Code base for profiling highly replicated differential gene expression RNA-seq.

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results

Personalized beyond Precision: Designing Unbiased Gold Standards to Improve Single-Subject Studies of Personal Genome Dynamics from Gene Products

Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values


The MR-Base platform supports systematic causal inference across the human phenome

Implementing MR-PRESSO and GCTA-GSMR for pleiotropy assessment in Mendelian randomization studies from a practitioner's perspective

Exploiting horizontal pleiotropy to search for causal pathways within a Mendelian randomization framework


Creative Commons Attribution 4.0 International

Table of Multiplexed Assay of Variant Effect (MAVE) studies

Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding

bioRxiv : the preprint server for biology

Accurate classification of BRCA1 variants with saturation genome editing

Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay

Massively parallel functional dissection of mammalian enhancers in vivo

Local fitness landscape of the green fluorescent protein

High-resolution mapping of protein sequence-function relationships

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

The spatial architecture of protein function and adaptation

Computational design of ligand-binding proteins with high affinity and selectivity

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay


Pushshift API

From Pretraining Data to Language Models to Downstream Tasks: Tracking the Trails of Political Biases Leading to Unfair NLP Models

COVID-Fact: Fact Extraction and Verification of Real-World Claims on COVID-19 Pandemic

Something's Brewing! Early Prediction of Controversy-causing Posts from Discussion Features

Detection of Mental Health from Reddit via Deep Contextualized Representations

International Workshop on Health Text Mining and Information Analysis

Personalized Response Generation via Generative Split Memory Network

North American Chapter of the Association for Computational Linguistics

Schizophrenia Detection Using Machine Learning Approach from Social Media Content

Native Language Cognate Effects on Second Language Lexical Choice

Detection of Suicidality Among Opioid Users on Reddit: Machine Learning–Based Approach

Are Deepfakes Concerning? Analyzing Conversations of Deepfakes on Reddit and Exploring Societal Implications

PROCEEDINGS OF THE 2022 CHI CONFERENCE ON HUMAN FACTORS IN COMPUTING SYSTEMS (CHI' 22)

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

Workshop on Biomedical Natural Language Processing


Language family classifications as Newick trees

Languages Support Efficient Communication about the Environment: Words for Snow Revisited

Making genealogical language classifications available for phylogenetic analysis

Defining and Counting Phonological Classes in Cross-linguistic Segment Databases


Muller diagrams excel at visualizing evolutionary dynamics of a population over time.  A common use case, and the intended use case during development, describes the abundance and succession of genotypes within a population derived from  sequencing data from samples at specified timepoints.  This provides a useful method of quickly discerning the evolutionary relationship between genotypes seen in a population and how this changes over time.

Parallel Evolution of Tobramycin Resistance across Species and Environments

On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis

Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance

Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis

Parallel genetic adaptation of Bacillus subtilis to different plant species

Species and condition shape the mutational spectrum in experimentally evolved biofilms

Following the Trail of One Million Genomes: Footprints of SARS-CoV-2 Adaptation to Humans


Create and manipulate stellar light curves!

Hot planets around cool stars -- two short-period mini-Neptunes
  transiting the late K-dwarf TOI-1260

Monthly Notices of the Royal Astronomical Society

TOI-2196 b: Rare planet in the hot Neptune desert transiting a G-type star

TOI-733 b: A planet in the small-planet radius valley orbiting a Sun-like star


Chapel-based Optimization

A comparative study of high-productivity high-performance programming languages for parallel metaheuristics

Towards ultra-scale Branch-and-Bound using a high-productivity language

Productivity-Aware Design and Implementation of Distributed Tree-Based Search Algorithms

An Incremental Parallel PGAS-based Tree Search Algorithm

International Symposium on High Performance Computing Systems and Applications

Dynamic Configuration of CUDA Runtime Variables for CDP-Based Divide-and-Conquer Algorithms


The MegaMorph version of GALAPAGOS

Galaxy And Mass Assembly (GAMA): understanding the wavelength dependence of galaxy structure with bulge-disc decompositions

Galapagos-2/Galfitm/Gama – Multi-wavelength measurement of galaxy structure: Separating the properties of spheroid and disk components in modern surveys

The KMOS Cluster Survey (KCS). III. Fundamental Plane of Cluster Galaxies atz≃ 1.80 in JKCS 041

Hubble Frontier Field Clusters and Their Parallel Fields: Photometric and Photometric Redshift Catalogs

Zenodo (CERN European Organization for Nuclear Research)

Euclid preparation. XXV. The Euclid Morphology Challenge -- Towards model-fitting photometry for billions of galaxies

HAL (Le Centre pour la Communication Scientifique Directe)

Euclid preparation


Fast genealogical relationship evaluation of bacterial isolates with WGS data.

Genome-by-genome approach for fast bacterial genealogical relationship evaluation

Comparative Genomics of Shiga Toxin-Producing Escherichia coli Strains Isolated from Pediatric Patients with and without Hemolytic Uremic Syndrome from 2000 to 2016 in Finland

High Prevalence and Persistence of Escherichia coli Strains Producing Shiga Toxin Subtype 2k in Goat Herds

Genomic Insights Into Clinical Shiga Toxin-Producing Escherichia coli Strains: A 15-Year Period Survey in Jönköping, Sweden

High prevalence and pathogenic potential of Shiga toxin-producing Escherichia coli strains in raw mutton and beef in Shandong, China


Carbon Dioxide Removal (CDR) Modeling Experiments

Emulating coupled atmosphere-ocean and carbon cycle models with a simpler model, MAGICC6 - Part 1: Model description and calibration

Pymagicc: A Python wrapper for the simple climate model MAGICC


CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification of environmental marker genes from sequencing-based community profiling studies.

Benthic eDNA metabarcoding provides accurate assessments of impact from oil extraction, and ecological insights

Planctomycetes as a Vital Constituent of the Microbial Communities Inhabiting Different Layers of the Meromictic Lake Sælenvannet (Norway)

Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

Shared and contrasting associations in the dynamic nano‐ and picoplankton communities of two close but contrasting sites from the Bay of Biscay


Compute mean telomere length from Whole Genome Sequencing data.

Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data

Telomere Length Maintenance and Its Transcriptional Regulation in Lynch Syndrome and Sporadic Colorectal Carcinoma


Readers and converters for ESA CCI Soil Moisture image and time series data. Written in Python.


:package: R/medoutcon: Efficient Causal Mediation Analysis with Natural and Interventional Direct/Indirect Effects

Double/Debiased Machine Learning for Treatment and Structural Parameters

Effect Decomposition in the Presence of an Exposure-Induced Mediator-Outcome Confounder

Cross-Validated Targeted Minimum-Loss-Based Estimation

Longitudinal Mediation Analysis with Time-varying Mediators and Exposures, with Application to Survival Outcomes

Nonparametric efficient causal mediation with intermediate confounders

Robust and Flexible Estimation of Stochastic Mediation Effects: A Proposed Method and Example in a Randomized Trial Setting

Nonparametric inference for interventional effects with multiple mediators

medoutcon: Nonparametric efficient causal mediation analysis with machine learning in R


Fiber Architecture Simulation Toolbox for 3D Polarized Light Imaging

Understanding fiber mixture by simulation in 3D Polarized Light Imaging

MEDUSA: A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres

Derivation of Fiber Orientations From Oblique Views Through Human Brain Sections in 3D-Polarized Light Imaging

fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI


a python package for reduced density matrix techniques

Linear and nonlinear spectroscopy from quantum master equations

A partially linearized spin-mapping approach for simulating nonlinear optical spectra

A simple improved low temperature correction for the hierarchical equations of motion.

Detailed balance in mixed quantum-classical mapping approaches

On detailed balance in nonadiabatic dynamics: From spin spheres to equilibrium ellipsoids


The Sloan Digital Sky Survey Quasar Catalog: Sixteenth Data Release

The Astrophysical Journal Supplement Series

The Completed SDSS-IV Extended Baryon Oscillation Spectroscopic Survey: Baryon Acoustic Oscillations with Lyα Forests

QuasarNET: Human-level spectral classification and redshifting with Deep Neural Networks

Detecting and Characterizing Mg ii Absorption in DESI Survey Validation Quasar Spectra

A striking relationship between dust extinction and radio detection in DESI QSOs: evidence for a dusty blow-out phase in red QSOs


Modified Gravity and Cosmology with Binary Black Holes' Population models : hierarchical bayesian inference package for constraining the Hubble constant, modified GW propagation and BBH population models with GWs.

Forecasting the Detection Capabilities of Third-generation Gravitational-wave Detectors Using GWFAST

Gravitational-wave cosmology with dark sirens: state of the art and perspectives for 3G detectors

Proceedings of 41st International Conference on High Energy physics — PoS(ICHEP2022)

Cosmology and Astrophysics with Standard Sirens and Galaxy Catalogs in View of Future Gravitational Wave Observations


Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly

BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly

Proceedings of the 51st International Conference on Parallel Processing


Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA

Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks

Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius

Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa

Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures

Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

Transcriptional biomarker discovery toward building a load stress reporting system for engineered Escherichia coli strains


A Scalable and Generalizable Pathloss Map Prediction

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

PMNet: Robust Pathloss Map Prediction via Supervised Learning


Speaker embedding (d-vector) trained with GE2E loss

Generalized End-to-End Loss for Speaker Verification

Investigating on Incorporating Pretrained and Learnable Speaker Representations for Multi-Speaker Multi-Style Text-to-Speech

JTubeSpeech: corpus of Japanese speech collected from YouTube for speech recognition and speaker verification

MediumVC: Any-to-any voice conversion using synthetic specific-speaker speeches as intermedium features

Back Translation for Speech-to-text Translation Without Transcripts

DASpeech: Directed Acyclic Transformer for Fast and High-quality Speech-to-Speech Translation

Probing Deep Speaker Embeddings for Speaker-related Tasks


DIA-NN - a universal automated software suite for DIA proteomics data analysis.

