Enabling easy statistical significance testing for deep neural networks.

From Masked Language Modeling to Translation: Non-English Auxiliary Tasks Improve Zero-shot Spoken Language Understanding

SkillSpan: Hard and Soft Skill Extraction from English Job Postings

deep-significance - Easy and Meaningful Statistical Significance Testing in the Age of Neural Networks

Cartography Active Learning

What Do You Mean by Relation Extraction? A Survey on Datasets and Study on Scientific Relation Classification

Experimental Standards for Deep Learning in Natural Language Processing Research

An Empirical Study on Cross-X Transfer for Legal Judgment Prediction

Kompetencer: Fine-grained Skill Classification in Danish Job Postings via Distant Supervision and Transfer Learning

DynDepNet: Learning Time-Varying Dependency Structures from fMRI Data via Dynamic Graph Structure Learning


Peregrine: Fast Genome Assembler Using SHIMMER Index

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

Human Genome Assembly in 100 Minutes


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

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

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

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

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

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

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

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

LongTron: Automated Analysis of Long Read Spliced Alignment Accuracy


redlistr: Tools for the IUCN Red List of Ecosystems and Species


Scalable analysis of large high-dimensional data

SCHNEL: Scalable clustering of high dimensional single-cell data

ManiVault: A Flexible and Extensible Visual Analytics Framework for High-Dimensional Data


The official implementation for Pseudo Numerical Methods for Diffusion Models on Manifolds (PNDM, PLMS | ICLR2022)

Denoising Diffusion Implicit Models

Score-Based Generative Modeling through Stochastic Differential Equations

Improved Denoising Diffusion Probabilistic Models

Fast Sampling of Diffusion Models with Exponential Integrator

DIRE for Diffusion-Generated Image Detection

Towards the Detection of Diffusion Model Deepfakes

Pyramidal Denoising Diffusion Probabilistic Models

Exact Diffusion Inversion via Bi-directional Integration Approximation

Lookahead Diffusion Probabilistic Models for Refining Mean Estimation


PyTorch implementation of MTAD-GAT (Multivariate Time-Series Anomaly Detection via Graph Attention Networks) by Zhao et. al (2020, https://arxiv.org/abs/2009.02040).

Detecting Spacecraft Anomalies Using LSTMs and Nonparametric Dynamic Thresholding

Multivariate Time-series Anomaly Detection via Graph Attention Network

Coupled Attention Networks for Multivariate Time Series Anomaly Detection

A Survey of Time Series Anomaly Detection Methods in the AIOps Domain

PatchAD: A Lightweight Patch-based MLP-Mixer for Time Series Anomaly Detection

Towards an Awareness of Time Series Anomaly Detection Models' Adversarial Vulnerability

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


Netease Youdao's open-source embedding and reranker models for RAG products.

DR-RAG: Applying Dynamic Document Relevance to Retrieval-Augmented
  Generation for Question-Answering

Tutorly: Turning Programming Videos Into Apprenticeship Learning Environments with LLMs

Understand What LLM Needs: Dual Preference Alignment for Retrieval-Augmented Generation


Drosophila transposable element canonical sequences

Engineered sex ratio distortion by X-shredding in the global agricultural pest Ceratitis capitata

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

Deep repeat resolution—the assembly of the Drosophila Histone Complex

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

Genomic analysis of P elements in natural populations of Drosophila melanogaster

Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line

ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements

Chromosome-specific maturation of the epigenome in the Drosophila male germline

Reconstructing the Invasion Route of the P-Element in Drosophila melanogaster Using Extant Population Samples


FD-MobileNet: Improved MobileNet with a Fast Downsampling Strategy

FixyNN: Efficient Hardware for Mobile Computer Vision via Transfer Learning

Real-time Artificial Intelligence for Accelerator Control: A Study at the Fermilab Booster

Open-source FPGA-ML codesign for the MLPerf Tiny Benchmark


Parallel Tensor Infrastructure (ParTI!)

Load-Balanced Sparse MTTKRP on GPUs

Efficient and effective sparse tensor reordering

International Conference on Supercomputing

ALTO: Adaptive Linearized Storage of Sparse Tensors

PROCEEDINGS OF THE 2021 ACM INTERNATIONAL CONFERENCE ON SUPERCOMPUTING, ICS 2021

A Parallel Sparse Tensor Benchmark Suite on CPUs and GPUs

Dynasor: A Dynamic Memory Layout for Accelerating Sparse MTTKRP for Tensor Decomposition on Multi-core CPU


A tool for text normalisation via character-level machine translation

A Large-Scale Comparison of Historical Text Normalization Systems

North American Chapter of the Association for Computational Linguistics

Adapting a State-of-the-Art Tagger for South Slavic Languages to Non-Standard Text

Proceedings of the 6th Workshop on Balto-Slavic Natural Language Processing

Dialect-to-Standard Normalization: A Large-Scale Multilingual Evaluation

Findings of the Association for Computational Linguistics: EMNLP 2023

A corpus-based study of 16th-century Slovene clitics and clitic-like elements


A tool for semi-automatic cell type classification

Cross-tissue immune cell analysis reveals tissue-specific features in humans

Innovative prognostic modeling in ESCC: leveraging scRNA-seq and bulk-RNA for dendritic cell heterogeneity analysis

Integrative single-cell analysis of LUAD: elucidating immune cell dynamics and prognostic modeling based on exhausted CD8+ T cells


Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

Reconstruction of ancient microbial genomes from the human gut

Maternal fecal microbiome predicts gestational age, birth weight and neonatal growth in rural Zimbabwe.

One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density

Wekemo Bioincloud: A user‐friendly platform for meta‐omics data analyses

Effect of Fecal Microbiota Transplantation Combined With Mediterranean Diet on Insulin Sensitivity in Subjects With Metabolic Syndrome

Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching

Signature of Alzheimer’s Disease in Intestinal Microbiome: Results From the AlzBiom Study

Assessing saliva microbiome collection and processing methods

Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration

Characterization of Bacterial Community Dynamics of the Human Mouth Throughout Decomposition via Metagenomic, Metatranscriptomic, and Culturing Techniques


code to run sei and obtain sei and sequence class predictions

A sequence-based global map of regulatory activity for deciphering human genetics

Hypothyroidism and rheumatoid arthritis: a two-sample Mendelian randomization study

Identification and Interpretation of eQTL and eGenes for Hodgkin Lymphoma Susceptibility

Sei framework resources (hg19 and hg38 FASTA files)

Zenodo (CERN European Organization for Nuclear Research)

Current genomic deep learning models display decreased performance in cell type-specific accessible regions


Large-Scale Multi-Label Text Classification on EU Legislation

A Survey on Text Classification: From Shallow to Deep Learning

An Empirical Study on Large-Scale Multi-Label Text Classification Including Few and Zero-Shot Labels


Reachability types: tracking aliasing and separation in higher-order functional programs

Proceedings of the ACM on Programming Languages

Polymorphic Reachability Types: Tracking Freshness, Aliasing, and Separation in Higher-Order Generic Programs

Modeling Reachability Types with Logical Relations

Graph IRs for Impure Higher-Order Languages (Technical Report)


(Linear-chain) Conditional random field in PyTorch.

NLRG at SemEval-2021 Task 5: Toxic Spans Detection Leveraging BERT-based Token Classification and Span Prediction Techniques

Meeting of the Association for Computational Linguistics

Aspect and Opinion Term Extraction for Hotel Reviews using Transfer Learning and Auxiliary Labels

New or Old? Exploring How Pre-Trained Language Models Represent Discourse Entities

International Conference on Computational Linguistics

DeepZensols: Deep Natural Language Processing Framework

Structured Refinement for Sequential Labeling


This repository is dedicated to the fit@TDS software. A python code aiming at the retrieving of material parameter from a TeraHertz time domain spectroscopy (TDS) measurements from a fit in the time domain.

THz-TDS Time-Trace Analysis for the Extraction of Material and Metamaterial Parameters

Broadband super-resolution Terahertz Time domain spectroscopy applied to Gas analysis


Python package to corrupt arbitrary images.

Benchmarking Robustness in Object Detection: Autonomous Driving when Winter is Coming

Benchmarking Neural Network Robustness to Common Corruptions and Surface Variations

RoboBEV: Towards Robust Bird's Eye View Perception under Corruptions

RoboDepth: Robust Out-of-Distribution Depth Estimation under Corruptions

The RoboDepth Challenge: Methods and Advancements Towards Robust Depth Estimation

Disentangled Variational Information Bottleneck for Multiview Representation Learning

Meaningfully Explaining Model Mistakes Using Conceptual Counterfactuals.

Noisy Learning for Neural ODEs Acts as a Robustness Locus Widening

Gradient Coreset for Federated Learning

Target-Aware Generative Augmentations for Single-Shot Adaptation


Zero-inflated dimensionality reduction algorithm for single-cell data

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

Computational approaches for interpreting scRNA-seq data

A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data

A deep adversarial variational autoencoder model for dimensionality reduction in single-cell RNA sequencing analysis

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion


WGS (Wheat) Robust Assembly Pipeline

Multiple wheat genomes reveal global variation in modern breeding

A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise

W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data


A deep learning toolkit for log-based anomaly detection

DeepLog: Anomaly Detection and Diagnosis from System Logs through Deep Learning

Conference on Computer and Communications Security

Robust log-based anomaly detection on unstable log data

Experience Report: Deep Learning-based System Log Analysis for Anomaly Detection

Leveraging Log Instructions in Log-based Anomaly Detection

LogAI: A Library for Log Analytics and Intelligence


Baselines models for GuacaMol benchmarks

Proximal Policy Optimization Algorithms

GuacaMol: Benchmarking Models for De Novo Molecular Design

Journal of chemical information and modeling

A Model to Search for Synthesizable Molecules

Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks

Guiding Deep Molecular Optimization with Genetic Exploration

DOCKSTRING: easy molecular docking yields better benchmarks for ligand design

Barking up the right tree: an approach to search over molecule synthesis DAGs


Evaluation of CNN-based Automatic Music Tagging Models

Semi-supervised Music Tagging Transformer

MusCaps: Generating Captions for Music Audio

Emotion Embedding Spaces for Matching Music to Stories

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

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


Julia implementation of EXPOKIT routines

Reach Set Approximation through Decomposition with Low-dimensional Sets and High-dimensional Matrices

Multi-Neutrino Entanglement and Correlations in Dense Neutrino Systems

QSWalk.jl: Julia package for quantum stochastic walks analysis

Quantum simulations of SO(5) many-fermion systems using qudits

Steps Toward Quantum Simulations of Hadronization and Energy-Loss in
  Dense Matter

Interacting quasiperiodic spin chains in the prethermal regime


Benchmark for Continuous Multi-Agent Robotic Control, based on OpenAI's Mujoco Gym environments.

