Polarized covariant radiative transport code

PATOKA: Simulating Electromagnetic Observables of Black Hole Accretion

The Astrophysical Journal Supplement Series

The Role of Adaptive Ray Tracing in Analyzing Black Hole Structure

Updated Transfer Coefficients for Magnetized Plasmas

Shadows of loop quantum black holes: semi-analytical simulations of loop quantum gravity effects on Sagittarius A* and M87*

Comparison of Polarized Radiative Transfer Codes Used by the EHT Collaboration

Modeling the inner part of M87 jet: confronting jet morphology with theory


DISTIL: Deep dIverSified inTeractIve Learning. An active/inter-active learning library built on py-torch for reducing labeling costs.

Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds

SIMILAR: Submodular Information Measures Based Active Learning In Realistic Scenarios

A Comparative Survey of Deep Active Learning

Effective Evaluation of Deep Active Learning on Image Classification Tasks

One-Round Active Learning

Zero-Round Active Learning

Data-Efficient Learning via Clustering-Based Sensitivity Sampling:
  Foundation Models and Beyond

Pareto Optimization for Active Learning under Out-of-Distribution Data Scenarios

A study of deep active learning methods to reduce labelling efforts in biomedical relation extraction


A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods

Robust enumeration of cell subsets from tissue expression profiles

xCell: digitally portraying the tissue cellular heterogeneity landscape

Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression

Comprehensive analyses of tumor immunity: implications for cancer immunotherapy

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

Comprehensive Benchmarking and Integration of Tumor Microenvironment Cell Estimation Methods

Digital cell quantification identifies global immune cell dynamics during influenza infection


FewCLUE 小样本学习测评基准，中文版

FewCLUE: A Chinese Few-shot Learning Evaluation Benchmark

What Makes Pre-trained Language Models Better Zero-shot Learners?

GlyphCRM: Bidirectional Encoder Representation for Chinese Character with its Glyph


AdaSeq: An All-in-One Library for Developing State-of-the-Art Sequence Understanding Models

Automated Concatenation of Embeddings for Structured Prediction

Zero-Shot Information Extraction via Chatting with ChatGPT

Named Entity and Relation Extraction with Multi-Modal Retrieval

Prompting ChatGPT in MNER: Enhanced Multimodal Named Entity Recognition with Auxiliary Refined Knowledge

DAMO-NLP at SemEval-2023 Task 2: A Unified Retrieval-augmented System for Multilingual Named Entity Recognition

Unsupervised Boundary-Aware Language Model Pretraining for Chinese Sequence Labeling

Modeling Label Correlations for Ultra-Fine Entity Typing with Neural Pairwise Conditional Random Field

DAMO-NLP at NLPCC-2022 Task 2: Knowledge Enhanced Robust NER for Speech Entity Linking

Recall, Expand and Multi-Candidate Cross-Encode: Fast and Accurate Ultra-Fine Entity Typing

D2KLab at SemEval-2023 Task 2: Leveraging T-NER to Develop a Fine-Tuned Multilingual Model for Complex Named Entity Recognition

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


Open morphology for Finnish

Measuring Lexical Quality of a Historical Finnish Newspaper Collection ― Analysis of Garbled OCR Data with Basic Language Technology Tools and Means

Omorfi —Free and open source morphological lexical database for Finnish

Nordic Conference of Computational Linguistics

Old Content and Modern Tools - Searching Named Entities in a Finnish OCRed Historical Newspaper Collection 1771-1910

Using Morphological Knowledge in Open-Vocabulary Neural Language Models

North American Chapter of the Association for Computational Linguistics

Ground Truth OCR Sample Data of Finnish Historical Newspapers and Journals in Data Improvement Validation of a re-OCRing Process

Abu-MaTran at WMT 2015 Translation Task: Morphological Segmentation and Web Crawling

Workshop on Statistical Machine Translation

Neural and rule-based Finnish NLP models—expectations, experiments and experiences

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

Initial Experiments in Data-Driven Morphological Analysis for Finnish

Proceedings of the Fourth International Workshop on Computatinal
          Linguistics of Uralic Languages

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

Apertium-fin-eng–Rule-based Shallow Machine Translation for WMT 2019 Shared Task

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


BEELINE: evaluation of algorithms for gene regulatory network inference

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

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

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

GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks


Violin Plots for Matlab

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

Ex vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy

Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy

Diverse states and stimuli tune olfactory receptor expression levels to modulate food-seeking behavior

Commonality and variation in mental representations of music revealed by a cross-cultural comparison of rhythm priors in 15 countries

Visualization of Sugar Content Distribution of White Strawberry by Near-Infrared Hyperspectral Imaging

Quantifying influence of human choice on the automated detection of Drosophila behavior by a supervised machine learning algorithm

Long-term transverse imaging of the hippocampus with glass microperiscopes

Dynamic fibronectin assembly and remodeling by leader neural crest cells prevents jamming in collective cell migration

Object detection neural network improves Fourier ptychography reconstruction


Scalable 1D Gaussian Processes in C++, Python, and Julia

Fast and Scalable Gaussian Process Modeling with Applications to Astronomical Time Series

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

Monthly notices of the Royal Astronomical Society

A planet within the debris disk around the pre-main-sequence star AU Microscopii

Gaussian Process Regression for Astronomical Time Series

The CARMENES search for exoplanets around M dwarfs. A Neptune-mass planet traversing the habitable zone around HD 180617

Gaussian process modelling of granulation and oscillations in red giant stars

Monthly Notices of the Royal Astronomical Society

Gaussian Process Modeling Fermi-LAT γ-Ray Blazar Variability: A Sample of Blazars with γ-Ray Quasi-periodicities

A hot Saturn on an eccentric orbit around the giant star K2-132

The Dark World: A Tale of WASP-43b in Reflected Light with HST WFC3/UVIS

Bayesian Methods for Exoplanet Science


A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores

Genetic comorbidity between major depression and cardio-metabolic traits, stratified by age at onset of major depression

Carolina Digital Repository (University of North Carolina at Chapel Hill)

Multivariate genetic analysis of personality and cognitive traits reveals abundant pleiotropy

Associations and limited shared genetic aetiology between bipolar disorder and cardiometabolic traits in the UK Biobank

The power of pathway-based polygenic risk scores

The genomics of childhood eating behaviours

Phenotypic Associations and Shared Genetic Etiology between Bipolar Disorder and Cardiometabolic Traits

Topic modeling identifies novel genetic loci associated with multimorbidities in UK Biobank

Genome-wide association study in 404,302 individuals identifies 7 significant loci for reaction time variability

medRxiv : the preprint server for health sciences


Openllet is an OWL 2 reasoner in Java, build on top of Pellet.

A Wikidata-based tool for building and visualising narratives

International Journal on Digital Libraries

A Comparative Study of Rule-Based Inference Engines for the Semantic Web

IEICE Transactions on Information and Systems

Ontological representation, classification and data-driven computing of phenotypes

An Ontology for Modeling Cultural Heritage Knowledge in Urban Tourism

A Declarative Model for Web Accessibility Requirements and its Implementation

OntoRepliCov: an Ontology-Based Approach for Modeling the SARS-CoV-2 Replication Process

Popularity-Driven Ontology Ranking Using Qualitative Features

Efficient TBox Reasoning with Value Restrictions using the wer Reasoner

Theory and Practice of Logic Programming

Natural Language to SPARQL Query Builder for Semantic Web Applications

Journal of Machine Intelligence and Data Science


zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs

CancerSCEM: a database of single-cell expression map across various human cancers

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

High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids


SoTA Abstract Meaning Representation (AMR) parsing with word-node alignments in Pytorch. Includes checkpoints and other tools such as statistical significance Smatch.

Transition-Based Dependency Parsing with Stack Long Short-Term Memory

Leveraging Abstract Meaning Representation for Knowledge Base Question Answering

Transition-based Parsing with Stack-Transformers

Structure-aware Fine-tuning of Sequence-to-sequence Transformers for Transition-based AMR Parsing

Maximum Bayes Smatch Ensemble Distillation for AMR Parsing

Pushing the Limits of AMR Parsing with Self-Learning

Inducing and Using Alignments for Transition-based AMR Parsing

Identification of Entailment and Contradiction Relations between Natural Language Sentences: A Neurosymbolic Approach


the pangenome graph builder

Graph pangenome captures missing heritability and empowers tomato breeding

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

Vcflib and tools for processing the VCF variant call format

Unbiased pangenome graphs

Superbubbles, Ultrabubbles, and Cacti

Journal of computational biology : a journal of computational molecular cell biology

Genome alignment with graph data structures: a comparison

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

A super-pangenome of the North American wild grape species

From the reference human genome to human pangenome: Premise, promise and challenge


An Unsteady Actuator Line Solver to Enable Adjoint Sensitivity Studies for Wake Steering

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


Package for fetching metadata and downloading data from SRA/ENA/GEO

pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive

A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study


An Arduino library to give environmental sensors a common interface of functions for use with Arduino-framework dataloggers, such as the EnviroDIY Mayfly.

Low-Cost, Open-Source, and Low-Power: But What to Do With the Data?


PDBFixer fixes problems in PDB files

An optimized chemical-genetic method for cell-specific metabolic labeling of RNA

The dynamic conformational landscape of the protein methyltransferase SETD8

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques

Molecular mechanism of LIP05 derived from Monascus purpureus YJX-8 for synthesizing fatty acid ethyl esters under aqueous phase

An Open-Source Molecular Builder and Free Energy Preparation Workflow

A Novel Machine Learning Approach Uncovers New and Distinctive Inhibitors for Cyclin-Dependent Kinase 9

The Dynamic Conformational Landscapes of the Protein Methyltransferase SETD8

Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study

Pre-bound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin-BPTI Complex Using Random Acceleration Molecular Dynamics Simulations

How Chromophore Labels Shape the Structure and Dynamics of a Peptide Hydrogel


A Julia package dedicated to simulating quantum many-body systems using Matrix Product States (MPS)

A critical lattice model for a Haagerup conformal field theory

Lattice regularisation and entanglement structure of the Gross-Neveu model

Efficient higher-order matrix product operators for time evolution

Higher Berry Curvature from the Wave Function I: Schmidt Decomposition
  and Matrix Product States

Infinite Grassmann time-evolving matrix product operator method in the steady state

The chiral Gross-Neveu model on the lattice via a Landau-forbidden phase transition


scikit-fmm is a Python extension module which implements the fast marching method.