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

A time-resolved proteomic and prognostic map of COVID-19

Single-Shot 10K Proteome Approach: Over 10,000 Protein Identifications by Data-Independent Acquisition-Based Single-Shot Proteomics with Ion Mobility Spectrometry

High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe

High-throughput proteomic sample preparation using pressure cycling technology

Optimization of Ultrafast Proteomics Using an LC-Quadrupole-Orbitrap Mass Spectrometer with Data-Independent Acquisition

A Comparative Analysis of Data Analysis Tools for Data-Independent Acquisition Mass Spectrometry


Code for the paper "Clinical Reading Comprehension: A Thorough Analysis of the emrQA Dataset" (ACL 2020)

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

Reading Wikipedia to Answer Open-Domain Questions

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


This project is a collection of tools for bioinformatic processing of ancient DNA data at the Harvard Medical School Reich Lab.

The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean

The Anglo-Saxon migration and the formation of the early English gene pool

A minimally destructive protocol for DNA extraction from ancient teeth

An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

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

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

A genetic history of the Balkans from Roman frontier to Slavic migrations


power spectrum and window function estimation

A Multi-tracer Analysis for the eBOSS galaxy sample based on the effective field theory of Large-scale structure

DESI 2024 III: Baryon Acoustic Oscillations from Galaxies and Quasars

The DESI One-Percent Survey: Modelling the clustering and halo occupation of all four DESI tracers with Uchuu

Optimal Reconstruction of Baryon Acoustic Oscillations for DESI 2024

HOD-Dependent Systematics for Luminous Red Galaxies in the DESI 2024 BAO Analysis

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

ELG Spectroscopic Systematics Analysis of the DESI Data Release 1


alfonso: ALgorithm For Non-Symmetric Optimization

A homogeneous interior-point algorithm for nonsymmetric convex conic optimization

Sum-of-squares optimization without semidefinite programming

Alfonso: Matlab Package for Nonsymmetric Conic Optimization

Performance enhancements for a generic conic interior point algorithm

Complexity Analysis of a Sampling-Based Interior Point Method for Convex Optimization


Programs for analysis and visualization of oceanographic HF radar data

The Global High Frequency Radar Network

Best Practices on High Frequency Radar Deployment and Operation for Ocean Current Measurement

Sensitivity of Skill Score Metric to Validate Lagrangian Simulations in Coastal Areas: Recommendations for Search and Rescue Applications

Integration of HF Radar Observations for an Enhanced Coastal Mean Dynamic Topography

Variational interpolation of high-frequency radar surface currents using DIVAnd


Deform meshes by reinforcement learning

Accelerating 3D Deep Learning with PyTorch3D

Mesh R-CNN

Kaolin: A PyTorch Library for Accelerating 3D Deep Learning Research

Modeling 3D Shapes by Reinforcement Learning


Causal inference is a critical task in various fields such as healthcare,economics, marketing and education. Recently, there have beensignificant advances through the application of machine learningtechniques, especially deep neural networks. Unfortunately, to-datemany of the proposed methods are evaluated on different (data,software/hardware, hyperparameter) setups and consequently it isnearly impossible to compare the efficacy of the available methodsor reproduce results presented in original research manuscripts.In this paper, we propose a causal inference toolbox (CauseBox)that addresses the aforementioned problems. At the time of thewriting, the toolbox includes seven state of the art causal inferencemethods and two benchmark datasets. By providing convenientcommand-line and GUI-based interfaces, theCauseBoxtoolboxhelps researchers fairly compare the state of the art methods intheir chosen application context against benchmark datasets.

Evaluation Methods and Measures for Causal Learning Algorithms

CauseBox: A Causal Inference Toolbox for Benchmarking Treatment Effect Estimators with Machine Learning Methods

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

Survey on Trustworthy Graph Neural Networks: From A Causal Perspective


General Inversion of Phase Technique (GIPhT)

Graph theory for analyzing pair-wise data: application to geophysical model parameters estimated from interferometric synthetic aperture radar data at Okmok volcano, Alaska

Geodetic Measurements and Numerical Models of Deformation at Coso Geothermal Field, California, USA, 2004–2016

Bayesian Inversion of Wrapped Satellite Interferometric Phase to Estimate Fault and Volcano Surface Ground Deformation Models

Journal of Geophysical Research: Solid Earth

Spatio-temporal analysis and volumetric characterization of interferometric synthetic aperture radar-observed deformation signatures related to underground and in situ leach mining


Library for discrete Lehmann representation of imaginary time Green's functions

Discrete Lehmann representation of imaginary time Green's functions

libdlr: Efficient imaginary time calculations using the discrete Lehmann representation

A fast time domain solver for the equilibrium Dyson equation

Low-rank Green's function representations applied to dynamical mean-field theory

cppdlr: Imaginary time calculations using the discrete Lehmann
  representation


Easily Process a Batch of Cox Models

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

Integrative genomic and transcriptomic analysis reveals immune subtypes and prognostic markers in ovarian clear cell carcinoma

A New Prognostic Risk Score: Based on the Analysis of Autophagy-Related Genes and Renal Cell Carcinoma

ezcox: An R/CRAN Package for Cox Model Batch Processing and Visualization


Code for: S.R. Qasim, H. Mahmood, and F. Shafait, Rethinking Table Recognition using Graph Neural Networks (2019)

Current Status and Performance Analysis of Table Recognition in Document Images With Deep Neural Networks

A Study on Reproducibility and Replicability of Table Structure Recognition Methods


R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)

An Introduction to the Analysis of Single-Cell RNA-Sequencing Data

Molecular therapy. Methods & clinical development

Single-Cell Transcriptional Profiling of Aortic Endothelium Identifies a Hierarchy from Endovascular Progenitors to Differentiated Cells

ascend: R package for analysis of single-cell RNA-seq data

Generation of human neural retina transcriptome atlas by single cell RNA sequencing


Convert biological neuronal networks to artificial recurrent neuronal networks

A mesoscale connectome of the mouse brain

A Weighted and Directed Interareal Connectivity Matrix for Macaque Cerebral Cortex

Three-Dimensional Reconstruction of Brain-wide Wiring Networks in Drosophila at Single-Cell Resolution

Wiring cost and topological participation of the mouse brain connectome

Specificity and robustness of long-distance connections in weighted, interareal connectomes

The Mouse Cortical Connectome, Characterized by an Ultra-Dense Cortical Graph, Maintains Specificity by Distinct Connectivity Profiles

Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template

Bio-instantiated recurrent neural networks: Integrating neurobiology-based network topology in artificial networks

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


GP Sinkhorn Implementation, paper: https://www.mdpi.com/1099-4300/23/9/1134

Solving Schrödinger Bridges via Maximum Likelihood

Entropic Neural Optimal Transport via Diffusion Processes

Energy-guided Entropic Neural Optimal Transport

Building the Bridge of Schrödinger: A Continuous Entropic Optimal Transport Benchmark

Light Schrödinger Bridge

Multi-marginal Schrödinger Bridges with Iterative Reference Refinement


STanford EArthquake Dataset (STEAD):A Global Data Set of Seismic Signals for AI

STanford EArthquake Dataset (STEAD): A Global Data Set of Seismic Signals for AI

INSTANCE – the Italian seismic dataset for machine learning

Scientometric Analysis of Artificial Intelligence (AI) for Geohazard Research

An automatic P-wave onset time picking method for mining-induced microseismic data based on long short-term memory deep neural network

Real-time Seismic Intensity Prediction using Self-supervised Contrastive GNN for Earthquake Early Warning

Automatic phase identification of earthquake based on the UBDN deep network

FastMapSVM: Classifying Complex Objects Using the FastMap Algorithm and Support-Vector Machines


A Matlab/Octave toolbox for stochastic Galerkin methods

Polynomial Chaos Expansion of random coefficients and the solution of stochastic partial differential equations in the Tensor Train format

Computation of the Response Surface in the Tensor Train data format

T-IFISS: a toolbox for adaptive FEM computation

Partial inversion of elliptic operator to speed up computation of likelihood in Bayesian inference

Post-Processing of High-Dimensional Data

Comparing theory based and higher-order reduced models for fusion simulation data


Scripts for calculating features and regression of prokaryote OGT

Predicting the optimal growth temperatures of prokaryotes using only genome derived features

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome

Microbial community of recently discovered Auka vent field sheds light on vent biogeography and evolutionary history of thermophily

Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin


AudioGPT: Understanding and Generating Speech, Music, Sound, and Talking Head

Fast-MD: Fast Multi-Decoder End-to-End Speech Translation with Non-Autoregressive Hidden Intermediates

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


Surfrider Europe's project Plastic Origins aims at mapping river plastic pollution. This citizen science project uses AI to detect litter on river banks. Results are put on a map and shared publicly. We welcome contributions from volunteers. Please, get in touch.


Word Mover's Distance from Matthew J Kusner's paper "From Word Embeddings to Document Distances"

Re-evaluating Automatic Metrics for Image Captioning

Re-evaluating Word Mover's Distance

Speeding up Word Mover's Distance and its variants via properties of distances between embeddings

Supervised Tree-Wasserstein Distance

Unbalanced Optimal Transport meets Sliced-Wasserstein

Unsupervised Sentence-embeddings by Manifold Approximation and Projection

Optimal Transport for Measures with Noisy Tree Metric

Word Tour: One-dimensional Word Embeddings via the Traveling Salesman Problem

Model Comparison for Semantic Grouping

Moving Other Way: Exploring Word Mover Distance Extensions


ML-Quadrat (ML2) is a Model-Driven Software Engineering (MDSE) tool with full code generation and out-of-the-box Machine Learning (ML) support at the modeling layer for creating smart services for the Internet of Things (IoT) and Cyber-Physical Systems (CPS).

ThingML+ Augmenting Model-Driven Software Engineering for the Internet of Things with Machine Learning

A model-driven approach to machine learning and software modeling for the IoT

From things' modeling language (ThingML) to things' machine learning (ThingML2)

Proceedings of the 23rd ACM/IEEE International Conference on Model Driven Engineering Languages and Systems: Companion Proceedings

Data Analytics and Machine Learning Methods, Techniques and Tool for Model-Driven Engineering of Smart IoT Services

International Conference on Software Engineering

Supporting AI Engineering on the IoT Edge through Model-Driven TinyML

Annual International Computer Software and Applications Conference

MDE4QAI: Towards Model-Driven Engineering for Quantum Artificial Intelligence

ML-Quadrat & DriotData: A Model-Driven Engineering Tool and a Low-Code Platform for Smart IoT Services

MDE for Machine Learning-Enabled Software Systems: A Case Study and
  Comparison of MontiAnna & ML-Quadrat


MgeEditing is an open source image and video editing toolbox based on MegEngine.

Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks

Image Super-Resolution Using Very Deep Residual Channel Attention Networks

Tracking Objects as Points

BasicVSR: The Search for Essential Components in Video Super-Resolution and Beyond

Learning Joint Spatial-Temporal Transformations for Video Inpainting

Video Super-Resolution with Recurrent Structure-Detail Network


The Galaxy Cluster ‘Pypeline’ for X-ray Temperature Maps

An X-ray and radio study of the Hubble Frontier Field cluster Abell S1063

LOFAR detection of a low-power radio halo in the galaxy cluster Abell 990

Monthly notices of the Royal Astronomical Society

P.037 Recurrency in mood disorders is related to bipolar course: pooled analysis of the BRIDGE and BRIDGE-II-MIX cohorts

On the origin of diffuse radio emission in Abell 85 – insights from new GMRT observations

Probing the Origin of Diffuse Radio Emission in the Cool Core of the Phoenix Galaxy Cluster

Simulating nearly edge-on sloshing in the galaxy cluster Abell 2199

Witnessing a Galaxy Cluster Merger with JWST and a Chandra X-Ray Temperature Map


Boris Computational Spintronics

Boris computational spintronics—High performance multi-mesh magnetic and spin transport modeling software

Emergence of transient domain wall skyrmions after ultrafast demagnetization

Efficient computation of demagnetizing fields for magnetic multilayers using multilayered convolution

Micromagnetic Monte Carlo method with variable magnetization length based on the Landau–Lifshitz–Bloch equation for computation of large-scale thermodynamic equilibrium states

Speeding Up Explicit Numerical Evaluation Methods for Micromagnetic Simulations Using Demagnetizing Field Polynomial Extrapolation


VirHostMatcher: matching hosts of viruses based on oligonucleotide frequency (ONF) comparison

Alignment-free d_2^* oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences

Review article: the human intestinal virome in health and disease

Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics

A computational approach to aid clinicians in selecting anti-viral drugs for COVID-19 trials


Towards agricultural autonomy: crop row detection under varying field conditions using deep learning

Deep learning‐based crop row detection for infield navigation of agri‐robots

Towards Infield Navigation: leveraging simulated data for crop row detection

Vision based Crop Row Navigation under Varying Field Conditions in Arable Fields


A fast, simple, multilingual tokenizer

BiLSTM-CRF for Persian Named-Entity Recognition ArmanPersoNERCorpus: the First Entity-Annotated Persian Dataset

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

Are the Multilingual Models Better? Improving Czech Sentiment with Transformers

¡Qué maravilla! Multimodal Sarcasm Detection in Spanish: a Dataset and a Baseline

WordTokenizers.jl: Basic tools for tokenizing natural language in Julia

Using Related Languages to Enhance Statistical Language Models

North American Chapter of the Association for Computational Linguistics


Diffusion Models Beat GANs on Image Synthesis

Elucidating the Design Space of Diffusion-Based Generative Models

Diffusion Posterior Sampling for General Noisy Inverse Problems

Label-Efficient Semantic Segmentation with Diffusion Models

Flow Matching for Generative Modeling

StyleGAN-XL: Scaling StyleGAN to Large Diverse Datasets

Diffusion Models for Adversarial Purification

Fast Sampling of Diffusion Models with Exponential Integrator

Improving Diffusion Models for Inverse Problems using Manifold Constraints

Come-Closer-Diffuse-Faster: Accelerating Conditional Diffusion Models for Inverse Problems through Stochastic Contraction


Visual Instruction Tuning

Generative Agents: Interactive Simulacra of Human Behavior

STICKERCONV: Generating Multimodal Empathetic Responses from Scratch


Qopen: Separation of intrinsic and scattering Q by envelope inversion

Seismic scattering and absorption parameters in the W-Bohemia/Vogtland region from elastic and acoustic radiative transfer theory

Measurement of intrinsic and scattering attenuation of shear waves in two sedimentary basins and comparison to crystalline sites in Germany

Crustal intrinsic and scattering attenuation of high‐frequency shear waves in the contiguous United States

Fast and Robust Earthquake Source Spectra and Moment Magnitudes from Envelope Inversion

Induced Earthquake Source Parameters, Attenuation, and Site Effects From Waveform Envelopes in the Fennoscandian Shield


Gaussian random variables.

Two-nucleon S -wave interactions at the SU(3) flavor-symmetric point with mud≈ msphys: A first lattice QCD calculation with the stochastic Laplacian Heaviside method

Bc→J/ψ form factors for the full q2 range from lattice…

Gluon gravitational structure of hadrons of different spin

FK /Fπ from Möbius domain-wall fermions solved on gradient-flowed HISQ ensembles

Gravitational form factors of the pion from lattice QCD

Improved information criteria for Bayesian model averaging in lattice field theory

Scale setting the Möbius domain wall fermion on gradient-flowed HISQ action using the omega baryon mass and the gradient-flow scales t0 and w0

Gravitational form factors of the proton from lattice QCD

Bs→Ds*
 form factors for the full
q2
 range from lattice QCD

Bottomonium precision tests from full lattice QCD: Hyperfine splitting,
ϒ
 leptonic width, and
b
 quark contribution to
e+e−→hadrons


Neural Machine Translation of Rare Words with Subword Units

Learning to Translate in Real-time with Neural Machine Translation

Simultaneous Machine Translation with Visual Context

Exploiting Multimodal Reinforcement Learning for Simultaneous Machine Translation


R library to normalize cytometry data

Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes

Immune Modulation with RANKL Blockade through Denosumab Treatment in Patients with Cancer

A conserved immune trajectory of recovery in hospitalized COVID-19 patients

bioRxiv : the preprint server for biology


☘ Code for Convex Aggregation for Opinion Summarization (Iso et al; Findings of EMNLP 2021)

MeanSum: A Neural Model for Unsupervised Multi-document Abstractive Summarization

Comparative Opinion Summarization via Collaborative Decoding

Automatically Evaluating Opinion Prevalence in Opinion Summarization


Engineering In-place (Shared-memory) Sorting Algorithms

BlockQuicksort: How Branch Mispredictions don't affect Quicksort

Simple and Fast BlockQuicksort using Lomuto's Partitioning Scheme

Performance Evaluation of Parallel Sortings on the Supercomputer Fugaku


PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics

SHR4z, a novel decoy effector from the haustorium of the parasitic weed Striga gesnerioides, suppresses host plant immunity

Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages

PlantTribes2: Tools for comparative gene family analysis in plant genomics


A python package for modeling and analysing transit light-curves.

emcee: The MCMC Hammer

Publications of the Astronomical Society of the Pacific

Water vapour in the atmosphere of the habitable-zone eight-Earth-mass planet K2-18 b

Early Release Science of the exoplanet WASP-39b with JWST NIRSpec G395H

A NEW APPROACH TO ANALYZING HST SPATIAL SCANS: THE TRANSMISSION SPECTRUM OF HD 209458 b

High-precision Stellar Limb-darkening in Exoplanetary Transits

The ExoTETHyS Package: Tools for Exoplanetary Transits around Host Stars

ExoClock Project. II. A Large-scale Integrated Study with 180 Updated Exoplanet Ephemerides

The Hubble WFC3 Emission Spectrum of the Extremely Hot Jupiter KELT-9b

ExoClock project: an open platform for monitoring the ephemerides of Ariel targets with contributions from the public

Near-IR Transmission Spectrum of HAT-P-32b using HST/WFC3


Evaluating Protein Transfer Learning with TAPE

Is Transfer Learning Necessary for Protein Landscape Prediction?

Contextual Lensing of Universal Sentence Representations

Fixed-Length Protein Embeddings using Contextual Lenses


pytrec_eval is an Information Retrieval evaluation tool for Python, based on the popular trec_eval.

Pytrec_eval: An Extremely Fast Python Interface to trec_eval

International ACM SIGIR Conference on Research and Development in Information Retrieval

Annotation Error Detection: Analyzing the Past and Present for a More Coherent Future

DoSSIER@COLIEE 2021: Leveraging dense retrieval and summarization-based re-ranking for case law retrieval

Efficient Self-Supervised Metric Information Retrieval: A Bibliography Based Method Applied to COVID Literature

OpenMatch: An Open Source Library for Neu-IR Research

Universal Vision-Language Dense Retrieval: Learning A Unified Representation Space for Multi-Modal Retrieval

The Power of Selecting Key Blocks with Local Pre-ranking for Long Document Information Retrieval

IR like a SIR: Sense-enhanced Information Retrieval for Multiple Languages

Zenodo (CERN European Organization for Nuclear Research)

Analyzing the Effectiveness of Listwise Reranking with Positional Invariance on Temporal Generalizability

How Can Context Help? Exploring Joint Retrieval of Passage and Personalized Context


Probabilistically split concatenated words using NLP based on English Wikipedia unigram frequencies.

An Effective BERT-Based Pipeline for Twitter Sentiment Analysis: A Case Study in Italian

Stance Detection in Web and Social Media: A Comparative Study

Inline Detection of Domain Generation Algorithms with Context-Sensitive Word Embeddings

AUGER: Automatically Generating Review Comments with Pre-training Models

Intercepting Hail Hydra: Real-time detection of Algorithmically Generated Domains

Journal of Network and Computer Applications

STAN: Towards Describing Bytecodes of Smart Contract

Exploiting Statistical and Structural Features for the Detection of Domain Generation Algorithms

Impersonation on Social Media: A Deep Neural Approach to Identify Ingenuine Content

Leveraging Knowledge Bases And Parallel Annotations For Music Genre Translation

SHAP Interpretations of Tree and Neural Network DNS Classifiers for Analyzing DGA Family Characteristics


scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development


Python module to compute and fit GRB afterglows.

A thousand days after the merger: Continued X-ray emission from GW170817

A search for optical and near-infrared counterparts of the compact binary merger GW190814

Proceedings of the International Astronomical Union

A tale of two mergers: constraints on kilonova detection in two short GRBs at z ∼ 0.5

Monthly Notices of the Royal Astronomical Society

GRMHD Simulations of Neutron-star Mergers with Weak Interactions: r-process Nucleosynthesis and Electromagnetic Signatures of Dynamical Ejecta

The early afterglow of GRB 190829A

Swift-XRT Follow-up of Gravitational-wave Triggers in the Second Advanced LIGO/Virgo Observing Run

The Astrophysical Journal Supplement Series


A library that includes Keras3 layers, blocks and models with pretrained weights, providing support for transfer learning, feature extraction, and more.