FACMAC: Factored Multi-Agent Centralised Policy Gradients

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

Off-the-Grid MARL: Datasets with Baselines for Offline Multi-Agent Reinforcement Learning

Counterfactual Conservative Q Learning for Offline Multi-agent Reinforcement Learning

Beyond Conservatism: Diffusion Policies in Offline Multi-agent Reinforcement Learning

Attacking c-MARL More Effectively: A Data Driven Approach


A uniform interface for a number of 2D and 3D maps of interstellar dust reddening/extinction.

Off the Beaten Path: Gaia Reveals GD-1 Stars outside of the Main Stream

GALExtin: an alternative online tool to determine the interstellar extinction in the Milky Way

Monthly Notices of the Royal Astronomical Society

Evidence for a Highly Opaque Large-scale Galaxy Void at the End of Reionization

R-band light-curve properties of Type Ia supernovae from the (intermediate) Palomar Transient Factory

Minute-cadence Observations of the LAMOST Fields with the TMTS: I. Methodology of Detecting Short-period Variables and Results from the first-year Survey

First Assessment of the Binary Lens OGLE-2015-BLG-0232

A joint Roman Space Telescope and Rubin Observatory synthetic wide-field imaging survey

Minute-cadence observations of the LAMOST fields with the TMTS: II. Catalogues of short-period variable stars from the first 2-yr surveys


Simulation and analysis framework for the Imaging X-ray Polarimetry Explorer

Discovery of strongly variable X-ray polarization in the neutron star low-mass X-ray binary transient XTE J1701−462

X-ray pulsar GRO J1008-57 as an orthogonal rotator

A Strong X-Ray Polarization Signal from the Magnetar 1RXS J170849.0-400910

Complex variations in X-ray polarization in the X-ray pulsar LS V +44 17/RX J0440.9+4431

Observations of 4U 1626–67 with the Imaging X-Ray Polarimetry Explorer

A polarimetrically oriented X-ray stare at the accreting pulsar EXO 2030+375

X-ray polarimetry of X-ray pulsar X Persei: another orthogonal rotator?

IXPE and XMM-Newton Observations of the Soft Gamma Repeater SGR 1806–20

X-ray polarimetry as a tool to measure the black hole spin in microquasars: simulations of IXPE capabilities

Monthly notices of the Royal Astronomical Society

Discovery of a variable energy-dependent X-ray polarization in the accreting neutron star GX 5-1


A Satellite Time Series Dataset for Crop Type Identification

Crop mapping from image time series: deep learning with multi-scale label hierarchies

Boost Precision Agriculture with Unmanned Aerial Vehicle Remote Sensing and Edge Intelligence: A Survey

BreizhCrops: A Time Series Dataset for Crop Type Mapping

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

A systematic review of the use of Deep Learning in Satellite Imagery for Agriculture


Avalanche fork adding RL support

Avalanche: an End-to-End Library for Continual Learning

Avalanche RL: a Continual Reinforcement Learning Library


SHallow shOtGUN profiler

Evaluating the Information Content of Shallow Shotgun Metagenomics

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

SHOGUN: a modular, accurate and scalable framework for microbiome quantification


CRyPTIC data processing pipelines

A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing ofM. tuberculosis

TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis

A data compendium of Mycobacterium tuberculosis antibiotic resistance

Rifampicin resistant Mycobacterium tuberculosis in Vietnam, 2020–2022

Journal of clinical tuberculosis and other mycobacterial diseases

Clockwork database


Softcite software mention recognizer, finding mentions and citations to software from within the academic literature

Softcite dataset: A dataset of software mentions in biomedical and economic research publications

Journal of the Association for Information Science and Technology

Mining Software Entities in Scientific Literature: Document-level NER for an Extremely Imbalance and Large-scale Task

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

Softcite software mention extraction from the CORD-19 publications


Whole exome sequencing pipeline including advanced variant annotation features and automated PDF reporting.

Knowledge bases and software support for variant interpretation in precision oncology

Challenges and Experiences Extending the cBioPortal for Cancer Genomics to a Molecular Tumor Board Platform

Studies in health technology and informatics

MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making

GMDS - openEHR Mapper - A Tool to Fuse Clinical and Genomic Data Using the openEHR Standard.

Use of Process Modelling for Optimization of Molecular Tumor Boards


Minia is a short-read assembler based on a de Bruijn graph

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

HASLR: Fast Hybrid Assembly of Long Reads

Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus) and their Blochmannia endosymbionts

Complete mitochondrial genome of the Antarctic copepod Tigriopus kingsejongenesis (Harpacticoida, Harpacticidae)


Transit and Radial velocity Interactive Fitting tool for Orbital analysis and N-body simulations: The Exo-Striker

A nearby transiting rocky exoplanet that is suitable for atmospheric investigation

An ultra-short-period transiting super-Earth orbiting the M3 dwarf TOI-1685

TESS exoplanet candidates validated with HARPS archival data

TOI-1201 b: A mini-Neptune transiting a bright and moderately young M dwarf

Two Jovian Planets around the Giant Star HD 202696: A Growing Population of Packed Massive Planetary Pairs around Massive Stars?

A detailed analysis of the Gl 486 planetary system

A Pair of Warm Giant Planets near the 2:1 Mean Motion Resonance around the K-dwarf Star TOI-2202*

The CARMENES search for exoplanets around M dwarfs

Four Jovian planets around low-luminosity giant stars observed by the EXPRESS and PPPS

HD 191939 revisited: New and refined planet mass determinations, and a new planet in the habitable zone


AtomDB project (www.atomdb.org)

PyAtomDB: Extending the AtomDB Atomic Database to Model New Plasma Processes and Uncertainties

XMM-Newton RGS Spectroscopy of the M31 Bulge. I. Evidence for a Past AGN Half a Million Years Ago

Plasma Diagnostics of the Supernova Remnant N132D using Deep XMM-Newton Observations with the Reflection Grating Spectrometer

R-matrix Electron-impact Excitation Data for the H- and He-like Ions with Z = 6−30

Identifying galaxy cluster mergers with deep neural networks using idealized Compton-y and X-ray maps

New radiative loss curve from updates to collisional excitation in the low-density, optically thin plasmas in SPEX


Python halo mass function calculator

The Dearth of z similar to 10 Galaxies in All HST Legacy Fields-The Rapid Evolution of the Galaxy Population in the First 500 Myr

HMFcalc: An Online Tool for Calculating Dark Matter Halo Mass Functions

The halo model as a versatile tool to predict intrinsic alignments

The Rest-frame Optical (900 nm) Galaxy Luminosity Function at z ∼ 4–7: Abundance Matching Points to Limited Evolution in the MSTAR/MHALO Ratio at z ≥ 4

A model for multiproperty galaxy cluster statistics

The impact of scatter in the galaxy UV luminosity to halo mass relation on Ly α visibility during the epoch of reionization

How well do we know the halo mass function?

Monthly Notices of the Royal Astronomical Society: Letters

ON THE CONTRIBUTION OF FLUORESCENCE TO LYα HALOS AROUND STAR-FORMING GALAXIES

TheHaloMod: An online calculator for the halo model

The Massive and Distant Clusters of WISE Survey: MOO J1142+1527, a 10^(15) M_⊙ Galaxy Cluster at z = 1.19


The new source code of the LinearFold, linear-time prediction for RNA secondary structures

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery


Inquisitive Parrots for Search

InPars: Unsupervised Dataset Generation for Information Retrieval

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

InPars-v2: Large Language Models as Efficient Dataset Generators for Information Retrieval

InPars: Data Augmentation for Information Retrieval using Large Language Models

Open-source Large Language Models are Strong Zero-shot Query Likelihood Models for Document Ranking

Multi-objective Representation Learning for Scientific Document Retrieval

InPars Toolkit: A Unified and Reproducible Synthetic Data Generation Pipeline for Neural Information Retrieval


Reduce - tool for adding and correcting hydrogens in PDB files

DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction

Machine Learning to Identify Flexibility Signatures of Class A GPCR Inhibition

Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design

DSDP: A Blind Docking Strategy Accelerated by GPUs

Modeling Molecular Structures with Intrinsic Diffusion Models


Parallel tempering MCMC sampler package written in Python

The NANOGrav 11-year Data Set: High-precision Timing of 45 Millisecond Pulsars

The Astrophysical Journal Supplement Series

The NANOGrav 11 Year Data Set: Pulsar-timing Constraints on the Stochastic Gravitational-wave Background

THE NANOGRAV NINE-YEAR DATA SET: LIMITS ON THE ISOTROPIC STOCHASTIC GRAVITATIONAL WAVE BACKGROUND

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

Pulsar Timing Array Constraints on Primordial Black Holes with NANOGrav 11-Year Dataset

The NANOGrav 11 yr Data Set: Limits on Gravitational Waves from Individual Supermassive Black Hole Binaries

Modeling the Uncertainties of Solar System Ephemerides for Robust Gravitational-wave Searches with Pulsar-timing Arrays

Constraining Cosmological Phase Transitions with the Parkes Pulsar Timing Array

Constraints on the Dynamical Environments of Supermassive Black-Hole Binaries Using Pulsar-Timing Arrays

DETECTING ECCENTRIC SUPERMASSIVE BLACK HOLE BINARIES WITH PULSAR TIMING ARRAYS: RESOLVABLE SOURCE STRATEGIES


In silico prediction of E. coli serotype

ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data

Molecular characterization of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae among the pediatric population in Qatar

Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island

Diversity of blaCTX-M-1-carrying plasmids recovered from Escherichia coli isolated from Canadian domestic animals