Physical interactions reduce the power of natural selection in growing yeast colonies

Renderable Neural Radiance Map for Visual Navigation

StorSeismic: A new paradigm in deep learning for seismic processing

A new framework for experimental design using Bayesian Evidential Learning: the case of wellhead protection area

Break: Bronchi Reconstruction by Geodesic Transformation and Skeleton Embedding

Workspace Aware Online Grasp Planning

Image patch analysis of sunspots and active regions. I. Intrinsic dimension and correlation analysis

Transfer learning for self-supervised, blind-spot seismic denoising

MORPHOLOGICAL MODELING OF COLD SPRAY COATINGS

Physics-Informed Graph Neural Network for Spatial-temporal Production Forecasting


Galaxy RNA workbench

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

The RNA workbench 2.0: next generation RNA data analysis

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


A semidefinite program solver for the conformal bootstrap.

TASI Lectures on the Conformal Bootstrap

A Semidefinite Program Solver for the Conformal Bootstrap

Carving out OPE space and precise O(2) model critical exponents

Scaling the semidefinite program solver SDPB

Weizmann Lectures on the Numerical Conformal Bootstrap

The Gross-Neveu-Yukawa archipelago

autoboot: a generator of bootstrap equations with global symmetry

Bootstrapping mixed correlators in N=4 super Yang-Mills

OPE coefficients in Argyres-Douglas theories

The Regge bootstrap, from linear to non-linear trajectories


A Julia package for large-scale tensor computations, with a hint of category theory

Chiral spin liquids on the kagome lattice with projected entangled simplex states

Lattice regularisation and entanglement structure of the Gross-Neveu model

Trimer states with ℤ_3 topological order in Rydberg atom arrays

Augmenting Density Matrix Renormalization Group with Disentanglers

Absence of Spin Liquid Phase in the J_1-J_2 Heisenberg model on the Square Lattice

Grassmann time-evolving matrix product operators for equilibrium quantum impurity problems

Augmenting Density Matrix Renormalization Group with Clifford Circuits

QSpace - An open-source tensor library for Abelian and non-Abelian
  symmetries

Chiral spin liquids with projected Gaussian fermionic entangled pair states

On the Magnetization of the 120^∘ order of the Spin-1/2 Triangular Lattice Heisenberg Model: a DMRG revisit


Deep GPs built on top of TensorFlow/Keras and GPflow

GPflux: A Library for Deep Gaussian Processes

Deep Gaussian Process Emulation using Stochastic Imputation

A Unifying Perspective on Non-Stationary Kernels for Deeper Gaussian Processes

Bellman: A Toolbox for Model-Based Reinforcement Learning in TensorFlow


Axon/Myelin segmentation using Deep Learning

AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks

Deep Active Learning for Axon-Myelin Segmentation on Histology Data

A simple and robust method for automating analysis of naïve and regenerating peripheral nerves

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

Automatic Axon and Myelin Segmentation of Microscopy Images and Morphometrics Extraction


Home page of project "KB"

A Manually-Curated Dataset of Fixes to Vulnerabilities of Open-Source Software

Detection, assessment and mitigation of vulnerabilities in open source dependencies

A Survey on Machine Learning Techniques for Source Code Analysis

A comparative study of vulnerability reporting by software composition analysis tools

Proceedings of the 15th ACM / IEEE International Symposium on Empirical Software Engineering and Measurement (ESEM)

SeqTrans: Automatic Vulnerability Fix Via Sequence to Sequence Learning

Multi-Granularity Detector for Vulnerability Fixes

A Survey on Automated Program Repair Techniques

The Used, the Bloated, and the Vulnerable: Reducing the Attack Surface of an Industrial Application

Automated Mapping of Vulnerability Advisories onto their Fix Commits in Open Source Repositories

Detecting Security Fixes in Open-Source Repositories using Static Code Analyzers


Modern Super Learning with Machine Learning Pipelines

Global land characterisation using land cover fractions at 100 m resolution

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

A Fundamental Measure of Treatment Effect Heterogeneity

txshift: Efficient estimation of the causal effects of stochastic interventions in R

Application of targeted maximum likelihood estimation in public health and epidemiological studies: a systematic review

An Easy Implementation of CV-TMLE

Effect of Sepsis on Death as Modified by Solid Organ Transplantation

Adaptive Sequential Design for a Single Time-Series

Causal isotonic calibration for heterogeneous treatment effects

Targeted learning in observational studies with multi-valued treatments: An evaluation of antipsychotic drug treatment safety


UCLID5: formal modeling, verification, and synthesis of computational systems

Verification of Quantitative Hyperproperties Using Trace Enumeration Relations

UCLID5: Multi-modal Formal Modeling, Verification, and Synthesis

A Methodology for Developing a Verifiable Aircraft Engine Controller from Formal Requirements

Synthesis in Uclid5


The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

A systematic assessment of current genome-scale metabolic reconstruction tools

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0.

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

ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic Reconstruction of a Non-model Species

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

Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (DGKA) as a potential therapeutic target for intrahepatic cholangiocarcinoma


a Medical Genetics Sequence Analysis Pipeline

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

MDM2, MDM4 and EGFR Amplifications and Hyperprogression in Metastatic Acral and Mucosal Melanoma

Distinct Mutation Patterns Reveal Melanoma Subtypes and Influence Immunotherapy Response in Advanced Melanoma Patients

First-line exome sequencing in Palestinian and Israeli Arabs with neurological disorders is efficient and facilitates disease gene discovery

European journal of human genetics : EJHG

Disruption of MeCP2–TCF20 complex underlies distinct neurodevelopmental disorders

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

Investigating the effects of additional truncating variants in DNA-repair genes on breast cancer risk in BRCA1-positive women

First submicroscopic inversion of the OPA1 gene identified in dominant optic atrophy - a case report

Diagnostic genome sequencing improves diagnostic yield: a prospective single-centre study in 1000 patients with inherited eye diseases

Transcriptional and Mutational Profiling of B-Other Acute Lymphoblastic Leukemia for Improved Diagnostics

Genome sequencing and transcriptome profiling in twins discordant for Mayer-Rokitansky-Küster-Hauser syndrome


High-performance reactive message-passing based Bayesian inference engine

Reactive Message Passing for Scalable Bayesian Inference

A Bayesian Modeling Approach to Situated Design of Personalized Soundscaping Algorithms

AIDA: An Active Inference-Based Design Agent for Audio Processing Algorithms


Context Broker and CEF building block for context data management which supports both the NGSI-LD and the NGSI-v2 APIs

A Standard-Based Open Source IoT Platform: FIWARE

VirIoT: A Cloud of Things That Offers IoT Infrastructures as a Service

Using FIWARE and blockchain in smart cities solutions

Overcoming the Barriers of Using Linked Open Data in Smart City Applications


Transportation Fuels Reporting System


Repository for the code of the Open Energy Platform (OEP) website. The OEP provides an interface to the Open Energy Family


Implementation of End-to-End Relation Extraction using LSTMs on Sequences and Tree Structures in ACL2016.

A Novel Cascade Binary Tagging Framework for Relational Triple Extraction

Joint entity recognition and relation extraction as a multi-head selection problem

Entity-Relation Extraction as Multi-Turn Question Answering

Neural End-to-End Learning for Computational Argumentation Mining

End-to-End Neural Relation Extraction with Global Optimization

Empirical Methods in Natural Language Processing

A Walk-based Model on Entity Graphs for Relation Extraction

Extracting Entities and Relations with Joint Minimum Risk Training

Pre-training Entity Relation Encoder with Intra-span and Inter-span Information

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

End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models


UNetFormer: A UNet-like transformer for efficient semantic segmentation of remote sensing urban scene imagery, ISPRS. Also, including other vision transformers and CNNs for satellite, aerial image and UAV image segmentation.

Isprs Journal of Photogrammetry and Remote Sensing

A Novel Transformer Based Semantic Segmentation Scheme for Fine-Resolution Remote Sensing Images

Transformer Meets Convolution: A Bilateral Awareness Network for Semantic Segmentation of Very Fine Resolution Urban Scene Images

PyramidMamba: Rethinking Pyramid Feature Fusion with Selective Space State Model for Semantic Segmentation of Remote Sensing Imagery

AN END-TO-END DEEP LEARNING WORKFLOW FOR BUILDING SEGMENTATION, BOUNDARY REGULARIZATION AND VECTORIZATION OF BUILDING FOOTPRINTS

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


Implementation of Deep IV: A Flexible Approach for Counterfactual Prediction

International Conference on Machine Learning

Auto IV: Counterfactual Prediction via Automatic Instrumental Variable Decomposition

Dual IV: A Single Stage Instrumental Variable Regression.

Markdowns in E-Commerce Fresh Retail: A Counterfactual Prediction and Multi-Period Optimization Approach

Instrumental Variables in Causal Inference and Machine Learning: A Survey

Causal Inference with Conditional Instruments using Deep Generative Models


Conv-TasNet: Surpassing Ideal Time–Frequency Magnitude Masking for Speech Separation

IEEE/ACM transactions on audio, speech, and language processing

Deep Multi-Frame MVDR Filtering for Single-Microphone Speech Enhancement

Deep Multi-Frame MVDR Filtering for Binaural Noise Reduction

Multi-Task Audio Source Separation

Integrating Statistical Uncertainty into Neural Network-Based Speech Enhancement

IEEE International Conference on Acoustics, Speech, and Signal Processing

Audio-visual Speech Separation with Adversarially Disentangled Visual Representation

Time-Domain Speech Super-Resolution With GAN Based Modeling for Telephony Speaker Verification


Code for reproducing f-AnoGAN training and anomaly scoring

Improved Training of Wasserstein GANs

Unsupervised Anomaly Detection with Generative Adversarial Networks to Guide Marker Discovery

The MVTec Anomaly Detection Dataset: A Comprehensive Real-World Dataset for Unsupervised Anomaly Detection

International Journal of Computer Vision

Beyond Dents and Scratches: Logical Constraints in Unsupervised Anomaly Detection and Localization

Proxy-bridged Image Reconstruction Network for Anomaly Detection in Medical Images

Anomaly Detection and Automatic Labeling for Solar Cell Quality Inspection Based on Generative Adversarial Network

