python


ROS# is a set of open source software libraries and tools in C# for communicating with ROS from .NET applications, in particular Unity3D

SEAN: Social Environment for Autonomous Navigation

SIGVerse: A Cloud-Based VR Platform for Research on Multimodal Human-Robot Interaction

Spatial Computing and Intuitive Interaction: Bringing Mixed Reality and Robotics Together

Accuracy and Repeatability Tests on HoloLens 2 and HTC Vive

Using Socially Expressive Mixed Reality Arms for Enhancing Low-Expressivity Robots

Augmented-Reality-Based Visualization of Navigation Data of Mobile Robots on the Microsoft Hololens -- Possibilities and Limitations

Design and Evaluation of an Augmented Reality Head-mounted Display Interface for Human Robot Teams Collaborating in Physically Shared Manufacturing Tasks

Programming Robots by Demonstration Using Augmented Reality

"Grip-that-there": An Investigation of Explicit and Implicit Task Allocation Techniques for Human-Robot Collaboration

Integrating Virtual Reality and Robotic Operation System (ROS) for AGV Navigation

EAI Endorsed Transactions on AI and Robotics


RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library.

Farview: Disaggregated Memory with Operator Off-loading for Database Engines

Regex matching with counting-set automata

Proceedings of the ACM on Programming Languages

Linear Parsing Expression Grammars

Mata, a Fast and Simple Finite Automata Library (Technical Report)

Sequential Circuits from Regular Expressions Revisited

Tagged Deterministic Finite Automata with Lookahead

Linear Matching of JavaScript Regular Expressions

The Design of a Verified Derivative-Based Parsing Tool for Regular Expressions

Stream Processing using Grammars and Regular Expressions

Derivative Based Extended Regular Expression Matching Supporting Intersection, Complement and Lookarounds


Towards Measuring Supply Chain Attacks on Package Managers for Interpreted Languages

Bad Snakes: Understanding and Improving Python Package Index Malware Scanning

DONAPI: Malicious NPM Packages Detector using Behavior Sequence
  Knowledge Mapping


An OMNeT-based simulator for low-power wireless networks such as Wireless Sensor Networks and Body Area Networks

Survey of Machine Learning Based Intrusion Detection Methods for Internet of Medical Things

A Comprehensive Study on LPWANs With a Focus on the Potential of LoRa/LoRaWAN Systems

IEEE Communications Surveys and Tutorials

Energy-efficient routing in the proximity of a complicated hole in wireless sensor networks

Joint Transmission Power Control and Relay Cooperation for WBAN Systems

An Optimized Relay Selection Technique to Improve the Communication Reliability in Wireless Sensor Networks

Mutual Aid Among Sensors: An Emergency Function for Sensor Networks

Combining Network Coding and Retransmission Techniques to Improve the Communication Reliability of Wireless Sensor Network

BNS: A Framework for Wireless Body Area Network Realistic Simulations

Priority and Traffic-Aware Contention-Based Medium Access Control Scheme for Multievent Wireless Sensor Networks

Cross-Layer Routing for a Mobility Support Protocol Based on Handover Mechanism in Cluster-Based Wireless Sensor Networks with Mobile Sink


Performance Modeling and Evaluation of Distributed Deep Learning Frameworks on GPUs

swCaffe: a Parallel Framework for Accelerating Deep Learning Applications on Sunway TaihuLight

Survey on Software Tools that Implement Deep Learning Algorithms on Intel/x86 and IBM/Power8/Power9 Platforms

Supercomputing Frontiers and Innovations


Federated Optimization in Heterogeneous Networks (MLSys '20)

Fast-Convergent Federated Learning

FedLab: A Flexible Federated Learning Framework

EasyFL: A Low-Code Federated Learning Platform for Dummies

ActPerFL: Active Personalized Federated Learning

Proceedings of the First Workshop on Federated Learning for Natural Language Processing (FL4NLP 2022)

FedGen: Generalizable Federated Learning for Sequential Data

FedDWA: Personalized Federated Learning with Dynamic Weight Adjustment

Federated Prompt Learning for Weather Foundation Models on Devices

Federated Learning for Clinical Structured Data: A Benchmark Comparison of Engineering and Statistical Approaches


This repository contains code used in the EMNLP 2019 paper "Learning Dynamic Context Augmentation for Global Entity Linking".

Neural Entity Linking: A Survey of Models Based on Deep Learning

Neural Fine-Grained Entity Type Classification with Hierarchy-Aware Loss

Improving Entity Linking by Modeling Latent Entity Type Information

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

Improving Few-Shot Domain Transfer for Named Entity Disambiguation with Pattern Exploitation

Findings of the Association for Computational Linguistics: EMNLP 2022


VulDeePecker: A Deep Learning-Based System for Vulnerability Detection

Proceedings 2018 Network and Distributed System Security Symposium

SySeVR: A Framework for Using Deep Learning to Detect Software Vulnerabilities

IEEE Transactions on Dependable and Secure Computing

Deep Learning based Vulnerability Detection: Are We There Yet?

Transformer-Based Language Models for Software Vulnerability Detection

Efficient Feature Selection for Static Analysis Vulnerability Prediction

Deep Cost-Sensitive Kernel Machine for Binary Software Vulnerability Detection

Pacific-Asia Conference on Knowledge Discovery and Data Mining

An Investigation of Quality Issues in Vulnerability Detection Datasets

2023 IEEE European Symposium on Security and Privacy Workshops (EuroS&PW)


Fully featured implementation of Routing Transformer

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

GLU Variants Improve Transformer

Efficient Content-Based Sparse Attention with Routing Transformers

ReZero is All You Need: Fast Convergence at Large Depth

ClusterFormer: Neural Clustering Attention for Efficient and Effective Transformer

Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)


CLIP-Adapter: Better Vision-Language Models with Feature Adapters

Enhancing CLIP with GPT-4: Harnessing Visual Descriptions as Prompts

CLIP4STR: A Simple Baseline for Scene Text Recognition with Pre-trained Vision-Language Model

XtremeCLIP: Extremely Parameter-efficient Tuning for Low-resource Vision Language Understanding

Findings of the Association for Computational Linguistics: ACL 2023


NLR-Annotator upload

Multiple wheat genomes reveal global variation in modern breeding

BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust

NRG1 functions downstream of EDS1 to regulate TIR-NLR-mediated plant immunity in Nicotiana benthamiana

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

The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire1[OPEN]

Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars

The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry

BED domain-containing NLR from wild barley confers resistance to leaf rust

Variation in plant Toll/Interleukin-1 receptor domain protein dependence on ENHANCED DISEASE SUSCEPTIBILITY 1

Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics

Genome-Wide Identification, Characterization, and Comparative Analysis of NLR Resistance Genes in Coffea spp.