Use of Genomics to Investigate Historical Importation of Shiga Toxin–Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand

Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella

Genome Informatics and Machine Learning-Based Identification of Antimicrobial Resistance-Encoding Features and Virulence Attributes in Escherichia coli Genomes Representing Globally Prevalent Lineages, Including High-Risk Clonal Complexes

Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada

Genomic Epidemiology and Antimicrobial Susceptibility Profile of Enterotoxigenic Escherichia coli From Outpatients With Diarrhea in Shenzhen, China, 2015–2020


Knowledge Independent Network Construction

Addressing noise in co-expression network construction

Identification of condition-specific biomarker systems in uterine cancer


OpenXAI : Towards a Transparent Evaluation of Model Explanations

OpenXAI: Towards a Transparent Evaluation of Model Explanations

Analyzing Explainer Robustness via Lipschitzness of Prediction Functions

InterpretCC: Intrinsic User-Centric Interpretability through Global Mixture of Experts

Uncovering Unique Concept Vectors through Latent Space Decomposition


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

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

International Journal of Computer Vision

Survey of Explainable AI Techniques in Healthcare

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


Python bindings for NCO


Cluster Investigation & Virus Epidemiology Tool

Transmission of paediatric respiratory syncytial virus and influenza in the wake of the COVID-19 pandemic

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks

Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface


Pipelines for the analysis of 10x single-cell RNA-sequencing data

The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages

Distinct fibroblast subsets drive inflammation and damage in arthritis

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments

Secondary influenza challenge triggers resident memory B cell migration and rapid relocation to boost antibody secretion at infected sites

Lipid-associated macrophages transition to an inflammatory state in human atherosclerosis, increasing the risk of cerebrovascular complications


Explaining the output of machine learning models with more accurately estimated Shapley values

Explaining individual predictions when features are dependent: More accurate approximations to Shapley values

SurvSHAP(t): Time-dependent explanations of machine learning survival models

Accelerating materials-space exploration for thermal insulators by mapping materials properties via artificial intelligence

groupShapley: Efficient prediction explanation with Shapley values for feature groups


Python Blob Detector and Source Finder

Unveiling the rarest morphologies of the LOFAR Two-metre Sky Survey radio source population with self-organised maps

CHANG-ES XII: A LOFAR and VLA view of the edge-on star-forming galaxy NGC 3556

The eROSITA Final Equatorial-Depth Survey (eFEDS): LOFAR view of brightest cluster galaxies and AGN feedback

Deep LOFAR 150 MHz imaging of the Bootes field: Unveiling the faint low-frequency sky

Nature of the unusual transient AT 2018cow from HI observations of its host galaxy

HAL (Le Centre pour la Communication Scientifique Directe)

Evolutionary Map of the Universe (EMU): A pilot search for diffuse, non-thermal radio emission in galaxy clusters with the Australian SKA Pathfinder

Radio source-component association for the LOFAR Two-metre Sky Survey with region-based convolutional neural networks

MeerKATHI -- an end-to-end data reduction pipeline for MeerKAT and other radio telescopes

The contribution of non-central radio galaxies to AGN feedback in rich galaxy clusters

A search for intercluster filaments with LOFAR and eROSITA


Global birdsong embeddings enable superior transfer learning for bioacoustic classification

BIRB: A Generalization Benchmark for Information Retrieval in Bioacoustics

Leveraging tropical reef, bird and unrelated sounds for superior
  transfer learning in marine bioacoustics


SmartSim Infrastructure Library Clients.

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

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

Combining machine learning with computational fluid dynamics using OpenFOAM and SmartSim


A collaborative software to download the energy database Marktstammdatenregister (MaStR)

Improving Data Reliability in Germany's Energy System: A Validation of Unit Locations of the Marktstammdatenregister


GUI for brightway2


Library that attributes resource use, waste, emissions, and loss to economic sectors

FLOWSA: A Python Package Attributing Resource Use, Waste, Emissions, and Other Flows to Industries


Experimentation procedure for Iterative Optimization Heuristics

IOHprofiler: A Benchmarking and Profiling Tool for Iterative Optimization Heuristics

IOHexperimenter: Benchmarking Platform for Iterative Optimization Heuristics

Benchmarking Algorithms for Submodular Optimization Problems Using IOHProfiler

Extensible Logging and Empirical Attainment Function for IOHexperimenter


A prototype implementation of Bao for PostgreSQL

Balsa: Learning a Query Optimizer Without Expert Demonstrations

Proceedings of the 2022 International Conference on Management of Data

Maliva: Using Machine Learning to Rewrite Visualization Queries Under Time Constraints

COOOL: A Learning-To-Rank Approach for SQL Hint Recommendations


Tokenization and pre-processing for Twitter data used to train classifiers.

THU_NGN at SemEval-2018 Task 3: Tweet Irony Detection with Densely connected LSTM and Multi-task Learning

North American Chapter of the Association for Computational Linguistics

SeerNet at SemEval-2018 Task 1: Domain Adaptation for Affect in Tweets

Modeling Personality Traits of Filipino Twitter Users

Proceedings of the Second Workshop on Computational Modeling of
          People's Opinions, Personality, and Emotions in Social Media

EvoMSA: A Multilingual Evolutionary Approach for Sentiment Analysis

IEEE Computational Intelligence Magazine

EmoNLP at SemEval-2018 Task 2: English Emoji Prediction with Gradient Boosting Regression Tree Method and Bidirectional LSTM

LT3 at SemEval-2019 Task 5: Multilingual Detection of Hate Speech Against Immigrants and Women in Twitter (hatEval)

THU_NGN at SemEval-2018 Task 1: Fine-grained Tweet Sentiment Intensity Analysis with Attention CNN-LSTM

YNU_oxz at SemEval-2020 Task 12: Bidirectional GRU with Capsule for Identifying Multilingual Offensive Language

International Workshop on Semantic Evaluation


Arabic edition of BERT pretrained language models

KUISAIL at SemEval-2020 Task 12: BERT-CNN for Offensive Speech Identification in Social Media

A review of sentiment analysis research in Arabic language

Arabic fake news detection based on deep contextualized embedding models

Pre-training Polish Transformer-based Language Models at Scale

ORCA: A Challenging Benchmark for Arabic Language Understanding

Hybrid Enhanced Universal Dependencies Parsing

International Workshop/Conference on Parsing Technologies


The WebSplit Benchmark introducing "Split and Rephrase" task

Split and Rephrase

Unsupervised Neural Text Simplification

Learning To Split and Rephrase From Wikipedia Edit History

Discourse-Aware Text Simplification: From Complex Sentences to Linked Propositions


Supplementary material for "When and Why Are Pre-trained Word Embeddings Useful for Neural Machine Translation?" at NAACL 2018

Beyond English-Centric Multilingual Machine Translation

When and Why are Pre-trained Word Embeddings Useful for Neural Machine Translation?

Multilingual Neural Machine Translation with Knowledge Distillation

The paradox of the compositionality of natural language: a neural machine translation case study

Motley: Benchmarking Heterogeneity and Personalization in Federated Learning

Unsupervised Pivot Translation for Distant Languages

Collective Wisdom: Improving Low-resource Neural Machine Translation using Adaptive Knowledge Distillation

A Study of Multilingual Neural Machine Translation

Language Graph Distillation for Low-Resource Machine Translation

Multilingual Neural Machine Translation: Can Linguistic Hierarchies Help?


"3D Human Texture Estimation from a Single Image with Transformers", ICCV 2021 Oral

3D Human Shape and Pose from a Single Low-Resolution Image with Self-Supervised Learning

Learning Spatial and Spatio-Temporal Pixel Aggregations for Image and Video Denoising

3D Human Pose, Shape and Texture from Low-Resolution Images and Videos


This project is a tensorflow implement of our work, ECM (emotional chatting machine).

Neural Responding Machine for Short-Text Conversation

Emotional Chatting Machine: Emotional Conversation Generation with Internal and External Memory

Learning to Express in Knowledge-Grounded Conversation


The repository for our open online course "Research on Corporate Transparency"

The financial reporting environment: Review of the recent literature

The Economics of Disclosure and Financial Reporting Regulation: Evidence and Suggestions for Future Research

Shaping Liquidity: On the Causal Effects of Voluntary Disclosure

Disclosure Processing Costs, Investors’ Information Choice, and Equity Market Outcomes: A Review

Creating Legitimacy for Sustainability Assurance Practices: Evidence from Sustainability Restatements

Non-GAAP Earnings Disclosure in Loss Firms

The marketization of a social movement: Activists, shareholders and CSR disclosure

On the Determinants and Effects of Corporate Tax Transparency: Review of an Emerging Literature

The Pitch: Managers’ Disclosure Choice During IPO Roadshows

Public Tax Disclosures and Investor Perceptions


Bayesian Change-Point Detection and Time Series Decomposition

ENSO-driven extreme oscillations in mean sea level destabilise critical shoreline mangroves—An emerging threat

Smoothing Splines for Discontinuous Signals

Detecting Change Intervals with Isolation Distributional Kernel


R package for analysing proteomics data

Proteus: an R package for downstream analysis of MaxQuant output

A Novel Enrichment Culture Highlights Core Features of Microbial Networks Contributing to Autotrophic Fe(II) Oxidation Coupled to Nitrate Reduction

Girding the loins? Direct evidence of the use of a medieval English parchment birthing girdle from biomolecular analysis

Surfactin Shows Relatively Low Antimicrobial Activity against Bacillus subtilis and Other Bacterial Model Organisms in the Absence of Synergistic Metabolites

LFQ-Based Peptide and Protein Intensity Differential Expression Analysis

Girding the loins? Direct evidence of the use of a medieval parchment birthing girdle from biomolecular analysis

Deep Proteome Profiling Reveals Signatures of Age and Sex Differences in Paw Skin and Sciatic Nerve of Naïve Mice


reference-guided aligner for next-generation sequencing technologies

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

A Novel Bipartite Centrosome Coordinates the Apicomplexan Cell Cycle

Whole transcriptome RNA-Seq allelic expression in human brain

Recent advancement in next-generation sequencing techniques and its computational analysis

Adaptive responses of yeast strains tolerant to acidic pH, acetate, and supraoptimal temperature

Empirical study on software and process quality in bioinformatics tools


Joint Embeddings of Chinese Words, Characters, and Fine-grained Subcharacter Components

VCWE: Visual Character-Enhanced Word Embeddings

Chinese Embedding via Stroke and Glyph Information: A Dual-channel View

A Hybrid Learning Scheme for Chinese Word Embedding

A Comparison on Fine-grained Pre-trained Embeddings for the WMT19Chinese-English News Translation Task

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


Technical document that specifies 0x protocol.

