Pipeline to build a massive tree from global data

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

The SARS-CoV-2 Alpha variant is associated with increased clinical severity of disease

The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis

Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining

Phylogenomic early warning signals for SARS-CoV-2 epidemic waves


LoveDA: A Remote Sensing Land-Cover Dataset for Domain Adaptive Semantic Segmentation

Hi-UCD: A Large-scale Dataset for Urban Semantic Change Detection in Remote Sensing Imagery

Multi-temporal urban semantic understanding based on GF-2 remote sensing imagery: from tri-temporal datasets to multi-task mapping


Multi-task deep learning framework for multi-omics data analysis

OmiEmbed: A Unified Multi-Task Deep Learning Framework for Multi-Omics Data

SubOmiEmbed: Self-supervised Representation Learning of Multi-omics Data for Cancer Type Classification

OmiTrans: Generative Adversarial Networks Based Omics-to-omics Translation Framework

A Fair Experimental Comparison of Neural Network Architectures for Latent Representations of Multi-Omics for Drug Response Prediction


This repo contains the codes for our paper Conditional Antibody Design as 3D Equivariant Graph Translation.

Antigen-Specific Antibody Design via Direct Energy-based Preference
  Optimization

Full-Atom Protein Pocket Design via Iterative Refinement


Pytorch implementation of SMIL: Multimodal Learning with Severely Missing Modality (AAAI 2021)

CentralNet: a Multilayer Approach for Multimodal Fusion

Multi-modal Learning with Missing Modality via Shared-Specific Feature Modelling

Multimodality in Meta-Learning: A Comprehensive Survey

Enhancing Multi-modal Learning: Meta-learned Cross-modal Knowledge Distillation for Handling Missing Modalities

RegBN: Batch Normalization of Multimodal Data with Regularization


SAITS: Self-Attention-based Imputation for Time Series

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


This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.

MGraphDTA: deep multiscale graph neural network for explainable drug–target binding affinity prediction

PADME: A Deep Learning-based Framework for Drug-Target Interaction Prediction

A deep learning method for drug-target affinity prediction based on sequence interaction information mining


Official Pytorch implementation of CutMix regularizer

CutMix: Regularization Strategy to Train Strong Classifiers with Localizable Features

Measuring Robustness to Natural Distribution Shifts in Image Classification

A U-Net Based Discriminator for Generative Adversarial Networks

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

On Feature Normalization and Data Augmentation

A Survey of Deep Learning for Scientific Discovery

KeepAugment: A Simple Information-Preserving Data Augmentation Approach

PixMatch: Unsupervised Domain Adaptation via Pixelwise Consistency Training

Rethinking the Pruning Criteria for Convolutional Neural Network

LaserMix for Semi-Supervised LiDAR Semantic Segmentation


An Implementation of Poptrie IP Routing Table Lookup Algorithm

Fast Longest Prefix Matching by Exploiting SIMD Instructions

Surgical DDoS Filtering With Fast LPM


利用bert预训练的中文模型进行文本分类  数据集中文情感分析语料chnsenticorp

Attention Is All You Need

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

Semi-supervised Sequence Learning

NEZHA: Neural Contextualized Representation for Chinese Language Understanding

A Fine-grained Interpretability Evaluation Benchmark for Neural NLP

WeLM: A Well-Read Pre-trained Language Model for Chinese

SeqGPT: An Out-of-the-box Large Language Model for Open Domain Sequence Understanding

ERNIE-Tiny : A Progressive Distillation Framework for Pretrained Transformer Compression

Exploiting Word Semantics to Enrich Character Representations of Chinese Pre-trained Models

Evaluation on ChatGPT for Chinese Language Understanding


Zero-Resource Knowledge-Grounded Dialogue Generation

Learning to Express in Knowledge-Grounded Conversation

Contextual Knowledge Learning For Dialogue Generation


Codes and Data for Scaling Relationship on Learning Mathematical Reasoning with Large Language Models

How Abilities in Large Language Models are Affected by Supervised Fine-tuning Data Composition

Query and Response Augmentation Cannot Help Out-of-domain Math Reasoning Generalization


Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ

Luciferase Expressing Preclinical Model Systems Representing the Different Molecular Subtypes of Colorectal Cancer

Differential CMS-Related Expression of Cell Surface Carbonic Anhydrases IX and XII in Colorectal Cancer Models—Implications for Therapy

International journal of molecular sciences


Stochastic Weight Averaging in PyTorch

Averaging Weights Leads to Wider Optima and Better Generalization

A Simple Baseline for Bayesian Uncertainty in Deep Learning

Pitfalls of In-Domain Uncertainty Estimation and Ensembling in Deep Learning

SWALP : Stochastic Weight Averaging in Low-Precision Training

Learning Neural Network Subspaces


Pytorch implementation of Sentiment Classification in Improved Semantic Representations From Tree-Structured Long Short-Term Memory Networks

Calibrating Deep Neural Networks using Focal Loss

Tell Me Why You Feel That Way: Processing Compositional Dependency for Tree-LSTM Aspect Sentiment Triplet Extraction (TASTE)

Leveraging Recursive Processing for Neural-Symbolic Affect-Target Associations

International Joint Conference on Neural Network


This toolkit consists of implementations of various graph-based semi-supervised learning (SSL) algorithms. Currently, three algorithms are implemented: Gaussian Random Fields (GRF), Adsorption, and Modified Adsorption (MAD). Junto also contains Hadoop-based implementations of these three algorithms.

Graph-based Semi-supervised Learning: A Comprehensive Review

Learning a Part-of-Speech Tagger from Two Hours of Annotation

North American Chapter of the Association for Computational Linguistics

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

Improving Statistical Machine Translation with a Multilingual Paraphrase Database

Empirical Methods in Natural Language Processing

Microblog Entity Linking by Leveraging Extra Posts

Bootstrapping via Graph Propagation

Meeting of the Association for Computational Linguistics

Microblog Emotion Classification by Computing Similarity in Text, Time, and Space

International Conference on Computational Linguistics

Minimally Supervised Classification to Semantic Categories using Automatically Acquired Symmetric Patterns

Semi-Supervised Lexicon Learning for Wide-Coverage Semantic Parsing

Learning to Route with Sparse Trajectory Sets---Extended Version


An attempt at replicating the Matching Networks for One Shot Learning in Tensorflow - Paper URL: https://arxiv.org/pdf/1606.04080.pdf

Matching Networks for One Shot Learning

Discriminative k-shot learning using probabilistic models

Learning from Few Samples: A Survey


AirSim is a simulator for drones, cars and more, built on Unreal Engine. We expand it with new implementations and sensor modalities.

AirSim: High-Fidelity Visual and Physical Simulation for Autonomous Vehicles

Physical LiDAR Simulation in Real-Time Engine

Cosys-AirSim: A Real-Time Simulation Framework Expanded for Complex Industrial Applications


Machine learning methods for astrophysics (photometric redshift and PDF estimation, star/galaxy classification etc.)

ANNz2: Photometric Redshift and Probability Distribution Function Estimation using Machine Learning

Publications of the Astronomical Society of the Pacific

Redshift distributions of galaxies in the Dark Energy Survey Science Verification shear catalogue and implications for weak lensing

Evaluation of probabilistic photometric redshift estimation approaches for The Rubin Observatory Legacy Survey of Space and Time (LSST)

Monthly Notices of the Royal Astronomical Society

Photometric redshifts for the Kilo-Degree Survey. Machine-learning analysis with artificial neural networks

Morpho-z: improving photometric redshifts with galaxy morphology

Statistical analysis of probability density functions for photometric redshifts through the KiDS-ESO-DR3 galaxies

The PAU Survey: narrow-band photometric redshifts using Gaussian processes

Degradation analysis in the estimation of photometric redshifts from non-representative training sets

The environment of QSO triplets at 1 ≲ z ≲ 1.5

Measuring photometric redshifts for high-redshift radio source surveys


Contrastive Self-supervised Sequential Recommendation with Robust Augmentation

Mutual Wasserstein Discrepancy Minimization for Sequential Recommendation


An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies

The mutational landscape of a prion-like domain

DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies

The genetic landscape for amyloid beta fibril nucleation accurately discriminates familial Alzheimer’s disease mutations

Mutations primarily alter the inclusion of alternatively spliced exons

The energetic and allosteric landscape for KRAS inhibition

An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation

Fitness landscape of a dynamic RNA structure


Tor anonymity network for SGX

SoK: A Systematic Review of TEE Usage for Developing Trusted Applications

Proceedings of the 18th International Conference on Availability, Reliability and Security

No Forking Way: Detecting Cloning Attacks on Intel SGX Applications

STELLA: Sparse Taint Analysis for Enclave Leakage Detection


Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals

Chromosome-level phased genome assembly of “Antonovka” identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1

Overnight Corticosterone and Gene Expression in Mouse Hippocampus: Time Course during Resting Period

The Chromosomal Distribution of Sex-Biased MicroRNAs in Drosophila is Nonadaptive

The Evidential Statistics of Genetic Assembly: Bootstrapping a Reference Sequence

Clonal composition and differentiation stage of human CD30+ B cells in reactive lymph nodes


Lane detection with PaddlePaddle. PPLanedet contains many SOTA methods, e.g. CondLaneNet, SCNN, RESA, RTFormer,UFLD

Spatial As Deep: Spatial CNN for Traffic Scene Understanding

Ultra Fast Structure-aware Deep Lane Detection

CondLaneNet: a Top-to-down Lane Detection Framework Based on Conditional Convolution

RESA: Recurrent Feature-Shift Aggregator for Lane Detection

CLRNet: Cross Layer Refinement Network for Lane Detection

End-to-End Lane detection with One-to-Several Transformer


Open-source stronger baseline for unsupervised or domain adaptive object re-ID.