Learning Invariant Representations for Reinforcement Learning without Reconstruction

Provable RL with Exogenous Distractors via Multistep Inverse Dynamics

Learning Representations for Pixel-based Control: What Matters and Why?

Learning Domain Invariant Representations in Goal-conditioned Block MDPs

Automatic Intrinsic Reward Shaping for Exploration in Deep Reinforcement Learning

Joint Representations for Reinforcement Learning with Multiple Sensors


Presenting Low-shot Visual Recognition by Shrinking and Hallucinating Features

Matching Networks for One Shot Learning

Low-shot Learning via Covariance-Preserving Adversarial Augmentation Networks

Learning from Few Samples: A Survey

Meta-learning algorithms for Few-Shot Computer Vision


Implementation of a classification framework from the paper Aggregated Residual Transformations for Deep Neural Networks

Shake-Shake regularization

Between-class Learning for Image Classification

Shakedrop Regularization for Deep Residual Learning

Memory-Efficient Implementation of DenseNets

Practices and Applications of Convolutional Neural Network-Based Computer Vision Systems in Animal Farming: A Review

Deep Networks from the Principle of Rate Reduction

Aerial Image Object Detection With Vision Transformer Detector (ViTDet)

GFF-CARVING: Graph Feature Fusion for the Recognition of Highly Varying and Complex Balinese Carving Motifs

Toward Runtime-Throttleable Neural Networks


Draw phylogenetic trees of tumor evolution

Single-cell analysis reveals new evolutionary complexity in uveal melanoma

Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data

Expression of PD-1 mitigates phagocytic activities TAM in osteosarcoma


Unofficial PyTorch implementation of "FixMatch: Simplifying Semi-Supervised Learning with Consistency and Confidence"

RETRIEVE: Coreset Selection for Efficient and Robust Semi-Supervised Learning

OpenMatch: Open-set Consistency Regularization for Semi-supervised Learning with Outliers

Antipodes of Label Differential Privacy: PATE and ALIBI

Improving Test-Time Adaptation via Shift-agnostic Weight Regularization and Nearest Source Prototypes

CrossNorm and SelfNorm for Generalization under Distribution Shifts

A Theory of Label Propagation for Subpopulation Shift

BARACK: Partially Supervised Group Robustness With Guarantees

Sample Efficiency of Data Augmentation Consistency Regularization

Adversarial Auto-Augment with Label Preservation: A Representation Learning Principle Guided Approach


Learning to query complex networks

Embedding Logical Queries on Knowledge Graphs

SE-KGE: A Location-Aware Knowledge Graph Embedding Model for Geographic Question Answering and Spatial Semantic Lifting

Message Passing Query Embedding

Contextual Graph Attention for Answering Logical Queries over Incomplete Knowledge Graphs

PROCEEDINGS OF THE 10TH INTERNATIONAL CONFERENCE ON KNOWLEDGE CAPTURE (K-CAP '19)


Purified Purine.

The History Began from AlexNet: A Comprehensive Survey on Deep Learning Approaches

Benchmarking Contemporary Deep Learning Hardware and Frameworks:A Survey of Qualitative Metrics

Purine: A bi-graph based deep learning framework

DeepFoldit -- A Deep Reinforcement Learning Neural Network Folding Proteins


A corpus of Biomedical papers annotated with mentions of UMLS entities.

MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts

Hierarchical Losses and New Resources for Fine-grained Entity Typing and Linking

Knowledge-Rich Self-Supervision for Biomedical Entity Linking

Generating Scientific Claims for Zero-Shot Scientific Fact Checking

Recognizing UMLS Semantic Types with Deep Learning

A survey on recent advances in named entity recognition

Ontology Enrichment from Texts: A Biomedical Dataset for Concept Discovery and Placement

BELB: a Biomedical Entity Linking Benchmark


Official pytorch Implementation of Relational Knowledge Distillation, CVPR 2019

Relational Knowledge Distillation

TEACHTEXT: CrossModal Generalized Distillation for Text-Video Retrieval

The State of Knowledge Distillation for Classification


Rank-1 89% (Single Query) on Market1501 with raw triplet loss, In Defense of the Triplet Loss for Person Re-Identification, using Pytorch

Beyond Part Models: Person Retrieval with Refined Part Pooling (and a Strong Convolutional Baseline)

Deep Generalized Max Pooling

Real-Time Person Re-identification at the Edge: A Mixed Precision Approach


ACL 2021: Question Answering over Temporal Knowledge Graphs

Tensor Decompositions for temporal knowledge base completion

Question Answering Over Temporal Knowledge Graphs

ForecastTKGQuestions: A Benchmark for Temporal Question Answering and Forecasting over Temporal Knowledge Graphs


Pick-a-Pic: An Open Dataset of User Preferences for Text-to-Image Generation

Confidence-aware Reward Optimization for Fine-tuning Text-to-Image
  Models


Machine learning tool to detect landslides from optical satellite imagery


HuBERT content encoders for: A Comparison of Discrete and Soft Speech Units for Improved Voice Conversion

HuBERT: Self-Supervised Speech Representation Learning by Masked Prediction of Hidden Units

LM-VC: Zero-Shot Voice Conversion via Speech Generation Based on Language Models

Distinctive and Natural Speaker Anonymization via Singular Value Transformation-Assisted Matrix

Adversarial Speaker Disentanglement Using Unannotated External Data for Self-supervised Representation-based Voice Conversion


Official implementation of MCVD: Masked Conditional Video Diffusion for Prediction, Generation, and Interpolation (https://arxiv.org/abs/2205.09853)

Pseudo Numerical Methods for Diffusion Models on Manifolds

Non Gaussian Denoising Diffusion Models

LDMVFI: Video Frame Interpolation with Latent Diffusion Models

Physion++: Evaluating Physical Scene Understanding that Requires Online Inference of Different Physical Properties

A Control-Centric Benchmark for Video Prediction


LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files

Genome-Wide Association Study Using Whole-Genome Sequencing Identifies a Genomic Region on Chromosome 6 Associated With Comb Traits in Nandan-Yao Chicken

Genome and haplotype provide insights into the population differentiation and breeding improvement of Gossypium barbadense

Genome-Wide Association Study Reveals That PvGUX1_1 Is Associated with Pod Stringlessness in Snap Bean (Phaseolus vulgaris L.)