SoK: Decentralized Finance (DeFi)

SoK: Decentralized Exchanges (DEX) with Automated Market Maker (AMM) Protocols

A Survey of Layer-Two Blockchain Protocols

Blockchain as IoT Economy Enabler: A Review of Architectural Aspects

Decentralized Finance (DeFi): A Survey

Explainable AI via Learning to Optimize

Who is gambling? Finding cryptocurrency gamblers using multi-modal retrieval methods

International Journal of Multimedia Information Retrieval


ICNet and PSPNet-50 in Tensorflow for real-time semantic segmentation

Pyramid Scene Parsing Network

Pruning Filters for Efficient ConvNets

ICNet for Real-Time Semantic Segmentation on High-Resolution Images

Real-time CNN-based Segmentation Architecture for Ball Detection in a Single View Setup

PROCEEDINGS OF THE 2ND INTERNATIONAL WORKSHOP ON MULTIMEDIA CONTENT ANALYSIS IN SPORTS, MMSPORTS 2019


project page for VinVL

VinVL: Revisiting Visual Representations in Vision-Language Models

GRIT: Faster and Better Image captioning Transformer Using Dual Visual Features

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

Improving Zero-shot Visual Question Answering via Large Language Models with Reasoning Question Prompts


WaveNet: A Generative Model for Raw Audio

Parallel WaveNet: Fast High-Fidelity Speech Synthesis

Deep Voice 3: Scaling Text-to-Speech with Convolutional Sequence Learning


Skeleton-based action recognition models in PyTorch, including Two-Stream CNN, HCN, HCN-Baseline, Ta-CNN and Dynamic GCN

Joint Distance Maps Based Action Recognition With Convolutional Neural Networks

International Conference on Multimedia and Expo

Co-occurrence Feature Learning from Skeleton Data for Action Recognition and Detection with Hierarchical Aggregation

Dynamic GCN: Context-enriched Topology Learning for Skeleton-based Action Recognition

Topology-aware Convolutional Neural Network for Efficient Skeleton-based Action Recognition


multi-agent deep reinforcement learning for networked system control.

Neural Message Passing for Quantum Chemistry

Learning Multiagent Communication with Backpropagation

Stabilising Experience Replay for Deep Multi-Agent Reinforcement Learning

Fully Decentralized Multi-Agent Reinforcement Learning with Networked Agents

Modeling Others using Oneself in Multi-Agent Reinforcement Learning

Multi-agent Reinforcement Learning for Networked System Control

An Introduction to Multi-Agent Reinforcement Learning and Review of its Application to Autonomous Mobility


An open-source toolbox for fast sampling of diffusion models. Official implementations of our papers published in ICML, CVPR, NeurIPS.

A Geometric Perspective on Diffusion Models

Fast ODE-based Sampling for Diffusion Models in Around 5 Steps

On the Trajectory Regularity of ODE-based Diffusion Sampling


Towards Deep Learning Models Resistant to Adversarial Attacks

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

Overfitting in adversarially robust deep learning

Bag of Tricks for Adversarial Training

Towards Bridging the gap between Empirical and Certified Robustness against Adversarial Examples

Calibrated Adversarial Training

On the Robustness of Neural Collapse and the Neural Collapse of Robustness


Windowed Adaptive Trimming for fastq files using quality

Novel Roles for the Polyphenol Oxidase Enzyme in Secondary Metabolism and the Regulation of Cell Death in Walnut

Cumulus Cell Transcripts Transit to the Bovine Oocyte in Preparation for Maturation

Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment

DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum

Sequencing the transcriptome of milk production: milk trumps mammary tissue

The Fumagillin Gene Cluster, an Example of Hundreds of Genes under veA Control in Aspergillus fumigatus

Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis

Genome-Wide Association and Genomic Prediction for Fry Color in Potato

(Per)Chlorate-Reducing Bacteria Can Utilize Aerobic and Anaerobic Pathways of Aromatic Degradation with (Per)Chlorate as an Electron Acceptor


GilBERTo: A pretrained language model based on RoBERTa for Italian

What the [MASK]? Making Sense of Language-Specific BERT Models

Pre-training Polish Transformer-based Language Models at Scale

IT5: Large-scale Text-to-text Pretraining for Italian Language Understanding and Generation

How "BERTology" Changed the State-of-the-Art also for Italian NLP

Proceedings of the Seventh Italian Conference on Computational Linguistics CLiC-it 2020

Bringing order into the realm of Transformer-based language models for artificial intelligence and law

A Machine Learning approach for Sentiment Analysis for Italian Reviews in Healthcare

Few-shot Named Entity Recognition with Cloze Questions

Agentività e telicità in GilBERTo: implicazioni cognitive

Coherent or Not? Stressing a Neural Language Model for Discourse Coherence in Multiple Languages

Findings of the Association for Computational Linguistics: ACL 2023


Multi-Planar UNet for autonomous segmentation of 3D medical images

U-Net: Convolutional Networks for Biomedical Image Segmentation

One Network to Segment Them All: A General, Lightweight System for Accurate 3D Medical Image Segmentation

Medical Image Computing and Computer-Assisted Intervention

The International Workshop on Osteoarthritis Imaging Knee MRI Segmentation Challenge: A Multi-Institute Evaluation and Analysis Framework on a Standardized Dataset

Deep Structure Learning using Feature Extraction in Trained Projection Space

UNet Architectures in Multiplanar Volumetric Segmentation -- Validated on Three Knee MRI Cohorts


Talking with Hands

A Comprehensive Review of Data-Driven Co-Speech Gesture Generation


The Emotional Voices Database: Towards Controlling the Emotional Expressiveness in Voice Generation Systems

The Emotional Voices Database: Towards Controlling the Emotion Dimension in Voice Generation Systems

Exploring Transfer Learning for Low Resource Emotional TTS

Review of end-to-end speech synthesis technology based on deep learning

A Methodology for Controlling the Emotional Expressiveness in Synthetic Speech -- a Deep Learning approach

MASS: Multi-task Anthropomorphic Speech Synthesis Framework


Models for automatic abstractive summarization

Deep Reinforcement Learning For Sequence to Sequence Models

Dataset for Automatic Summarization of Russian News

Communications in computer and information science

Advances of Transformer-Based Models for News Headline Generation

Importance of Copying Mechanism for News Headline Generation


Global phylogenies of SARS-CoV-2 sequences

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

Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike

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

Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2

bioRxiv : the preprint server for biology

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

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows

Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

Early and ongoing importations of SARS-CoV-2 in Canada

Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA

medRxiv : the preprint server for health sciences


Mutation system for Java programs, including OO mutation operators.

Mutation testing in the wild: findings from GitHub

Zenodo (CERN European Organization for Nuclear Research)

Metamorphic relation prioritization for effective regression testing

Enhance Combinatorial Testing With Metamorphic Relations

IEEE Transactions on Software Engineering


Network Reverse Engineering through AP inference of Mutual Information

Single-cell analyses reveal YAP/TAZ as regulators of stemness and cell plasticity in glioblastoma

A single-cell survey of cellular hierarchy in acute myeloid leukemia

Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Frontiers in cell and developmental biology

Evaluating Pruning Methods in Gene Network Inference

Single-cell protein activity analysis reveals a novel subpopulation of chondrocytes and the corresponding key master regulator proteins associated with anti-senescence and OA progression

The chromatin modulating NSL complex regulates genes and pathways genetically linked to Parkinson’s disease


[CVPR 2020 Workshop] A PyTorch GAN library that reproduces research results for popular GANs.

Pros and Cons of GAN Evaluation Measures: New Developments

InfoMax-GAN: Improved Adversarial Image Generation via Information Maximization and Contrastive Learning

A Systematic Survey of Regularization and Normalization in GANs

A New Perspective on Stabilizing GANs Training: Direct Adversarial Training

Mimicry: Towards the Reproducibility of GAN Research

On Sampling with Approximate Transport Maps

Local-Global MCMC kernels: the best of both worlds

Exploring the Effect of High-frequency Components in GANs Training

BIGRoC: Boosting Image Generation via a Robust Classifier


Official TensorFlow Implementation of Adversarial Training for Free! which trains robust models at no extra cost compared to natural training.

Adversarial Training for Free!

You Only Propagate Once: Accelerating Adversarial Training via Maximal Principle

Bag of Tricks for Adversarial Training

Efficient Adversarial Training with Transferable Adversarial Examples


r:trån is a road space model transformer library for OpenDRIVE, CityGML and beyond

CITYGML AND THE STREETS OF NEW YORK -A PROPOSAL FOR DETAILED STREET SPACE MODELLING

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

Detailed Streetspace Modelling for Multiple Applications: Discussions on the Proposed CityGML 3.0 Transportation Model

ISPRS International Journal of Geo-Information

Spatio-Semantic Road Space Modeling for Vehicle–Pedestrian Simulation to Test Automated Driving Systems

REQUIREMENT ANALYSIS OF 3D ROAD SPACE MODELS FOR AUTOMATED DRIVING


Code base for the precision, recall, density, and coverage metrics for generative models. ICML 2020.