Machine Learning in NextG Networks via Generative Adversarial Networks

IEEE Transactions on Cognitive Communications and Networking

The role of noise in denoising models for anomaly detection in medical images

EvAn: Neuromorphic Event-Based Sparse Anomaly Detection


Material from the DARPA Transparent Computing Program

HOLMES: Real-time APT Detection through Correlation of Suspicious Information Flows

THREATRACE: Detecting and Tracing Host-Based Threats in Node Level Through Provenance Graph Learning

GrAALF:Supporting Graphical Analysis of Audit Logs for Forensics

RAPTOR: Advanced Persistent Threat Detection in Industrial IoT via Attack Stage Correlation

Kairos: Practical Intrusion Detection and Investigation using Whole-system Provenance

Xanthus: Push-button Orchestration of Host Provenance Data Collection

Proceedings of the 3rd International Workshop on Practical Reproducible Evaluation of Computer Systems

Recommender Systems in Cybersecurity

LogKernel: A Threat Hunting Approach Based on Behaviour Provenance Graph and Graph Kernel Clustering

Combating Advanced Persistent Threats: Challenges and Solutions

Ostinato: Cross-host Attack Correlation Through Attack Activity Similarity Detection


Instruction THroughput Estimator using MAchine Learning (ITHEMAL)

Ithemal: Accurate, Portable and Fast Basic Block Throughput Estimation using Deep Neural Networks

BHive: A Benchmark Suite and Measurement Framework for Validating x86-64 Basic Block Performance Models

PROCEEDINGS OF THE 2019 IEEE INTERNATIONAL SYMPOSIUM ON WORKLOAD CHARACTERIZATION (IISWC 2019)

Facile: Fast, Accurate, and Interpretable Basic-Block Throughput Prediction

IEEE International Symposium on Workload Characterization

AnICA: Analyzing Inconsistencies in Microarchitectural Code Analyzers


VISIbility Based Line Extraction

Detecting Weak Spectral Lines in Interferometric Data through Matched Filtering

The First Detection of 13C17O in a Protoplanetary Disk: A Robust Tracer of Disk Gas Mass

An Unbiased ALMA Spectral Survey of the LkCa 15 and MWC 480 Protoplanetary Disks

Dust Continuum Emission and the Upper Limit Fluxes of Submillimeter Water Lines of the Protoplanetary Disk around HD 163296 Observed by ALMA

The Excitation Conditions of CN in TW Hya


Code for the paper "High Speed and High Dynamic Range Video with an Event Camera" (T-PAMI, 2019).

Learning to Super Resolve Intensity Images from Events

Experimental Comparison between Event and Global Shutter Cameras

OpenESS: Event-based Semantic Scene Understanding with Open Vocabularies


A simplified PyTorch implementation of "SeqGAN: Sequence Generative Adversarial Nets with Policy Gradient." (Yu, Lantao, et al.)

Code-Switched Language Models Using Neural Based Synthetic Data from Parallel Sentences

From Machine Translation to Code-Switching: Generating High-Quality Code-Switched Text

OodGAN: Generative Adversarial Network for Out-of-Domain Data Generation

Multilingual Transfer Learning for Code-Switched Language and Speech Neural Modeling

Russian Natural Language Generation: Creation of a Language Modelling Dataset and Evaluation with Modern Neural Architectures


The GitHub open source software repository on interpreting super-resolution CNNs for sub-pixel motion compensation in video coding

Improved CNN-Based Learning of Interpolation Filters for Low-Complexity Inter Prediction in Video Coding

Interpreting CNN For Low Complexity Learned Sub-Pixel Motion Compensation In Video Coding

International Conference on Information Photonics

Interpreting Super-Resolution CNNs for Sub-Pixel Motion Compensation in Video Coding

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


NOVOPlasty - The organelle assembler and heteroplasmy caller

NOVOPlasty: de novo assembly of organelle genomes from whole genome data

A systematic comparison of chloroplast genome assembly tools

Unraveling heteroplasmy patterns with NOVOPlasty

Eight Million Years of Satellite DNA Evolution in Grasshoppers of the Genus Schistocerca Illuminate the Ins and Outs of the Library Hypothesis

Improved Methods for Acetocarmine and Haematoxylin Staining to Visualize Chromosomes in the Filamentous Green Alga Zygnema (Charophyta)

bioRxiv : the preprint server for biology

Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing

Complete Chloroplast Genome Analysis of Two Important Medicinal Alpinia Species: Alpinia galanga and Alpinia kwangsiensis


Long read / genome alignment software

Weighted minimizer sampling improves long read mapping

Long-read mapping to repetitive reference sequences using Winnowmap2

A long read mapping method for highly repetitive reference sequences

Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery


Bilinear attention networks for visual question answering

Bilinear Attention Networks

Cycle-Consistency for Robust Visual Question Answering

Nougat: Neural Optical Understanding for Academic Documents

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

Cross-Media Keyphrase Prediction: A Unified Framework with Multi-Modality Multi-Head Attention and Image Wordings

Learning from Lexical Perturbations for Consistent Visual Question Answering

Guiding Visual Question Answering with Attention Priors


[NeurIPS 2019] Learning Imbalanced Datasets with Label-Distribution-Aware Margin Loss

Imbalance Trouble: Revisiting Neural-Collapse Geometry

Escaping Saddle Points for Effective Generalization on Class-Imbalanced Data

Supercharging Imbalanced Data Learning With Energy-based Contrastive Representation Transfer

Learning to Re-weight Examples with Optimal Transport for Imbalanced Classification

Class Balancing GAN with a Classifier in the Loop

Decoupled Training for Long-Tailed Classification With Stochastic Representations

Background Splitting: Finding Rare Classes in a Sea of Background


Easy generative modeling in PyTorch

beta-VAE: Learning Basic Visual Concepts with a Constrained Variational Framework

International Conference on Learning Representations

Stochastic Gradient VB and the Variational Auto-Encoder

Neural Discrete Representation Learning

A Neural Algorithm of Artistic Style

Pixel Recurrent Neural Networks

Conditional Image Generation with PixelCNN Decoders

NICE: Non-linear Independent Components Estimation

Generating Diverse High-Fidelity Images with VQ-VAE-2

Generative Pretraining from Pixels

Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention


Exact Combinatorial Optimization with Graph Convolutional Neural Networks (NeurIPS 2019)

Ecole: A Gym-like Library for Machine Learning in Combinatorial Optimization Solvers

Learning a Large Neighborhood Search Algorithm for Mixed Integer Programs

Learning Cut Selection for Mixed-Integer Linear Programming via Hierarchical Sequence Model

Lookback for Learning to Branch

A Fast Graph Neural Network-Based Method for Winner Determination in Multi-Unit Combinatorial Auctions

Rethinking the Capacity of Graph Neural Networks for Branching Strategy

Promoting Generalization for Exact Solvers via Adversarial Instance Augmentation

Distributional MIPLIB: a Multi-Domain Library for Advancing ML-Guided
  MILP Methods


Neural Machine Translation of Rare Words with Subword Units

Fully Character-Level Neural Machine Translation without Explicit Segmentation

A Character-Level Decoder without Explicit Segmentation for Neural Machine Translation

How Grammatical is Character-level Neural Machine Translation? Assessing MT Quality with Contrastive Translation Pairs

Normalizing Medieval German Texts: from rules to deep learning

A Neural Approach to Language Variety Translation

Character-level Chinese-English Translation through ASCII Encoding

Neural machine translation of Basque

European Association for Machine Translation Conferences/Workshops

Character-level Transformer-based Neural Machine Translation

Improved English to Russian Translation by Neural Suffix Prediction


A collection of succinct data structures

From Theory to Practice: Plug and Play with Succinct Data Structures

Log(Graph): A Near-Optimal High-Performance Graph Representation

A Framework of Dynamic Data Structures for String Processing

Hypersuccinct Trees -- New universal tree source codes for optimal compressed tree data structures and range minima

Parallel Construction of Compact Planar Embeddings

Entropy Trees and Range-Minimum Queries In Optimal Average-Case Space


Methods to compute Local Inverse Simpson's Index (LISI)

Fast, sensitive, and accurate integration of single cell data with Harmony

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes

FastIntegration: a versatile R package for accessing and integrating large-scale single-cell RNA-seq data


Repository for the paper "Planning to Explore via Self-Supervised World Models"

Model-Based Active Exploration

Curiosity-Driven Exploration via Latent Bayesian Surprise

Reparameterized Policy Learning for Multimodal Trajectory Optimization


Generative adversarial network for generating electronic health records.

Generating Multi-label Discrete Patient Records using Generative Adversarial Networks

GAN-Leaks: A Taxonomy of Membership Inference Attacks against Generative Models

Conference on Computer and Communications Security

Differentially Private Synthetic Medical Data Generation using Convolutional GANs

GAN-Leaks: A Taxonomy of Membership Inference Attacks against GANs

Generating Synthetic but Plausible Healthcare Record Datasets

Generative Adversarial Networks for Synthetic Data Generation: A Comparative Study


Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope

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

The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy

Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

A Barcode-Based Phylogenetic Characterization of Phytophthora cactorum Identifies Two Cosmopolitan Lineages with Distinct Host Affinities and the First Report of Phytophthora pseudotsugae in California

Cuban history of CRF19 recombinant subtype of HIV-1

Simulation data for the estimation of numerical constants for approximating pairwise evolutionary distances between amino acid sequences


Corruption and Perturbation Robustness (ICLR 2019)

Benchmarking Neural Network Robustness to Common Corruptions and Perturbations

Bayesian Deep Learning and a Probabilistic Perspective of Generalization

Improving robustness against common corruptions by covariate shift adaptation

Masked Siamese Networks for Label-Efficient Learning

A simple way to make neural networks robust against diverse image corruptions

Simulating a Primary Visual Cortex at the Front of CNNs Improves Robustness to Image Perturbations

Benchmarking Neural Network Robustness to Common Corruptions and Surface Variations

Towards Stable Test-Time Adaptation in Dynamic Wild World

Multiobjective Evolutionary Design of Deep Convolutional Neural Networks for Image Classification

Boosting Adversarial Training with Hypersphere Embedding


A library for factorization machines and polynomial networks for classification and regression in Python.

On the Computational Efficiency of Training Neural Networks

Android Malware Detection Based on Factorization Machine

Supervised Learning for Non-Sequential Data: A Canonical Polyadic Decomposition Approach

Supervised Learning for Non-Sequential Data with the Canonical Polyadic Decomposition.