Contrastive Learning of Structured World Models

Physion: Evaluating Physical Prediction from Vision in Humans and Machines

Better Set Representations For Relational Reasoning

The Impact of Negative Sampling on Contrastive Structured World Models


Side Channels Analysis and Deep Learning

Deep learning for side-channel analysis and introduction to ASCAD database

Reinforcement Learning for Hyperparameter Tuning in Deep Learning-based Side-channel Analysis

IACR Transactions on Cryptographic Hardware and Embedded Systems

Strength in Numbers: Improving Generalization with Ensembles in Machine Learning-based Profiled Side-channel Analysis

Exploring Feature Selection Scenarios for Deep Learning-based Side-channel Analysis

Ranking Loss: Maximizing the Success Rate in Deep Learning Side-Channel Analysis

Information Theory-based Evolution of Neural Networks for Side-channel Analysis

Auto-tune POIs: Estimation of distribution algorithms for efficient side-channel analysis

An Enhanced Convolutional Neural Network in Side-Channel Attacks and Its Visualization

No (good) loss no gain: systematic evaluation of loss functions in deep learning-based side-channel analysis

Side-channel analysis against ANSSI’s protected AES implementation on ARM: end-to-end attacks with multi-task learning


Assembler for NVIDIA Maxwell architecture

Tensor Comprehensions: Framework-Agnostic High-Performance Machine Learning Abstractions

Dissecting the NVIDIA Volta GPU Architecture via Microbenchmarking

Dissecting the NVidia Turing T4 GPU via Microbenchmarking

Modeling Deep Learning Accelerator Enabled GPUs

maxDNN: An Efficient Convolution Kernel for Deep Learning with Maxwell GPUs

Verified instruction-level energy consumption measurement for NVIDIA GPUs

Low Overhead Instruction Latency Characterization for NVIDIA GPGPUs

Implementing Strassen's Algorithm with CUTLASS on NVIDIA Volta GPUs

Cimple: Instruction and Memory Level Parallelism

RegDem: Increasing GPU Performance via Shared Memory Register Spilling


Implementation of Dreamer v3 in pytorch.

Mastering Diverse Domains through World Models

World Models via Policy-Guided Trajectory Diffusion

MAMBA: an Effective World Model Approach for Meta-Reinforcement Learning

Hieros: Hierarchical Imagination on Structured State Space Sequence World Models


Linear Assignmment Problem solver using Jonker-Volgenant algorithm - Python 3 native module.

OoDAnalyzer: Interactive Analysis of Out-of-Distribution Samples

High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE

Comparing temporal graphs using dynamic time warping

Exploring the Deep Feature Space of a Cell Classification Neural Network


Detection of pseudogene candidates in bacterial and archaeal genomes.

Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes

Anaerobic endosymbiont generates energy for ciliate host by denitrification

Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

Genomic Features of Salmonella enterica Subspecies houtenae Serotype 45:g,z51:- Isolated from Multiple Abdominal Abscesses of an African Fat-Tailed Gecko, United States, 2020

Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis


Beyond I.I.D.: Three Levels of Generalization for Question Answering on Knowledge Bases

Would You Ask it that Way? Measuring and Improving Question Naturalness for Knowledge Graph Question Answering

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

Few-shot Transfer Learning for Knowledge Base Question Answering: Fusing Supervised Models with In-Context Learning


A pipeline for running AMRfinderPlus and collating results into functional classes

Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

Prolonged Outbreak of Multidrug-Resistant Shigella sonnei Harboring bla(CTX-M-27) in Victoria, Australia

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria

Genomic Epidemiology and Antimicrobial Resistance Mechanisms of Imported Typhoid in Australia

Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

Resistance to first-line antibiotic therapy among patients with uncomplicated acute cystitis in Melbourne, Australia: prevalence, predictors and clinical impact

Hidden Resistances: How Routine Whole-Genome Sequencing Uncovered an Otherwise Undetected blaNDM-1 Gene in Vibrio alginolyticus from Imported Seafood


We propose EfficientDerain for high-efficiency single-image deraining at AAAI 2021. The latest extended version has been accepted by IJCV at 2024. Please check the released code at https://github.com/tsingqguo/efficientderainplus and paper at https://arxiv.org/pdf/2201.02366.

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

Not Just Streaks: Towards Ground Truth for Single Image Deraining

Uncertainty-Aware Cascaded Dilation Filtering for High-Efficiency Deraining


Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

In Vivo Validation of Alternative FDXR Transcripts in Human Blood in Response to Ionizing Radiation

International journal of molecular sciences

The Increase in the Drug Resistance of Acute Myeloid Leukemia THP-1 Cells in High-Density Cell Culture Is Associated with Inflammatory-like Activation and Anti-Apoptotic Bcl-2 Proteins

Transcript capture and ultradeep long-read RNA sequencing (CAPLRseq) to diagnose HNPCC/Lynch syndrome

In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing

Single-Molecule RNA Sequencing Reveals IFNγ-Induced Differential Expression of Immune Escape Genes in Merkel Cell Polyomavirus–Positive MCC Cell Lines


Image Signal Processor

Gradient-Based Feature Extraction From Raw Bayer Pattern Images

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

Software-Defined Imaging: A Survey

Adversarial RAW: Image-Scaling Attack Against Imaging Pipeline


Color palette package in R inspired by works at the Metropolitan Museum of Art in New York

Spectral neural approximations for models of transcriptional dynamics

Theory of photonic crystal polaritons in periodically patterned multilayer waveguides

Pitfalls of machine learning models for protein-protein interactions

Geographical and economic influences on neuroimaging modality choice

Evolution and diversification of the momilactone biosynthetic gene cluster in the genusOryza


AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia

Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Molecular characterization and antimicrobial susceptibility testing of clinical and non-clinical Brucella melitensis and Brucella abortus isolates from Egypt

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria

Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria

Analysis of the Molecular Diversity Among Cronobacter Species Isolated From Filth Flies Using Targeted PCR, Pan Genomic DNA Microarray, and Whole Genome Sequencing Analyses

Genomic Epidemiology and Antimicrobial Resistance Mechanisms of Imported Typhoid in Australia

ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa

Characterization of NDM-5-producing Enterobacteriaceae isolates from retail grass carp (Ctenopharyngodon idella) and evidence of bla_(NDM-5)-bearing IncHI2 plasmid transfer between ducks and fish

Prevalence of Enterococcus spp. and the Whole-Genome Characteristics of Enterococcus faecium and Enterococcus faecalis Strains Isolated from Free-Living Birds in Poland


AIXIjs - General Reinforcement Learning in the Browser

Count-Based Exploration in Feature Space for Reinforcement Learning

Universal Reinforcement Learning Algorithms: Survey and Experiments

AIXIjs: A Software Demo for General Reinforcement Learning

Generalised Discount Functions applied to a Monte-Carlo AImu Implementation


Official code for "Towards Photo-Realistic Virtual Try-On by Adaptively Generating↔Preserving Image Content"，CVPR‘20 https://arxiv.org/abs/2003.05863

Per Garment Capture and Synthesis for Real-time Virtual Try-on


Overview of the data QC, code, and GWAS summary output from the 2017 UK Biobank data release

Transancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders

A generalized linear mixed model association tool for biobank-scale data

Zenodo (CERN European Organization for Nuclear Research)

Neuropsychiatric Genetics of African Populations-Psychosis (NeuroGAP-Psychosis): a case-control study protocol and GWAS in Ethiopia, Kenya, South Africa and Uganda

Insights from complex trait fine-mapping across diverse populations

Genomic Risk Factors for Cervical Cancer

Causal Association Between Tea Consumption and Kidney Function: A Mendelian Randomization Study

Variability in Brain Structure and Function Reflects Lack of Peer Support

Recent shifts in the genomic ancestry of Mexican Americans may alter the genetic architecture of biomedical traits

Epigenome-wide association study of seizures in childhood and adolescence

Deciphering the Biological Mechanisms Underlying the Genome-Wide Associations between Computerized Device Use and Psychiatric Disorders


Pairwise multilevel comparison using adonis

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations

Fecal Microbiota Transplantation Controls Murine Chronic Intestinal Inflammation by Modulating Immune Cell Functions and Gut Microbiota Composition

Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple

Metagenomic evidence for co-occurrence of antibiotic, biocide and metal resistance genes in pigs

Salivary Microbiome and Cigarette Smoking: A First of Its Kind Investigation in Jordan

International journal of environmental research and public health

Microbial composition in seasonal time series of free tropospheric air and precipitation reveals community separation

More Than “Push” and “Pull”? Plant-Soil Feedbacks of Maize Companion Cropping Increase Chemical Plant Defenses Against Herbivores

Diet and gut microbiome enterotype are associated at the population level in African buffalo

The multifactorial nature of beak and skull shape evolution in parrots and cockatoos (Psittaciformes)

Nitrification inhibitors effectively target N2O-producing Nitrosospira spp. in tropical soil


A framework for Big Data Optimization with multi-objective metaheuristics

jMetalSP: A framework for dynamic multi-objective big data optimization

InDM2: Interactive Dynamic Multi-Objective Decision Making Using Evolutionary Algorithms

Multi-objective Big Data Optimization with jMetal and Spark

Dynamic Multi-Objective Optimization with jMetal and Spark: A Case Study


A suite of rust libraries for secure multi-party computation

Circa: Stochastic ReLUs for Private Deep Learning

AutoPrivacy: Automated Layer-wise Parameter Selection for Secure Neural Network Inference

AESPA: Accuracy Preserving Low-degree Polynomial Activation for Fast Private Inference


PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow

A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events

Genomic consequences of domestication of the Siamese fighting fish

Genomes of the cosmopolitan fruit pest Bactrocera dorsalis (Diptera: Tephritidae) reveal its global invasion history and thermal adaptation

An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Long-read HiFi Sequencing Correctly Assembles Repetitive heavy fibroin Silk Genes in New Moth and Caddisfly Genomes

Representing sex chromosomes in genome assemblies

Convergent Rewiring of the Virulence Regulatory Network Promotes Adaptation of Ralstonia solanacearum on Resistant Tomato

Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg


A Neural Machine Translation implementation in Chainer

An Empirical Comparison of Simple Domain Adaptation Methods for Neural Machine Translation

言語処理学会年次大会発表論文集(Web)

Enabling Multi-Source Neural Machine Translation By Concatenating Source Sentences In Multiple Languages

Kyoto University Participation to WAT 2016

International Conference on Computational Linguistics

Kyoto-NMT: a Neural Machine Translation implementation in Chainer

Kyoto University Participation to WAT 2017

Neural Machine Translation: Basics, Practical Aspects and Recent Trends

International Joint Conference on Natural Language Processing

Kyoto University MT System Description for IWSLT 2017

International Workshop on Spoken Language Translation


Python3 scripts to manipulate FASTA and FASTQ files

IVA: accurate de novo assembly of RNA virus genomes

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

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

Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing

Nearly Complete Genome Sequence of Brugia malayi Strain FR3

HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

Easy and Accurate Reconstruction of Whole HIV Genomes from Short-Read Sequence Data


The monorepo that powers the GreenDB.

GreenDB: Toward a Product-by-Product Sustainability Database

GreenDB: A Product-by-Product Sustainability Database

GreenDB -- A Dataset and Benchmark for Extraction of Sustainability Information of Consumer Goods


Computer vision library for wildfire detection  Deep learning models in PyTorch & ONNX for inference on edge devices (e.g. Raspberry Pi)


Convert a PDDL domain into an OpenAI Gym environment.