Reliable Fidelity and Diversity Metrics for Generative Models

The Spatially-Correlative Loss for Various Image Translation Tasks

Instance-Conditioned GAN

FreGAN: Exploiting Frequency Components for Training GANs under Limited Data

CG-NeRF: Conditional Generative Neural Radiance Fields

Heavy-tailed denoising score matching

Aligning Synthetic Medical Images with Clinical Knowledge using Human Feedback

VidMuse: A Simple Video-to-Music Generation Framework with Long-Short-Term Modeling


Efficient face emotion recognition in photos and videos

Classifying Emotions and Engagement in Online Learning Based on a Single Facial Expression Recognition Neural Network

IEEE Transactions on Affective Computing

Facial expression and attributes recognition based on multi-task learning of lightweight neural networks

Symposium on Intelligent Systems and Informatics

Frame-level Prediction of Facial Expressions, Valence, Arousal and Action Units for Mobile Devices

EmotiEffNet Facial Features in Uni-task Emotion Recognition in Video at ABAW-5 competition

Neural Network Model for Video-Based Analysis of Student's Emotions in E-Learning

HSE-NN Team at the 4th ABAW Competition: Multi-task Emotion Recognition and Learning from Synthetic Images

HSEmotion Team at the 7th ABAW Challenge: Multi-Task Learning and Compound Facial Expression Recognition


Software for processing and analyzing STARmap experiments.

UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

SpaGE: Spatial Gene Enhancement using scRNA-seq

Accurate inference of genome-wide spatial expression with iSpatial

SpatialMap: Spatial Mapping of Unmeasured Gene Expression Profiles in Spatial Transcriptomic Data Using Generalized Linear Spatial Models


Perceiver-Actor: A Multi-Task Transformer for Robotic Manipulation

GNFactor: Multi-Task Real Robot Learning with Generalizable Neural Feature Fields

Large-Scale Actionless Video Pre-Training via Discrete Diffusion for
  Efficient Policy Learning


Attention over nodes in Graph Neural Networks using PyTorch (NeurIPS 2019)

Benchmarking Graph Neural Networks

Understanding Attention and Generalization in Graph Neural Networks

Automated Data Augmentations for Graph Classification


Library of swarm optimization algorithms.

Comparison of Meta-Heuristics for the Planning of Meshed Power Systems

Comparing Single-Objective Optimization Protocols for Calibrating the Birds Nest Aquifer Model—A Problem Having Multiple Local Optima

International journal of environmental research and public health

Introducing Ulimisana Optimization Algorithm Based on Ubuntu Philosophy


Software for generating a brain-predicted age value, using Gaussian Processes regression, implemented in R

Bias-adjustment in neuroimaging-based brain age frameworks: A robust scheme

Brain-age is associated with progression to dementia in memory clinic patients

Prediction of brain age using structural magnetic resonance imaging: A comparison of accuracy and test-retest reliability of publicly available software packages

Integrated methylome and phenome study of the circulating proteome reveals markers pertinent to brain health

Accelerated brain aging in major depressive disorder and antidepressant treatment response: A CAN-BIND report

Linking Brain Age Gap to Mental and Physical Health in the Berlin Aging Study II

Neuroimaging-Based Brain Age Estimation: A Promising Personalized Biomarker in Neuropsychiatry

Longitudinal trajectories of brain age in young individuals at familial risk of mood disorder from the Scottish Bipolar Family Study

Network Modeling Sex Differences in Brain Integrity and Metabolic Health

Health-related heterogeneity in brain aging and associations with longitudinal change in cognitive function


Code for "Stochastic Optimization of Sorting Networks using Continuous Relaxations", ICLR 2019.

Stochastic Optimization of Sorting Networks via Continuous Relaxations

Abductive Knowledge Induction From Raw Data

ProtoGate: Prototype-based Neural Networks with Local Feature Selection for Tabular Biomedical Data


Unsupervised Domain Adaptive Re-Identification: Theory and Practice

A formal approach to good practices in Pseudo-Labeling for Unsupervised Domain Adaptive Re-Identification

Improving Unsupervised Domain Adaptive Re-Identification Via Source-Guided Selection of Pseudo-Labeling Hyperparameters


SEACR: Sparse Enrichment Analysis for CUT&RUN

Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag

Multifactorial chromatin regulatory landscapes at single cell resolution

A modified CUT&RUN protocol and analysis pipeline to identify transcription factor binding sites in human cell lines

Improved CUT&RUN chromatin profiling and analysis tools

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

Simultaneous CUT&Tag profiling of the accessible and silenced regulome in single cells


Estimate the total emissions for popular CryptoArt platforms.


Graph Classification with Graph Convolutional Networks in PyTorch (NeurIPS 2018 Workshop)

Understanding Attention and Generalization in Graph Neural Networks

Spectral Multigraph Networks for Discovering and Fusing Relationships in Molecules

The Impact of Global Structural Information in Graph Neural Networks Applications

International Conference on Data Technologies and Applications


한글 자모 분리/조합 작업을 위한 툴킷

Investigating an Effective Character-level Embedding in Korean Sentence Classification

Zero-shot North Korean to English Neural Machine Translation by Character Tokenization and Phoneme Decomposition

Meeting of the Association for Computational Linguistics

KoSpeech: Open-Source Toolkit for End-to-End Korean Speech Recognition

Towards an Efficient Code-Mixed Grapheme-to-Phoneme Conversion in an Agglutinative Language: A Case Study on To-Korean Transliteration

Workshop on Computational Approaches to Code Switching


Color composite image creation, mostly following the Lupton, Wherry et al (2004) algorithm.

Space Warps – I. Crowdsourcing the discovery of gravitational lenses

Monthly Notices of the Royal Astronomical Society

Space Warps– II. New gravitational lens candidates from the CFHTLS discovered through citizen science

LinKS: discovering galaxy-scale strong lenses in the Kilo-Degree Survey using convolutional neural networks

Testing convolutional neural networks for finding strong gravitational lenses in KiDS

Imaging extended emission-line regions of obscured AGN with the Subaru Hyper Suprime-Cam Survey

Lenses In VoicE (LIVE): Searching for strong gravitational lenses in the VOICE@VST survey using Convolutional Neural Networks

Survey of Gravitationally lensed Objects in HSC Imaging (SuGOHI) - X. Strong Lens Finding in The HSC-SSP using Convolutional Neural Networks


SemEval-2021 Task 1: Lexical Complexity Prediction

CompLex: A New Corpus for Lexical Complexity Prediction from Likert Scale Data

Predicting lexical complexity in English texts: the Complex 2.0 dataset

cs60075_team2 at SemEval-2021 Task 1 : Lexical Complexity Prediction using Transformer-based Language Models pre-trained on various text corpora


code for "AttentiveNAS Improving Neural Architecture Search via Attentive Sampling"

AttentiveNAS: Improving Neural Architecture Search via Attentive Sampling

AlphaNet: Improved Training of Supernets with Alpha-Divergence

Supernet Training for Federated Image Classification under System Heterogeneity


Official repository for "Revisiting Weakly Supervised Pre-Training of Visual Perception Models". https://arxiv.org/abs/2201.08371.

Expediting Large-Scale Vision Transformer for Dense Prediction without Fine-tuning


[T-PAMI'22] [Jittor & Pytorch] Multiway Non-rigid Point Cloud Registration via Learned Functional Map Synchronization

Multiway Non-Rigid Point Cloud Registration via Learned Functional Map Synchronization

Fast and Robust Non-Rigid Registration Using Accelerated Majorization-Minimization


This repository contains the code used to produce the Global Flood Database and assess changes in population exposed to floods.

Satellite imaging reveals increased proportion of population exposed to floods


Scene Graph Generation by Iterative Message Passing

Neural Motifs: Scene Graph Parsing with Global Context

Mapping Images to Scene Graphs with Permutation-Invariant Structured Prediction


Code associated with the Don't Stop Pretraining ACL 2020 paper

Don't Stop Pretraining: Adapt Language Models to Domains and Tasks

Should We Be Pre-training? An Argument for End-task Aware Training as an Alternative

Efficient Domain Adaptation of Language Models via Adaptive Tokenization

G-MAP: General Memory-Augmented Pre-trained Language Model for Domain Tasks

Task Adaptive Pretraining of Transformers for Hostility Detection


PyTorch code for "Learning Temporal Attention in Dynamic Graphs with Bilinear Interactions"

Language Models Can Improve Event Prediction by Few-Shot Abductive Reasoning

Distill2Vec: Dynamic Graph Representation Learning with Knowledge Distillation

On the Predictive Accuracy of Neural Temporal Point Process Models for Continuous-time Event Data

Learning Representation over Dynamic Graph using Aggregation-Diffusion Mechanism


nway -- Bayesian cross-matching of astronomical catalogues

Finding counterparts for All-sky X-ray surveys with Nway: a Bayesian algorithm for cross-matching multiple catalogues

The XMM-SERVS survey: new XMM-Newton point-source catalog for the
  XMM-LSS field

First constraints on the AGN X-ray luminosity function at z ~ 6 from an eROSITA-detected quasar

The eROSITA Final Equatorial-Depth Survey (eFEDS): A multiwavelength view of WISE mid-infrared galaxies/active galactic nuclei

The ROSAT Raster survey in the north ecliptic pole field

An XMM-Newton View of the Andromeda Galaxy as Explored in a Legacy Survey (New-ANGELS). I. The X-Ray Source Catalog

The Astrophysical Journal Supplement Series

Revisiting X-Ray-bright Optically Normal Galaxies with the Chandra Source Catalog

The Chandra Source Catalog Normal Galaxy Sample


中文自然语言推理数据集（A large-scale Chinese Nature language inference and Semantic similarity calculation Dataset）

Collective Human Opinions in Semantic Textual Similarity

SDA: Simple Discrete Augmentation for Contrastive Sentence Representation Learning


[CVPR 2021 Best Student Paper Honorable Mention, Oral] Official PyTorch code for ClipBERT, an efficient framework for end-to-end learning on image-text and video-text tasks.

Less is More: ClipBERT for Video-and-Language Learning via Sparse Sampling

Revealing Single Frame Bias for Video-and-Language Learning

SQA3D: Situated Question Answering in 3D Scenes

AssistSR: Task-oriented Video Segment Retrieval for Personal AI Assistant

AssistSR: Affordance-centric Question-driven Video Segment Retrieval

The Multi-Modal Video Reasoning and Analyzing Competition


A tensorflow implementation of Knowledge Graph Convolutional Networks

Knowledge Graph Convolutional Networks for Recommender Systems

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

Multi-Task Feature Learning for Knowledge Graph Enhanced Recommendation


Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

Comprehensive identification of transposable element insertions using multiple sequencing technologies

Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder

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


A simple and effective LLM pruning approach.