Fake News Challenge

A Retrospective Analysis of the Fake News Challenge Stance-Detection Task

Disinformation, Misinformation, and Fake News in Social Media

Combining Similarity Features and Deep Representation Learning for Stance Detection in the Context of Checking Fake News

Investigating Rumor News Using Agreement-Aware Search

International Conference on Information and Knowledge Management

SIRIUS-LTG: An Entity Linking Approach to Fact Extraction and Verification

Proceedings of the First Workshop on Fact Extraction and VERification (FEVER)

Exploiting stance hierarchies for cost-sensitive stance detection of Web documents

Journal of Intelligent Information Systems

On the use of text augmentation for stance and fake news detection

Journal of Information and Telecommunication

UofA-Truth at Factify 2022 : Transformer And Transfer Learning Based Multi-Modal Fact-Checking

APSN: Adversarial Pseudo-Siamese Network for Fake News Stance Detection

Veritas Annotator: Discovering the Origin of a Rumour

Proceedings of the Second Workshop on Fact Extraction and VERification (FEVER)


This is a code repository to efficiently train a deconvolutional neural network with rectified linear units.

Do Deep Neural Networks Learn Facial Action Units When Doing Expression Recognition?

How Deep Neural Networks Can Improve Emotion Recognition on Video Data

Super-Resolution via Deep Learning

Self-Tuned Deep Super Resolution

An Analysis of Unsupervised Pre-training in Light of Recent Advances

Decomposition-Based Domain Adaptation for Real-World Font Recognition


Understand and test language model architectures on synthetic tasks.

Zoology: Measuring and Improving Recall in Efficient Language Models

Simple linear attention language models balance the recall-throughput
  tradeoff

HGRN2: Gated Linear RNNs with State Expansion

Understanding the differences in Foundation Models: Attention, State
  Space Models, and Recurrent Neural Networks

Just read twice: closing the recall gap for recurrent language models


Efficient TLS termination inside Intel SGX enclaves for existing applications

Util::Lookup: Exploiting key decoding in cryptographic libraries

STELLA: Sparse Taint Analysis for Enclave Leakage Detection

Using SGX for Meta-Transactions Support in Ethereum DApps


COMmon Bayesian Optimization

COMBO: An efficient Bayesian optimization library for materials science

Bayesian optimization of chemical composition: a comprehensive framework
  and its application to RFe_12-type magnet compounds

Machine learning in materials modeling—fundamentals and the opportunities in 2D materials

Continuous surrogate-based optimization algorithms are well-suited for expensive discrete problems

Communications in computer and information science

Fourier Representations for Black-Box Optimization over Categorical Variables

First-principles investigation of Nd(Fe,M)12 (M = K--Br) and Nd(Fe,Cr,Co,Ni,Ge,As)12: Possible enhancers of Curie temperature for NdFe12 magnetic compounds


Towards Gene Expression Convolutions using Gene Interaction Graphs

Deep Learning on Graphs: A Survey

Is graph-based feature selection of genes better than random?


Automatic White Matter Bundle Segmentation

Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning

An overview of deep learning in medical imaging focusing on MRI

TractSeg - Fast and accurate white matter tract segmentation

Combined tract segmentation and orientation mapping for bundle-specific tractography

Prevalence of white matter pathways coming into a single white matter voxel orientation: The bottleneck issue in tractography

Tract orientation mapping for bundle-specific tractography

Population-based tract-to-region connectome of the human brain and its hierarchical topology

Detecting microstructural deviations in individuals with deep diffusion MRI tractometry

Fiber tractography bundle segmentation depends on scanner effects, vendor effects, acquisition resolution, diffusion sampling scheme, diffusion sensitization, and bundle segmentation workflow

Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation


[ECCV2022] PETR: Position Embedding Transformation for Multi-View 3D Object Detection & [ICCV2023] PETRv2: A Unified Framework for 3D Perception from Multi-Camera Images

Cross Modal Transformer: Towards Fast and Robust 3D Object Detection

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

Are We Ready for Vision-Centric Driving Streaming Perception? The ASAP Benchmark


A collection of datasets for the purpose of emotion recognition/detection in speech.

The Ryerson Audio-Visual Database of Emotional Speech and Song (RAVDESS): A dynamic, multimodal set of facial and vocal expressions in North American English

ShEMO -- A Large-Scale Validated Database for Persian Speech Emotion Detection

DEMoS: an Italian emotional speech corpus

Towards a standard set of acoustic features for the processing of emotion in speech.

The Perceived Emotion of Isolated Synthetic Audio: The EmoSynth Dataset and Results


NicheNet: predict active ligand-target links between interacting cells

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair

Defining human mesenchymal and epithelial heterogeneity in response to oral inflammatory disease

TIM3+ TRBV11-2 T cells and IFNγ signature in patrolling monocytes and CD16+ NK cells delineate MIS-C

Single cell atlas identifies lipid-processing and immunomodulatory endothelial cells in healthy and malignant breast

Computational Approaches and Challenges in Spatial Transcriptomics

基因组蛋白质组与生物信息学报

Single-cell atlas of keratoconus corneas revealed aberrant transcriptional signatures and implicated mechanical stretch as a trigger for keratoconus pathogenesis

Endothelial Zeb2 preserves the hepatic angioarchitecture and protects against liver fibrosis

Mapping the Spatial Dynamics of the Human Oral Mucosa in Chronic Inflammatory Disease


Leave One Feature Out Importance


Flexible audio loudness meter in Python with implementation of ITU-R BS.1770-4 loudness algorithm

LibriMix: An Open-Source Dataset for Generalizable Speech Separation

Surfboard: Audio Feature Extraction for Modern Machine Learning

HUI-Audio-Corpus-German: A high quality TTS dataset

CLEAR: A Dataset for Compositional Language and Elementary Acoustic Reasoning

Pheme: Efficient and Conversational Speech Generation

Leveraging Neural Representations for Audio Manipulation


Calling and Phasing of Single-Nucleotide and Structural Variants of the LDLR Gene Using Oxford Nanopore MinION

International journal of molecular sciences

ONT long-read WGS for variant discovery and orthogonal confirmation of short read WGS derived genetic variants in clinical genetic testing


Density estimation likelihood-free inference. No longer actively developed see https://github.com/mackelab/sbi instead

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

Automatic Posterior Transformation for Likelihood-Free Inference

Flexible statistical inference for mechanistic models of neural dynamics

SBI -- A toolkit for simulation-based inference

Distinct synaptic transfer functions in same-type photoreceptors

Near-optimal rotation of colour space by zebrafish cones in vivo


Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

Computer vision for pattern detection in chromosome contact maps

Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice


A Python interface for reinforcement learning environments

Magnetic control of tokamak plasmas through deep reinforcement learning

dm_control: Software and Tasks for Continuous Control

AndroidEnv: A Reinforcement Learning Platform for Android

Using Unity to Help Solve Intelligence

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

Learning Robust Real-Time Cultural Transmission without Human Data

Mava: a research library for distributed multi-agent reinforcement learning in JAX

Gymnasium: A Standard Interface for Reinforcement Learning Environments

PufferLib: Making Reinforcement Learning Libraries and Environments Play Nice


int8_t and int16_t matrix multiply based on https://arxiv.org/abs/1705.01991

The Sockeye 2 Neural Machine Translation Toolkit at AMTA 2020

Sharp Models on Dull Hardware: Fast and Accurate Neural Machine Translation Decoding on the CPU

Edinburgh's Submissions to the 2020 Machine Translation Efficiency Task

Workshop on Neural Generation and Translation

Compressing Neural Machine Translation Models with 4-bit Precision

Efficient Machine Translation with Model Pruning and Quantization

Speed-optimized, Compact Student Models that Distill Knowledge from a Larger Teacher Model: the UEDIN-CUNI Submission to the WMT 2020 News Translation Task

Empirical Methods in Natural Language Processing


Elementary Multiperspective Material Ontology (EMMO)

Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering

Journal of Chemical and Engineering Data

A Perspective on Digital Knowledge Representation in Materials Science and Engineering

Ontology-Based Process Modelling-with Examples of Physical Topologies

Agent-OM: Leveraging LLM Agents for Ontology Matching

Knowledge Graph Question Answering for Materials Science (KGQA4MAT): Developing Natural Language Interface for Metal-Organic Frameworks Knowledge Graph (MOF-KG)

CateCom: A Practical Data-Centric Approach to Categorization of Computational Models

Integrating Extended Non-destructive Testing in the Life Cycle Management of Bonded Products—Some Perspectives

Towards Enhancing Open Innovation Efficiency: A Method for Ontological Integration of BPMN and EMMO

Conference on Computer Science and Information Systems

Insights from an OTTR-centric Ontology Engineering Methodology

A materials terminology knowledge graph automatically constructed from text corpus


OpenModelica Microgrid Gym (OMG): An OpenAI Gym Environment for Microgrids


Systematic conservation prioritization in R

Economics and optics influence funding for ecological restoration in a nation-wide program


Public repository for the Monte Python Code

Early Dark Energy can Resolve the Hubble Tension

Early dark energy does not restore cosmological concordance

Oscillating scalar fields and the Hubble tension: A resolution with novel signatures

Cosmic microwave background bounds on primordial black holes including dark matter halo accretion

The BAO+BBN take on the Hubble tension

Journal of Cosmology and Astroparticle Physics

Constraining early dark energy with large-scale structure

Early dark energy is not excluded by current large-scale structure data

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

Limits on wCDM from the EFTofLSS with the PyBird code

Hints of Early Dark Energy in Planck, SPT, and ACT data: new physics or systematics?


This is a repository of public data sources for Recommender Systems (RS).