Planning with Learned Object Importance in Large Problem Instances using Graph Neural Networks

PDDLGym: Gym Environments from PDDL Problems

GLIB: Efficient Exploration for Relational Model-Based Reinforcement Learning via Goal-Literal Babbling

WorldCoder, a Model-Based LLM Agent: Building World Models by Writing
  Code and Interacting with the Environment

pyRDDLGym: From RDDL to Gym Environments

GLIB: Exploration via Goal-Literal Babbling for Lifted Operator Learning

The Sandbox Environment for Generalizable Agent Research (SEGAR)


The Chroma Software System for Lattice QCD

A per-cent-level determination of the nucleon axial coupling from quantum chromodynamics

Λ_b →Λ^*(1520)ℓ^+ℓ^- form factors from lattice
  QCD

Λ_c →Λ^*(1520) form factors from lattice QCD and improved analysis of the Λ_b →Λ^*(1520) and Λ_b →Λ_c^*(2595,2625) form factors

Λb→Λc*(2595,2625)ℓ−ν¯
 form factors from lattice QCD

Simulating the Weak Death of the Neutron in a Femtoscale Universe with Near-Exascale Computing

SIMULATeQCD: A simple multi-GPU lattice code for QCD calculations

Charm-baryon semileptonic decays and the strange Λ^* resonances: New insights from lattice QCD

Exclusive semileptonic B_s→ K ℓ ν decays on the lattice

Lattice gauge ensembles and data management

Status of next-generation Λ_b → p, Λ, Λ_c form-factor calculations


A multi-programming language benchmark for LLMs

StarCoder: may the source be with you!

SantaCoder: don't reach for the stars!

MultiPL-E: A Scalable and Polyglot Approach to Benchmarking Neural Code Generation

IEEE Transactions on Software Engineering

MultiPL-E: A Scalable and Extensible Approach to Benchmarking Neural Code Generation

Deep Learning Based Code Generation Methods: A Literature Review

Neural Machine Translation for Code Generation

Generative Software Engineering


Complete Matlab pipeline for large scale calcium imaging data analysis

Suite2p: beyond 10,000 neurons with standard two-photon microscopy

Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data

Two-photon calcium imaging of the medial prefrontal cortex and hippocampus without cortical invasion

Engineered AAVs for non-invasive gene delivery to rodent and non-human primate nervous systems

Reinforcement Learning Recruits Somata and Apical Dendrites across Layers of Primary Sensory Cortex

The essential role of recurrent processing for figure-ground perception in mice

HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium-Imaging Movies

Fast wide-volume functional imaging of engineered in vitro brain tissues

Multiplane Calcium Imaging Reveals Disrupted Development of Network Topology in Zebrafish pcdh19 Mutants

Activity-dependent organization of prefrontal hub-networks for associative learning and signal transformation


15MW reference wind turbine repository developed in conjunction with IEA Wind

Comparison of loads from HAWC2 and OpenFAST for the IEA Wind 15 MW Reference Wind Turbine

SCIENCE OF MAKING TORQUE FROM WIND (TORQUE 2020), PTS 1-5

Structural Optimisation of Offshore Direct-Drive Wind Turbine Generators Including Static and Dynamic Analyses


An intuitive library to extract features from time series.

TSFEL: Time Series Feature Extraction Library

Early Classification of Time Series. Cost-based Optimization Criterion and Algorithms

IMU-Based Fitness Activity Recognition Using CNNs for Time Series Classification

Early and Revocable Time Series Classification


Identify and quantify MHC eluted peptides from mass spectrometry raw data

The nf-core framework for community-curated bioinformatics pipelines

MHCflurry: open-source class I MHC binding affinity prediction

A Deeper Look into Comet—Implementation and Features

Journal of the American Society for Mass Spectrometry

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

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

MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

FRED 2: an immunoinformatics framework for Python


A Wikidata Python module integrating the MediaWiki API and the Wikidata SPARQL endpoint

Wikidata as a knowledge graph for the life sciences

Using Shape Expressions (ShEx) to Share RDF Data Models and to Guide Curation with Rigorous Validation

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

Joint Open Knowledge Base Canonicalization and Linking

A protocol for adding knowledge to Wikidata, a case report

Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience

Statistical Knowledge Assessment for Large Language Models

The Janus System: Multi-paradigm Programming in Prolog and Python

International Conference on Logic Programming

COMBO: A Complete Benchmark for Open KG Canonicalization


This repository is for developing study packages for OHDSI studies. Once completed, they can be moved to the StudyProtocols repository.

Feasibility and Evaluation of a Large-Scale External Validation Approach for Patient-Level Prediction in an International Data Network: Validation of models predicting stroke in female patients newly diagnosed with atrial fibrillation.

Identifying the DEAD: Development and Validation of a Patient-Level Model to Predict Death Status in Population-Level Claims Data

Inferring disease severity in rheumatoid arthritis using predictive modeling in administrative claims databases

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality

Supplementing claims data analysis using self-reported data to develop a probabilistic phenotype model for current smoking status


Data on COVID-19 (coronavirus) cases, deaths, hospitalizations, tests • All countries • Updated daily by Our World in Data

A global database of COVID-19 vaccinations

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

A cross-country database of COVID-19 testing

Predicting the growth and trend of COVID-19 pandemic using machine learning and cloud computing

Collectivism predicts mask use during COVID-19

Consumer Responses to the COVID-19 Crisis: Evidence from Bank Account Transaction Data

Quantifying the effects of the COVID-19 pandemic on gender equality on health, social, and economic indicators: a comprehensive review of data from March, 2020, to September, 2021

Unrepresentative big surveys significantly overestimated US vaccine uptake

Online misinformation is linked to early COVID-19 vaccination hesitancy and refusal

Lancet COVID-19 Commission Statement on the occasion of the 75th session of the UN General Assembly


Deep Graph Infomax (https://arxiv.org/abs/1809.10341)

A Comprehensive Survey on Graph Neural Networks

IEEE transactions on neural networks and learning systems

Graph Neural Networks: A Review of Methods and Applications

Deep Graph Infomax

Deep Learning on Graphs: A Survey

Graph Self-Supervised Learning: A Survey

A Comprehensive Survey on Pretrained Foundation Models: A History from BERT to ChatGPT

Self-supervised Heterogeneous Graph Neural Network with Co-contrastive Learning

Anomaly Detection on Attributed Networks via Contrastive Self-Supervised Learning