Very Deep Convolutional Networks for Large-Scale Image Recognition

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

Rethinking the Inception Architecture for Computer Vision

MobileNetV2: Inverted Residuals and Linear Bottlenecks

EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks

Xception: Deep Learning with Depthwise Separable Convolutions

A ConvNet for the 2020s

GhostNet: More Features from Cheap Operations

EfficientNetV2: Smaller Models and Faster Training

RepVGG: Making VGG-style ConvNets Great Again


User Simulation for Task-Completion Dialogues

Deep Reinforcement Learning: An Overview

Neural Approaches to Conversational AI

End-to-End Task-Completion Neural Dialogue Systems

Towards End-to-End Reinforcement Learning of Dialogue Agents for Information Access

Deep Reinforcement Learning

A User Simulator for Task-Completion Dialogues

BBQ-Networks: Efficient Exploration in Deep Reinforcement Learning for Task-Oriented Dialogue Systems

Self-Supervised Dialogue Learning

Goal-oriented Dialogue Policy Learning from Failures

User Simulation for Evaluating Information Access Systems


What and How Well You Performed? A Multitask Learning Approach to Action Quality Assessment

Uncertainty-aware Score Distribution Learning for Action Quality Assessment

A Survey of Video-based Action Quality Assessment

2021 International Conference on Networking Systems of AI (INSAI)

GAIA: Rethinking Action Quality Assessment for AI-Generated Videos


Hierarchical probabilistic 3D U-Net, with attention mechanisms (— -, ) and a nested decoder structure with deep supervision (—++). Built in TensorFlow 2.5. Configured for voxel-level clinically significant prostate cancer detection in multi-channel 3D bpMRI scans.

End-to-end prostate cancer detection in bpMRI via 3D CNNs: Effects of attention mechanisms, clinical priori and decoupled false positive reduction

A Hierarchical Probabilistic U-Net for Modeling Multi-Scale Ambiguities

Anatomical and Diagnostic Bayesian Segmentation in Prostate MRI - Should Different Clinical Objectives Mandate Different Loss Functions?

Encoding Clinical Priori in 3D Convolutional Neural Networks for Prostate Cancer Detection in bpMRI


NCrystal : a library for thermal neutron transport in crystals and other materials

Fast neutron sensitivity of neutron detectors based on Boron-10 converter layers

Performance evaluation of the Boron Coated Straws detector with Geant4

Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment

Time- and energy-resolved effects in the boron-10 based multi-grid and helium-3 based thermal neutron detectors

A simulational study of the indirect-geometry neutron spectrometer BIFROST at the European Spallation Source, from neutron source position to detector position

Investigation of neutron scattering in the Multi-Blade detector with Geant4 simulations

HighNESS Conceptual Design Report


Partial Entropy Decomposition and Partial Information Decomposition with pointwise surprisal measures

Measuring Multivariate Redundant Information with Pointwise Common Change in Surprisal

Simple Acoustic Features Can Explain Phoneme-Based Predictions of Cortical Responses to Speech

Representational interactions during audiovisual speech entrainment: Redundancy in left posterior superior temporal gyrus and synergy in left motor cortex

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

Exact Partial Information Decompositions for Gaussian Systems Based on Dependency Constraints

MAXENT3D_PID: An Estimator for the Maximum-Entropy Trivariate Partial Information Decomposition


tools to find circRNAs in RNA-seq data

The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis in mammals

Present Scenario of Circular RNAs (circRNAs) in Plants

Circular RNAs: Methodological challenges and perspectives in cardiovascular diseases

Journal of cellular and molecular medicine

Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq

Genome-wide identification and functional analysis of circRNAs in Zea mays

Circular RNAs in the cardiovascular system

Supplementation with Milk-Derived Extracellular Vesicles Shapes the Gut Microbiota and Regulates the Transcriptomic Landscape in Experimental Colitis

Disease-Associated Circular RNAs: From Biology to Computational Identification

Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis

Computational approaches for circRNAs prediction and in silico characterization


Proteome-Wide Association Study

PWAS: proteome-wide association study—linking genes and phenotypes by functional variation in proteins


BRIE: Bayesian Regression for Isoform Estimate in Single Cells

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

BRIE: transcriptome-wide splicing quantification in single cells

BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq

Journal of translational genetics and genomics


The Caltech Fish Counting Dataset

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

HOTA: A Higher Order Metric for Evaluating Multi-object Tracking

International journal of computer vision

The Caltech Fish Counting Dataset: A Benchmark for Multiple-Object Tracking and Counting

Align and Distill: Unifying and Improving Domain Adaptive Object
  Detection


Fast interstellar dust extinction laws in Python

A Large Fraction of Hydrogen-rich Supernova Progenitors Experience Elevated Mass Loss Shortly Prior to Explosion

The Koala: A Fast Blue Optical Transient with Luminous Radio Emission from a Starburst Dwarf Galaxy at z = 0.27

extinction v0.3.0

Evidence for Late-stage Eruptive Mass Loss in the Progenitor to SN2018gep, a Broad-lined Ic Supernova: Pre-explosion Emission and a Rapidly Rising Luminous Transient

SN 2017ein and the Possible First Identification of a Type Ic Supernova Progenitor

Nebular spectra of 111 Type Ia supernovae disfavour single-degenerate progenitors

A Search for Extragalactic Fast Blue Optical Transients in ZTF and the Rate of AT2018cow-like Transients

A detailed spectroscopic study of Tidal Disruption Events

SN 2016iet: The Pulsational or Pair Instability Explosion of a Low-metallicity Massive CO Core Embedded in a Dense Hydrogen-poor Circumstellar Medium

Precision angular diameters for 16 southern stars with VLTI/PIONIER


Translation Error Rate (TER)

Findings of the WMT 2020 Shared Task on Quality Estimation

Empirical Methods in Natural Language Processing

Findings of the WMT 2018 Shared Task on Quality Estimation

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

Findings of the WMT 2021 Shared Task on Quality Estimation

Machine Translation Quality and Post-Editor Productivity

Conference of the Association for Machine Translation in the Americas

PhoMT: A High-Quality and Large-Scale Benchmark Dataset for Vietnamese-English Machine Translation

PosEdiOn: Post-Editing Assessment in PythOn

European Association for Machine Translation Conferences/Workshops

Mismatching-Aware Unsupervised Translation Quality Estimation For Low-Resource Languages

Advancing Semi-Supervised Learning for Automatic Post-Editing: Data-Synthesis by Mask-Infilling with Erroneous Terms

RESHAPE: Reverse-Edited Synthetic Hypotheses for Automatic Post-Editing


Code for "NODE-GAM: Neural Generalized Additive Model for Interpretable Deep Learning"

How Interpretable and Trustworthy are GAMs?

Interpretability with full complexity by constraining feature information


A parallel, open-source geothermal flow simulator


Pyramid Scene Parsing Network, CVPR2017.

Pyramid Scene Parsing Network

On the Robustness of Semantic Segmentation Models to Adversarial Attacks

Benchmarking the Robustness of Semantic Segmentation Models

A Deep Learning Approach for Meibomian Gland Atrophy Evaluation in Meibography Images

Translational vision science & technology

Context-Aware Saliency Detection for Image Retargeting Using Convolutional Neural Networks

Application of Three Deep Learning Schemes Into Oceanic Eddy Detection

An Exploration of Recent Intelligent Image Analysis Techniques for Visual Pavement Surface Condition Assessment

Color Constancy via Multi-Scale Region-Weighed Network Guided by Semantics

A Multiscale-Based Adjustable Convolutional Neural Network for Multiple Organ Segmentation

Wireless Communications and Mobile Computing


Fighting an Infodemic: COVID-19 Fake News Dataset

National Conference on Artificial Intelligence

A Heuristic-driven Uncertainty based Ensemble Framework for Fake News Detection in Tweets and News Articles

A Heuristic-driven Ensemble Framework for COVID-19 Fake News Detection

Model-Agnostic and Diverse Explanations for Streaming Rumour Graphs


MaskFusion: Real-Time Recognition, Tracking and Reconstruction of Multiple Moving Objects

BundleTrack: 6D Pose Tracking for Novel Objects without Instance or Category-Level 3D Models

RGB-D Odometry and SLAM

Evaluating the Impact of Semantic Segmentation and Pose Estimation on Dense Semantic SLAM


replication package for  From Commit Message Generation to History-Aware Commit Message Completion, ASE 2023

CodeT5: Identifier-aware Unified Pre-trained Encoder-Decoder Models for Code Understanding and Generation

Automating Code Review Activities by Large-Scale Pre-training

RACE: Retrieval-Augmented Commit Message Generation


GPU accelerated source code for motion compensation of multi-stack MRI data

An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI

NeSVoR: Implicit Neural Representation for Slice-to-Volume Reconstruction in MRI

PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI


:package: Non-parametric Causal Effects Based on Modified Treatment Policies :crystal_ball:

Nonparametric Causal Effects Based on Longitudinal Modified Treatment Policies

When effects cannot be estimated: redefining estimands to understand the effects of naloxone access laws

Comparison of a Target Trial Emulation Framework vs Cox Regression to Estimate the Association of Corticosteroids With COVID-19 Mortality

Effect of Sepsis on Death as Modified by Solid Organ Transplantation


Object Hallucination in Image Captioning

Speaking the Same Language: Matching Machine to Human Captions by Adversarial Training

Mitigating Gender Bias in Captioning Systems

Looking for Confirmations: An Effective and Human-Like Visual Dialogue Strategy


Pre-trained models and language resources for Natural Language Processing in Polish

Combining Neural and Knowledge-Based Approaches to Named Entity Recognition in Polish

Evaluation of Sentence Representations in Polish

Sentiment Analysis with Contextual Embeddings and Self-Attention

Hybrid retrievers with generative re-rankers

Conference on Computer Science and Information Systems

Analyzing the Influence of Language Model-Generated Responses in Mitigating Hate Speech on Social Media Directed at Ukrainian Refugees in Poland


Fast K-Medoids clustering in Python with FasterPAM

Faster k-Medoids Clustering: Improving the PAM, CLARA, and CLARANS Algorithms

Fast and Eager k-Medoids Clustering: O(k) Runtime Improvement of the PAM, CLARA, and CLARANS Algorithms