User Behavior Simulation with Large Language Model based Agents

Recommender Systems: A Primer

Evaluation Measures of Individual Item Fairness for Recommender Systems: A Critical Study


A Latex style and template for paper preprints (based on NIPS style)

A Comprehensive Overview and Survey of Recent Advances in Meta-Learning

A Deep CNN Architecture with Novel Pooling Layer Applied to Two Sudanese Arabic Sentiment Datasets

Weak phases and CP-symmetry tests in sequential decays of entangled double-strange baryons

A Brief Summary of Interactions Between Meta-Learning and Self-Supervised Learning

A Brief Survey of Associations Between Meta-Learning and General AI

Empirically Classifying Network Mechanisms

Cross-Corpus Multilingual Speech Emotion Recognition: Amharic vs. Other Languages

A Survey of Personality, Persona, and Profile in Conversational Agents and Chatbots

Dynamic Bayesian Neural Networks

The orbital Lense–Thirring precession in a strong field


A tool to map bisulfite converted sequence reads and determine cytosine methylation states

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

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

Introduction to Single-Cell DNA Methylation Profiling Methods

H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity

Drivers underpinning the malignant transformation of giant cell tumour of bone

Abstract 2659: 5-methylcytosine (m5C) RNA modification controls the innate immune response to virus infection by regulating type I interferons

Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells

BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS

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


A fast stabilizer circuit library.

Suppressing quantum errors by scaling a surface code logical qubit

A Fault-Tolerant Honeycomb Memory

Relaxing Hardware Requirements for Surface Code Circuits using Time-dynamics

Benchmarking the Planar Honeycomb Code

A Pair Measurement Surface Code on Pentagons

Microarchitectures for Heterogeneous Superconducting Quantum Computers

SymPhase: Phase Symbolization for Fast Simulation of Stabilizer Circuits


Read-based phasing of genomic variants, also called haplotype assembly

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

Organ-specific genome diversity of replication-competent SARS-CoV-2

A graph-based approach to diploid genome assembly

Genotyping, sequencing and analysis of 140,000 adults from Mexico City

A chromosome-level reference genome and pangenome for barn swallow population genomics


Repository for the development and release of ISRaD data and tools


A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling

In vitro microvessels for the study of angiogenesis and thrombosis

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

Analysis of a mathematical model for COVID-19 population dynamics in Lagos, Nigeria

Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range

Mass and Information Feedbacks through Receptor Endocytosis Govern Insulin Signaling as Revealed Using a Parameter-free Modeling Framework

Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics

Mathematical modeling of COVID-19 in 14.8 million individuals in Bahia, Brazil

Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites

A protocol for dynamic model calibration

PEtab—Interoperable specification of parameter estimation problems in systems biology

Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression.


A Python package for flavour physics phenomenology in the Standard model and beyond

The Belle II Physics Book

Progress of Theoretical and Experimental Physics

Rare b decays meet high-mass Drell-Yan

flavio: a Python package for flavour and precision phenomenology in the Standard Model and beyond

Anatomy of
    ε '/ε
 ε ′ / ε beyond the standard model

Anomalies in B mesons decays: a phenomenological approach

Anomalies in B mesons decays: Present status and future collider prospects


Analysis framework and collection of process-oriented diagnostics for weather and climate simulations

Effects of the Horizontal Scales of the Cloud‐Resolving Model on Tropical Cyclones in the Superparameterized Community Atmosphere Model

Dataset for SPCAM TC paper

Zenodo (CERN European Organization for Nuclear Research)


Qkit framework

A quantum engineer's guide to superconducting qubits

Granular aluminium as a superconducting material for high-impedance quantum circuits

Control of the coupling strength and linewidth of a cavity magnon-polariton

Complex temperature dependence of coupling and dissipation of cavity magnon polaritons from millikelvin to room temperature

Local sensing with the multilevel ac Stark effect

Introducing coherent time control to cavity magnon-polariton modes

State preparation of a fluxonium qubit with feedback from a custom FPGA-based platform

Magnons at low excitations: Observation of incoherent coupling to a bath of two-level systems

Transmon qubit in a magnetic field: Evolution of coherence and transition frequency

Versatile Configuration and Control Framework for Real-Time Data Acquisition Systems


James Webb Space Telescope PSF simulation tool

The chemical enrichment in the early Universe as probed by JWST via direct metallicity measurements at z~8

JexoSim: a time-domain simulator of exoplanet transit spectroscopy with JWST

Monthly notices of the Royal Astronomical Society

Active Galactic Nuclei Selection and Demographics: A New Age with JWST/MIRI

Constrained Reference Star Differential Imaging: Enabling High-Fidelity Imagery of Highly Structured Circumstellar Disks

The Near Infrared Imager and Slitless Spectrograph for JWST. V. Kernel Phase Imaging and Data Analysis

Transiting Exoplanet Yields for the Roman Galactic Bulge Time Domain Survey Predicted from Pixel-level Simulations

J0107a: A Barred Spiral Dusty Star-forming Galaxy at z = 2.467

Point spread function modelling for astronomical telescopes: a review focused on weak gravitational lensing studies

Frontiers in Astronomy and Space Sciences

Quantifying the Escape of Lyα at z ≈ 5–6: A Census of Lyα Escape Fraction with Hα-emitting Galaxies Spectroscopically Confirmed by JWST and VLT/MUSE

The Astrophysical Journal Supplement Series

Quantifying the escape of Lyα at z≈ 5-6: a census of Lyα escape fraction with Hα emitting galaxies spectroscopically confirmed by JWST and VLT/MUSE


Asynchronous Distributed Hyperparameter Optimization.

Hyperparameter optimization: Foundations, algorithms, best practices, and open challenges

HyperNOMAD: Hyperparameter optimization of deep neural networks using mesh adaptive direct search

Emergent Communication under Competition

Limitations of weak labels for embedding and tagging

Use of static surrogates in hyperparameter optimization


SPADE: Support for Provenance Auditing in Distributed Environments

Xanthus: Push-button Orchestration of Host Provenance Data Collection

Proceedings of the 3rd International Workshop on Practical Reproducible Evaluation of Computer Systems

Kellect: a Kernel-Based Efficient and Lossless Event Log Collector for Windows Security


Codebase for ECCV18 "The Sound of Pixels"

The Sound of Pixels

Co-Separating Sounds of Visual Objects

TriBERT: Full-body Human-centric Audio-visual Representation Learning for Visual Sound Separation

Visually Guided Sound Source Separation With Audio-Visual Predictive Coding

IEEE transactions on neural networks and learning systems


Dataset to assess the disentanglement properties of unsupervised learning methods

A Style-Based Generator Architecture for Generative Adversarial Networks

Disentangling by Factorising

Isolating Sources of Disentanglement in Variational Autoencoders

Visual Prompt Tuning

On Variational Bounds of Mutual Information

Interpretable Machine Learning: Fundamental Principles and 10 Grand Challenges

Implicit 3D Orientation Learning for 6D Object Detection from RGB Images

Variational Inference of Disentangled Latent Concepts from Unlabeled Observations

Scaling Vision Transformers to 22 Billion Parameters

A Large-scale Study of Representation Learning with the Visual Task Adaptation Benchmark


PyTorch code for ICLR 2019 paper: Global-to-local Memory Pointer Networks for Task-Oriented Dialogue https://arxiv.org/pdf/1901.04713

A Survey of Knowledge-enhanced Text Generation

Dynamic Fusion Network for Multi-Domain End-to-end Task-Oriented Dialog

Contextualize Knowledge Bases with Transformer for End-to-end Task-Oriented Dialogue Systems

Learning to Memorize in Neural Task-Oriented Dialogue Systems

Intention Reasoning Network for Multi-Domain End-to-end Task-Oriented Dialogue

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


Code for the ICML 2021 (long talk) paper: "ViLT: Vision-and-Language Transformer Without Convolution or Region Supervision"

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

MixGen: A New Multi-Modal Data Augmentation

A Joint Study of Phrase Grounding and Task Performance in Vision and Language Models


Efficient PyTorch Hessian eigendecomposition tools!

Hessian-based Analysis of Large Batch Training and Robustness to Adversaries

An Empirical Investigation of the Role of Pre-training in Lifelong Learning

Improving Generalization in Federated Learning by Seeking Flat Minima

Accelerated Stochastic Power Iteration

The Generalization-Stability Tradeoff In Neural Network Pruning

Directional Pruning of Deep Neural Networks

Pruning artificial neural networks: a way to find well-generalizing, high-entropy sharp minima

Sharpness-Aware Minimization Revisited: Weighted Sharpness as a Regularization Term

Irreducible Curriculum for Language Model Pretraining


Pytorch implementation of Generative Adversarial Text-to-Image Synthesis paper

Improved Training of Wasserstein GANs

Improved Techniques for Training GANs

Wasserstein GAN

Generative Adversarial Text to Image Synthesis


An implementation of the Contrast Predictive Coding (CPC) method to train audio features in an unsupervised fashion.

Representation Learning with Contrastive Predictive Coding

Unsupervised pretraining transfers well across languages

The Zero Resource Speech Benchmark 2021: Metrics and baselines for unsupervised spoken language modeling

A Comparison of Discrete and Soft Speech Units for Improved Voice Conversion

Self-supervised Representation Learning with Relative Predictive Coding

Conditional Contrastive Learning: Removing Undesirable Information in Self-Supervised Representations.

MBrain: A Multi-channel Self-Supervised Learning Framework for Brain Signals

Comparison of Self-Supervised Speech Pre-Training Methods on Flemish Dutch


Strategic Dialogue Management via Deep Reinforcement Learning

SimpleDS: A Simple Deep Reinforcement Learning Dialogue System

Deep Reinforcement Learning for Multi-Domain Dialogue Systems

A Data-Efficient Deep Learning Approach for Deployable Multimodal Social Robots

Training an Interactive Humanoid Robot Using Multimodal Deep Reinforcement Learning


Hetionet: an integrative network of disease

TISSUES 2.0: an integrative web resource on mammalian tissue expression

Database : the journal of biological databases and curation

Knowledge-based Biomedical Data Science 2019

Scientific Language Models for Biomedical Knowledge Base Completion: An Empirical Study

An open source knowledge graph ecosystem for the life sciences

Graph Chain-of-Thought: Augmenting Large Language Models by Reasoning on
  Graphs

Establish the expected number of induced motifs on unlabeled graphs through analytical models

An Open-Source Knowledge Graph Ecosystem for the Life Sciences


Monocular Depth Estimation Toolbox based on MMSegmentation.

DepthFormer: Exploiting Long-range Correlation and Local Information for Accurate Monocular Depth Estimation

BinsFormer: Revisiting Adaptive Bins for Monocular Depth Estimation

DatasetDM: Synthesizing Data with Perception Annotations Using Diffusion Models

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

The RoboDepth Challenge: Methods and Advancements Towards Robust Depth Estimation


A fast, robust Python library to check for offensive language in strings.