Self-Supervised Learning on Graphs: Contrastive, Generative, or Predictive

GraphZoom: A multi-level spectral approach for accurate and scalable graph embedding


SimpleShot: Revisiting Nearest-Neighbor Classification for Few-Shot Learning

Using Shape to Categorize: Low-Shot Learning with an Explicit Shape Bias

Few-shot Learning as Cluster-induced Voronoi Diagrams: A Geometric Approach

Learning Dense Object Descriptors from Multiple Views for Low-shot Category Generalization


Experiment code for "Deep Reinforcement Learning in a Handful of Trials using Probabilistic Dynamics Models"

Context-aware Dynamics Model for Generalization in Model-Based Reinforcement Learning

Off-Dynamics Reinforcement Learning: Training for Transfer with Domain Classifiers

Calibrated Model-Based Deep Reinforcement Learning

On-Policy Robot Imitation Learning from a Converging Supervisor

LS3: Latent Space Safe Sets for Long-Horizon Visuomotor Control of Sparse Reward Iterative Tasks


Application for making ENCODE Blacklists

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Control of neurogenic competence in mammalian hypothalamic tanycytes

Global discovery of lupus genetic risk variant allelic enhancer activity

Liquid biopsy epigenomic profiling for cancer subtyping

Histone deacetylase 1 and 2 drive differentiation and fusion of progenitor cells in human placental trophoblasts

Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice

Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells

The TH1 cell lineage-determining transcription factor T-bet suppresses TH2 gene expression by redistributing GATA3 away from TH2 genes

Mapping the evolving landscape of super-enhancers during cell differentiation

Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data


SOM-DST: Efficient Dialogue State Tracking by Selectively Overwriting Memory (ACL 2020)

MultiWOZ 2.4: A Multi-Domain Task-Oriented Dialogue Dataset with Essential Annotation Corrections to Improve State Tracking Evaluation

Towards Fair Evaluation of Dialogue State Tracking by Flexible Incorporation of Turn-level Performances

Comprehensive Study: How the Context Information of Different Granularity Affects Dialogue State Tracking?

Multi-Domain Dialogue State Tracking based on State Graph

Multi-Domain Dialogue State Tracking - A Purely Transformer-Based Generative Approach.


VIRULIGN: fast codon-correct alignment and annotation of viral genomes

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

Potential Associations of Mutations within the HIV-1 Env and Gag Genes Conferring Protease Inhibitor (PI) Drug Resistance


Resources for the "Evaluating the Factual Consistency of Abstractive Text Summarization" paper

GSum: A General Framework for Guided Neural Abstractive Summarization

QAFactEval: Improved QA-Based Factual Consistency Evaluation for Summarization

Human-like Summarization Evaluation with ChatGPT

Improving Factual Consistency of Abstractive Summarization via Question Answering

Noisy Self-Knowledge Distillation for Text Summarization

Rome was built in 1776: A Case Study on Factual Correctness in Knowledge-Grounded Response Generation

FFCI: A Framework for Interpretable Automatic Evaluation of Summarization

CDEvalSumm: An Empirical Study of Cross-Dataset Evaluation for Neural Summarization Systems

DialSummEval: Revisiting Summarization Evaluation for Dialogues

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


Implementation of Efficient Off-policy Meta-learning via Probabilistic Context Variables (PEARL)

Efficient Off-Policy Meta-Reinforcement Learning via Probabilistic Context Variables

VariBAD: A Very Good Method for Bayes-Adaptive Deep RL via Meta-Learning

Offline Meta-Reinforcement Learning with Online Self-Supervision

Improving Generalization in Meta-RL with Imaginary Tasks from Latent Dynamics Mixture

Context Meta-Reinforcement Learning via Neuromodulation

Meta-Model-Based Meta-Policy Optimization

State Regularized Policy Optimization on Data with Dynamics Shift

Learning Action Translator for Meta Reinforcement Learning on Sparse-Reward Tasks

Improving Context-Based Meta-Reinforcement Learning with Self-Supervised Trajectory Contrastive Learning

Meta-Learning Parameterized Skills


bead-based normalization of mass cytometry data

Distinct predictive biomarker candidates for response to anti-CTLA-4 and anti-PD-1 immunotherapy in melanoma patients

Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy

TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate

Reduced CD27−IgD− B Cells in Blood and Raised CD27−IgD− B Cells in Gut-Associated Lymphoid Tissue in Inflammatory Bowel Disease

Harnessing CD3 diversity to optimize CAR T cells

Treated HIV Infection Alters Phenotype but Not HIV-Specific Function of Peripheral Blood Natural Killer Cells

Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia

Single cell profiling at the maternal–fetal interface reveals a deficiency of PD-L1+ non-immune cells in human spontaneous preterm labor

CNS Repopulation by Hematopoietic-Derived Microglia-Like Cells Corrects Progranulin deficiency


Learning Deep CNN Denoiser Prior for Image Restoration (CVPR, 2017) (Matlab)

Image Restoration by Iterative Denoising and Backward Projections

Plug-and-Play Unplugged: Optimization Free Reconstruction using Consensus Equilibrium

Plug-and-Play gradient-based denoisers applied to CT image enhancement

Denoising single images by feature ensemble revisited


causalimages: An R package for performing causal inference with image and image sequence data

Image-based Treatment Effect Heterogeneity

Integrating Earth Observation Data into Causal Inference: Challenges and Opportunities

Estimating Causal Effects Under Image Confounding Bias with an Application to Poverty in Africa


Dataset and codes for ACL 2019 DocRED: A Large-Scale Document-Level Relation Extraction Dataset.