A Simple and Effective Pruning Approach for Large Language Models

Compressing LLMs: The Truth is Rarely Pure and Never Simple

Decoding Compressed Trust: Scrutinizing the Trustworthiness of Efficient
  LLMs Under Compression

SLEB: Streamlining LLMs through Redundancy Verification and Elimination
  of Transformer Blocks

Draft & Verify: Lossless Large Language Model Acceleration via Self-Speculative Decoding


Binary releases of Vaa3D and related software components

TeraVR empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain

Microglial morphometric analysis: so many options, so little consistency

An imaging analysis protocol to trace, quantify, and model multi-signal neuron morphology


MSE5540/6640 Materials Informatics course at the University of Utah

Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties.

Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals

Self-referencing embedded strings (SELFIES): A 100% robust molecular string representation

Machine Learning for Materials Scientists: An Introductory Guide Towards Best Practices

Benchmarking materials property prediction methods: the Matbench test set and Automatminer reference algorithm

Machine Learning Directed Search for Ultraincompressible, Superhard Materials

Journal of the American Chemical Society

Predicting materials properties without crystal structure: deep representation learning from stoichiometry

Can machine learning identify the next high-temperature superconductor? Examining extrapolation performance for materials discovery

Machine Learning and Energy Minimization Approaches for Crystal Structure Predictions: A Review and New Horizons

Compositionally restricted attention-based network for materials property predictions


An open-source implementation of SEAL for link prediction in open graph benchmark (OGB) datasets.

Link Prediction Based on Graph Neural Networks

Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning

Learning from Counterfactual Links for Link Prediction

Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction

Algorithm and System Co-design for Efficient Subgraph-based Graph Representation Learning

Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking

Revisiting Link Prediction: A Data Perspective

SUREL+: Moving from Walks to Sets for Scalable Subgraph-based Graph Representation Learning

Link Prediction without Graph Neural Networks


FastSpeech: Fast, Robust and Controllable Text to Speech

VRAIN-UPV MLLP's system for the Blizzard Challenge 2021


active learning + reusable workflows + likelihood free inference

A Trust Crisis In Simulation-Based Inference? Your Posterior Approximations Can Be Unfaithful

Compositional Score Modeling for Simulation-based Inference

Towards Reliable Simulation-Based Inference with Balanced Neural Ratio Estimation

Balancing Simulation-based Inference for Conservative Posteriors

AI for Science: An Emerging Agenda


TGL: A General Framework for Temporal GNN Training on Billion-Scale Graphs

Do We Really Need Complicated Model Architectures For Temporal Networks?

Spear and Shield: Adversarial Attacks and Defense Methods for Model-Based Link Prediction on Continuous-Time Dynamic Graphs

On the Generalization Capability of Temporal Graph Learning Algorithms:
  Theoretical Insights and a Simpler Method

A survey of dynamic graph neural networks


ggplot extension: options for tailored facets, multiple colourscales and miscellaneous

Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis

Entropy predicts sensitivity of pseudorandom seeds


Bird tracking - GPS tracking network for large birds

GPS tracking data of Lesser Black-backed Gulls and Herring Gulls breeding at the southern North Sea coast

GPS tracking data of Eurasian oystercatchers (Haematopus ostralegus) from the Netherlands and Belgium

O_WESTERSCHELDE - Eurasian oystercatchers (Haematopus ostralegus, Haematopodidae) breeding in East Flanders (Belgium)

O_SCHIERMONNIKOOG - Eurasian oystercatchers (Haematopus ostralegus, Haematopodidae) breeding on Schiermonnikoog (the Netherlands)

LBBG_ZEEBRUGGE - Lesser black-backed gulls (Larus fuscus, Laridae) breeding at the southern North Sea coast (Belgium and the Netherlands)

MH_ANTWERPEN - Western marsh harriers (Circus aeruginosus, Accipitridae) breeding near Antwerp (Belgium)

O_BALGZAND - Eurasian oystercatchers (Haematopus ostralegus, Haematopodidae) wintering on Balgzand (the Netherlands)

HG_OOSTENDE - Herring gulls (Larus argentatus, Laridae) breeding at the southern North Sea coast (Belgium)

LBBG_JUVENILE - Juvenile lesser black-backed gulls (Larus fuscus, Laridae) hatched in Zeebrugge (Belgium)

O_VLIELAND - Eurasian oystercatchers (Haematopus ostralegus, Haematopodidae) breeding and wintering on Vlieland (the Netherlands)


CUDA-Warp RNN-Transducer

Speech Recognition with Deep Recurrent Neural Networks

Sequence Transduction with Recurrent Neural Networks

Synchronous Transformers for End-to-End Speech Recognition

Cross Attention Augmented Transducer Networks for Simultaneous Translation

Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

BAT: Boundary aware transducer for memory-efficient and low-latency ASR


Code for "Text Generation from Knowledge Graphs with Graph Transformers"

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

A Survey of Knowledge-enhanced Text Generation

Repulsive Attention: Rethinking Multi-head Attention as Bayesian Inference

Identifying Semantic Induction Heads to Understand In-Context Learning

Generalized Supervised Attention for Text Generation


Collection of functions and jupyter notebooks to partially automate running a capacity test following ASTM E2848.


L-BFGS-B, converted from Fortran to C, with Matlab wrapper

Generalized Canonical Polyadic Tensor Decomposition

Learning the Sampling Pattern for MRI

Sketching for Large-Scale Learning of Mixture Models

DTF: Deep Tensor Factorization for Predicting Anticancer Drug Synergy

Data-driven regularization of Wasserstein barycenters with an application to multivariate density registration

Data Assimilation Methods for Neuronal State and Parameter Estimation

The Journal of Mathematical Neuroscience

A Flexible Optimization Framework for Regularized Matrix-Tensor Factorizations With Linear Couplings

IEEE Journal on Selected Topics in Signal Processing

Real-Time Non-Rigid 3D Respiratory Motion Estimation for MR-Guided Radiotherapy Using MR-MOTUS

Estimating Higher-Order Moments Using Symmetric Tensor Decomposition

SIAM Journal on Matrix Analysis and Applications

Riemannian preconditioned algorithms for tensor completion via tensor ring decomposition


C Code generation for NMPC

Aerial navigation in obstructed environments with embedded nonlinear model predictive control

Nonlinear Model Predictive Control for Distributed Motion Planning in Road Intersections Using PANOC

Real-Time Distributed Automation Of Road Intersections


[ICLR 2022] code for "How Much Can CLIP Benefit Vision-and-Language Tasks?" https://arxiv.org/abs/2107.06383

In Defense of Grid Features for Visual Question Answering

Reliable Visual Question Answering: Abstain Rather Than Answer Incorrectly

When are Lemons Purple? The Concept Association Bias of Vision-Language Models

Understanding Multimodal Procedural Knowledge by Sequencing Multimodal Instructional Manuals


Local Burden of Disease

Mapping 123 million neonatal, infant and child deaths between 2000 and 2017

Mapping child growth failure across low- and middle-income countries

Mapping diphtheria-pertussis-tetanus vaccine coverage in Africa, 2000–2016: a spatial and temporal modelling study

Mapping local patterns of childhood overweight and wasting in low- and middle-income countries between 2000 and 2017

Mapping geographical inequalities in oral rehydration therapy coverage in low-income and middle-income countries, 2000–17

The overlapping burden of the three leading causes of disability and death in sub-Saharan African children


Invertible conditional GANs for image editing

Unsupervised Representation Learning with Deep Convolutional Generative Adversarial Networks

AttGAN: Facial Attribute Editing by Only Changing What You Want

DeepFakes and Beyond: A Survey of Face Manipulation and Fake Detection

Invertible Conditional GANs for image editing

Fader Networks: Manipulating Images by Sliding Attributes

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

DNA-GAN: Learning Disentangled Representations from Multi-Attribute Images

An Introduction to Digital Face Manipulation

Handbook of Digital Face Manipulation and Detection


Data sets from subject/item type studies in Psychology and Linguistics

Parsimonious Mixed Models

Statistical Methods for Linguistic Research: Foundational Ideas - Part I

The cave of Shadows. Addressing the human factor with generalized additive mixed models

Bayesian linear mixed models using Stan: A tutorial for psychologists, linguists, and cognitive scientists

That’s not quite it: An experimental investigation of (non‑)exhaustivity in clefts

Tracking your emotions: An eye-tracking study on reader's engagement with perspective during text comprehension

Quarterly journal of experimental psychology (2006)

Production of prosodic cues in coordinate name sequences addressing varying interlocutors

Laboratory Phonology: Journal of the Association for Laboratory Phonology

Remember they were emotional - Effects of emotional qualifiers during sentence processing


Inference-Time Intervention: Eliciting Truthful Answers from a Language Model

PoLLMgraph: Unraveling Hallucinations in Large Language Models via State
  Transition Dynamics

Adaptive Activation Steering: A Tuning-Free LLM Truthfulness Improvement
  Method for Diverse Hallucinations Categories


A Toolkit for Using EnergyPlus in R.

eplusr: A framework for integrating building energy simulation and data-driven analytics


MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.