Pile of Law: Learning Responsible Data Filtering from the Law and a 256GB Open-Source Legal Dataset

Composing Ensembles of Pre-trained Models via Iterative Consensus

Not All Counterhate Tweets Elicit the Same Replies: A Fine-Grained Analysis

Proceedings of the 12th Joint Conference on Lexical and Computational Semantics (*SEM 2023)

Exploring a Multi-Layered Cross-Genre Corpus of Document-Level Semantic Relations

Ask Language Model to Clean Your Noisy Translation Data


Code for the ICML 2023 paper "SparseGPT: Massive Language Models Can Be Accurately Pruned in One-Shot".

Compressing LLMs: The Truth is Rarely Pure and Never Simple

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

Sparse Fine-tuning for Inference Acceleration of Large Language Models


This repository contains data indexes from NIST's Genome in a Bottle project.

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

ARCS: scaffolding genome drafts with linked reads

Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase

Combining callers improves the detection of copy number variants from whole-genome sequencing

European journal of human genetics : EJHG

High-coverage, long-read sequencing of Han Chinese trio reference samples

Accurate sequencing of DNA motifs able to form alternative (non-B) structures

Managing genomic variant calling workflows with Swift/T

WFA-GPU: gap-affine pairwise read-alignment using GPUs

DeBreak: Deciphering the exact breakpoints of structural variations using long sequencing reads

A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples


Creative Commons Attribution 4.0 International

A first-of-its-kind acoustic simulation platform for audio-visual embodied AI research. It supports training and evaluating multiple tasks and applications.

SoundSpaces: Audio-Visual Navigation in 3D Environments

Learning to Set Waypoints for Audio-Visual Navigation

SoundSpaces 2.0: A Simulation Platform for Visual-Acoustic Learning

Dynamical Audio-Visual Navigation: Catching Unheard Moving Sound Sources in Unmapped 3D Environments


Atomic interaction potentials based on artificial neural networks

Recent advances and applications of deep learning methods in materials science

Sensitivity and dimensionality of atomic environment representations used for machine learning interatomic potentials.

AENET-LAMMPS and AENET-TINKER: Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials.

Molecular dynamics simulations of heat transport using machine-learned potentials: A mini-review and tutorial on GPUMD with neuroevolution potentials

AI-Aided Mapping of the Structure-Composition-Conductivity Relationships of Glass-Ceramic Lithium Thiophosphate Electrolytes


Code for RL experiments in "Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks"

Benchmarking Deep Reinforcement Learning for Continuous Control

Unsupervised Meta-Learning for Reinforcement Learning

Deep Reinforcement Learning

A Model-based Approach for Sample-efficient Multi-task Reinforcement Learning

Model-Agnostic Meta-Learning using Runge-Kutta Methods


This is a complete package of recent deep learning methods for 3D point clouds in pytorch (with pretrained models).

PointNet: Deep Learning on Point Sets for 3D Classification and Segmentation

Dynamic Graph CNN for Learning on Point Clouds

PointConv: Deep Convolutional Networks on 3D Point Clouds

Deep Closest Point: Learning Representations for Point Cloud Registration

PCN: Point Completion Network

PointNetLK: Robust & Efficient Point Cloud Registration using PointNet

PPFNet: Global Context Aware Local Features for Robust 3D Point Matching

FlowNet3D: Learning Scene Flow in 3D Point Clouds

RPM-Net: Robust Point Matching Using Learned Features

PRNet: Self-Supervised Learning for Partial-to-Partial Registration


Official implementation of project Honeybee (CVPR 2024)

MMBench: Is Your Multi-modal Model an All-around Player?

MME: A Comprehensive Evaluation Benchmark for Multimodal Large Language Models

SEED-Bench: Benchmarking Multimodal LLMs with Generative Comprehension

Honeybee: Locality-enhanced Projector for Multimodal LLM


MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

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

Computational and structural biotechnology journal

Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear (Pyrus bretschneideri) Fruit

International journal of molecular sciences

Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana

Improved Methods for Acetocarmine and Haematoxylin Staining to Visualize Chromosomes in the Filamentous Green Alga Zygnema (Charophyta)

bioRxiv : the preprint server for biology

The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery

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

Genome-wide characterization and expression analysis of α-amylase and β-amylase genes underlying drought tolerance in cassava

Genome-Wide Identification and Analysis of the NAC Transcription Factor Gene Family in Garden Asparagus (Asparagus officinalis)


A pre-trained GPT model for Python code completion and generation

CERT: Continual Pre-Training on Sketches for Library-Oriented Code Generation

When Language Model Meets Private Library

A Survey on Large Language Models for Software Engineering

BAMBOO: A Comprehensive Benchmark for Evaluating Long Text Modeling Capacities of Large Language Models

BigCodeBench: Benchmarking Code Generation with Diverse Function Calls
  and Complex Instructions


Code for "ATISS: Autoregressive Transformers for Indoor Scene Synthesis", NeurIPS 2021

Fast and Flexible Indoor Scene Synthesis via Deep Convolutional Generative Models

SceneFormer: Indoor Scene Generation with Transformers

MIME: Human-Aware 3D Scene Generation

InstructScene: Instruction-Driven 3D Indoor Scene Synthesis with
  Semantic Graph Prior

CLIP-Layout: Style-Consistent Indoor Scene Synthesis with Semantic Furniture Embedding

COFS: COntrollable Furniture layout Synthesis


PyTorch code for end-to-end spoken language understanding (SLU) with ASR-based transfer learning

Speech Model Pre-training for End-to-End Spoken Language Understanding

Using Speech Synthesis to Train End-to-End Spoken Language Understanding Models

Speech to Text Adaptation: Towards an Efficient Cross-Modal Distillation

Leveraging Acoustic and Linguistic Embeddings from Pretrained speech and language Models for Intent Classification

Exploring Teacher-Student Learning Approach for Multi-Lingual Speech-to-Intent Classification


Code for the paper "Ordered Neurons: Integrating Tree Structures into Recurrent Neural Networks"

Compound Probabilistic Context-Free Grammars for Grammar Induction

Can RNNs learn Recursive Nested Subject-Verb Agreements?

Span-Based Neural Buffer: Towards Efficient and Effective Utilization of Long-Distance Context for Neural Sequence Models

THIRTY-FOURTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, THE THIRTY-SECOND INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE AND THE TENTH AAAI SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE

Ensemble Distillation for Unsupervised Constituency Parsing


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

Whole genome sequencing in clinical and public health microbiology

A Brief Review of Software Tools for Pangenomics

基因组蛋白质组与生物信息学报

Epidemic Dynamics of Vibrio parahaemolyticus Illness in a Hotspot of Disease Emergence, Galicia, Spain

Melioidosis in a Resident of Texas with No Recent Travel History, United States

Burkholderia thailandensis Isolated from Infected Wound, Arkansas, USA

In silico Identification of Serovar-Specific Genes for Salmonella Serotyping

Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes

Burkholderia species in human infections in Mexico: Identification of B. cepacia, B. contaminans, B. multivorans, B. vietnamiensis,B. pseudomallei and a new Burkholderia species

Subclinical Burkholderia pseudomallei Infection Associated with Travel to the British Virgin Islands


[ECCV 2022] Official implementation of the paper: Audio-Visual Segmentation

Audio-Visual Segmentation

Audio-Visual Segmentation with Semantics

Referred by Multi-Modality: A Unified Temporal Transformer for Video Object Segmentation

A Closer Look at Audio-Visual Segmentation


Predict Gender from Names Using Historical Data

The Pandemic Penalty: The gendered effects of COVID-19 on scientific productivity

Socius: Sociological Research for a Dynamic World

The Effect of Gender in the Publication Patterns in Mathematics

Uncovering Latent Biases in Text: Method and Application to Peer Review

Gender representation and academic achievement among STEM-interested students in college STEM courses.

What’s Under the Big Tent? A Study of ADHO Conference Abstracts, 2004-2014

Addressing the Gender Gap: Using Quantitative and Qualitative Methods to Illuminate Women’s Fisheries Participation

Authors and editors assort on gender and geography in high-rank ecological publications

Fleshing Out Models of Gender in English-Language Novels (1850 – 2000)

ChatGPT Is More Likely to Be Perceived as Male Than Female

COVID-19 and Gender Differences in Family Medicine Scholarship


Statistical NLG for spoken dialogue systems

Composite Task-Completion Dialogue Policy Learning via Hierarchical Deep Reinforcement Learning

The E2E Dataset: New Challenges For End-to-End Generation

Evaluating the State-of-the-Art of End-to-End Natural Language Generation: The E2E NLG Challenge

Sequence-to-Sequence Generation for Spoken Dialogue via Deep Syntax Trees and Strings

PROCEEDINGS OF THE 54TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS (ACL 2016), VOL 2

Semantic Noise Matters for Neural Natural Language Generation

Findings of the E2E NLG Challenge

A Context-aware Natural Language Generator for Dialogue Systems

Annual Meeting of the Special Interest Group on Discourse and Dialogue

Controlling Personality-Based Stylistic Variation with Neural Natural Language Generators

Training a Natural Language Generator From Unaligned Data

PROCEEDINGS OF THE 53RD ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS AND THE 7TH INTERNATIONAL JOINT CONFERENCE ON NATURAL LANGUAGE PROCESSING, VOL 1

Can Neural Generators for Dialogue Learn Sentence Planning and Discourse Structuring?


TOFlow: Video Enhancement with Task-Oriented Flow

International Journal of Computer Vision

Deep Contextual Video Compression

Video Super Resolution Based on Deep Learning: A Comprehensive Survey

VFIMamba: Video Frame Interpolation with State Space Models


A curated list of awesome Active Learning

Active Learning

Synthesis lectures on artificial intelligence and machine learning

Consistency-based Semi-supervised Active Learning: Towards Minimizing Labeling Cost

Active Semi-Supervised Learning Using Sampling Theory for Graph Signals

Ask me better questions

Active learning using on-line algorithms

Deep Reinforcement Active Learning for Medical Image Classification

Medical Image Computing and Computer-Assisted Intervention


The plan validation system.