Coreferential Reasoning Learning for Language Representation

ERICA: Improving Entity and Relation Understanding for Pre-trained Language Models via Contrastive Learning

Global-to-Local Neural Networks for Document-Level Relation Extraction

DREEAM: Guiding Attention with Evidence for Improving Document-Level Relation Extraction

Document-Level Relation Extraction with Sentences Importance Estimation and Focusing

Dual Supervision Framework for Relation Extraction with Distant Supervision and Human Annotation

Boosting Document-Level Relation Extraction by Mining and Injecting Logical Rules

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

Mention-centered Graph Neural Network for Document-level Relation Extraction

Self-distillation framework for document-level relation extraction in low-resource environments


Rethinking Data Augmentation for Image Super-resolution (CVPR 2020)

Avoiding Overfitting: A Survey on Regularization Methods for Convolutional Neural Networks

Rethinking Data Augmentation for Image Super-resolution: A Comprehensive Analysis and a New Strategy

Generative Adversarial Networks for Image Augmentation in Agriculture: A Systematic Review


Circle C++ shaders

Supporting Unified Shader Specialization by Co-opting C++ Features

Proceedings of the ACM on Computer Graphics and Interactive Techniques

Development in Vulkan: a domain-specific approach

Труды Института системного программирования РАН

Unified Shader Programming in C


Learning audio concepts from natural language supervision

CLAP Learning Audio Concepts from Natural Language Supervision

Natural Language Supervision For General-Purpose Audio Representations

GAMA: A Large Audio-Language Model with Advanced Audio Understanding and
  Complex Reasoning Abilities


【CVPR'2023】Bidirectional Cross-Modal Knowledge Exploration for Video Recognition with Pre-trained Vision-Language Models

Revisiting Classifier: Transferring Vision-Language Models for Video Recognition

Cap4Video: What Can Auxiliary Captions Do for Text-Video Retrieval?


A Pytorch implementation of DeepCrack and RoadNet projects.

Predicting Depth, Surface Normals and Semantic Labels with a Common Multi-Scale Convolutional Architecture

Crack Detection as a Weakly-Supervised Problem: Towards Achieving Less Annotation-Intensive Crack Detectors

Weakly-Supervised Crack Detection

TrueDeep: A systematic approach of crack detection with less data

Revealing the Underlying Patterns: Investigating Dataset Similarity, Performance, and Generalization


Data/Code Repository for https://api.semanticscholar.org/CorpusID:218470122

SciREX: A Challenge Dataset for Document-Level Information Extraction

ToolQA: A Dataset for LLM Question Answering with External Tools

Document-level Entity-based Extraction as Template Generation

CitationIE: Leveraging the Citation Graph for Scientific Information Extraction

Automatic Error Analysis for Document-level Information Extraction

Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)


mutation(barcode) caller for 10x single cell data

A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

Spatially resolved clonal copy number alterations in benign and malignant tissue

Early activation of inflammatory pathways in UBA1-mutated hematopoietic stem and progenitor cells in VEXAS

Loss of SYNCRIP unleashes APOBEC-driven mutagenesis, tumor heterogeneity, and AR-targeted therapy resistance in prostate cancer

Genetic and Transcriptional Contributions to Relapse in Normal Karyotype Acute Myeloid Leukemia


ACL2023 - AlignScore, a metric for factual consistency evaluation.

AlignScore: Evaluating Factual Consistency with a Unified Alignment Function

TofuEval: Evaluating Hallucinations of LLMs on Topic-Focused Dialogue
  Summarization


Offline Reinforcement Learning (aka Batch Reinforcement Learning) on Atari 2600 games

An Optimistic Perspective on Offline Reinforcement Learning

Implicit Under-Parameterization Inhibits Data-Efficient Deep Reinforcement Learning

Challenges and Opportunities in Offline Reinforcement Learning from Visual Observations


SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer

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

A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer

Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies

Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex

LongTron: Automated Analysis of Long Read Spliced Alignment Accuracy


ParsBERT: Transformer-based Model for Persian Language Understanding

XL-WiC: A Multilingual Benchmark for Evaluating Semantic Contextualization

ParsiNLU: A Suite of Language Understanding Challenges for Persian

Exploiting BERT to Improve Aspect-Based Sentiment Analysis Performance on Persian Language


Python3 bindings for the Compact Language Detector v3 (CLD3)

Geographically-Balanced Gigaword Corpora for 50 Language Varieties

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

HC4: A New Suite of Test Collections for Ad Hoc CLIR

Cultural Convergence: Insights into the behavior of misinformation networks on Twitter

Code-Switched Text Synthesis in Unseen Language Pairs

Analysing the effectiveness of Twitter as an equitable community communication tool for international conferences


A neural word aligner based on multilingual BERT

Word Alignment by Fine-tuning Embeddings on Parallel Corpora

Improving Translation Faithfulness of Large Language Models via Augmenting Instructions

Frustratingly Easy Label Projection for Cross-lingual Transfer

Deliberate then Generate: Enhanced Prompting Framework for Text Generation

Constructing Code-mixed Universal Dependency Forest for Unbiased Cross-lingual Relation Extraction

Improving Machine Translation with Large Language Models: A Preliminary Study with Cooperative Decoding

Adapting Offline Speech Translation Models for Streaming with Future-Aware Distillation and Inference

Cross-Align: Modeling Deep Cross-lingual Interactions for Word Alignment

Learning Contextualised Cross-lingual Word Embeddings and Alignments for Extremely Low-Resource Languages Using Parallel Corpora

EVALIGN: Visual Evaluation of Translation Alignment Models

Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations


SISTR (Salmonella In Silico Typing Resource) command-line tool

The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

Typing methods based on whole genome sequencing data

Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria

Mobilome-driven partitions of the resistome in Salmonella

Prevalence and Antibiotic Resistance of Salmonella and Campylobacter Isolates from Raw Chicken Breasts in Retail Markets in the United States and Comparison to Data from the Plant Level

Carbapenem resistance in extensively drug-resistant Salmonella enterica serovar Agona and AmpC β-lactamase-producing S. Infantis.

Rural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data

Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing

Raw meat-based diet for pets: a neglected source of human exposure to Salmonella and pathogenic Escherichia coli clones carrying mcr, Portugal, September 2019 to January 2020


microsatellite instability detection using tumor only or paired tumor-normal data

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

Patient-derived xenografts and organoids model therapy response in prostate cancer

Molecular and Computational Methods for the Detection of Microsatellite Instability in Cancer

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability

基因组蛋白质组与生物信息学报

Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers

Analysis pipelines for cancer genome sequencing in mice

Immunotherapy in Metastatic Colorectal Cancer: Could the Latest Developments Hold the Key to Improving Patient Survival?