Constraints on Cosmology and Baryonic Feedback with the Deep Lens Survey Using Galaxy–Galaxy and Galaxy–Mass Power Spectra

Early Release Science of the exoplanet WASP-39b with JWST NIRISS

A broadband thermal emission spectrum of the ultra-hot Jupiter WASP-18b

ULYSSES: Universal LeptogeneSiS Equation Solver

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

Water in the terrestrial planet-forming zone of the PDS 70 disk

Zenodo (CERN European Organization for Nuclear Research)

Carbon monoxide emission lines reveal an inverted atmosphere in the ultra hot Jupiter WASP-33 b consistent with an eastward hot spot

An Updated Mass–Radius Analysis of the 2017–2018 NICER Data Set of PSR J0030+0451

Dark Energy Survey Year 3 results: Galaxy-halo connection from galaxy-galaxy lensing

KERN

Bayesian comparison of interacting modified holographic Ricci dark energy scenarios


Validation of Exoplanet Signals using a Probabilistic Algorithm--- calculating false positive probabilities for transit signals

FALSE POSITIVE PROBABILITIES FOR ALL KEPLER OBJECTS OF INTEREST: 1284 NEWLY VALIDATED PLANETS AND 428 LIKELY FALSE POSITIVES

Stellar and planetary properties of K2 campaign 1 candidates and validation of 17 planets, including a planet receiving Earth-like insolation

K2 DISCOVERS A BUSY BEE: AN UNUSUAL TRANSITING NEPTUNE FOUND IN THE BEEHIVE CLUSTER

The K2-138 System: A Near-resonant Chain of Five Sub-Neptune Planets Discovered by Citizen Scientists

An exomoon survey of 70 cool giant exoplanets and the new candidate Kepler-1708 b-i

DISCOVERY AND VALIDATION OF A HIGH-DENSITY SUB-NEPTUNE FROM THE K2 MISSION

TWO SMALL TEMPERATE PLANETS TRANSITING NEARBY M DWARFS IN K2 CAMPAIGNS 0 AND 1

Validation of Small Kepler Transiting Planet Candidates in or near the Habitable Zone

37 new validated planets in overlapping K2 campaigns

Monthly notices of the Royal Astronomical Society

A PSF-based Approach to TESS High quality data Of Stellar clusters (PATHOS) - IV. Candidate exoplanets around stars in open clusters: frequency and age-planetary radius distribution


Interpretation of cell states using reference single-cell maps

Interpretation of T cell states from single-cell transcriptomics data using reference atlases

A CD4+ T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections

Single-cell transcriptome landscape of circulating CD4+ T cell populations in autoimmune diseases

Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses

SPICA: Swiss portal for immune cell analysis

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


HiCMA: Hierarchical Computations on Manycore Architectures

Tile Low-Rank Approximation of Large-Scale Maximum Likelihood Estimation on Manycore Architectures

Hierarchical algorithms on hierarchical architectures

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

Solving Acoustic Boundary Integral Equations Using High Performance Tile Low-Rank LU Factorization

Efficiency assessment of approximated spatial predictions for large datasets


A comprehensive, unified and modular event extraction toolkit.

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

Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer

KoLA: Carefully Benchmarking World Knowledge of Large Language Models

The Devil is in the Details: On the Pitfalls of Event Extraction Evaluation

OmniEvent: A Comprehensive, Fair, and Easy-to-Use Toolkit for Event Understanding

CorefPrompt: Prompt-based Event Coreference Resolution by Measuring Event Type and Argument Compatibilities


Chemical Kinetics For Exoplanetary Atmospheres

VULCAN: An Open-source, Validated Chemical Kinetics Python Code for Exoplanetary Atmospheres

A solar C/O and sub-solar metallicity in a hot Jupiter atmosphere

Photochemically-produced SO_2 in the atmosphere of WASP-39b

A Comparative Study of Atmospheric Chemistry with VULCAN

A broadband thermal emission spectrum of the ultra-hot Jupiter WASP-18b

ANALYTICAL MODELS OF EXOPLANETARY ATMOSPHERES. III. GASEOUS C–H–O–N CHEMISTRY WITH NINE MOLECULES

Inferring Shallow Surfaces on Sub-Neptune Exoplanets with JWST

SO2, silicate clouds, but no CH4 detected in a warm Neptune.

Evidence for disequilibrium chemistry from vertical mixing in hot Jupiter atmospheres

Atmospheric compositions and observability of nitrogen-dominated ultra-short-period super-Earths


fast phage annotation program

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Predicting stop codon reassignment improves functional annotation of bacteriophages

bioRxiv : the preprint server for biology

Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages


Python code for Biased tracers in redshift space

The Hubble tension in light of the Full-Shape analysis of Large-Scale Structure data

Journal of Cosmology and Astroparticle Physics

Limits on wCDM from the EFTofLSS with the PyBird code

Early modified gravity in light of the H0 tension and LSS data

BOSS Correlation Function analysis from the Effective Field Theory of Large-Scale Structure

Dark sector to restore cosmological concordance

Updated constraints from the effective field theory analysis of the BOSS power spectrum on early dark energy

Constraining decaying dark matter with BOSS data and the effective field theory of large-scale structures

Limits on primordial non-Gaussianities from BOSS galaxy-clustering data

Consistency of effective field theory analyses of the BOSS power spectrum

Limits on clustering and smooth quintessence from the EFTofLSS


The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

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

The genome of broomcorn millet

Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution

The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales

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

Genomic basis of homoploid hybrid speciation within chestnut trees

High-depth resequencing reveals hybrid population and insecticide resistance characteristics of fall armyworm (Spodoptera frugiperda) invading China

Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation

The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation

Meliaceae genomes provide insights into wood development and limonoids biosynthesis


Protein-compound affinity prediction through unified RNN-CNN

DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks

ATOM3D: Tasks On Molecules in Three Dimensions

A brief review of protein–ligand interaction prediction

Computational and structural biotechnology journal

Pretraining model for biological sequence data

Trends and Potential of Machine Learning and Deep Learning in Drug Study at Single-Cell Level


Numerical Manufacturing And Design Tool (NuMAD) -- A design tool for wind and water turbine composite blades

Land-based wind turbines with flexible rail-transportable blades - Part 2: 3D finite element design optimization of the rotor blades


TensorFlow port of PyTorch Image Models (timm) - image models with pretrained weights.

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

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

A ConvNet for the 2020s

Segment Anything

Pyramid Vision Transformer: A Versatile Backbone for Dense Prediction without Convolutions

MLP-Mixer: An all-MLP Architecture for Vision

PVT v2: Improved baselines with Pyramid Vision Transformer

Going deeper with Image Transformers

MetaFormer is Actually What You Need for Vision

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


R package for extracting and visualizing mutational patterns in base substitution catalogues

MutationalPatterns: comprehensive genome-wide analysis of mutational processes

Transient commensal clonal interactions can drive tumor metastasis

Stratification of HPV‐associated and HPV‐negative oropharyngeal squamous cell carcinomas based on DNA methylation epigenotypes

The chemotherapeutic drug CX-5461 is a potent mutagen in cultured human cells

The cytidine deaminase APOBEC3G drives cancer mutagenesis and clonal evolution in bladder cancer


Fetch NCDC ISD, TMY3, or CZ2010 weather data that corresponds to ZIP Code Tabulation Areas or Latitude/Longitude.


Analysis and Optimization of Loss Functions for Multiclass, Top-k, and Multilabel Classification

Multi-Label Sampling based on Local Label Imbalance

Synthetic Oversampling of Multi-Label Data based on Local Label Distribution


binned motif enrichment analysis and visualisation

monaLisa: an R/Bioconductor package for identifying regulatory motifs

A unique bipartite Polycomb signature regulates stimulus-response transcription during development

Reorganization of postmitotic neuronal chromatin accessibility for maturation of serotonergic identity


Chapel HyperGraph Library (CHGL) - HPC-class Hypergraphs in Chapel

Hypernetwork Science via High-Order Hypergraph Walks

Hypernetwork Science: From Multidimensional Networks to Computational Topology

Analyzing, Exploring, and Visualizing Complex Networks via Hypergraphs using SimpleHypergraphs.jl

Topological Simplifications of Hypergraphs


Novelty-inclusive microbial community profiling of shotgun metagenomes

Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution

Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient

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

Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities

Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf

Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline


The Constrained and Unconstrained Testing Environment with safe threads (CUTEst) for optimization software

A Globally Convergent Gradient Method with Momentum

Accelerated derivative-free spectral residual method for nonlinear systems of equations

Model-Based Derivative-Free Optimization Methods and Software


A Python framework for sequence labeling evaluation(named-entity recognition, pos tagging, etc...)

Improving Multilingual Models with Language-Clustered Vocabularies

Multi-Domain Goal-Oriented Dialogues (MultiDoGO): Strategies toward Curating and Annotating Large Scale Dialogue Data

Empirical Methods in Natural Language Processing

Indic-Transformers: An Analysis of Transformer Language Models for Indian Languages

Learning to Classify Intents and Slot Labels Given a Handful of Examples

No One Left Behind: Inclusive Federated Learning over Heterogeneous Devices

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

LINGUIST: Language Model Instruction Tuning to Generate Annotated Utterances for Intent Classification and Slot Tagging

PERT: Pre-training BERT with Permuted Language Model

Joint Chinese Word Segmentation and Part-of-speech Tagging via Multi-channel Attention of Character N-grams

International Conference on Computational Linguistics

Downstream Datasets Make Surprisingly Good Pretraining Corpora

Event Causality Identification with Causal News Corpus - Shared Task 3, CASE 2022


dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data

Mapping the developing human immune system across organs

Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins

The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres

Early human lung immune cell development and its role in epithelial cell fate


Woltka: a versatile meta'omic data classifier

Effects of ‘Healthy’ Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References

Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing

The Impact of Maternal Asthma on the Preterm Infants' Gut Metabolome and Microbiome - The Microbiome, Atopic Disease, and Prematurity (MAP) Study


:bike: Extract data from public hire bicycle systems


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

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

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

Microscopic understanding of magnetic interactions in bilayer CrI 3

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

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

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

Dynamic symmetry breaking and spin splitting in metal halide perovskites

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

Research Portal (Queen's University Belfast)

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

ComDMFT: A massively parallel computer package for the electronic structure of correlated-electron systems


Home of Arachne and other Arkouda functionality provided by researchers at NJIT

Arachne: An Arkouda Package for Large-Scale Graph Analytics

IEEE Conference on High Performance Extreme Computing

Contour Algorithm for Connectivity

High-Performance Truss Analytics in Arkouda

International Conference on High Performance Computing

Property Graphs in Arachne


Geometric operations on polytopes of any dimension

Learning Strategy-Aware Linear Classifiers

Multi-Agent Safety Verification using Symmetry Transformations

Grinding the Space: Learning to Classify Against Strategic Agents

A Consistency Constraint-Based Approach to Coupled State Constraints in Distributed Model Predictive Control


gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS.