Fast k-medoids Clustering in Rust and Python

Clustering by Direct Optimization of the Medoid Silhouette

Medoid Silhouette clustering with automatic cluster number selection


Assemblies from HPP Year 1 production

A draft human pangenome reference

The Dynamic Structure and Rapid Evolution of Human Centromeric Satellite DNA

Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Sigmoni: classification of nanopore signal with a compressed pangenome index

bioRxiv : the preprint server for biology


aspect-based sentiment classification

Interactive Attention Networks for Aspect-Level Sentiment Classification

Aspect Level Sentiment Classification with Deep Memory Network

Effective LSTMs for Target-Dependent Sentiment Classification

Left-Center-Right Separated Neural Network for Aspect-based Sentiment Analysis with Rotatory Attention


[Paper][ISWC 2021] Zero-shot Visual Question Answering using Knowledge Graph

Knowledge Graphs Meet Multi-Modal Learning: A Comprehensive Survey

FVQA 2.0: Introducing Adversarial Samples into Fact-based Visual Question Answering


Statistics and visualization for amplicon data

Exploring the Plasticity of Diet on Gut Microbiota and Its Correlation with Gut Health

Experimental Warming Has Not Affected the Changes in Soil Organic Carbon During the Growing Season in an Alpine Meadow Ecosystem on the Qinghai–Tibet Plateau

Bacillus amyloliquefaciens alleviates the pathological injuries in mice infected with Schistosoma japonicum by modulating intestinal microbiome

Frontiers in cellular and infection microbiology

The vaginal microbial signatures of preterm birth woman

Investigation of bacterial and fungal population structure on environmental surfaces of three medical institutions during the COVID-19 pandemic


[NeurIPS 2020] Blind Video Temporal Consistency via Deep Video Prior

Neural Radiance Flow for 4D View Synthesis and Video Processing

AuxAdapt: Stable and Efficient Test-Time Adaptation for Temporally Consistent Video Semantic Segmentation

Deep Video Prior for Video Consistency and Propagation


see README

A Comparative Study on Recent Neural Spoofing Countermeasures for Synthetic Speech Detection

Investigating self-supervised front ends for speech spoofing countermeasures

Spoofed training data for speech spoofing countermeasure can be efficiently created using neural vocoders

Investigating Active-learning-based Training Data Selection for Speech Spoofing Countermeasure

Improving LPCNet-based Text-to-Speech with Linear Prediction-structured Mixture Density Network

A Practical Guide to Logical Access Voice Presentation Attack Detection

Can Large-Scale Vocoded Spoofed Data Improve Speech Spoofing Countermeasure with a Self-Supervised Front End?

Period VITS: Variational Inference with Explicit Pitch Modeling for End-to-end Emotional Speech Synthesis

Estimating the Confidence of Speech Spoofing Countermeasure

One-class learning towards generalized voice spoofing detection.


Tensorflow Implementation of R-Net

Attention Is All You Need

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

A Theoretically Grounded Application of Dropout in Recurrent Neural Networks

Machine Comprehension Using Match-LSTM and Answer Pointer

SberQuAD -- Russian Reading Comprehension Dataset: Description and
  Analysis

Difficulty Controllable Generation of Reading Comprehension Questions

Difficulty Controllable Question Generation for Reading Comprehension.

Comparative Analysis of Neural QA models on SQuAD

MemoReader: Large-Scale Reading Comprehension through Neural Memory Controller

Towards Inference-Oriented Reading Comprehension: ParallelQA


Official GitHub repository for the Text-Guided Video Editing (TGVE) competition of LOVEU Workshop @ CVPR'23.

High-Resolution Image Synthesis with Latent Diffusion Models

CLIPScore: A Reference-free Evaluation Metric for Image Captioning

Tune-A-Video: One-Shot Tuning of Image Diffusion Models for Text-to-Video Generation

CVPR 2023 Text Guided Video Editing Competition

Edit Temporal-Consistent Videos with Image Diffusion Model

MAG-Edit: Localized Image Editing in Complex Scenarios via Mask-Based Attention-Adjusted Guidance


[ICLR'23 Spotlight & IJCV'24] MapTR: Structured Modeling and Learning for Online Vectorized HD Map Construction

MapTRv2: An End-to-End Framework for Online Vectorized HD Map Construction

PolyDiffuse: Polygonal Shape Reconstruction via Guided Set Diffusion Models

Mind the map! Accounting for existing map information when estimating online HDMaps from sensor data

MapNeXt: Revisiting Training and Scaling Practices for Online Vectorized HD Map Construction

Is Your HD Map Constructor Reliable under Sensor Corruptions?


Free and open-source application (command line and GUI) providing QSAR models predictions as well as applicability domain and accuracy assessment for physicochemical properties, environmental fate and toxicological endpoints. ==================>Download the latest compiled version from the "releases" tab and run the executable installer.

PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

OPERA models for predicting physicochemical properties and environmental fate endpoints

CERAPP: Collaborative Estrogen Receptor Activity Prediction Project

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

Open-source QSAR models for pKa prediction using multiple machine learning approaches

An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling

CATMoS: Collaborative Acute Toxicity Modeling Suite

Predictive Models for Acute Oral Systemic Toxicity: A Workshop to Bridge the Gap from Research to Regulation.

Computational toxicology (Amsterdam, Netherlands)


[ICCV2021] Official PyTorch implementation of Segmenter: Transformer for Semantic Segmentation

How to train your ViT? Data, Augmentation, and Regularization in Vision Transformers

Rethinking Range View Representation for LiDAR Segmentation

Evaluating transformer-based semantic segmentation networks for pathological image segmentation

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

Improving Predictive Performance and Calibration by Weight Fusion in Semantic Segmentation

White Matter Hyperintensities Segmentation Using Probabilistic TransUNet


Shared BERT model for 4 languages of Bulgarian, Czech, Polish and Russian. Slavic NER model.

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

Tuning Multilingual Transformers for Language-Specific Named Entity Recognition

Meeting of the Association for Computational Linguistics

Tuning Multilingual Transformers for Named Entity Recognition on Slavic Languages

7TH WORKSHOP ON BALTO-SLAVIC NATURAL LANGUAGE PROCESSING (BSNLP'2019)

Pre-training Polish Transformer-based Language Models at Scale

Transfer Learning for Czech Historical Named Entity Recognition

Recent Advances in Natural Language Processing


The official PyTorch implementation of Towards Fast, Accurate and Stable 3D Dense Face Alignment, ECCV 2020.

Evaluation of Various State of the Art Head Pose Estimation Algorithms for Clinical Scenarios

AniTalker: Animate Vivid and Diverse Talking Faces through Identity-Decoupled Facial Motion Encoding

Geometrically Adaptive Dictionary Attack on Face Recognition

State of the Art of Quality Assessment of Facial Images

BabyNet: Reconstructing 3D faces of babies from uncalibrated photographs


SBX: Stable Baselines Jax (SB3 + Jax)

Proximal Policy Optimization Algorithms

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

Addressing Function Approximation Error in Actor-Critic Methods

Controlling Overestimation Bias with Truncated Mixture of Continuous Distributional Quantile Critics

Dropout Q-Functions for Doubly Efficient Reinforcement Learning

Smooth Exploration for Robotic Reinforcement Learning

CrossQ: Batch Normalization in Deep Reinforcement Learning for Greater Sample Efficiency and Simplicity


An R package for computing the Standardized Precipitation-Evapotranspiration Index (SPEI), Penman-Monteith and other reference evapotranspiration, SPI, etc.

Evaluation of bias correction methods for a multivariate drought index: case study of the Upper Jhelum Basin


中文法律LLaMA (LLaMA for Chinese legel domain)

Lawyer LLaMA Technical Report

Large Language Models in Law: A Survey

Continual Learning of Large Language Models: A Comprehensive Survey

AviationGPT: A Large Language Model for the Aviation Domain

Chain-of-Discussion: A Multi-Model Framework for Complex Evidence-Based
  Question Answering


The implementation of Temporal Generative Adversarial Nets with Singular Value Clipping

Adversarial Video Generation on Complex Datasets

Generating Videos with Dynamics-aware Implicit Generative Adversarial Networks

Lower Dimensional Kernels for Video Discriminators

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

Temporal Shift GAN for Large Scale Video Generation


A maze generator and solver written in Python, which uses a backtracker algorithm and Djikstra's algorithm.

Heuristic Search Planning with Deep Neural Networks using Imitation, Attention and Curriculum Learning

Optimize Planning Heuristics to Rank, not to Estimate Cost-to-Goal


Benchmarks for Model-Based Optimization

Design-Bench: Benchmarks for Data-Driven Offline Model-Based Optimization

Conservative Objective Models for Effective Offline Model-Based Optimization

RoMA: Robust Model Adaptation for Offline Model-based Optimization

Diffusion Models as Constrained Samplers for Optimization with Unknown
  Constraints


CNS (Computational Neuroscience) Lab project for age/sex classification of fMRI scans

Spatio-Temporal Graph Convolution for Resting-State fMRI Analysis

Learning Dynamic Graph Representation of Brain Connectome with Spatio-Temporal Attention

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


R package containing useful functions for mutational signature analysis

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment

Copy number signatures predict chromothripsis and clinical outcomes in newly diagnosed multiple myeloma

The impact of rare germline variants on human somatic mutation processes

Mutational topography reflects clinical neuroblastoma heterogeneity

Zenodo (CERN European Organization for Nuclear Research)

A comprehensive comparison of tools for fitting mutational signatures


Asynchronous Methods for Deep Reinforcement Learning

Pre-training with non-expert human demonstration for deep reinforcement learning

Jointly Pre-training with Supervised, Autoencoder, and Value Losses for Deep Reinforcement Learning

Vision-based deep execution monitoring


COsmological N-body CodE in PyThon

νCONCEPT: cosmological neutrino simulations from the non-linear Boltzmann hierarchy

Journal of Cosmology and Astroparticle Physics

Fully relativistic treatment of decaying cold dark matter in N-body simulations

The cosmological simulation code CON CEPT  1.0

CONCEPT - The COsmological N-body CodE in PyThon


Documentation assets for Quorum

Performance Benchmarking and Optimizing Hyperledger Fabric Blockchain Platform

Trade-offs between Distributed Ledger Technology Characteristics

IDMoB: IoT Data Marketplace on Blockchain

Blockchain Enabled Industrial Internet of Things Technology

IEEE Transactions on Computational Social Systems

Distributed Ledger Technology Review and Decentralized Applications Development Guidelines