Neurofibromatosis type 1 mosaicism in patients with constitutional mismatch repair deficiency

Immune checkpoint inhibitor‐related molecular markers predict prognosis in extrahepatic cholangiocarcinoma

Therapeutic HDAC inhibition in hypermutant diffuse intrinsic pontine glioma


Pytorch implementation of DCGAN, WGAN-CP, WGAN-GP

Unsupervised Representation Learning with Deep Convolutional Generative Adversarial Networks

Improved Training of Wasserstein GANs

Wasserstein GAN

A Note on the Inception Score

Ten years of generative adversarial nets (GANs): a survey of the state-of-the-art

Enhancing Mechanical Metamodels With a Generative Model-Based Augmented Training Dataset

TiAda: A Time-scale Adaptive Algorithm for Nonconvex Minimax Optimization

MaWGAN: A Generative Adversarial Network to Create Synthetic Data from Datasets with Missing Data


Creative Commons Attribution 4.0 International

Chemical Methods Ontology

NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany

Establishing a Common Nutritional Vocabulary - From Food Production to Diet

Overview of chemical ontologies

Visual and Semantic Enrichment of Analytical Chemistry Literature Searches by Combining Text Mining and Computational Chemistry

Structuring superconductor data with ontology: reproducing historical datasets as knowledge bases

Science and Technology of Advanced Materials: Methods

Ontologies for increasing the FAIRness of plant research data


a minimal C++ interval tree implementation

HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications

HINT: A Hierarchical Index for Intervals in Main Memory

HINT: a hierarchical interval index for Allen relationships

Faster and Smaller Two-Level Index for Network-Based Trajectories

String Processing and Information Retrieval


Creative Commons Attribution Share Alike 4.0 International

The official repository for the EuroCrops dataset.

EuroCrops: The Largest Harmonized Open Crop Dataset Across the European Union

Challenges and Opportunities of Large Transnational Datasets: A Case Study on European Administrative Crop Data

Boosting Crop Classification by Hierarchically Fusing Satellite, Rotational, and Contextual Data

Harnessing Administrative Data Inventories to Create a Reliable Transnational Reference Database for Crop Type Monitoring

IGARSS 2022 - 2022 IEEE International Geoscience and Remote Sensing Symposium


A CVXPY extension for convex-concave programming

Learning Fair Rule Lists

Optimization Method for Wide Beam Sonar Transmit Beamforming

Stochastic Neural Networks for Automatic Cell Tracking in Microscopy Image Sequences of Bacterial Colonies

A Note on the Hausdorff Distance Between Norm Balls and Their Linear Maps


Code for Nature energy manuscript


Package for direction dependent calibration

The LOFAR Two-meter Sky Survey: Deep Fields Data Release 1

Disk-jet coupling in the 2017/2018 outburst of the Galactic black hole candidate X-ray binary MAXI J1535-571

CUBICAL - fast radio interferometric calibration suite exploiting complex optimization

Monthly Notices of the Royal Astronomical Society

Convolutional deep denoising autoencoders for radio astronomical images

MKT J170456.2-482100: the first transient discovered by MeerKAT

Zenodo (CERN European Organization for Nuclear Research)

The twisted jets of Circinus X-1

Monthly notices of the Royal Astronomical Society

Spectropolarimetry and photometry of the early afterglow of the gamma-ray burst GRB 191221B

MERGHERS pilot: MeerKAT discovery of diffuse emission in nine massive Sunyaev-Zel'dovich-selected galaxy clusters from ACT

The LOFAR LBA Sky Survey: Deep Fields I. The Boötes Field

LOFAR Deep Fields: probing a broader population of polarized radio galaxies in ELAIS-N1


TN93 fast distance calculator

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Using HIV Networks to Inform Real Time Prevention Interventions

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Early Antiretroviral Therapy Is Associated with Lower HIV DNA Molecular Diversity and Lower Inflammation in Cerebrospinal Fluid but Does Not Prevent the Establishment of Compartmentalized HIV DNA Populations

Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy

SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

bioRxiv : the preprint server for biology

Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions

Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection

Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial


PRIDE Inspector is a Java desktop application to visualise and Quality Assessment on Mass Spectrometry data and Proteomics

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics

Evaluation of Unconventional Protein Secretion by Saccharomyces cerevisiae and other Fungi

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics


Doodler. A web application built with plotly/dash for image segmentation with minimal supervision. Plays nicely with segmentation gym, https://github.com/Doodleverse/segmentation_gym

Human-in-the-Loop Segmentation of Earth Surface Imagery

A 1.2 Billion Pixel Human-Labeled Dataset for Data-Driven Classification of Coastal Environments


The complete set of tools for energy consumption analysis of programming languages, using Computer Language Benchmark Game

Evaluation of Rust code verbosity, understandability and complexity


An online tool for forest management scenario planning


An efficient implementation of the popular sequence models for text generation, summarization, and translation tasks. https://arxiv.org/pdf/2106.04718.pdf

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

AMMUS : A Survey of Transformer-based Pretrained Models in Natural Language Processing

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

FastSeq: Make Sequence Generation Faster

EL-Attention: Memory Efficient Lossless Attention for Generation


A tool for retrosynthetic planning

AiZynthFinder: A Fast Robust and Flexible Open-Source Software for Retrosynthetic Planning

Datasets and Their Influence on the Development of Computer Assisted Synthesis Planning Tools in the Pharmaceutical Domain

Retrosynthetic Accessibility Score (RAscore) - Rapid Machine Learned Synthesizability Classification from AI Driven Retrosynthetic Planning

Clustering of Synthetic Routes Using Tree Edit Distance

Journal of chemical information and modeling

Fast prediction of distances between synthetic routes with deep learning

Machine Learning: Science and Technology

Beyond Games: A Systematic Review of Neural Monte Carlo Tree Search Applications

A Quick Policy to Filter Reactions Based on Feasibility in AI-Guided Retrosynthetic Planning

GitAgent: Facilitating Autonomous Agent with GitHub by Tool Extension

AiZynthFinder 4.0: developments based on learnings from 3 years of industrial application

Directly Optimizing for Synthesizability in Generative Molecular Design
  using Retrosynthesis Models


Next-Gen Sequencing tools from the Horvath Lab

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets

RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data

ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data

SCReadCounts: Estimation of cell-level SNVs from scRNA-seq data

SCExecute: cell barcode-stratified analyses of scRNA-seq data