Performance Measures and a Data Set for Multi-Target, Multi-Camera Tracking

Person Transfer GAN to Bridge Domain Gap for Person Re-Identification

Group-aware Label Transfer for Domain Adaptive Person Re-identification

Exploiting Sample Uncertainty for Domain Adaptive Person Re-Identification

Dynamic Gradient Reactivation for Backward Compatible Person Re-identification


[ICLR'21] FedBN: Federated Learning on Non-IID Features via Local Batch Normalization

FedLab: A Flexible Federated Learning Framework

Efficient Split-Mix Federated Learning for On-Demand and In-Situ Customization

FedWon: Triumphing Multi-domain Federated Learning Without Normalization

FedER: Federated Learning through Experience Replay and Privacy-Preserving Data Synthesis


Breaking the Softmax Bottleneck: A High-Rank RNN Language Model

FRAGE: Frequency-Agnostic Word Representation

Understanding and Improving Knowledge Distillation

Sigsoftmax: Reanalysis of the Softmax Bottleneck

Direct Output Connection for a High-Rank Language Model

Target Conditioned Sampling: Optimizing Data Selection for Multilingual Neural Machine Translation

Revisiting Representation Degeneration Problem in Language Modeling

An Empirical Study of Building a Strong Baseline for Constituency Parsing

PROCEEDINGS OF THE 56TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS, VOL 2

Contextual Temperature for Language Modeling

Cross Entropy of Neural Language Models at Infinity—A New Bound of the Entropy Rate


Meteor Automatic Translation Evaluation System

Enhancing AMR-to-Text Generation with Dual Graph Representations

Unsupervised Multimodal Neural Machine Translation with Pseudo Visual Pivoting

VALHALLA: Visual Hallucination for Machine Translation

Towards User-Driven Neural Machine Translation

Neural machine translation of literary texts from English to Slovene


an AI algorithm for detecting trash in geolocated images

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

A Survey on Waste Detection and Classification Using Deep Learning

SWDet: Anchor-Based Object Detector for Solid Waste Detection in Aerial Images

IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing


A steganalysis tool for detecting LSB steganography in images

StegExpose - A Tool for Detecting LSB Steganography

EvilModel 2.0: Bringing Neural Network Models into Malware Attacks

Multitask Identity-Aware Image Steganography via Minimax Optimization

An Efficient Light-weight LSB steganography with Deep learning Steganalysis

MalModel: Hiding Malicious Payload in Mobile Deep Learning Models with Black-box Backdoor Attack

Cover-aware Steganalysis


Large Deformation Diffeomorphic Image Registration with Laplacian Pyramid Networks

Conditional Deformable Image Registration with Convolutional Neural Network

ORRN: An ODE-based Recursive Registration Network for Deformable Respiratory Motion Estimation with Lung 4DCT Images

Spatially Covariant Image Registration with Text Prompts

: Approximate Diffeomorphisms via Gradient Inverse Consistency


Going beyond BEDMAP2 using a super resolution deep neural network. Also a convenient flat file data repository for high resolution bed elevation datasets around Antarctica.

DeepBedMap: Using a deep neural network to better resolve the bed topography of Antarctica

EGU General Assembly Conference Abstracts


Clermont PCR method In-Silico

Decreasing prevalence of contamination with extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) in retail chicken meat in the Netherlands

Prevalence and Genomic Characteristics of mcr-Positive Escherichia coli Strains Isolated from Humans, Pigs, and Foods in China

Whole-Genome Characterisation of ESBL-Producing E. coli Isolated from Drinking Water and Dog Faeces from Rural Andean Households in Peru


Detect and align similar passages

Language Resources for Historical Newspapers: the Impresso Collection

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

Studying the History of the Arabic Language: Language Technology and a Large-Scale Historical Corpus

Readers' engagement through digital social reading on Twitter: the TwLetteratura case study

Algorithmic Analysis of Medieval Arabic Biographical Collections

Shamela: A Large-Scale Historical Arabic Corpus

Tracking Textual Similarities in Neo-Latin Drama Networks

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION

impresso Text Reuse at Scale. An interface for the exploration of text reuse data in semantically enriched historical newspapers


A Tensorflow implementation of Collaborative Metric Learning (CML)

Collaborative Metric Learning

Sequential Recommendation via Stochastic Self-Attention

Sampling-Decomposable Generative Adversarial Recommender

Topology Distillation for Recommender System

Bidirectional Distillation for Top-K Recommender System

Improving Collaborative Metric Learning with Efficient Negative Sampling

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

Loss Aversion in Recommender Systems: Utilizing Negative User Preference to Improve Recommendation Quality

Unbiased Knowledge Distillation for Recommendation

Rethinking Collaborative Metric Learning: Toward an Efficient Alternative Without Negative Sampling

IEEE transactions on pattern analysis and machine intelligence

The Minority Matters: A Diversity-Promoting Collaborative Metric Learning Algorithm


DCT (discrete cosine transform) functions for pytorch

Viewmaker Networks: Learning Views for Unsupervised Representation Learning

Language Through a Prism: A Spectral Approach for Multiscale Language Representations

Frequency Domain-based Dataset Distillation

Automatic Differentiation for Inverse Problems in X-ray Imaging and Microscopy

Separable Layers Enable Structured Efficient Linear Substitutions


Neural macine translation soft alignment visualisations for web and command line

Paying Attention to Multi-Word Expressions in Neural Machine Translation

Debugging Neural Machine Translations

Hybrid Machine Translation by Combining Output from Multiple Machine Translation Systems

Debugging Translations of Transformer-based Neural Machine Translation Systems


The Electricity Transformer dataset is collected to support the further investigation on the long sequence forecasting problem.

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

Are Transformers Effective for Time Series Forecasting?

A Time Series is Worth 64 Words: Long-term Forecasting with Transformers

CoST: Contrastive Learning of Disentangled Seasonal-Trend Representations for Time Series Forecasting

SCINet: Time Series Modeling and Forecasting with Sample Convolution and Interaction

SAITS: Self-Attention-based Imputation for Time Series

ETSformer: Exponential Smoothing Transformers for Time-series Forecasting

Triformer: Triangular, Variable-Specific Attentions for Long Sequence Multivariate Time Series Forecasting

TCCT: Tightly-coupled convolutional transformer on time series forecasting

TSMixer: Lightweight MLP-Mixer Model for Multivariate Time Series Forecasting

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


Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription

Genetic Dissection of the RNA Polymerase II Transcription Cycle

Identification and prediction of developmental enhancers in sea urchin embryos

Evolution of promoter-proximal pausing enabled a new layer of transcription control

Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis


Code for  "PPDM: Parallel Point Detection and Matching for Real-time Human-Object Interaction Detection".

QPIC: Query-Based Pairwise Human-Object Interaction Detection with Image-Wide Contextual Information

MSTR: Multi-Scale Transformer for End-to-End Human-Object Interaction Detection


Generic TCR-epitope recognition prediction using CNN approach on both known and novel epitopes

Can we predict T cell specificity with digital biology and machine learning?

AttnTAP: A Dual-input Framework Incorporating the Attention Mechanism for Accurately Predicting TCR-peptide Binding

Interpretable deep learning to uncover the molecular binding patterns determining TCR–epitope interactions

MATE-Pred: Multimodal Attention-based TCR-Epitope interaction Predictor

BATMAN: Improved T cell receptor cross-reactivity prediction benchmarked on a comprehensive mutational scan database

bioRxiv : the preprint server for biology


Official repository for the paper "Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval"

ProGen2: Exploring the Boundaries of Protein Language Models

Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval

RITA: a Study on Scaling Up Generative Protein Sequence Models

Accurate and Definite Mutational Effect Prediction with Lightweight Equivariant Graph Neural Networks

Ensemble Learning with Supervised Methods Based on Large-Scale Protein Language Models for Protein Mutation Effects Prediction

International journal of molecular sciences

Multi-level Protein Representation Learning for Blind Mutational Effect Prediction


EmbedRank: Unsupervised Keyphrase Extraction using Sentence Embeddings (official implementation)

Simple Unsupervised Keyphrase Extraction using Sentence Embeddings

Unsupervised Keyphrase Extraction for Web Pages

Topic Aware Contextualized Embeddings for High Quality Phrase Extraction


The Pantheon+ Analysis: SuperCal-fragilistic Cross Calibration, Retrained SALT2 Light-curve Model, and Calibration Systematic Uncertainty

The Pantheon+ analysis: Improving the redshifts and peculiar velocities of Type Ia supernovae used in cosmological analyses

The state of the dark energy equation of state circa 2023

Progress in direct measurements of the Hubble constant

Cosmic chronometers to calibrate the ladders and measure the curvature of the Universe. A model-independent study

The Dipole of the Pantheon+SH0ES Data

Investigating dark energy by electromagnetic frequency shifts

The tension in the absolute magnitude of Type Ia supernovae

Testing the cosmological principle with the Pantheon+ sample and the region-fitting method

Effects of Type Ia Supernovae Absolute Magnitude Priors on the Hubble Constant Value


Benchmark of federated learning. Dedicated to the community.

SCAFFOLD: Stochastic Controlled Averaging for Federated Learning

Personalized Federated Learning: A Meta-Learning Approach

Adaptive Federated Optimization

Measuring the Effects of Non-Identical Data Distribution for Federated Visual Classification

Clustered Federated Learning: Model-Agnostic Distributed Multi-Task Optimization under Privacy Constraints

Model-Contrastive Federated Learning

Personalized Federated Learning with Moreau Envelopes

Ditto: Fair and Robust Federated Learning Through Personalization

FedMD: Heterogenous Federated Learning via Model Distillation

Federated Learning with Personalization Layers


:package: R/haldensify: Highly Adaptive Lasso Conditional Density Estimation

Causal mediation analysis for stochastic interventions

Journal of the Royal Statistical Society Series B: Statistical Methodology

hal9001: Scalable highly adaptive lasso regression in R

Efficient nonparametric inference on the effects of stochastic interventions under two‐phase sampling, with applications to vaccine efficacy trials

Nonparametric inverse probability weighted estimators based on the highly adaptive lasso

Nonparametric causal mediation analysis for stochastic interventional (in)direct effects

Targeted Maximum Likelihood Based Estimation for Longitudinal Mediation Analysis

Causal Inference for Continuous Multiple Time Point Interventions


Stochastic Answer Networks (SAN) for Machine Reading Comprehension

ReCoRD: Bridging the Gap between Human and Machine Commonsense Reading Comprehension

Stochastic Answer Networks for Machine Reading Comprehension

Conversing by Reading: Contentful Neural Conversation with On-demand Machine Reading

Multi-task Learning with Sample Re-weighting for Machine Reading Comprehension

Stochastic Answer Networks for Natural Language Inference

Stochastic Answer Networks for SQuAD 2.0


StorageVET 2.0 is a valuation model for analysis of energy storage technologies and some other energy resources paired with storage. The tool can be used as a standalone model, or integrated with other power system models, thanks to its open-source Python framework. Download the executable environment and learn more at https://www.storagevet.com.