From Byzantine Replication to Blockchain: Consensus is only the Beginning

Novel and Secure Blockchain Framework for Health Applications in IoT

The Nubo Virtual Services Marketplace

Design and Evaluation of Smart-Contract-based System Operations for Permissioned Blockchain-based Systems

Tubu-io Decentralized Application Development & Test Workbench


ProPara (Process Paragraph Comprehension) dataset and models

Reasoning about Actions and State Changes by Injecting Commonsense Knowledge

Building Dynamic Knowledge Graphs from Text using Machine Reading Comprehension

Be Consistent! Improving Procedural Text Comprehension using Label Consistency

Knowledge-Aware Procedural Text Understanding with Multi-Stage Training

Coalescing Global and Local Information for Procedural Text Understanding

Reasoning over Entity-Action-Location Graph for Procedural Text Understanding

Entity Tracking via Effective Use of Multi-Task Learning Model and Mention-guided Decoding

Procedural Text Understanding via Scene-Wise Evolution

ParallelPARC: A Scalable Pipeline for Generating Natural-Language Analogies


LAMMPS interface for phonon calculations using phonopy

DP-GEN: A concurrent learning platform for the generation of reliable deep learning based potential energy models

Phonons in twisted transition-metal dichalcogenide bilayers: Ultrasoft phasons and a transition from a superlubric to a pinned phase

Thermoelastic properties of bridgmanite using deep-potential molecular dynamics

Development of the RF-MEAM Interatomic Potential for the Fe-C System to Study the Temperature-Dependent Elastic Properties


Unofficial implementation of AlpaGasus

GPT-4 Technical Report

AlpaGasus: Training A Better Alpaca with Fewer Data

Instruction Tuning With Loss Over Instructions


Study on the applicability of Direct Feedback Alignment to neural view synthesis, recommender systems, geometric learning, and natural language processing.

Direct Feedback Alignment Scales to Modern Deep Learning Tasks and Architectures

Credit Assignment Through Broadcasting a Global Error Vector

Adversarial Robustness by Design Through Analog Computing And Synthetic Gradients


Portable command-line tool to query bioinformatics APIs, data, databases and files.

Somatic inflammatory gene mutations in human ulcerative colitis epithelium

Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases

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

miR-219 Cooperates with miR-338 in Myelination and Promotes Myelin Repair in the CNS

Manifold Roles of CCR7 and Its Ligands in the Induction and Maintenance of Bronchus-Associated Lymphoid Tissue

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models


Learn and L3 embedding from audio/video pairs

Look, Listen and Learn

Self-supervised audio representation learning for mobile devices

Learnable Irrelevant Modality Dropout for Multimodal Action Recognition on Modality-Specific Annotated Videos


Code for the paper "Contrastive Learning Inverts the Data Generating Process".

CITRIS: Causal Identifiability from Temporal Intervened Sequences

Causal Representation Learning for Instantaneous and Temporal Effects in Interactive Systems

Towards efficient representation identification in supervised learning


An open information extraction system that provides compact extractions

MinIE: Minimizing Facts in Open Information Extraction

Empirical Methods in Natural Language Processing

OPIEC: An Open Information Extraction Corpus

On Generating Fact-Infused Question Variations

IELM: An Open Information Extraction Benchmark for Pre-Trained Language Models


SFU Opinion and Comments Corpus

News recommender system: a review of recent progress, challenges, and opportunities

The FRENK Datasets of Socially Unacceptable Discourse in Slovene and English

Corpora Annotated with Negation: An Overview

International Conference on Computational Logic

Classifying Constructive Comments

A corpus analysis of online news comments using the Appraisal framework

Journal of Corpora and Discourse Studies


This is the GitHub repository for our ICLR22 paper: "You are AllSet: A Multiset Function Framework for Hypergraph Neural Networks"

CHGNN: A Semi-Supervised Contrastive Hypergraph Learning Network

From Hypergraph Energy Functions to Hypergraph Neural Networks


Framework for converting QA-SRL to Open-IE and evaluating Open IE parsers.

Creating a Large Benchmark for Open Information Extraction

Span Model for Open Information Extraction on Accurate Corpus

Graphene: Semantically-Linked Propositions in Open Information Extraction

An Evaluation of PredPatt and Open IE via Stage 1 Semantic Role Labeling

International Conference on Computational Semantics

Summarizing Unstructured Logs in Online Services

DetIE: Multilingual Open Information Extraction Inspired by Object Detection

Graphene: A Context-Preserving Open Information Extraction System

Fact-aware Sentence Split and Rephrase with Permutation Invariant Training

Hierarchical Knowledge Graphs: A Novel Information Representation for Exploratory Search Tasks


A PyTorch implementation of ACM SIGKDD 2019 paper "Predicting Dynamic Embedding Trajectory in Temporal Interaction Networks"

Intensity-Free Learning of Temporal Point Processes

TCL: Transformer-based Dynamic Graph Modelling via Contrastive Learning

UNIPoint: Universally Approximating Point Processes Intensities

Spectral Transform Forms Scalable Transformer

Efficient Dynamic Graph Representation Learning at Scale

Modeling Inter-Dependence Between Time and Mark in Multivariate Temporal Point Processes

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

From Static to Dynamic Node Embeddings

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

Advances in AI for web integrity, equity, and well-being


Cross-Lingual Entity Alignment via Joint Attribute-Preserving Embedding, ISWC 2017

Cross-lingual Entity Alignment via Joint Attribute-Preserving Embedding

Knowledge Association with Hyperbolic Knowledge Graph Embeddings

SelfKG: Self-Supervised Entity Alignment in Knowledge Graphs

Time-aware Graph Neural Network for Entity Alignment between Temporal Knowledge Graphs

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

JarKA: Modeling Attribute Interactions for Cross-lingual Knowledge Alignment

On the Ambiguity of Rank-Based Evaluation of Entity Alignment or Link Prediction Methods

A Fused Gromov-Wasserstein Framework for Unsupervised Knowledge Graph Entity Alignment

Knowledge Graph Entity Alignment with Graph Convolutional Networks: Lessons Learned

A Self-supervised Method for Entity Alignment

Multi-Modal Entity Alignment Method Based on Feature Enhancement


[NeurIPS 2022] Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphs

Variational Graph Auto-Encoders

Pareto Invariant Risk Minimization: Towards Mitigating the Optimization Dilemma in Out-of-Distribution Generalization

Learning Invariant Molecular Representation in Latent Discrete Space


Official repository for the paper "Masksembles for Uncertainty Estimation" (CVPR 2021).

BatchEnsemble: An Alternative Approach to Efficient Ensemble and Lifelong Learning

Masksembles for Uncertainty Estimation

Packed-Ensembles for Efficient Uncertainty Estimation

Low-field magnetic resonance image enhancement via stochastic image quality transfer


Multilingual Large Language Models Evaluation Benchmark

Measuring Massive Multitask Language Understanding

Okapi: Instruction-tuned Large Language Models in Multiple Languages with Reinforcement Learning from Human Feedback

Quantifying Multilingual Performance of Large Language Models Across
  Languages

Aurora-M: The First Open Source Multilingual Language Model Red-teamed
  according to the U.S. Executive Order


Domain adaptation made easy. Fully featured, modular, and customizable.

Domain-Adversarial Training of Neural Networks

Unsupervised Domain Adaptation by Backpropagation

Learning Transferable Features with Deep Adaptation Networks

Adversarial Discriminative Domain Adaptation

Deep CORAL: Correlation Alignment for Deep Domain Adaptation

Conditional Adversarial Domain Adaptation

Maximum Classifier Discrepancy for Unsupervised Domain Adaptation

Unsupervised Domain Adaptation with Residual Transfer Networks

Sliced Wasserstein Discrepancy for Unsupervised Domain Adaptation

A DIRT-T Approach to Unsupervised Domain Adaptation


Code for our CVPR 2019 paper, HPLFlowNet: Hierarchical Permutohedral Lattice FlowNet for Scene Flow Estimation on Large-scale Point Clouds.

FLOT: Scene Flow on Point Clouds Guided by Optimal Transport

RMS-FlowNet: Efficient and Robust Multi-Scale Scene Flow Estimation for Large-Scale Point Clouds

RMS-FlowNet++: Efficient and Robust Multi-Scale Scene Flow Estimation for Large-Scale Point Clouds

International Journal of Computer Vision


Truly Conversational Search is the next logic step in the journey to generate intelligent and useful AI. To understand what this may mean, researchers have voiced a continuous desire to study how people currently converse with search engines. Traditionally, the desire to produce such a comprehensive dataset has been limited because those who have this data (Search Engines) have a responsibility to their users to maintain their privacy and cannot share the data publicly in a way that upholds the trusts users have in the Search Engines. Given these two powerful forces we believe we have a dataset and paradigm that meets both sets of needs: A artificial public dataset that approximates the true data and an ability to evaluate model performance on the real user behavior. What this means is we released a public dataset which is generated by creating artificial sessions using embedding similarity and will test on the original data. To say this again: we are not releasing any private user data but are releasing what we believe to be a good representation of true user interactions.

MS MARCO: A Human Generated MAchine Reading COmprehension Dataset

Few-Shot Generative Conversational Query Rewriting

TREC CAsT 2019: The Conversational Assistance Track Overview

Multi-Stage Conversational Passage Retrieval: An Approach to Fusing Term Importance Estimation and Neural Query Rewriting

Query Reformulation using Query History for Passage Retrieval in Conversational Search

Contrastive Multi-document Question Generation

Enhancing User Behavior Sequence Modeling by Generative Tasks for Session Search


accurate LiftOver tool for new genome assemblies

Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference

BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies


Unsupervised multilabel image segmentation (color/gray/multichannel) based on the Potts  model (aka piecewise constant Mumford-Shah model)

Fast Partitioning of Vector-Valued Images

An image reconstruction model regularized by edge-preserving diffusion and smoothing for limited-angle computed tomography

A Weighted Difference of Anisotropic and Isotropic Total Variation for Relaxed Mumford-Shah Color and Multiphase Image Segmentation

Difference of anisotropic and isotropic TV for segmentation under blur and Poisson noise

An Efficient Smoothing and Thresholding Image Segmentation Framework with Weighted Anisotropic-Isotropic Total Variation


Benchmarking Deep Reinforcement Learning for Continuous Control

Imitating Driver Behavior with Generative Adversarial Networks

Learning Temporal Strategic Relationships using Generative Adversarial Imitation Learning


DSMIL: Dual-stream multiple instance learning networks for tumor detection in Whole Slide Image

Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning

MixUp-MIL: Novel Data Augmentation for Multiple Instance Learning and a Study on Thyroid Cancer Diagnosis

Scalable Set Encoding with Universal Mini-Batch Consistency and Unbiased Full Set Gradient Approximation


Meta-Learning with Differentiable Convex Optimization

Charting the Right Manifold: Manifold Mixup for Few-shot Learning

Iterative label cleaning for transductive and semi-supervised few-shot learning

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


Official code for the NeurIPS 2022 paper "Shape, Light, and Material Decomposition from Images using Monte Carlo Rendering and Denoising".