AutoPlanBench: : Automatically generating benchmarks for LLM planners from PDDL

TwoStep: Multi-agent Task Planning using Classical Planners and Large
  Language Models

Vision-Language Interpreter for Robot Task Planning


Code release for "Cut and Learn for Unsupervised Object Detection and Instance Segmentation" and "VideoCutLER: Surprisingly Simple Unsupervised Video Instance Segmentation"

Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour

The devil is in the object boundary: towards annotation-free instance
  segmentation using Foundation Models


[MICCAI 2019 Young Scientist Award] [MEDIA 2020 Best Paper Award] Models Genesis

Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis

Models Genesis

Transferable Visual Words: Exploiting the Semantics of Anatomical Patterns for Self-Supervised Learning

SAM: Self-Supervised Learning of Pixel-Wise Anatomical Embeddings in Radiological Images

Advancing 3D Medical Image Analysis with Variable Dimension Transform based Supervised 3D Pre-training

Universal and Extensible Language-Vision Models for Organ Segmentation and Tumor Detection from Abdominal Computed Tomography

Transfer Learning for Segmentation Problems: Choose the Right Encoder and Skip the Decoder

Brain Anatomy Prior Modeling to Forecast Clinical Progression of Cognitive Impairment with Structural MRI

AbdomenAtlas: A large-scale, detailed-annotated, & multi-center dataset for efficient transfer learning and open algorithmic benchmarking


Deep learning toolbox based on PyTorch for hyperspectral data classification.

Spectral–Spatial Classification of Hyperspectral Imagery with 3D Convolutional Neural Network

Going Deeper With Contextual CNN for Hyperspectral Image Classification

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

Deep Learning for Classification of Hyperspectral Data: A Comparative Review

IEEE Geoscience and Remote Sensing Magazine

HSI-CNN: A Novel Convolution Neural Network for Hyperspectral Image

Exploring Cross-Domain Pretrained Model for Hyperspectral Image Classification

IEEE Transactions on Geoscience and Remote Sensing

A High-Performance Spectral-Spatial Residual Network for Hyperspectral Image Classification with Small Training Data

DEEP FEATURE EXTRACTION BASED ON DYNAMIC GRAPH CONVOLUTIONAL NETWORKS FOR ACCELERATED HYPERSPECTRAL IMAGE CLASSIFICATION

XXIV ISPRS CONGRESS: IMAGING TODAY, FORESEEING TOMORROW, COMMISSION III

Training Methods of Multi-Label Prediction Classifiers for Hyperspectral Remote Sensing Images


Repo for reproduction of sequential social dilemmas

Multi-agent Reinforcement Learning in Sequential Social Dilemmas

Social Influence as Intrinsic Motivation for Multi-Agent Deep Reinforcement Learning

Inequity aversion improves cooperation in intertemporal social dilemmas

The Importance of Credo in Multiagent Learning

IQ-Flow: Mechanism Design for Inducing Cooperative Behavior to Self-Interested Agents in Sequential Social Dilemmas

Learning to Learn Group Alignment: A Self-Tuning Credo Framework with Multiagent Teams

Emergent Cooperation under Uncertain Incentive Alignment


Various speech datasets made available to the public

Earnings-21: A Practical Benchmark for ASR in the Wild

Earnings-22: A Practical Benchmark for Accents in the Wild

Updated Corpora and Benchmarks for Long-Form Speech Recognition

Implementing contextual biasing in GPU decoder for online ASR


RL starter files in order to immediately train, visualize and evaluate an agent without writing any line of code

State Entropy Maximization with Random Encoders for Efficient Exploration

Value Function Spaces: Skill-Centric State Abstractions for Long-Horizon Reasoning

Poisoning Deep Reinforcement Learning Agents with In-Distribution Triggers

Simplifying Deep Reinforcement Learning via Self-Supervision

Decentralized Reinforcement Learning: Global Decision-Making via Local Economic Transactions

Exploring through Random Curiosity with General Value Functions

Flexible Attention-Based Multi-Policy Fusion for Efficient Deep Reinforcement Learning

Heterogeneous Knowledge for Augmented Modular Reinforcement Learning

Maximum Entropy On-Policy Actor-Critic via Entropy Advantage Estimation


Flops counter for convolutional networks in pytorch framework

Green AI

Intriguing Findings of Frequency Selection for Image Deblurring

PRGC: Potential Relation and Global Correspondence Based Joint Relational Triple Extraction

Less Is More: Fast Multivariate Time Series Forecasting with Light Sampling-oriented MLP Structures

Deep Gradient Learning for Efficient Camouflaged Object Detection

WORD: A large scale dataset, benchmark and clinical applicable study for abdominal organ segmentation from CT image

DiCyc: GAN-based deformation invariant cross-domain information fusion for medical image synthesis

Diffusion Probabilistic Model Made Slim

TF-GridNet: Integrating Full- and Sub-Band Modeling for Speech Separation

DeciWatch: A Simple Baseline for 10x Efficient 2D and 3D Pose Estimation


Terrier IR Platform

Shopping Queries Dataset: A Large-Scale ESCI Benchmark for Improving Product Search

Meta-evaluation of Conversational Search Evaluation Metrics

ACM transactions on office information systems

Heuristic Feature Selection for Clickbait Detection


Soil Incubation Database sidb

Interactions among temperature, moisture, and oxygen concentrations in controlling decomposition rates in a boreal forest soil

Decomposability of soil organic matter over time: the Soil Incubation Database (SIDb, version 1.0) and guidance for incubation procedures


Intel:registered: Homomorphic Encryption Acceleration Library accelerates modular arithmetic operations used in homomorphic encryption

Intel HEXL: Accelerating Homomorphic Encryption with Intel AVX512-IFMA52

FDFB: Full Domain Functional Bootstrapping Towards Practical Fully Homomorphic Encryption

Accelerating Encrypted Computing on Intel GPUs

Verifiable Fully Homomorphic Encryption

SoK: Fully Homomorphic Encryption Accelerators

CryptoTL: Private, Efficient and Secure Transfer Learning


R raster package https://rspatial.github.io/raster/reference/raster-package.html

A standardized catalogue of spectral indices to advance the use of remote sensing in Earth system research

Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)

Picks in the Fabric of a Polyploidy Complex: Integrative Species Delimitation in the Tetraploid Leucanthemum Mill. (Compositae, Anthemideae) Representatives


NRPy+, BlackHoles@Home, SENRv2, and the NRPy+ Jupyter Tutorial: Python-Based Code Generation for Numerical Relativity... and Beyond!

General relativistic hydrodynamics on a moving-mesh I: static space–times

Monthly Notices of the Royal Astronomical Society

Bound Debris Expulsion from Neutron Star Merger Remnants

NRPyCritCol & SFcollapse1D: an open-source, user-friendly toolkit to study critical phenomena

Exploring pathways to forming twin stars


UIUC/PPL version of ChaNGa

The formation of ultradiffuse galaxies in the RomulusC galaxy cluster simulation

The formation of isolated ultradiffuse galaxies in romulus25

A New Signal Model for Axion Cavity Searches from N-body Simulations

The AGORA High-resolution Galaxy Simulations Comparison Project. III. Cosmological Zoom-in Simulation of a Milky Way–mass Halo

THE EFFECTS OF ANGULAR MOMENTUM ON HALO PROFILES

The Role of Mass and Environment on Satellite Distributions around Milky Way Analogs in the Romulus25 Simulation

Simulating gravitational motion, gas dynamics, and structure in the cosmos

Extracting Insights from Astrophysics Simulations


Elephant is the Electrophysiology Analysis Toolkit

Perineuronal nets stabilize the grid cell network

Uncertainpy: A Python Toolbox for Uncertainty Quantification and Sensitivity Analysis in Computational Neuroscience

Neural Latents Benchmark '21: Evaluating latent variable models of neural population activity

Massively parallel recordings in macaque motor cortex during an instructed delayed reach-to-grasp task

Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection

The Journal of neuroscience : the official journal of the Society for Neuroscience

CalciumGAN: A Generative Adversarial Network Model for Synthesising Realistic Calcium Imaging Data of Neuronal Populations.

Acceleration of the SPADE Method Using a Custom-Tailored FP-Growth Implementation

Linear Time GPs for Inferring Latent Trajectories from Neural Spike Trains

Dopaminergic and Cholinergic Modulation of Large Scale Networks in silico Using Snudda


A suite of tools for managing crowdsourcing tasks from the inception through to data packaging for research use.

Improving Question Answering Model Robustness with Synthetic Adversarial Data Generation

Models in the Loop: Aiding Crowdworkers with Generative Annotation Assistants

Analyzing Dynamic Adversarial Training Data in the Limit

Reasoning over Public and Private Data in Retrieval-Based Systems

LEGOEval: An Open-Source Toolkit for Dialogue System Evaluation via Crowdsourcing

Training Models to Generate, Recognize, and Reframe Unhelpful Thoughts

Mephisto: A Framework for Portable, Reproducible, and Iterative Crowdsourcing


FASTA/FASTQ pre-processing programs

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

RNA-Seq Perspectives to Improve Clinical Diagnosis

Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids

Dynamics of the Fouling Layer Microbial Community in a Membrane Bioreactor

Variation in Crossover Frequencies Perturb Crossover Assurance Without Affecting Meiotic Chromosome Segregation in Saccharomyces cerevisiae

Hypothalamic transcriptomic alterations in male and female California mice (Peromyscus californicus) developmentally exposed to bisphenol A or ethinyl estradiol

Transcriptomic Effects of the Cell Cycle Regulator LGO in Arabidopsis Sepals

Continental-Scale Patterns Reveal Potential for Warming-Induced Shifts in Cattle Diet

Global forensic geolocation with deep neural networks

Rational attenuation of RNA viruses with zinc finger antiviral protein


Creative Commons Attribution Share Alike 4.0 International

KorNLI and KorSTS: New Benchmark Datasets for Korean Natural Language Understanding

Exploring the Data Efficiency of Cross-Lingual Post-Training in Pretrained Language Models

Reference and Document Aware Semantic Evaluation Methods for Korean Language Summarization


SOTA Semantic Segmentation Models in PyTorch

A ConvNet for the 2020s

SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers

Unified Perceptual Parsing for Scene Understanding

PVT v2: Improved baselines with Pyramid Vision Transformer

MetaFormer is Actually What You Need for Vision

Visual attention network

ResNet strikes back: An improved training procedure in timm

Semantic Flow for Fast and Accurate Scene Parsing

HarDNet: A Low Memory Traffic Network

UniFormer: Unifying Convolution and Self-attention for Visual Recognition


This Repostory contains the pretrained DTLN-aec model for real-time acoustic echo cancellation.