Clonal dynamics of haematopoiesis across the human lifespan

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

phylodyn: an R package for phylodynamic simulation and inference

Estimating effective population size changes from preferentially sampled genetic sequences

Clonality and timing of relapsing colorectal cancer metastasis revealed through whole-genome single-cell sequencing


Everything you need to create an LLM Agent—tools, prompts, frameworks, and models—all in one place.

A Survey on Large Language Model based Autonomous Agents

MetaAgents: Simulating Interactions of Human Behaviors for LLM-based Task-oriented Coordination via Collaborative Generative Agents

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


ANYstructure is the ultimate steel structure design tool for plate fields and cylinders. Weight optimization for all structures with machine learning capabilities. Calculations are based on DNV standards and rules.


Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Proteogenomic characterization of pancreatic ductal adenocarcinoma

A Curated Resource for Phosphosite-specific Signature Analysis

Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Kinome Array Profiling of Patient-Derived Pancreatic Ductal Adenocarcinoma Identifies Differentially Active Protein Tyrosine Kinases

Proteogenomics of diffuse gliomas reveal molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms

PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα

Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy

Clinically relevant glioblastoma patient-derived xenograft models to guide drug development and identify molecular signatures

Common Germline Risk Variants Impact Somatic Alterations and Clinical Features across Cancers

Rat deconvolution as knowledge miner for immune cell trafficking from toxicogenomics databases


Solving two-dimensional spin models with tensor networks (powered by PyTorch)

UvA-DARE (Digital Competing States in the t-J Model: Uniform d-Wave State versus Stripe State versus Stripe State

Differentiable Programming Tensor Networks

Faster methods for contracting infinite two-dimensional tensor networks

Simulating Chiral Spin Liquids with Projected Entangled-Pair States

Static and dynamical signatures of Dzyaloshinskii-Moriya interactions in the Heisenberg model on the kagome lattice

Field-induced Bose-Einstein condensation and supersolid in the two-dimensional Kondo necklace

Incommensurate order with translationally invariant projected entangled-pair states: Spiral states and quantum spin liquid on the anisotropic triangular lattice

variPEPS -- a versatile tensor network library for variational ground state simulations in two spatial dimensions

Variational tensor network operator

Simulating Spin Dynamics of Supersolid States in a Quantum Ising Magnet


Score-based Generative Models (Diffusion Models) for Speech Enhancement and Dereverberation

Speech Enhancement and Dereverberation With Diffusion-Based Generative Models

Speech Enhancement with Score-Based Generative Models in the Complex STFT Domain

StoRM: A Diffusion-Based Stochastic Regeneration Model for Speech Enhancement and Dereverberation

Analysing Diffusion-based Generative Approaches Versus Discriminative Approaches for Speech Restoration

Reducing the Prior Mismatch of Stochastic Differential Equations for Diffusion-based Speech Enhancement

Target Speech Extraction with Conditional Diffusion Model

Noise-aware Speech Enhancement using Diffusion Probabilistic Model

Diffusion-Based Speech Enhancement with Joint Generative and Predictive Decoders

Investigating the Design Space of Diffusion Models for Speech Enhancement

Unsupervised speech enhancement with diffusion-based generative models


A general and accurate MACs / FLOPs profiler for PyTorch models

ColBERT: Efficient and Effective Passage Search via Contextualized Late Interaction over BERT

PolyLaneNet: Lane Estimation via Deep Polynomial Regression

Not All Patches are What You Need: Expediting Vision Transformers via Token Reorganizations

Is Attention Better Than Matrix Decomposition?

LongLoRA: Efficient Fine-tuning of Long-Context Large Language Models

Multi-resolution HuBERT: Multi-resolution Speech Self-Supervised Learning with Masked Unit Prediction

Lightweight Composite Re-Ranking for Efficient Keyword Search with BERT

A Systematic Study of Knowledge Distillation for Natural Language Generation with Pseudo-Target Training

Profiling Neural Blocks and Design Spaces for Mobile Neural Architecture Search

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

PPCD-GAN: Progressive Pruning and Class-Aware Distillation for Large-Scale Conditional GANs Compression


A Pythonic API for working with OWID's data catalog.


LibSA4Py: Light-weight static analysis for extracting type hints and features

Type4Py: Practical Deep Similarity Learning-Based Type Inference for Python

Proceedings of the 44th International Conference on Software Engineering

ManyTypes4Py: A Benchmark Python Dataset for Machine Learning-based Type Inference

Cross-Domain Evaluation of a Deep Learning-Based Type Inference System


PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

CARB-ES-19 Multicenter Study of Carbapenemase-Producing Klebsiella pneumoniae and Escherichia coli From All Spanish Provinces Reveals Interregional Spread of High-Risk Clones Such as ST307/OXA-48 and ST512/KPC-3

Carbapenemase-Producing Klebsiella pneumoniae From Transplanted Patients in Brazil: Phylogeny, Resistome, Virulome and Mobile Genetic Elements Harboring blaKPC–2 or blaNDM–1

Characterization of E. coli Isolates Producing Extended Spectrum Beta-Lactamase SHV-Variants from the Food Chain in Germany

Carbapenemase-Producing Klebsiella pneumoniae in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types

Dissection of Highly Prevalent qnrS1-Carrying IncX Plasmid Types in Commensal Escherichia coli from German Food and Livestock

Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B2 products sold on the Belgian market using whole-genome sequencing


A Multilingual and Multilevel Representation Learning Toolkit for NLP

Distributed Representations of Sentences and Documents

BilBOWA: Fast Bilingual Distributed Representations without Word Alignments

UsingWord Embedding for Cross-Language Plagiarism Detection

MultiVec: a Multilingual and Multilevel Representation Learning Toolkit for NLP

CompiLIG at SemEval-2017 Task 1: Cross-Language Plagiarism Detection Methods for Semantic Textual Similarity

Bilingual Embeddings and Word Alignments for Translation Quality Estimation

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

Discovering Light Verb Constructions and their Translations from Parallel Corpora without Word Alignment

Proceedings of the 13th Workshop on Multiword Expressions (MWE 2017)


mapping functions to support openair


A suite of tools to explore protein structures with Protein Blocks :snake:

Protein flexibility in the light of structural alphabets

Extension of the classical classification of β-turns

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins

Database : the journal of biological databases and curation

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

Global analysis of VHHs framework regions with a structural alphabet

Investigation of the impact of PTMs on the protein backbone conformation

Data set of intrinsically disordered proteins analysed at a local protein conformation level


Dreem One Shot Detector

DOSED: a deep learning approach to detect multiple sleep micro-events in EEG signal

A deep learning architecture to detect events in EEG signals during sleep

AI vs Humans for the diagnosis of sleep apnea


A sybil-resilient distributed learning protocol.

Mitigating Sybils in Federated Learning Poisoning

Privacy Side Channels in Machine Learning Systems

SaFL: Sybil-aware Federated Learning with Application to Face Recognition


This is CASA eMERLIN pipeline to calibrate data from the e-MERLIN array. Please fork the repository before making any changes and read the Coding Practices page in the wiki. Please add issues with the pipeline in the issues tab.

Investigating the spectral age problem with powerful radio galaxies

Monthly notices of the Royal Astronomical Society

WISDOM project - VIII. Multiscale feedback cycles in the brightest cluster galaxy NGC 0708

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

Software and techniques for VLBI data processing and analysis

An early peak in the radio light curve of short-duration gamma-ray burst 200826A

VLBI observations of GRB 201015A, a relatively faint GRB with a hint of very high-energy gamma-ray emission

Sub-kpc radio jets in the brightest central galaxy of the cool-core galaxy cluster RXJ1720.1+2638

Radio jets in NGC 1068 with e-MERLIN and VLA: structure and morphology


LogMap: An Ontology Alignment and Alignment Repair System

Logic-based assessment of the compatibility of UMLS ontology sources

MELT - Matching EvaLuation Toolkit

Ontology mapping for semantically enabled applications

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative

Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching

Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-based Modules

Breaking-down the Ontology Alignment Task with a Lexical Index and Neural Embeddings

Prediction of adverse biological effects of chemicals using knowledge graph embeddings

Uncertainty in Automated Ontology Matching: Lessons Learned from an Empirical Experimentation

Exploring Wasserstein Distance across Concept Embeddings for Ontology Matching


Simple tools to work with the Initial Mass Function

Improving the open cluster census

S^5: Probing the Milky Way and Magellanic Clouds potentials with the 6-D map of the Orphan-Chenab stream

Population synthesis of accreting white dwarfs: rates and evolutionary pathways of H and He novae

The Radcliffe wave as the gas spine of the Orion arm

Demographics of Protoplanetary Disks: A Simulated Population of Edge-on Systems

Faint Stars in a Faint Galaxy. II. The Low-mass Stellar Initial Mass Function of the Boötes I Ultrafaint Dwarf Spheroidal Galaxy

CMZoom. IV. Incipient High-mass Star Formation throughout the Central Molecular Zone

Monoceros OB4: a new association in Gaia DR2

Monthly Notices of the Royal Astronomical Society: Letters

Clustered Formation of Massive Stars within an Ionized Rotating Disk


A comprehensive benchmark of Graph Structure Learning (NeurIPS 2023 Datasets and Benchmarks Track)

Hierarchical Graph Pooling with Structure Learning

Graph-Revised Convolutional Network

GSLB: The Graph Structure Learning Benchmark


Tree edit distance using the Zhang Shasha algorithm

Does String-Based Neural MT Learn Source Syntax?