OpenIllumination: A Multi-Illumination Dataset for Inverse Rendering Evaluation on Real Objects

Ghost on the Shell: An Expressive Representation of General 3D Shapes


Fast expectation maximization for microbial source tracking

FEAST: fast expectation-maximization for microbial source tracking

Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab

Chicken Manure and Mushroom Residues Affect Soil Bacterial Community Structure but Not the Bacterial Resistome When Applied at the Same Rate of Nitrogen for 3 Years

Gut microbiota composition in the sympatric and diet‐sharing Drosophila simulans and Dicranocephalus wallichii bowringi shaped largely by community assembly processes rather than regional species pool

Determination of a criminal suspect using environmental plant DNA metabarcoding technology

Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides

The molecular impact of life in an indoor environment

Multi-dimensional investigation and distribution characteristics analysis of gut microbiota of different marine fish in Fujian Province of China


Automatic differentiation with weighted finite-state transducers.

Differentiable Weighted Finite-State Transducers

Powerful and Extensible WFST Framework for RNN-Transducer Losses

Parallel Composition of Weighted Finite-State Transducers


Repo to the paper "Message Passing Neural PDE Solvers"

Message Passing Neural PDE Solvers

PDE-Refiner: Achieving Accurate Long Rollouts with Neural PDE Solvers

Physics-Embedded Neural Networks: Graph Neural PDE Solvers with Mixed Boundary Conditions

DySLIM: Dynamics Stable Learning by Invariant Measure for Chaotic
  Systems


Social Ways: Learning Multi-Modal Distributions of Pedestrian Trajectories with GANs (CVPR 2019)

InfoGAN: Interpretable Representation Learning by Information Maximizing Generative Adversarial Nets

Social GAN: Socially Acceptable Trajectories with Generative Adversarial Networks

Improving Movement Predictions of Traffic Actors in Bird's-Eye View Models using GANs and Differentiable Trajectory Rasterization


Supervision Exists Everywhere: A Data Efficient Contrastive Language-Image Pre-training Paradigm

PyramidCLIP: Hierarchical Feature Alignment for Vision-language Model Pretraining

Democratizing Contrastive Language-Image Pre-training: A CLIP Benchmark of Data, Model, and Supervision

UniCLIP: Unified Framework for Contrastive Language-Image Pre-training

HiCLIP: Contrastive Language-Image Pretraining with Hierarchy-aware Attention

SoftCLIP: Softer Cross-modal Alignment Makes CLIP Stronger

Revisiting Multimodal Representation in Contrastive Learning: From Patch and Token Embeddings to Finite Discrete Tokens

Boosting Visual-Language Models by Exploiting Hard Samples

Misalign, Contrast then Distill: Rethinking Misalignments in Language-Image Pretraining


Camoscio: An Italian instruction-tuned language model based on LLaMA

LLaMA: Open and Efficient Foundation Language Models

LoRA: Low-Rank Adaptation of Large Language Models

Self-Instruct: Aligning Language Models with Self-Generated Instructions

Camoscio: an Italian Instruction-tuned LLaMA

PejorativITy: Disambiguating Pejorative Epithets to Improve Misogyny
  Detection in Italian Tweets


A spherical convolutional neural network for cosmology (TFv1).

DeepSphere: Efficient spherical convolutional neural network with HEALPix sampling for cosmological applications

DeepSphere: a graph-based spherical CNN

DeepSphere: towards an equivariant graph-based spherical CNN

DeepSphere: a graph-based spherical CNN (ICLR'20 spotlight)

CMB delensing with deep learning


Nanopore data  assembler

Efficient assembly of nanopore reads via highly accurate and intact error correction

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

Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

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

A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data

Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses

Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit

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

Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L.

Near-Chromosome-Level Genome Assembly of the Dark Septate Endophyte Laburnicola rhizohalophila: A Model for Investigating Root-Fungus Symbiosis


Generate IGV style locus tracks from bigWig files in R

SIAH ubiquitin E3 ligases as modulators of inflammatory gene expression

Trackplot: a fast and lightweight R script for epigenomic enrichment plots


Energy-based Out-of-distribution Detection

Provable Guarantees for Understanding Out-of-distribution Detection

Reliable and Trustworthy Machine Learning for Health Using Dataset Shift Detection

Breaking Down Out-of-Distribution Detection: Many Methods Based on OOD Training Data Estimate a Combination of the Same Core Quantities

Feed Two Birds with One Scone: Exploiting Wild Data for Both Out-of-Distribution Generalization and Detection

Towards Accurate Open-Set Recognition via Background-Class Regularization

Hybrid Energy Based Model in the Feature Space for Out-of-Distribution Detection

Gradient-Regularized Out-of-Distribution Detection


Dataset for NAACL 2021 paper: "DART: Open-Domain Structured Data Record to Text Generation"

Prefix-Tuning: Optimizing Continuous Prompts for Generation

Control Prefixes for Parameter-Efficient Text Generation

Parameter-Efficient Tuning on Layer Normalization for Pre-trained Language Models

Self-supervised Graph Masking Pre-training for Graph-to-Text Generation

Discourse-Aware Soft Prompting for Text Generation


A novel method to tune language models. Codes and datasets for paper ``GPT understands, too''.

GPT Understands, Too

P-Tuning v2: Prompt Tuning Can Be Comparable to Fine-tuning Universally Across Scales and Tasks

TransPrompt: Towards an Automatic Transferable Prompting Framework for Few-shot Text Classification

Making Pre-trained Language Models End-to-end Few-shot Learners with Contrastive Prompt Tuning

Towards Unified Prompt Tuning for Few-shot Text Classification

Parameter-Efficient Prompt Tuning Makes Generalized and Calibrated Neural Text Retrievers

Discrete Prompt Optimization via Constrained Generation for Zero-shot Re-ranker


Sandbox for training deep learning networks

Deep Residual Learning for Image Recognition

Very Deep Convolutional Networks for Large-Scale Image Recognition

U-Net: Convolutional Networks for Biomedical Image Segmentation

Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift

Densely Connected Convolutional Networks

Squeeze-and-Excitation Networks

Rethinking the Inception Architecture for Computer Vision

MobileNetV2: Inverted Residuals and Linear Bottlenecks

CBAM: Convolutional Block Attention Module

EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks


Sentence paraphrase generation at the sentence level

Automatic Fact-guided Sentence Modification

Abstractive Snippet Generation

WEB CONFERENCE 2020: PROCEEDINGS OF THE WORLD WIDE WEB CONFERENCE (WWW 2020)

Effective Data Augmentation Approaches to End-to-End Task-Oriented Dialogue

Reading Between the Demographic Lines: Resolving Sources of Bias in Toxicity Classifiers


Associated Repository for "Translation between Molecules and Natural Language"

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

MolXPT: Wrapping Molecules with Text for Generative Pre-training

Leveraging Biomolecule and Natural Language through Multi-Modal
  Learning: A Survey


Challenges in Data-to-Document Generation

Data-to-Text Generation with Content Selection and Planning

Revisiting Challenges in Data-to-Text Generation with Fact Grounding

Grounding NBA Matchup Summaries

Proceedings of the 14th International Conference on Natural Language Generation


A library to conduct ranking experiments with transformers.

On the Calibration and Uncertainty of Neural Learning to Rank Models

Weakly Supervised Label Smoothing

Do the Findings of Document and Passage Retrieval Generalize to the Retrieval of Responses for Dialogues?

Moving Stuff Around: A study on efficiency of moving documents into memory for Neural IR models


Natural Questions (NQ) contains real user questions issued to Google search, and answers found from Wikipedia by annotators. NQ is designed for the training and evaluation of automatic question answering systems.

A Survey on Machine Reading Comprehension: Tasks, Evaluation Metrics and Benchmark Datasets

Proving Test Set Contamination in Black Box Language Models

Recitation-Augmented Language Models

InPars-Light: Cost-Effective Unsupervised Training of Efficient Rankers

RAG Does Not Work for Enterprises


A Survey of Machine Unlearning

To Be Forgotten or To Be Fair: Unveiling Fairness Implications of Machine Unlearning Methods

Machine Unlearning

Proof of Unlearning: Definitions and Instantiation

Label-Agnostic Forgetting: A Supervision-Free Unlearning in Deep Models

CaMU: Disentangling Causal Effects in Deep Model Unlearning


E2E system with LF-MMI; word N-gram for Mandarin

LAE: Language-Aware Encoder for Monolingual and Multilingual ASR

Consistent Training and Decoding for End-to-End Speech Recognition Using Lattice-Free MMI

Improving Mandarin End-to-End Speech Recognition With Word N-Gram Language Model

Integrating Lattice-Free MMI Into End-to-End Speech Recognition

IEEE/ACM Transactions on Audio, Speech, and Language Processing

Automatic Prosody Annotation with Pre-Trained Text-Speech Model


A Live Movie Rating Dataset Collected From Twitter

Next Item Recommendation with Self-Attention

Evaluating Recommender Systems: Survey and Framework

Combining similarity and sentiment in opinion mining for product recommendation

Journal of Intelligent Information Systems

HCF-CRS: A Hybrid Content based Fuzzy Conformal Recommender System for providing recommendations with confidence

ConceptExplorer: Visual Analysis of Concept Drifts in Multi-source Time-series Data

Learning Transferrable Parameters for Long-tailed Sequential User Behavior Modeling

Coupled Variational Recurrent Collaborative Filtering

Text-based Sentiment Analysis and Music Emotion Recognition


The official repo of Qwen-Audio (通义千问-Audio) chat & pretrained large audio language model proposed by Alibaba Cloud.