Journal of chemical theory and computation

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

The Motion Paradigm of Pre-Dock Zearalenone Hydrolase Predictions with Molecular Dynamics and the Docking Phase with Umbrella Sampling


1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

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

Hi-C analysis: from data generation to integration

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

Chromosome Structure I: Loop extrusion or boundary:boundary pairing?

lncRNA read-through regulates the BX-C insulator Fub-1

Chromosome Structure II: Stem-loops and circle-loops

Systematic characterization of regulatory variants of blood pressure genes

The insulating activity of theDrosophilaBX-C chromatin boundaryFub-1is parasegmentally regulated by lncRNA read-through


腾讯事务处理技术验证系统（Tencent Transaction Processing Testbed System）

Systematic definition and classification of data anomalies in DBMS (English Version)

Coo: Consistency Check for Transactional Databases


Multiple Scattering Theory code for first principles calculations

Ab initio approaches to high-entropy alloys: a comparison of CPA, SQS, and supercell methods

An investigation of high entropy alloy conductivity using first-principles calculations

Averaged cluster approach to including chemical short-range order in KKR-CPA

Tests on the Accuracy and Scalability of the Full-Potential DFT Method Based on Multiple Scattering Theory


Large scale graph learning on a single machine.

Marius: Learning Massive Graph Embeddings on a Single Machine

SMORE: Knowledge Graph Completion and Multi-hop Reasoning in Massive Knowledge Graphs

MariusGNN: Resource-Efficient Out-of-Core Training of Graph Neural Networks


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

The CMS monitoring infrastructure and applications

Exploiting Apache Spark platform for CMS computing analytics

The evolution of the CMS monitoring infrastructure

Big data solutions for CMS computing monitoring and analytics


The TLA Proof Manager

Formal Verification of Multi-Paxos for Distributed Consensus

Towards an Automatic Proof of Lamport's Paxos

Simpler Specifications and Easier Proofs of Distributed Algorithms Using History Variables

Smart Casual Verification of CCF's Distributed Consensus and Consistency
  Protocols


Generalized Out-of-Distribution Detection: A Survey

ViM: Out-Of-Distribution with Virtual-logit Matching

OpenOOD: Benchmarking Generalized Out-of-Distribution Detection

OpenOOD v1.5: Enhanced Benchmark for Out-of-Distribution Detection

Full-Spectrum Out-of-Distribution Detection

Nearest Neighbor Guidance for Out-of-Distribution Detection

DiffGuard: Semantic Mismatch-Guided Out-of-Distribution Detection using Pre-trained Diffusion Models

Neuron Activation Coverage: Rethinking Out-of-distribution Detection and Generalization

Diffusion Denoising Process for Perceptron Bias in Out-of-distribution Detection

NECO: NEural Collapse Based Out-of-distribution detection


Package for dynamical modeling of power grids

PowerDynamics.jl - An experimentally validated open-source package for the dynamical analysis of power grids.


Modular Multiobjective (Hyper) Neuro-Evolution of Augmenting Topologies + MAP-Elites: Java code for evolving intelligent agents in Ms. Pac-Man, Tetris, and more, as well as code for Procedural Content Generation in Mario, Zelda, Minecraft, and more!

CPPN2GAN: Combining Compositional Pattern Producing Networks and GANs for Large-scale Pattern Generation

Genetic and Evolutionary Computation Conference

Illuminating the Space of Beatable Lode Runner Levels Produced By Various Generative Adversarial Networks

Using Multiple Generative Adversarial Networks to Build Better-Connected Levels for Mega Man

Hybrid Encoding for Generating Large Scale Game Level Patterns With Local Variations

Evolving Flying Machines in Minecraft Using Quality Diversity


An easy-to-use reinforcement learning library for research and education.

UCB Momentum Q-learning: Correcting the bias without forgetting

Kernel-Based Reinforcement Learning: A Finite-Time Analysis

Near Instance-Optimal PAC Reinforcement Learning for Deterministic MDPs

Online Policy Optimization for Robust MDP

Optimistic Posterior Sampling for Reinforcement Learning with Few Samples and Tight Guarantees

Bandits Corrupted by Nature: Lower Bounds on Regret and Robust Optimistic Algorithm

Model-free Posterior Sampling via Learning Rate Randomization

Entropy Regularized Reinforcement Learning with Cascading Networks

Adversarial Online Multi-Task Reinforcement Learning


Python library for supernova cosmology

Sifting for Sapphires: Systematic Selection of Tidal Disruption Events in iPTF

The Astrophysical journal. Supplement series

SALT3-NIR: Taking the Open-source Type Ia Supernova Model to Longer Wavelengths for Next-generation Cosmological Measurements

Out of One, Many: Distinguishing Time Delays from Lensed Supernovae

Deep learning unresolved lensed light curves


Supernova Analysis package

The Pantheon+ Analysis: The Full Dataset and Light-Curve Release

The Dark Energy Survey supernova programme: modelling selection efficiency and observed core-collapse supernova contamination

Monthly Notices of the Royal Astronomical Society

SNIa Cosmology Analysis Results from Simulated LSST Images: From Difference Imaging to Constraints on Dark Energy

The Young Supernova Experiment Data Release 1 (YSE DR1): Light Curves and Photometric Classification of 1975 Supernovae

Fink: early supernovae Ia classification using active learning

The Dark Energy Survey: Cosmology Results With ~1500 New High-redshift Type Ia Supernovae Using The Full 5-year Dataset

Using Host Galaxy Photometric Redshifts to Improve Cosmological Constraints with Type Ia Supernovae in the LSST Era

First Impressions: Early-time Classification of Supernovae Using Host-galaxy Information and Shallow Learning

The Dark Energy Survey Supernova Program: Cosmological Analysis and Systematic Uncertainties

Using rest-frame optical and NIR data from the RAISIN survey to explore the redshift evolution of dust laws in SN Ia host galaxies


A diverse suite of scalable reinforcement learning environments in JAX

Podracer architectures for scalable Reinforcement Learning

Jumanji: a Diverse Suite of Scalable Reinforcement Learning Environments in JAX

QDax: A Library for Quality-Diversity and Population-based Algorithms with Hardware Acceleration

Combinatorial Optimization with Policy Adaptation using Latent Space Search

XLand-MiniGrid: Scalable Meta-Reinforcement Learning Environments in JAX


Open source implementation of "Neural Message Passing for Quantum Chemistry"

Graph Neural Networks: A Review of Methods and Applications

Deep Learning on Graphs: A Survey

Expressive Graph Informer Networks


A collection of small-sample, high-dimensional microarray data sets to assess machine-learning algorithms and models.

Second-generation p-values: Improved rigor, reproducibility, & transparency in statistical analyses

Data Generators for Learning Systems Based on RBF Networks

IEEE transactions on neural networks and learning systems

On the Use of Random Forest for Two-Sample Testing

An update on statistical boosting in biomedicine

Distance-based classifier by data transformation for high-dimension, strongly spiked eigenvalue models

A Novel Hybrid Classification Method Based on the Opposition-Based Seagull Optimization Algorithm

Targeted Random Projection for Prediction From High-Dimensional Features

Journal of the American Statistical Association

Classification for high-dimension low-sample size data

Assessing Methods for Evaluating the Number of Components in Non-Negative Matrix Factorization

Sparse quadratic classification rules via linear dimension reduction


Data and analysis for the BuzzFeed News article, "Hyperpartisan Facebook Pages Are Publishing False And Misleading Information At An Alarming Rate."

A Stylometric Inquiry into Hyperpartisan and Fake News

Hong Kong Protests: Using Natural Language Processing for Fake News Detection on Twitter

IFIP advances in information and communication technology

Monant Medical Misinformation Dataset: Mapping Articles to Fact-Checked Claims

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

Disinformation Detection: A review of linguistic feature selection and classification models in news veracity assessments


3D city model viewer for Mac

Tools for BIM-GIS Integration (IFC Georeferencing and Conversions): Results from the GeoBIM Benchmark 2019

ISPRS International Journal of Geo-Information

Reference study of IFC software support: The GeoBIM benchmark 2019—Part I

A DATA STRUCTURE TO INCORPORATE VERSIONING IN 3D CITY MODELS

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

Multisource spatial data integration for use cases applications

Visualising higher-dimensional space-time and space-scale objects as projections to ℝ^3


Molweni: A Challenge Multiparty Dialogues-based Machine Reading Comprehension Dataset with Discourse Structure

Speaker-Aware Discourse Parsing on Multi-Party Dialogues

Task-Aware Self-Supervised Framework for Dialogue Discourse Parsing

Findings of the Association for Computational Linguistics: EMNLP 2023


Code release for Hu et al. Learning to Reason: End-to-End Module Networks for Visual Question Answering. in ICCV, 2017

A Corpus for Reasoning About Natural Language Grounded in Photographs

CLEVR-Dialog: A Diagnostic Dataset for Multi-Round Reasoning in Visual Dialog

Fooling Vision and Language Models Despite Localization and Attention Mechanism

Can you fool AI with adversarial examples on a visual Turing test

Mimic and Fool: A Task-Agnostic Adversarial Attack

Inverse Visual Question Answering: A New Benchmark and VQA Diagnosis Tool

Language Features Matter: Effective Language Representations for Vision-Language Tasks

Probing Cross-Modal Representations in Multi-Step Relational Reasoning

Workshop on Representation Learning for NLP


GQA: Training Generalized Multi-Query Transformer Models from Multi-Head Checkpoints

UL2: Unifying Language Learning Paradigms

LongT5: Efficient Text-To-Text Transformer for Long Sequences

Scaling Up Models and Data with  and

MAGVIT: Masked Generative Video Transformer

All You May Need for VQA are Image Captions

CoLT5: Faster Long-Range Transformers with Conditional Computation

PropSegmEnt: A Large-Scale Corpus for Proposition-Level Segmentation and Entailment Recognition

Alternating Gradient Descent and Mixture-of-Experts for Integrated Multimodal Perception

mLongT5: A Multilingual and Efficient Text-To-Text Transformer for Longer Sequences


CheXstray: Real-time Multi-Modal Data Concordance for Drift Detection in Medical Imaging AI

CheXstray: A Real-Time Multi-Modal Monitoring Workflow for Medical Imaging AI

MEDICAL IMAGE COMPUTING AND COMPUTER ASSISTED INTERVENTION, MICCAI 2023, PT III