Empirical Methods in Natural Language Processing

Generating Sentences from Disentangled Syntactic and Semantic Spaces

A Multi-Task Approach for Disentangling Syntax and Semantics in Sentence Representations

Cost-effective End-to-end Information Extraction for Semi-structured Document Images

Automated Clustering and Program Repair for Introductory Programming Assignments

Role of persistent cascades in diffusion

Leveraging Natural Supervision for Language Representation Learning and Generation

MEEL: Multi-Modal Event Evolution Learning


This Is the Moment for Probabilistic Loops

Solving Invariant Generation for Unsolvable Loops

Strong Invariants Are Hard: On the Hardness of Strongest Polynomial Invariants for (Probabilistic) Programs

Proceedings of the ACM on programming languages

(Un)Solvable Loop Analysis

Automated Sensitivity Analysis for Probabilistic Loops


SPM tools to get the best of mass univariate analyses

Simultaneous EEG-fMRI during a neurofeedback task, a brain imaging dataset for multimodal data integration

Recommendations of Choice of Head Coil and Prescan Normalize Filter Depend on Region of Interest and Task

Pros and Cons of Using the Informed Basis Set to Account for Hemodynamic Response Variability with Developmental Data

Validation of a New Coil Array Tailored for Dog Functional Magnetic Resonance Imaging Studies

Sailing in rough waters: Examining volatility of fMRI noise

Brain network changes and cognitive function after cardiac arrest

Weakened effective connectivity between salience network and default mode network during resting state in adolescent depression


Tools for visualising microbial community amplicon data

ampvis2: an R package to analyse and visualise 16S rRNA amplicon data

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

High Diversity and Functional Potential of Undescribed “Acidobacteriota” in Danish Wastewater Treatment Plants

Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome

Process conditions affect microbial diversity and activity in a haloalkaline biodesulfurization system


Data package: time series of load, wind and solar generation


Density Estimation Likelihood-Free Inference with neural density estimators and adaptive acquisition of simulations

Sequential Neural Likelihood: Fast Likelihood-free Inference with Autoregressive Flows

Fast likelihood-free cosmology with neural density estimators and active learning

SBI -- A toolkit for simulation-based inference

Benchmarking Simulation-Based Inference

Likelihood-free inference with emulator networks

Nuisance hardened data compression for fast likelihood-free inference

Simulation-based Inference of Reionization Parameters from 3D Tomographic 21 cm Light-cone Images

Solving high-dimensional parameter inference: marginal posterior densities & Moment Networks

Cosmic shear: Inference from forward models

Sum of the masses of the Milky Way and M31: A likelihood-free inference approach


A toolkit to help generate renewable energy generation time-series for energy systems analysis

Robust design of a future 100% renewable european energy supply system with hydrogen infrastructure

International journal of hydrogen energy


Snow Microwave Radiative Transfert model to compute thermal emission and backscatter from snowpack

SMRT: an active–passive microwave radiative transfer model for snow with multiple microstructure and scattering formulations (v1.0)

The Microwave Snow Grain Size: A New Concept to Predict Satellite Observations Over Snow‐Covered Regions

Forward modelling of synthetic-aperture radar (SAR) backscatter during lake ice melt conditions using the Snow Microwave Radiative Transfer (SMRT) model


custom resolver

Environmental drivers of under-ice phytoplankton bloom dynamics in the Arctic Ocean

Bloom termination of the toxic dinoflagellate Alexandrium catenella: Vertical migration behavior, sediment infiltration, and benthic cyst yield

Green Edge ice camp campaigns: understanding the processes controlling the under-ice Arctic phytoplankton spring bloom

Assessment of holographic microscopy for quantifying marine particle size and concentration

Shifts in Phytoplankton Community Structure Across an Anticyclonic Eddy Revealed From High Spectral Resolution Lidar Scattering Measurements

Characterizing coastal phytoplankton seasonal succession patterns on the West Antarctic Peninsula

Plankton Imagery Data Inform Satellite‐Based Estimates of Diatom Carbon

A Recirculating Eddy Promotes Subsurface Particle Retention in an Antarctic Biological Hotspot

Length, width, shape regularity, and chain structure: time series analysis of phytoplankton morphology from imagery

Imaging Technologies Build Capacity and Accessibility in Phytoplankton Species Identification Expertise for Research and Monitoring: Lessons Learned During the COVID-19 Pandemic


a bash pipeline for RAD sequencing

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

Signatures of selection underpinning rapid coral adaptation to the world’s warmest reefs

A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination

Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies

Zenodo (CERN European Organization for Nuclear Research)

Genetic patterns in peripheral marine populations of the fusilier fish Caesio cuning within the Kuroshio Current

Location and Species Matters: Variable Influence of the Environment on the Gene Flow of Imperiled, Native and Invasive Cottontails

Weak Genetic Isolation and Putative Phenotypic Selection in the Wild Carnation Dianthus virgineus (Caryophyllaceae)


Calculates Hydrologic Indicator stats and fundamental properties of daily streamflow for a given set of data

Regionalization for Ungauged Catchments — Lessons Learned From a Comparative Large‐Sample Study

A high-resolution streamflow and hydrological metrics dataset for ecological modeling using a regression model

Assessing Environmental Flow Targets Using Pre-Settlement Land Cover: A SWAT Modeling Application

Species-Richness Responses to Water-Withdrawal Scenarios and Minimum Flow Levels: Evaluating Presumptive Standards in the Tennessee and Cumberland River Basins

Assessing the Difference between Soil and Water Assessment Tool (SWAT) Simulated Pre-Development and Observed Developed Loading Regimes

Disentangling the effect of climatic and hydrological predictor variables on benthic macroinvertebrate distributions from predictive models


This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

PCSF: An R-package for network-based interpretation of high-throughput data

Clinical protein science in translational medicine targeting malignant melanoma

Computational Analysis of Phosphoproteomics Data in Multi‐Omics Cancer Studies

Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data

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

Functional stratification of cancer drugs through integrated network similarity


CBE Thermal Comfort Tool for ASHRAE-55

comf: An R Package for Thermal Comfort Studies


A collection of baselines for the MineRL environment/datasets & the NeurIPS 2021 MineRL competitions

The MineRL Competition on Sample Efficient Reinforcement Learning using Human Priors

Action Space Shaping in Deep Reinforcement Learning

Retrospective Analysis of the 2019 MineRL Competition on Sample Efficient Reinforcement Learning


A free audio dataset of spoken digits. An audio version of MNIST.

SMIL: Multimodal Learning with Severely Missing Modality

Scalable optical learning operator

FrugalML: How to Use ML Prediction APIs More Accurately and Cheaply

Towards Empirical Sandwich Bounds on the Rate-Distortion Function

Spike encoding techniques for IoT time-varying signals benchmarked on a neuromorphic classification task

On Lightweight Privacy-preserving Collaborative Learning for Internet of Things by Independent Random Projections

Did the Model Change? Efficiently Assessing Machine Learning API Shifts

When Noise meets Chaos: Stochastic Resonance in Neurochaos Learning

Multiplierless MP-Kernel Machine For Energy-efficient Edge Devices

A Simple Lifelong Learning Approach


The Super-Resolution for Renewable Resource Data (sup3r) software uses generative adversarial networks to create synthetic high-resolution wind and solar spatiotemporal data from coarse low-resolution inputs.

Super Resolution for Renewable Energy Resource Data With Wind From Reanalysis Data (Sup3rWind) and Application to Ukraine


Tools for processing UMI RNA-tag data

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

SCANPY: large-scale single-cell gene expression data analysis

Power analysis of single-cell RNA-sequencing experiments

A single-cell survey of Drosophila blood

Human sensorimotor organoids derived from healthy and amyotrophic lateral sclerosis stem cells form neuromuscular junctions

Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells


LCIA Formatter

Life Cycle Data Interoperability Improvements through Implementation of the Federal LCA Commons Elementary Flow List


Developer Version of the R package CAST: Caret Applications for Spatio-Temporal models

Predicting into unknown space? Estimating the area of applicability of spatial prediction models


Source code for ClimateLearn

ClimateLearn: Benchmarking Machine Learning for Weather and Climate Modeling


Code for the in-dev PrediXcan Project

webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study

Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer’s dementia


massively-parallel cosmology simulator

Strong Bound on Canonical Ultralight Axion Dark Matter from the Lyman-Alpha Forest

Modeling biased tracers at the field level

The ASTRID simulation: the evolution of Supermassive Black Holes

The ASTRID simulation: galaxy formation and reionization

An efficient and accurate hybrid method for simulating non-linear neutrino structure

Bayesian emulator optimisation for cosmology: application to the Lyman-alpha forest

Journal of Cosmology and Astroparticle Physics

An emulator for the Lyman-α forest

New limits on light dark matter - proton cross section from the cosmic large-scale structure.

An emulator for the Lyman-α forest in beyond-ΛCDM cosmologies

Inhomogeneous He ii reionization in hydrodynamic simulations


Quetzal is a modeling library designed for transport planning and traffic forecasts


Fast Linearized Coronagraph Optimizer (FALCO) in MATLAB

Fast linearized coronagraph optimizer (FALCO) I: a software toolbox for rapid coronagraphic design and wavefront correction

Space Telescopes and Instrumentation 2018: Optical, Infrared, and Millimeter Wave

Review of high-contrast imaging systems for current and future ground- and space-based telescopes I. Coronagraph design methods and optical performance metrics

High-contrast Demonstration of an Apodized Vortex Coronagraph

End-to-end numerical modeling of the Roman Space Telescope coronagraph

High contrast demonstrations of novel scalar vortex coronagraph designs at the high contrast spectroscopy testbed

Techniques and Instrumentation for Detection of Exoplanets X

Flight designs and pupil error mitigation for the bowtie shaped pupil coronagraph on the Nancy Grace Roman Space Telescope

Journal of Astronomical Telescopes, Instruments, and Systems

Laboratory demonstration of the wrapped staircase scalar vortex coronagraph

Topological designs for scalar vortex coronagraphs

Space Telescopes and Instrumentation 2022: Optical, Infrared, and Millimeter Wave

Achromatizing scalar vortex coronagraphs with radial phase mask dimples


Python Library for Automating Molecular Simulations

Generalization of Intrinsic Orbitals to Kramers-Paired Quaternion Spinors, Molecular Fragments, and Valence Virtual Spinors

Journal of chemical theory and computation

Frequency Range Selection Method for Vibrational Spectra

The journal of physical chemistry letters

Characterization of excited states in time-dependent density functional theory using localized molecular orbitals.