Qwen-Audio: Advancing Universal Audio Understanding via Unified Large-Scale Audio-Language Models

An Embarrassingly Simple Approach for LLM with Strong ASR Capacity

Explainable Multimodal Emotion Reasoning

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

CrossCheckGPT: Universal Hallucination Ranking for Multimodal Foundation Models

AffectGPT: Dataset and Framework for Explainable Multimodal Emotion
  Recognition


Code for "Generative Code Modeling with Graphs" (ICLR'19)

Learning to Represent Programs with Graphs

Generative Code Modeling with Graphs

Open Vocabulary Learning on Source Code with a Graph-Structured Cache


Official Pytorch implementation of ReBias (Learning De-biased Representations with Biased Representations), ICML 2020

Latent Adversarial Debiasing: Mitigating Collider Bias in Deep Neural Networks

Mitigating Dataset Bias by Using Per-sample Gradient

Learning Debiased Models with Dynamic Gradient Alignment and Bias-conflicting Sample Mining

Fighting Fire with Fire: Contrastive Debiasing without Bias-free Data via Generative Bias-transformation


Official PyTorch implementation of "AASIST: Audio Anti-Spoofing using Integrated Spectro-Temporal Graph Attention Networks"

SASV 2022: The First Spoofing-Aware Speaker Verification Challenge

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

Audio Deepfake Detection: A Survey

Anti-Spoofing Using Transfer Learning with Variational Information Bottleneck

Phase-Aware Spoof Speech Detection Based on Res2Net with Phase Network

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

EmoFake: An Initial Dataset for Emotion Fake Audio Detection

Malafide: a novel adversarial convolutive noise attack against deepfake and spoofing detection systems

Audio Anti-Spoofing Detection: A Survey


EdgeCloudSim: An Environment for Performance Evaluation of Edge Computing Systems

All one needs to know about fog computing and related edge computing paradigms: A complete survey

Edge-Cloud Continuum Solutions for Urban Mobility Prediction and Planning

Effect of RSU Placement on Autonomous Vehicle V2I Scenarios

Balkan Journal of Electrical and Computer Engineering

Edge to Cloud Tools: A Multivocal Literature Review


Source code about machine learning and security.

CyExec*: A High-Performance Container-Based Cyber Range With Scenario Randomization

Security Information Sharing in Smart Grids: Persisting Security Audits to the Blockchain

An exploratory study on the predominant programming paradigms in Python code

Proceedings of the 30th ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering

Hacking Neural Networks: A Short Introduction


official code repo for paper "CogView2: Faster and Better Text-to-Image Generation via Hierarchical Transformers"

CogView: Mastering Text-to-Image Generation via Transformers

Toward Verifiable and Reproducible Human Evaluation for Text-to-Image Generation

Auditing Gender Presentation Differences in Text-to-Image Models


Code to support training, evaluating and interacting neural network dialog models, and training them with reinforcement learning. Code to deploy a web server which hosts the models live online is available at: https://github.com/asmadotgh/neural_chat_web

A Hierarchical Recurrent Encoder-Decoder For Generative Context-Aware Query Suggestion

Way Off-Policy Batch Deep Reinforcement Learning of Implicit Human Preferences in Dialog

A Hierarchical Latent Variable Encoder-Decoder Model for Generating Dialogues

A Hierarchical Latent Structure for Variational Conversation Modeling

Approximating Interactive Human Evaluation with Self-Play for Open-Domain Dialog Systems

Human-centric Dialog Training via Offline Reinforcement Learning

Hierarchical Reinforcement Learning for Open-Domain Dialog

Discovering Dialog Structure Graph for Open-Domain Dialog Generation


Software for the visualization of sequence-function relationships

Logomaker: beautiful sequence logos in Python

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

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


RAFT: Recurrent All-Pairs Field Transforms for Optical Flow

Learning N:M Fine-grained Structured Sparse Neural Networks From Scratch

Particle Video Revisited: Tracking Through Occlusions Using Point Trajectories

Consistent View Synthesis with Pose-Guided Diffusion Models

Deep Equilibrium Optical Flow Estimation

Imposing Consistency for Optical Flow Estimation

A Simple and Powerful Global Optimization for Unsupervised Video Object Segmentation

360° Optical Flow using Tangent Images

DistractFlow: Improving Optical Flow Estimation via Realistic Distractions and Pseudo-Labeling

MAMo: Leveraging Memory and Attention for Monocular Video Depth Estimation


Learning Gradient Fields for Shape Generation

LION: Latent Point Diffusion Models for 3D Shape Generation

ChartPointFlow for Topology-Aware 3D Point Cloud Generation

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


Detecting sites of genomic enrichment

ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response

Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius

PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

Abstract 1687: Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma

Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression

Interleukin-33 Signaling Controls the Development of Iron-Recycling Macrophages

Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain

Release of promoter–proximal paused Pol II in response to histone deacetylase inhibition

TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex

Cardiac endothelial cells maintain open chromatin and expression of cardiomyocyte myofibrillar genes


A citation recommendation system that allows users to find relevant citations for their paper drafts. The tool is backed by Semantic Scholar's OpenCorpus dataset.

Construction of the Literature Graph in Semantic Scholar

Content-Based Citation Recommendation

Navigation-based candidate expansion and pretrained language models for citation recommendation

Learning Neural Textual Representations for Citation Recommendation


Test DRAM for bit flips caused by the rowhammer problem

The RowHammer Problem and Other Issues We May Face as Memory Becomes Denser

PThammer: Cross-User-Kernel-Boundary Rowhammer through Implicit Accesses

CATTmew: Defeating Software-Only Physical Kernel Isolation

IEEE Transactions on Dependable and Secure Computing

RowHammer and Beyond

Understanding Rowhammer Attacks through the Lens of a Unified Reference Framework

TeleHammer : A Stealthy Cross-Boundary Rowhammer Technique

GhostKnight: Breaching Data Integrity via Speculative Execution

TeleHammer: A Formal Model of Implicit Rowhammer


[Neurips 2023] T2I-CompBench: A Comprehensive Benchmark for Open-world Compositional Text-to-image Generation

Scaling Rectified Flow Transformers for High-Resolution Image Synthesis

PixArt-α: Fast Training of Diffusion Transformer for Photorealistic Text-to-Image Synthesis

CoMat: Aligning Text-to-Image Diffusion Model with Image-to-Text Concept
  Matching


On the detection of synthetic images generated by diffusion models

AEROBLADE: Training-Free Detection of Latent Diffusion Images Using
  Autoencoder Reconstruction Error

Synthetic Image Detection: Highlights from the IEEE Video and Image Processing Cup 2022 Student Competition

DeepFake-O-Meter v2.0: An Open Platform for DeepFake Detection

RIGID: A Training-free and Model-Agnostic Framework for Robust
  AI-Generated Image Detection


Unsupervised Deep Embedding for Clustering Analysis

Towards K-means-friendly Spaces: Simultaneous Deep Learning and Clustering

Deep Divergence-Based Approach to Clustering

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

Attentive Representation Learning With Adversarial Training for Short Text Clustering

TC-DWA:Text Clustering with Dual Word-Level Augmentation

Proceedings of the AAAI Conference on Artificial Intelligence

Prognostic value of B-score for predicting joint replacement in the context of osteoarthritis phenotypes: Data from the osteoarthritis initiative


A foundation model for knowledge graph reasoning

Towards Foundation Models for Knowledge Graph Reasoning

A Benchmark to Understand the Role of Knowledge Graphs on Large Language Model's Accuracy for Question Answering on Enterprise SQL Databases

LLM as Prompter: Low-resource Inductive Reasoning on Arbitrary Knowledge
  Graphs

Zero-shot Logical Query Reasoning on any Knowledge Graph


Tensorflow implementation for learning an image-to-image translation without input-output pairs. https://arxiv.org/pdf/1703.10593.pdf

Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks

XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings

A single neural network for cone-beam computed tomography-based radiotherapy of head-and-neck, lung and breast cancer

Generative Adversarial Networks for MR-CT Deformable Image Registration

Jekyll: Attacking Medical Image Diagnostics using Deep Generative Models

IEEE European Symposium on Security and Privacy

Neural network augmented wave-equation simulation

A Quantitative Analysis of the Taxonomy of Artistic Styles


The unified repository for few-shot font generation methods. This repository includes FUNIT (ICCV'19), DM-Font (ECCV'20), LF-Font (AAAI'21) and MX-Font (ICCV'21).

Artistic Glyph Image Synthesis via One-Stage Few-Shot Learning

Multiple Heads are Better than One: Few-shot Font Generation with Multiple Localized Experts

Few-shot Font Generation with Weakly Supervised Localized Representations


RETAIN: Interpretable Predictive Model in Healthcare using Reverse Time Attention Mechanism

RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism

Medical Concept Representation Learning from Electronic Health Records and its Application on Heart Failure Prediction

Change Matters: Medication Change Prediction with Recurrent Residual Networks

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

CATNet: Cross-event Attention-based Time-aware Network for Medical Event Prediction

The Right Tool for the Job: Open-Source Auditing Tools in Machine Learning

Attention-based neural networks for clinical prediction modelling on electronic health records


[ICCV 2017] Torch code for Grad-CAM

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

VQA: Visual Question Answering

Grad-CAM: Why did you say that?

Deep learning for the prediction of early on-treatment response in metastatic colorectal cancer from serial medical imaging

Adaptive Deep Learning through Visual Domain Localization

GWSkyNet-Multi: A Machine-learning Multiclass Classifier for LIGO–Virgo Public Alerts


Passage Re-ranking with BERT

Question Rewriting for Conversational Question Answering

Learning-to-Rank with BERT in TF-Ranking

A Comparison of Question Rewriting Methods for Conversational Passage Retrieval

Beyond Factuality: A Comprehensive Evaluation of Large Language Models as Knowledge Generators

Ultra-High Dimensional Sparse Representations with Binarization for Efficient Text Retrieval

A Little Bit Is Worse Than None: Ranking with Limited Training Data

Explicit Query Rewriting for Conversational Dense Retrieval

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

Learning Representations and Agents for Information Retrieval