Acoustic echo cancellation with the dual-signal transformation LSTM network

F-T-LSTM based Complex Network for Joint Acoustic Echo Cancellation and Speech Enhancement

Real-time speech enhancement with dynamic attention span


NeuroSAT: Learning a SAT Solver from Single-Bit Supervision

Graph-based Semi-supervised Learning: A Comprehensive Review

Addressing Variable Dependency in GNN-based SAT Solving


Pytorch implementations of density estimation algorithms: BNAF, Glow, MAF, RealNVP, planar flows

FormulaZero: Distributionally Robust Online Adaptation via Offline Population Synthesis

Featurized Density Ratio Estimation

Imitation with Neural Density Models

Bridging Mean-Field Games and Normalizing Flows with Trajectory Regularization

Addressing Distribution Shift in Time Series Forecasting with Instance
  Normalization Flows


Domain-Adversarial Neural Network in Tensorflow

Support and Invertibility in Domain-Invariant Representations

Missing-Class-Robust Domain Adaptation by Unilateral Alignment

IEEE Transactions on Industrial Electronics

Mutual Information-Based Disentangled Neural Networks for Classifying Unseen Categories in Different Domains: Application to Fetal Ultrasound Imaging

Distributional Adversarial Networks

SPADE: Semi-supervised Anomaly Detection under Distribution Mismatch


Neural network model, suitable for multi-agent learning. https://arxiv.org/abs/1605.07736

Deep Learning on Graphs: A Survey

Learning Multiagent Communication with Backpropagation


Connectome Computation System

Shifting gradients of macroscale cortical organization mark the transition from childhood to adolescence

Individual Variability and Test-Retest Reliability Revealed by Ten Repeated Resting-State Brain Scans over One Month

Assessing Variations in Areal Organization for the Intrinsic Brain: From Fingerprints to Reliability

Temporal stability of functional brain modules associated with human intelligence

Charting brain growth in tandem with brain templates at school age

Fluctuations between high- and low-modularity topology in time-resolved functional connectivity

Moving Beyond Processing and Analysis-Related Variation in Neuroscience

DREAM: A Toolbox to Decode Rhythms of the Brain System

Anxiety correlates with cortical surface area in subjective cognitive decline: APOE ε4 carriers versus APOE ε4 non-carriers

Mind-Body Practice Changes Fractional Amplitude of Low Frequency Fluctuations in Intrinsic Control Networks


[CAAI AIR'24] Bilateral Reference for High-Resolution Dichotomous Image Segmentation

ViTMatte: Boosting Image Matting with Pretrained Plain Vision Transformers

GCoNet+: A Stronger Group Collaborative Co-Salient Object Detector

Memory-aided Contrastive Consensus Learning for Co-salient Object Detection


Code and Pretrained model for IGCV3

IGCV2: Interleaved Structured Sparse Convolutional Neural Networks

IGCV3: Interleaved Low-Rank Group Convolutions for Efficient Deep Neural Networks

Deeply-Fused Nets

Interleaved Group Convolutions for Deep Neural Networks

Deep Convolutional Neural Networks with Merge-and-Run Mappings


VMamba: Visual State Space Models，code is based on mamba

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

A ConvNet for the 2020s

Mamba: Linear-Time Sequence Modeling with Selective State Spaces

VMamba: Visual State Space Model

Swin-UMamba: Mamba-based UNet with ImageNet-based pretraining

LocalMamba: Visual State Space Model with Windowed Selective Scan

Serpent: Scalable and Efficient Image Restoration via Multi-scale
  Structured State Space Models


Humanoid robotics prototyping environment based on OpenRAVE

ZMP Support Areas for Multicontact Mobility Under Frictional Constraints

Multi-contact Walking Pattern Generation based on Model Preview Control of 3D COM Accelerations

Capturability-based Pattern Generation for Walking with Variable Height

When to make a step? Tackling the timing problem in multi-contact locomotion by TOPP-MPC

Dynamic Walking over Rough Terrains by Nonlinear Predictive Control of the Floating-base Inverted Pendulum

Biped Stabilization by Linear Feedback of the Variable-Height Inverted Pendulum Model

Balance control using both ZMP and COM height variations: A convex boundedness approach

Balance of Humanoid robot in Multi-contact and Sliding Scenarios.


Learning to Cluster Faces (CVPR 2019, CVPR 2020)

Linkage Based Face Clustering via Graph Convolution Network

Learning to Cluster Faces on an Affinity Graph

Learning to Cluster Faces via Confidence and Connectivity Estimation

Learning to Cluster Faces via Transformer

Graph Convolutional Network Based Semi-Supervised Learning on Multi-Speaker Meeting Data


Machine Learning and Artificial Intelligence for Medicine.

PATE-GAN: Generating Synthetic Data with Differential Privacy Guarantees

International Conference on Learning Representations

GANITE: Estimation of Individualized Treatment Effects using Generative Adversarial Nets

Bayesian Inference of Individualized Treatment Effects using Multi-task Gaussian Processes

INVASE: Instance-wise Variable Selection using Neural Networks

Limits of Estimating Heterogeneous Treatment Effects: Guidelines for Practical Algorithm Design

International Conference on Machine Learning

Nonparametric Estimation of Heterogeneous Treatment Effects: From Theory to Learning Algorithms

AutoPrognosis: Automated Clinical Prognostic Modeling via Bayesian Optimization with Structured Kernel Learning

CASTLE: Regularization via Auxiliary Causal Graph Discovery

Scalable Bayesian Inverse Reinforcement Learning

KnockoffGAN: Generating Knockoffs for Feature Selection using Generative Adversarial Networks


HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Associations of the intestinal microbiome with the complement system in neovascular age-related macular degeneration

Comparing Circadian Rhythmicity in the Human Gut Microbiome

Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition

Correlation of gut microbiota and metabolic functions with the antibody response to the BBIBP-CorV vaccine

Bugs as features (part 1): concepts and foundations for the compositional data analysis of the microbiome–gut–brain axis

Insights into the Composition of a Co-Culture of 10 Probiotic Strains (OMNi BiOTiC® AAD10) and Effects of Its Postbiotic Culture Supernatant


Predictive Soil Mapping with R (book)


Simple baselines and RNNs for predicting human motion in tensorflow. Presented at CVPR 17.

On human motion prediction using recurrent neural networks

Human Motion Prediction via Learning Local Structure Representations and Temporal Dependencies

Investigating Pose Representations and Motion Contexts Modeling for 3D Motion Prediction

IEEE transactions on pattern analysis and machine intelligence

Deep Learning for Vision-based Prediction: A Survey

Focusing on What is Relevant: Time-Series Learning and Understanding using Attention


A Large-scale Study of Representation Learning with the Visual Task Adaptation Benchmark

Comparing Transfer and Meta Learning Approaches on a Unified Few-Shot Classification Benchmark

An Evolutionary Approach to Dynamic Introduction of Tasks in Large-scale Multitask Learning Systems

A Continual Development Methodology for Large-scale Multitask Dynamic ML Systems

A Multiagent Framework for the Asynchronous and Collaborative Extension of Multitask ML Systems

Self-supervised visual learning in the low-data regime: a comparative
  evaluation


Covid-19 Twitter dataset for non-commercial research use and pre-processing scripts - under active development

A large-scale COVID-19 Twitter chatter dataset for open scientific research -- an international collaboration

Understanding the Public Discussion About the Centers for Disease Control and Prevention During the COVID-19 Pandemic Using Twitter Data: Text Mining Analysis Study

ESTeR: Combining Word Co-occurrences and Word Associations for Unsupervised Emotion Detection

A comparative study of Bot Detection techniques methods with an application related to Covid-19 discourse on Twitter

A large-scale COVID-19 Twitter chatter dataset for open scientific research - an international collaboration

Zenodo (CERN European Organization for Nuclear Research)

Visual Analytics of Twitter and Social Media Dataflows: a Casestudy of COVID-19 Rumors

Users’ Reactions to Announced Vaccines Against COVID-19 Before Marketing in France: Analysis of Twitter Posts

Cooperative Network Learning for Large-Scale and Decentralized Graphs


Software that can perform photorealistic style transfer without the need of any post-processing steps.

Deep Photo Style Transfer

A Closed-form Solution to Photorealistic Image Stylization

Photorealistic Style Transfer via Wavelet Transforms

Diffusion-based Image Translation using Disentangled Style and Content Representation

Let There be Light: Improved Traffic Surveillance via Detail Preserving Night-to-Day Transfer

On the Road to Online Adaptation for Semantic Image Segmentation

DeepObjStyle: Deep Object-based Photo Style Transfer

DILIE: Deep Internal Learning for Image Enhancement


Benchmark Suite for Machine Learning Interatomic Potentials for Materials

Moment Tensor Potentials: A Class of Systematically Improvable Interatomic Potentials

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

The MLIP package: Moment Tensor Potentials with MPI and Active Learning

Scaling deep learning for materials discovery

Through the eyes of a descriptor: Constructing complete, invertible descriptions of atomic environments

Compact atomic descriptors enable accurate predictions via linear models

Implementing a neural network interatomic model with performance portability for emerging exascale architectures

Spline-based neural network interatomic potentials: blending classical and machine learning models


A Benchmarking Study of Embedding-based Entity Alignment for Knowledge Graphs, VLDB 2020

A benchmarking study of embedding-based entity alignment for 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

OntoEA: Ontology-guided Entity Alignment via Joint Knowledge Graph Embedding

A Comprehensive Survey on Automatic Knowledge Graph Construction

Unsupervised Knowledge Graph Alignment by Probabilistic Reasoning and Semantic Embedding

Knowing the No-match: Entity Alignment with Dangling Cases

ActiveEA: Active Learning for Neural Entity Alignment

Knowledge graph embedding methods for entity alignment: experimental review

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

EAGER: Embedding-Assisted Entity Resolution for Knowledge Graphs


An R package for creating Q-Q and manhattan plots from GWAS results

qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

Assessing genome assembly quality using the LTR Assembly Index (LAI)

Genetics of structural connectivity and information processing in the brain

Developmental language disorder – a comprehensive study of more than 46,000 individuals

Thirty novel sequence variants impacting human intracranial volume

Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding

Genetic and epidemiological analyses of infection load and its relationship with psychiatric disorders