Enhancing ReaxFF for Molecular Dynamics Simulations of Lithium-Ion Batteries: An interactive reparameterization protocol


netZooPy is a network biology package implemented in Python.

gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit

Cell-Specific Gene Networks and Drivers in Rheumatoid Arthritis Synovial Tissues

bioRxiv : the preprint server for biology

Gene Network Analyses Identify Co-regulated Transcription Factors and BACH1 as a Key Driver in Rheumatoid Arthritis Fibroblast-like Synoviocytes


Wind Plant Integrated System Design and Engineering Model

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

Distributed Aerodynamic Control using Active Trailing-Edge Flaps for Large Wind Turbines

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

Land-based wind turbines with flexible rail transportable blades – Part II: 3D FEM design optimization of the rotor blades


Java (convolutional or fully-connected) neural network implementation with plugin for Weka. Uses dropout and rectified linear units.

A Fast Incremental Gaussian Mixture Model

Identification of Wearable Devices with Bluetooth

IEEE Transactions on Sustainable Computing

Detecting and Classifying Human Touches in a Social Robot Through Acoustic Sensing and Machine Learning

Word Embeddings-Based Uncertainty Detection in Financial Disclosures

Meeting of the Association for Computational Linguistics

Scalable and Incremental Learning of Gaussian Mixture Models


Asymptotic Improvements to Quantum Circuits via Qutrits

PROCEEDINGS OF THE 2019 46TH INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE (ISCA '19)

Resource-Efficient Quantum Computing by Breaking Abstractions

New Abstractions for Quantum Computing


Virtual Adversarial Training (VAT) implementation for PyTorch

Virtual Adversarial Training: A Regularization Method for Supervised and Semi-Supervised Learning

Unlabeled Data Improves Adversarial Robustness

Distributional Smoothing with Virtual Adversarial Training

Interpolation-Based Contrastive Learning for Few-Label Semi-Supervised Learning

Supercharging Imbalanced Data Learning With Energy-based Contrastive Representation Transfer

SLIDE: a surrogate fairness constraint to ensure fairness consistency


Assembler for raw de novo genome assembly of long uncorrected reads.

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

Hybridization dynamics and extensive introgression in the Daphnia longispina species complex: new insights from a high-quality Daphnia galeata reference genome

Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi

Chromosomal rearrangements with stable repertoires of genes and transposable elements in an invasive forest-pathogenic fungus


The source code of ISWC2020 paper "Temporal Knowledge Graph completion based on time series Gaussian embedding " and COLING2020 paper "TeRo: A Time-aware Knowledge Graph Embedding via Temporal Rotation "

Temporal Knowledge Graph Embedding Model based on Additive Time Series Decomposition

Temporal Knowledge Graph Completion using a Linear Temporal Regularizer and Multivector Embeddings

North American Chapter of the Association for Computational Linguistics

RotateQVS: Representing Temporal Information as Rotations in Quaternion Vector Space for Temporal Knowledge Graph Completion

Hyperbolic Temporal Knowledge Graph Embeddings with Relational and Time Curvatures

Few-Shot Inductive Learning on Temporal Knowledge Graphs using Concept-Aware Information

ECOLA: Enhancing Temporal Knowledge Embeddings with Contextualized Language Representations


Knowledge-Preserving Incremental Social Event Detection via Heterogeneous GNNs

Relational Prompt-based Pre-trained Language Models for Social Event
  Detection

Heterogeneous Social Event Detection via Hyperbolic Graph Representations


Read trimming tool for Illumina NGS data.

WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

Detection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA

Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains

Genomic Analysis of a Highly Virulent NDM-1-Producing Escherichia coli ST162 Infecting a Pygmy Sperm Whale (Kogia breviceps) in South America

MIG-seq is an effective method for high-throughput genotyping in wheat (Triticum spp.)

DNA research : an international journal for rapid publication of reports on genes and genomes

The complete mitochondrial genome of Cycas debaoensis revealed unexpected static evolution in gymnosperm species

Genomic Perspectives on Aeromonas salmonicida subsp. salmonicida Strain 890054 as a Model System for Pathogenicity Studies and Mitigation of Fish Infections

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution

The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in Klebsiella spp


Architecture-level Fault Injection Tool for GPU Application Resilience Evaluation

NVBitFI: Dynamic Fault Injection for GPUs

Enabling Software Resilience in GPGPU Applications via Partial Thread Protection

Characterizing a Neutron-Induced Fault Model for Deep Neural Networks

Characterizing Impacts of Storage Faults on HPC Applications: A Methodology and Insights


Do Pre-trained Models Benefit Knowledge Graph Completion? A Reliable Evaluation and a Reasonable Approach

Findings of the Association for Computational Linguistics: ACL 2022

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


Codes for papers: 1. Graph Convolutional Network for Recommendation with Low-pass Collaborative Filters (ICML). 2. Less is More: Exploring Simple and Powerful Low-pass Graph Convolutional Network for Recommendation. 3. Self-propagation Graph Neural Network for Recommendation (TKDE).

Self-Propagation Graph Neural Network for Recommendation

IEEE Transactions on Knowledge and Data Engineering

Low-Pass Graph Convolutional Network for Recommendation

THIRTY-SIXTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE / THIRTY-FOURTH CONFERENCE ON INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE / TWELVETH SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE


Lightning Fast Language Prediction

Enriching Word Vectors with Subword Information

Bag of Tricks for Efficient Text Classification

FastText.zip: Compressing text classification models

Automatic Language Identification in Texts: A Survey

The LMU Munich Unsupervised Machine Translation System for WMT19

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

Great Expectations: Unsupervised Inference of Suspense, Surprise and Salience in Storytelling


TOGA: A Neural Method for Test Oracle Generation

Proceedings of the 44th International Conference on Software Engineering

Towards More Realistic Evaluation for Neural Test Oracle Generation

Neural-Based Test Oracle Generation: A Large-Scale Evaluation and Lessons Learned

Proceedings of the 31st ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering

Revisiting and Improving Retrieval-Augmented Deep Assertion Generation


A curated list of resources relevant to doing Biomedical Information Extraction (including BioNLP)

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation

A framework for information extraction from tables in biomedical literature

International Journal on Document Analysis and Recognition (IJDAR)

The Colorado Richly Annotated Full Text (CRAFT) Corpus: Multi-Model Annotation in the Biomedical Domain

Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text

Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine.


Auxiliary Classifier Generative Adversarial Networks in Keras

Conditional Image Synthesis With Auxiliary Classifier GANs

A Bayesian Data Augmentation Approach for Learning Deep Models

Fast-converging Conditional Generative Adversarial Networks for Image Synthesis


SILO Language Models: Isolating Legal Risk In a Nonparametric Datastore

Infini-gram: Scaling Unbounded n-gram Language Models to a Trillion
  Tokens

DataComp-LM: In search of the next generation of training sets for
  language models

Time is Encoded in the Weights of Finetuned Language Models

MINT-1T: Scaling Open-Source Multimodal Data by 10x: A Multimodal
  Dataset with One Trillion Tokens

Scaling Retrieval-Based Language Models with a Trillion-Token Datastore


My fork of Alex Krizhevsky's cuda-convnet from 2013 where I added dropout, among other features.

Improving neural networks by preventing co-adaptation of feature detectors

Controlling Over-generalization and its Effect on Adversarial Examples Generation and Detection

Towards Dependable Deep Convolutional Neural Networks (CNNs) with Out-distribution Learning

Out-distribution training confers robustness to deep neural networks


PyCrown - Fast raster-based individual tree segmentation for LiDAR data


Using graph network to solve PDEs

Neural Operator: Learning Maps Between Function Spaces

Neural Operator: Graph Kernel Network for Partial Differential Equations

Multipole Graph Neural Operator for Parametric Partial Differential Equations

Physics-Informed Deep Neural Operator Networks

Nonlocal kernel network (NKN): A stable and resolution-independent deep neural network

Approximate Bayesian Neural Operators: Uncertainty Quantification for Parametric PDEs

Neural Operator: Is data all you need to model the world? An insight into the impact of Physics Informed Machine Learning


Code for the Gaze360: Physically Unconstrained Gaze Estimation in the Wild Dataset

An Objective System for Quantitative Assessment of Television Viewing Among Children (Family Level Assessment of Screen Use in the Home-Television): System Development Study


Graph Transformer Architecture. Source code for "A Generalization of Transformer Networks to Graphs", DLG-AAAI'21.

Equivariant and Stable Positional Encoding for More Powerful Graph Neural Networks

Privacy-Enhancing Digital Contact Tracing with Machine Learning for Pandemic Response: A Comprehensive Review

Learning Flexible Body Collision Dynamics with Hierarchical Contact Mesh Transformer

Gradformer: Graph Transformer with Exponential Decay


Code for paper "Hierarchical Text Classification with Reinforced Label Assignment" EMNLP 2019

Empirical Methods in Natural Language Processing

Hierarchical Interdisciplinary Topic Detection Model for Research Proposal Classification

Interdisciplinary Fairness in Imbalanced Research Proposal Topic Inference: A Hierarchical Transformer-based Method with Selective Interpolation


Source code for ACL 2019 paper "GEAR: Graph-based Evidence Aggregating and Reasoning for Fact Verification"

Natural Language Inference with Self-Attention for Veracity Assessment of Pandemic Claims

Graph Sequential Network for Reasoning over Sequences

GLAF: Global-to-Local Aggregation and Fission Network for Semantic Level Fact Verification

International Conference on Computational Linguistics


face-cluster-by-infomap 一种无监督人脸聚类方法，在开源数据集上取得SOTA效果

Linkage Based Face Clustering via Graph Convolution Network

Learning to Cluster Faces on an Affinity Graph

Learning to Cluster Faces via Confidence and Connectivity Estimation


Helper scripts for processing and visualization of phylogenetics datasets

Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

Phylogenomics Yields New Insight Into Relationships Within Vernonieae (Asteraceae)

The Deep Evolutionary Relationships of the Morphologically Heterogeneous Nolinoideae (Asparagaceae) Revealed by Transcriptome Data

Species Delimitation and Conservation in Taxonomically Challenging Lineages: The Case of Two Clades of Capurodendron (Sapotaceae) in Madagascar

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

Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis

Resolving the phylogeny of Thladiantha (Cucurbitaceae) with three different target capture pipelines

Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics


8th place solution to Zindi's FarmPin Crop Detection Challenge

mixup: Beyond Empirical Risk Minimization

A disciplined approach to neural network hyper-parameters: Part 1 -- learning rate, batch size, momentum, and weight decay

Tile2Vec: Unsupervised representation learning for spatially distributed data


This repository provides train＆test code, dataset, det.&rec. annotation, evaluation script, annotation tool, and ranking.

Shape Robust Text Detection with Progressive Scale Expansion Network

Empowering Things With Intelligence: A Survey of the Progress, Challenges, and Opportunities in Artificial Intelligence of Things

Scene Text Detection and Recognition: The Deep Learning Era

Curved scene text detection via transverse and longitudinal sequence connection

Detecting Curve Text in the Wild: New Dataset and New Solution

ICDAR2019 Robust Reading Challenge on Arbitrary-Shaped Text (RRC-ArT)

Text Recognition in the Wild: A Survey

Scene Text Detection in Natural Images: A Review


SOTOPIA: Interactive Evaluation for Social Intelligence in Language Agents

LLM-Deliberation: Evaluating LLMs with Interactive Multi-Agent Negotiation Games

How Well Can LLMs Negotiate? NegotiationArena Platform and Analysis


R Interface to the Spectra Library for Large Scale Eigenvalue and SVD Problems

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

Natural variation in C. elegans arsenic toxicity is explained by differences in branched chain amino acid metabolism

The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits

Natural variation in fecundity is correlated with species-wide levels of divergence in Caenorhabditis elegans

sparsegl: An R Package for Estimating Sparse Group Lasso


Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

Pan-Cancer Integrative Histology-Genomic Analysis via Interpretable Multimodal Deep Learning

Deep Biological Pathway Informed Pathology-Genomic Multimodal Survival Prediction

Cross-modality Attention-based Multimodal Fusion for Non-small Cell Lung Cancer (NSCLC) Patient Survival Prediction


On Evaluation of Embodied Navigation Agents

iGibson 1.0: A Simulation Environment for Interactive Tasks in Large Realistic Scenes

Robot Navigation in Constrained Pedestrian Environments using Reinforcement Learning

Principles and Guidelines for Evaluating Social Robot Navigation Algorithms


RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.

Expression dynamics of repetitive DNA in early human embryonic development

easyCLIP analysis of RNA-protein interactions incorporating absolute quantification

SETDB1 fuels the lung cancer phenotype by modulating epigenome, 3D genome organization and chromatin mechanical properties

A versatile mouse model of epitope-tagged histone H3.3 to study epigenome dynamics


Tensorflow implementation of Ordinary Differential Equation Solvers with full GPU support

Neural Ordinary Differential Equations

Universal Differential Equations for Scientific Machine Learning

Data-driven reduced order modeling of environmental hydrodynamics using deep autoencoders and neural ODEs

A two stages Deep Learning Architecture for Model Reduction of Parametric Time-Dependent Problems


Bridging deep learning and logical reasoning using a differentiable satisfiability solver.

SATNet: Bridging deep learning and logical reasoning using a differentiable satisfiability solver

Techniques for Symbol Grounding with SATNet

Assessing SATNet's Ability to Solve the Symbol Grounding Problem

Refining neural network predictions using background knowledge

Learning to Solve Constraint Satisfaction Problems with Recurrent Transformer


mmCIF-based extension dictionary for computed structure models

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

The impact of AlphaFold Protein Structure Database on the fields of life sciences

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models


Official Pytorch implementation of GANILLA

GANILLA: Generative Adversarial Networks for Image to Illustration Translation

MISS GAN: A Multi-IlluStrator style generative adversarial network for image to illustration translation

Generative Adversarial Networks for photo to Hayao Miyazaki style cartoons


A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

Multi-state design of flexible proteins predicts sequences optimal for conformational change

Prediction of Contact Residues in Anti-HIV Neutralizing Antibody by Deep Learning

Conserved and divergent chaperoning effects of Hsp60/10 chaperonins on protein folding landscapes

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


Transfusion: Understanding Transfer Learning for Medical Imaging

SVCCA: Singular Vector Canonical Correlation Analysis for Deep Learning Dynamics and Interpretability

Insights on representational similarity in neural networks with canonical correlation

A Survey of Deep Learning for Scientific Discovery

Ecco: An Open Source Library for the Explainability of Transformer Language Models

Explainable Clinical Decision Support from Text

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

Selectivity considered harmful: evaluating the causal impact of class selectivity in DNNs

Syntactic Perturbations Reveal Representational Correlates of Hierarchical Phrase Structure in Pretrained Language Models

Embracing Federated Learning: Enabling Weak Client Participation via Partial Model Training

Revisiting Hidden Representations in Transfer Learning for Medical Imaging


Script for parsing SAM/BAM files for coverage statistics

Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater

“Frozen evolution” of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence

Bacteriophages Roam the Wheat Phyllosphere

Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

Direct Nanopore Sequencing of Human Cytomegalovirus Genomes from High-Viral-Load Clinical Samples

Evolutionary stasis of an RNA virus indicates arbovirus re-emergence triggered by accidental release


Riemannian geometry and automatic differentiation for optimization problems of quantum physics and quantum technologies

QGOpt: Riemannian optimization for quantum technologies

Classification of the Fashion-MNIST Dataset on a Quantum Computer


GIZA++ is a statistical machine translation toolkit that is used to train IBM Models 1-5 and an HMM word alignment model. This package also contains the source for the mkcls tool which generates the word classes necessary for training some of the alignment models.

Curriculum Pre-training for End-to-End Speech Translation

Saliency-driven Word Alignment Interpretation for Neural Machine Translation

Accurate Word Alignment Induction from Neural Machine Translation

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

International Conference on Information and Knowledge Management

Controllable data synthesis method for grammatical error correction

Recursive Neural Network Based Preordering for English-to-Japanese Machine Translation

Zero-Shot Translation Quality Estimation with Explicit Cross-Lingual Patterns

Constraint Translation Candidates: A Bridge between Neural Query Translation and Cross-lingual Information Retrieval

Alignment-free Cross-lingual Semantic Role Labeling

Construction of an Evaluation Corpus for Grammatical Error Correction for Learners of Japanese as a Second Language

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


Graph Clustering Merger

MAGUS: Multiple sequence Alignment using Graph clUStering

Recursive MAGUS: scalable and accurate multiple sequence alignment

UPP2: fast and accurate alignment of datasets with fragmentary sequences

The Maximum Weight Trace Alignment Merging Problem

HMMerge: an ensemble method for multiple sequence alignment

Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem

IEEE/ACM transactions on computational biology and bioinformatics


Continual reinforcement learning baselines: experiment specifications, implementation of existing methods, and common metrics. Easily extensible to new methods.

CORA: Benchmarks, Baselines, and Metrics as a Platform for Continual Reinforcement Learning Agents

Continual Learning In Environments With Polynomial Mixing Times

Self-Activating Neural Ensembles for Continual Reinforcement Learning

Evaluating Continual Learning on a Home Robot


OpenFOAM Foundation development repository

Basic verification of a numerical framework applied to a morphology adaptive multifield two‐fluid model considering bubble motions

International Journal for Numerical Methods in Fluids

Building Retrofitting through Coupling of Building Energy Simulation-Optimization Tool with CFD and Daylight Programs

multiRegionFoam -- A Unified Multiphysics Framework for Multi-Region Coupled Continuum-Physical Problems


Efficient and general syntactical decoding for Large Language Models

Synchromesh: Reliable code generation from pre-trained language models

Grammar-Constrained Decoding for Structured NLP Tasks without Finetuning

SynCode: LLM Generation with Grammar Augmentation


Produce elegant shaded error bars in MATLAB

Lipid peroxidation regulates long-range wound detection through 5-lipoxygenase in zebrafish.

Flagellar energetics from high-resolution imaging of beating patterns in tethered mouse sperm

A Recursive Markov Boundary-Based Approach to Causal Structure Learning

Post-explant profiling of subcellular-scale carbon fiber intracortical electrodes and surrounding neurons enables modeling of recorded electrophysiology

The Panopticon—Assessing the Effect of Starvation on Prolonged Fly Activity and Place Preference

Sub-picoliter Traceability of Microdroplet Gravimetry and Microscopy


High Availability Shared Pipeline Engine

The Breakthrough Listen Search for Intelligent Life: A Wideband Data Recorder System for the Robert C. Byrd Green Bank Telescope

Publications of the Astronomical Society of the Pacific

Bifrost: a Python/C++ Framework for High-Throughput Stream Processing in Astronomy

Spectrometers and Polyphase Filterbanks in Radio Astronomy

The Breakthrough Listen search for intelligent life: Wide-bandwidth digital instrumentation for the CSIRO Parkes 64-m telescope

Publications of the Astronomical Society of Australia

The design and implementation of a ROACH2+GPU based correlator on the Tianlai dish array

Wideband Array Signal Processing with Real-Time Adaptive Interference Mitigation


Lexicons for the Multilingual UCREL Semantic Analysis System

Lexical Coverage Evaluation of Large-scale Multilingual Semantic Lexicons for Twelve Languages

Tagging Named Entities in 19th Century and Modern Finnish Newspaper Material with a Finnish Semantic Tagger

Nordic Conference of Computational Linguistics

Creating and Validating Multilingual Semantic Representations for Six Languages: Expert versus Non-Expert Crowds

Proceedings of the 1st Workshop on Sense, Concept and Entity
          Representations and their Applications

FiST – towards a free Semantic Tagger of modern standard Finnish

Proceedings of the Fifth International Workshop on Computational Linguistics for Uralic Languages


Documentation for dynamic machine learning systems.

Datasheets for Datasets

Model Cards for Model Reporting

Proceedings of the Conference on Fairness, Accountability, and Transparency

Reward Reports for Reinforcement Learning

Choices, Risks, and Reward Reports: Charting Public Policy for Reinforcement Learning Systems


[DEPRECATED] Command line tools for recording, replaying and mirroring touchscreen events for Android

Prompting Is All You Need: Automated Android Bug Replay with Large Language Models

Translating Video Recordings of Mobile App Usages into Replayable Scenarios

International Conference on Software Engineering

GIFdroid: Automated Replay of Visual Bug Reports for Android Apps

Translating Video Recordings of Complex Mobile App UI Gestures into Replayable Scenarios

Visual Identification of Mobile App GUI Elements for Automated Robotic Testing

Computational intelligence and neuroscience

Learning-Replay Based Automated Robotic Testing for Mobile App

Towards Efficient Record and Replay: A Case Study in WeChat


Alluvial diagrams

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life.

A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury

Reconfiguration of Cortical Networks in MDD Uncovered by Multiscale Community Detection with fMRI

Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells

Concordance of Immunohistochemistry-Based and Gene Expression-Based Subtyping in Breast Cancer

Comparison of metadata with relevance for bibliometrics between Microsoft Academic Graph and OpenAlex until 2020

Computational identification of repurposed drugs against viruses causing epidemics and pandemics via drug-target network analysis

Scores of a specific field-normalized indicator calculated with different approaches of field-categorization: Are the scores different or similar?

New insights into the epidemiology of Listeria monocytogenes – A cross-sectoral retrospective genomic analysis in the Netherlands (2010–2020)

Using visualisation methods to analyse referral networks within community health care among patients aged 65 years and over


Exoplanet Planet Simulator (PlaSim extended for different planet types (including tidally-locked) and evolution on geological timescales--glaciers and carbon cycle)

Haze Optical Depth in Exoplanet Atmospheres Varies with Rotation Rate: Implications for Observations

A Large Repository of 3D Climate Model Outputs for Community Analysis and Postprocessing

Water Vapour Transit Ambiguities for Habitable M-Earths


Hazel v2.0: synthesis and inversion of Stokes profiles caused by the joint action of atomic level polarization and the Hanle and Zeeman effects

Detecting Magnetic Fields in Exoplanets with Spectropolarimetry of the Helium Line at 1083 nm

Determining the dynamics and magnetic fields in He I 10830 Å during a solar filament eruption

Three-dimensional magnetic field structure of a flux-emerging region in the solar atmosphere

Magnetic field fluctuations in the shocked umbral chromosphere


Neural Code Comprehension: A Learnable Representation of Code Semantics

Convolutional Neural Networks over Tree Structures for Programming Language Processing

A Literature Study of Embeddings on Source Code

How could Neural Networks understand Programs?


Hosts the Multiface dataset, which is a multi-view dataset of multiple identities performing a sequence of facial expressions.

Deep Appearance Models for Face Rendering

Mixture of Volumetric Primitives for Efficient Neural Rendering

MeshTalk: 3D Face Animation from Speech using Cross-Modality Disentanglement

Pixel Codec Avatars

Learning Compositional Radiance Fields of Dynamic Human Heads

Multiface: A Dataset for Neural Face Rendering


A Python library for spectral modelling and RADEX

The distribution and origin of C2H in NGC 253 from ALCHEMI

PROPERTIES OF THE MOLECULAR CORES OF LOW LUMINOSITY OBJECTS

The First Spatially-resolved Detection of ^13CN in a Protoplanetary
  Disk and Evidence for Complex Carbon Isotope Fractionation


INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search

Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology

Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS

Screening of Bacteriocinogenic Lactic Acid Bacteria and Their Characterization as Potential Probiotics

Persistent contamination of raw milk by Campylobacter jejuni ST-883

Longitudinal Study of Shiga Toxin-Producing Escherichia coli and Campylobacter jejuni on Finnish Dairy Farms and in Raw Milk

Advanced Research Infrastructure for Experimentation in genomicS (ARIES): a lustrum of Galaxy experience

Streptococcus canis Are a Single Population Infecting Multiple Animal Hosts Despite the Diversity of the Universally Present M-Like Protein SCM

Evidence for the Dissemination to Humans of Methicillin-Resistant Staphylococcus aureus ST398 through the Pork Production Chain: A Study in a Portuguese Slaughterhouse

Identification of polysaccharide capsules among extensively drug-resistant genitourinary Haemophilus parainfluenzae isolates

Genome–scale approach to study the genetic relatedness among Brucella melitensis strains


An R package to hold and facilitate interaction with natural earth map data :earth_africa:

CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast

Indian genetic heritage in Southeast Asian populations

Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites

Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago

Adulis and the transshipment of baboons during classical antiquity

The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients.

Genetic Diversity and Structure of a Diverse Population of Picea sitchensis Using Genotyping-by-Sequencing


A library implementing different string similarity and distance measures using Python.

Inspo: Writing Stories with a Flock of AIs and Humans

Bidirectional Interactions With Humpback Whale Singer Using Concrete Sound Elements


The project is a platform of zero learning with a library of games.

Deep Reinforcement Learning

Deep Learning for General Game Playing with Ludii and Polygames

AI and Wargaming

Efficient Reasoning in Regular Boardgames


Multiple-Instance Support Vector Machines

Attention-based Deep Multiple Instance Learning

Extracting microRNA-gene relations from biomedical literature using distant supervision

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data

Pain Intensity Estimation from Mobile Video Using 2D and 3D Facial Keypoints

Theory and Algorithms for Shapelet-Based Multiple-Instance Learning

pyLEMMINGS: Large Margin Multiple Instance Classification and Ranking for Bioinformatics Applications


Data and models for the SciFact verification task.

DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter

BEIR: A Heterogenous Benchmark for Zero-shot Evaluation of Information Retrieval Models

Fact or Fiction: Verifying Scientific Claims

Generating Scientific Claims for Zero-Shot Scientific Fact Checking

Abstract, Rationale, Stance: A Joint Model for Scientific Claim Verification

Cocktail: A Comprehensive Information Retrieval Benchmark with
  LLM-Generated Documents Integration


ECMAScript parsing infrastructure for multipurpose analysis

Visualizing JIT Compiler Graphs

Measurement of the Usage of Web Clips in Underground Economy

Visualizing The Intermediate Representation of Just-in-Time Compilers


GHEtool is an open-source tool for borefield sizing and ground temperature evolution plotting.

Validated combined first and last year borefield sizing methodology.

Building Simulation Conference proceedings

GHEtool: An open-source tool for borefield sizing in Python


generation of Sobol low-discrepancy sequence (LDS) for the Julia language

Surrogate Assisted Methods for the Parameterisation of Agent-Based Models

A Quasi–Monte Carlo Method With Krylov Linear Solvers for Multigroup Neutron Transport Simulations

Measure transport with kernel mean embeddings

Deterministic and quasi-random sampling of optimized Gaussian mixture distributions for vibronic Monte Carlo

Density estimation in RKHS with application to Korobov spaces in high dimensions

Global Sensitivity Analysis Applied to Train Traffic Rescheduling: A Comparative Study


A Python package for modelling the Australian National Electricity Market dispatch procedure


A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.

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

Twelve years of SAMtools and BCFtools

From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Nextflow enables reproducible computational workflows

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

BCFtools/csq: haplotype-aware variant consequences

WhatsHap: fast and accurate read-based phasing

Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates


Metabolome Annotation Workflow

MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry

Toward a Framework for Integrative, FAIR, and Reproducible Management of Data on the Dynamic Balance of Microbial Communities

Untargeted metabolomics to expand the chemical space of the marine diatom Skeletonema marinoi

Analysis of Metabolomics and Transcriptomics Data to Assess Interactions in Microalgal Co-culture ofSkeletonema marinoiandPrymnesium parvum

Implementation of FAIR Practices in Computational Metabolomics Workflows - A Case Study


Keyphrase Generation

Convolutional Sequence to Sequence Learning

Deep Keyphrase Generation

Simple Recurrent Units for Highly Parallelizable Recurrence

One Size Does Not Fit All: Generating and Evaluating Variable Number of Keyphrases

TNT-KID: Transformer-based neural tagger for keyword identification

An Empirical Study on Neural Keyphrase Generation

Does Order Matter? An Empirical Study on Generating Multiple Keyphrases as a Sequence

UniKeyphrase: A Unified Extraction and Generation Framework for Keyphrase Prediction

Keyphrase Extraction with Incomplete Annotated Training Data

Proceedings of the Seventh Workshop on Noisy User-generated Text (W-NUT 2021)

General-to-Specific Transfer Labeling for Domain Adaptable Keyphrase Generation


FlauBERT: Unsupervised Language Model Pre-training for French

BARThez: a Skilled Pretrained French Sequence-to-Sequence Model

Pre-training Polish Transformer-based Language Models at Scale

FlauBERT : des modèles de langue contextualisés pré-entraînés pour le français (FlauBERT : Unsupervised Language Model Pre-training for French)

ASR-Generated Text for Language Model Pre-training Applied to Speech Tasks

Using ASR-Generated Text for Spoken Language Modeling

Proceedings of BigScience Episode #5 -- Workshop on Challenges & Perspectives in Creating Large Language Models

UoR-NCL at SemEval-2022 Task 3: Fine-Tuning the BERT-Based Models for Validating Taxonomic Relations

Proceedings of the 16th International Workshop on Semantic Evaluation (SemEval-2022)

Word Sense Disambiguation for Automatic Translation of Medical Dialogues into Pictographs

Recent Advances in Natural Language Processing


Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

Overcoming Data Bottlenecks in Genomic Pathogen Surveillance

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing

Applied Bioinformatics and Public Health Microbiology: challenges, discoveries and innovations during a pandemic

hAMRoaster: a tool for comparing performance of AMR gene detection software

hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling

The first report of the mobile colistin resistance gene, mcr-10.1, in Kenya and a novel mutation in the phoQ gene (S244T) in a colistin-resistant Enterobacter cloacae clinical isolate


Flexible Framework for Parallel PDE Parameter Estimation in Julia

A fast marching algorithm for the factored eikonal equation

jInv -- a flexible Julia package for PDE parameter estimation

Full waveform inversion guided by travel time tomography


Pure Python Spell Checking http://pyspellchecker.readthedocs.io/en/latest/

Quilt-1M: One Million Image-Text Pairs for Histopathology

Learning to combine Grammatical Error Corrections

CharacterBERT and Self-Teaching for Improving the Robustness of Dense Retrievers on Queries with Typos

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

Diamonds in the Rough: Generating Fluent Sentences from Early-Stage Drafts for Academic Writing Assistance

MaintNet: A Collaborative Open-Source Library for Predictive Maintenance Language Resources

Cross-lingual Transfer Learning for Grammatical Error Correction

International Conference on Computational Linguistics

(Almost) Unsupervised Grammatical Error Correction using Synthetic Comparable Corpus

Workshop on Innovative Use of NLP for Building Educational Applications

GRUBERT: A GRU-Based Method to Fuse BERT Hidden Layers for Twitter Sentiment Analysis

International Joint Conference on Natural Language Processing

Fashion-IQ 2020 Challenge 2nd Place Team's Solution

Towards Unsupervised Grammatical Error Correction using Statistical Machine Translation with Synthetic Comparable Corpus


Python version of the SGP4 satellite position library

Wide-Scale Monitoring of Satellite Lifetimes: Pitfalls and a Benchmark Dataset

Pulsar and Magnetar Navigation with Fermi/GBM and GECAM

Generating Realistic Two-Line Elements for Notional Space Vehicles and Constellations


A system that seamlessly integrates Big Data processing and machine learning model serving in distributed relational database

Serving Deep Learning Models with Deduplication from Relational Databases

A Comparison of Decision Forest Inference Platforms from A Database Perspective


PyTorch implementations of neural network models for keyword spotting

Deep Residual Learning for Small-Footprint Keyword Spotting

An Experimental Analysis of the Power Consumption of Convolutional Neural Networks for Keyword Spotting

Honk: A PyTorch Reimplementation of Convolutional Neural Networks for Keyword Spotting

PQK: Model Compression via Pruning, Quantization, and Knowledge Distillation

Prototypical Metric Transfer Learning for Continuous Speech Keyword Spotting With Limited Training Data

Fighting Voice Spam with a Virtual Assistant Prototype

JavaScript Convolutional Neural Networks for Keyword Spotting in the Browser: An Experimental Analysis


Pathfinding and search testbed/visualization suite. Current code is in PDB-refactor branch.

Multi-Agent Pathfinding with Continuous Time

Iterative Budgeted Exponential Search

Ultrafast Euclidean Shortest Path Computation Using Hub Labeling

THIRTY-SEVENTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, VOL 37 NO 10

Efficiently computing alternative paths in game maps


A numerical solver package for a wide range of quantum lattice models based on many-variable Variational Monte Carlo method

Restricted Boltzmann machine learning for solving strongly correlated quantum systems

mVMC—Open-source software for many-variable variational Monte Carlo method

Competition among Superconducting, Antiferromagnetic, and Charge Orders with Intervention by Phase Separation in the 2D Holstein-Hubbard Model.

Correlation-induced superconductivity dynamically stabilized and enhanced by laser irradiation

Excitons and Dark Fermions as Origins of Mott Gap, Pseudogap and Superconductivity in Cuprate Superconductors — General Concept and Basic Formalism Based on Gap Physics

Journal of the Physical Society of Japan

Spin nematics in frustrated spin-dimer systems with bilayer structure

Update of ℋΦ: Newly added functions and methods in versions 2 and 3

Optimized implementation for calculation and fast-update of Pfaffians installed to the open-source fermionic variational solver mVMC

Ground state of the S=1/2 pyrochlore Heisenberg antiferromagnet: A quantum spin liquid emergent from dimensional reduction

MateriApps LIVE! and MateriApps Installer: Environment for starting and scaling up materials science simulations


Galactic Dynamics in python

galpy: A python LIBRARY FOR GALACTIC DYNAMICS

The Astrophysical Journal Supplement Series

Vertical waves in the solar neighbourhood in Gaia DR2

Chemodynamics of the Milky Way. I. The first year of APOGEE data

HAL (Le Centre pour la Communication Scientifique Directe)

Confirming chemical clocks: asteroseismic age dissection of the Milky Way disc(s)

Monthly Notices of the Royal Astronomical Society

Universality of free fall from the orbital motion of a pulsar in a stellar triple system

Evidence from APOGEE for the presence of a major building block of the halo buried in the inner Galaxy

Monthly notices of the Royal Astronomical Society

Apocenter Pile-up: Origin of the Stellar Halo Density Break

Linear perturbation theory for tidal streams and the small-scale CDM power spectrum

DYNAMICAL MODELING OF TIDAL STREAMS

A time-resolved picture of our Milky Way’s early formation history


VIP is a python package/library for angular, reference star and spectral differential imaging for exoplanet/disk detection through high-contrast imaging.

VIP: Vortex Image Processing package for high-contrast direct imaging

Near-infrared scattered light properties of the HR4796A dust ring: a measured scattering phase function from 13.6deg to 166.6deg

Discovery of a low-mass companion inside the debris ring surrounding the F5V star HD 206893

VLT/SPHERE robust astrometry of the HR8799 planets at milliarcsecond-level accuracy Orbital architecture analysis with PyAstrOFit

Deep exploration of Epsilon Eridani with Keck Ms-band vortex coronagraphy and radial velocities: mass and orbital parameters of the giant exoplanet

Low-rank plus sparse decomposition for exoplanet detection in direct imaging ADI sequences

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

Separating extended disc features from the protoplanet in PDS 70 using VLT/SINFONI

Are the spiral arms in the MWC 758 protoplanetary disc driven by a companion inside the cavity?

STIM map: detection map for exoplanets imaging beyond asymptotic Gaussian residual speckle noise


A collection of Java libraries for basic AI algorithms (JAICore) and automated software composition, in particular AutoML (softwareconfiguration)

ML-Plan: Automated machine learning via hierarchical planning

Automated Multi-Label Classification based on ML-Plan

Single and Parallel Machine Scheduling with Variable Release Dates


Moses, the machine translation system

MASS: Masked Sequence to Sequence Pre-training for Language Generation

Dual Learning for Machine Translation

Findings of the 2016 Conference on Machine Translation

Meeting of the Association for Computational Linguistics

Unsupervised Neural Machine Translation

Beyond English-Centric Multilingual Machine Translation

Population Based Training of Neural Networks

Pay Less Attention with Lightweight and Dynamic Convolutions

Massive Exploration of Neural Machine Translation Architectures

Graph Convolutional Encoders for Syntax-aware Neural Machine Translation

Structured Attention Networks


Implementation of spatio-temporal graph convolutional network with PyTorch

Traffic Flow Prediction with Vehicle Trajectories

THIRTY-FIFTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, THIRTY-THIRD CONFERENCE ON INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE AND THE ELEVENTH SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE

Uncertainty Quantification of Sparse Travel Demand Prediction with Spatial-Temporal Graph Neural Networks

Urban Regional Function Guided Traffic Flow Prediction

Uncertainty Quantification via Spatial-Temporal Tweedie Model for Zero-inflated and Long-tail Travel Demand Prediction

Residual Correction in Real-Time Traffic Forecasting

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


Succinct Data Structure Library

Large-Scale Pattern Search Using Reduced-Space On-Disk Suffix Arrays

E2FM: an encrypted and compressed full-text index for collections of
  genomic sequences


NeurIPS'19: Meta-Weight-Net: Learning an Explicit Mapping For Sample Weighting (Pytorch implementation for noisy labels).

Learning from Noisy Labels with Deep Neural Networks: A Survey

Robust Semi-Supervised Learning with Out of Distribution Data.

DAC-MR: Data Augmentation Consistency Based Meta-Regularization for Meta-Learning


Genome free discovery and classification of miRNAs from small RNA-Seq with random forests

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests

Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants

International journal of molecular sciences

The Multiverse of Plant Small RNAs: How Can We Explore It?


Question Answering task using Deep Learning on SQuAD dataset

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

SQuAD: 100,000+ Questions for Machine Comprehension of Text

Bidirectional Attention Flow for Machine Comprehension


OpenAlpaca: A Fully Open-Source Instruction-Following Model Based On OpenLLaMA

PandaGPT: One Model To Instruction-Follow Them All

Sight Beyond Text: Multi-Modal Training Enhances LLMs in Truthfulness and Ethics

Understanding and Patching Compositional Reasoning in LLMs


Transcriptional burst kinetics inference and analysis described in the article "Genomic encoding of transcriptional burst kinetics" (Larsson et. al 2019).

Neural network aided approximation and parameter inference of non-Markovian models of gene expression

Elastic dosage compensation by X-chromosome upregulation

Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance

Enhanced chromatin accessibility contributes to X chromosome dosage compensation in mammals

Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics


Project site for "Your Classifier is Secretly an Energy-Based Model and You Should Treat it Like One"

Your Classifier is Secretly an Energy Based Model and You Should Treat it Like One

Controversial stimuli: Pitting neural networks against each other as models of human cognition

No MCMC for me: Amortized sampling for fast and stable training of energy-based models

Scalable Bayesian Inverse Reinforcement Learning

Strictly Batch Imitation Learning by Energy-based Distribution Matching

Hybrid Discriminative-Generative Training via Contrastive Learning

JEM++: Improved Techniques for Training JEM

Towards Understanding the Generative Capability of Adversarially Robust Classifiers

Hamiltonian Dynamics with Non-Newtonian Momentum for Rapid Sampling

An Algorithm for Out-Of-Distribution Attack to Neural Network Encoder


Dynamic Key-Value Memory Networks for Knowledge Tracing

Knowledge Query Network: How Knowledge Interacts with Skills

Modeling Hint-Taking Behavior and Knowledge State of Students with Multi-Task Learning

Student Performance Prediction Using Dynamic Neural Models

Empirical Evaluation of Deep Learning Models for Knowledge Tracing: Of Hyperparameters and Metrics on Performance and Replicability

Deep Knowledge Tracing with Learning Curves


The Platinum Genomes Truthset

De novo assembly of haplotype-resolved genomes with trio binning

Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes

Lossy Compressor Preserving Variant Calling through Extended BWT

Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies

Thousands of human mutation clusters are explained by short-range template switching


Bundle Recommendation with Graph Convolutional Networks

Bundle Recommendation and Generation with Graph Neural Networks

IEEE Transactions on Knowledge and Data Engineering

Accurate Bundle Matching and Generation via Multitask Learning with Partially Shared Parameters

Economic Recommender Systems -- A Systematic Review