A Julia/JuMP Package for Maximizing Algebraic Connectivity of Undirected Weighted Graphs

On maximizing algebraic connectivity of networks for various engineering applications

Synthesizing Robust Communication Networks for Unmanned Aerial Vehicles With Resource Constraints

Volume 1: Adaptive Control; Advanced Vehicle Propulsion Systems; Aerospace Systems; Autonomous Systems; Battery Modeling; Biochemical Systems; Control Over Networks; Control Systems Design; Cooperativ

Optimal Robust Network Design: Formulations and Algorithms for
  Maximizing Algebraic Connectivity


Variational quantum Gibbs state preparation with a truncated Taylor series

Variational Quantum Singular Value Decomposition

Variational quantum algorithms for trace distance and fidelity estimation

TensorCircuit: a Quantum Software Framework for the NISQ Era

VSQL: Variational Shadow Quantum Learning for Classification

Quantum Self-Attention Neural Networks for Text Classification

Practical distributed quantum information processing with LOCCNet

Concentration of Data Encoding in Parameterized Quantum Circuits

Quantum Artificial Intelligence for the Science of Climate Change

Q^2Chemistry: A quantum computation platform for quantum chemistry


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


Repository containing the open source code of works published at the FBK MT unit.

Diverse Beam Search: Decoding Diverse Solutions from Neural Sequence Models

Over-Generation Cannot Be Rewarded: Length-Adaptive Average Lagging for Simultaneous Speech Translation

Efficient yet Competitive Speech Translation: FBK@IWSLT2022

Does Simultaneous Speech Translation need Simultaneous Models?

Attention as a Guide for Simultaneous Speech Translation

Who Are We Talking About? Handling Person Names in Speech Translation

Dodging the Data Bottleneck: Automatic Subtitling with Automatically
  Segmented ST Corpora

Direct Speech Translation for Automatic Subtitling

TransLLaMa: LLM-based Simultaneous Translation System

AlignAtt: Using Attention-based Audio-Translation Alignments as a Guide for Simultaneous Speech Translation


fit piecewise linear data for a specified number of line segments

An Automatic Method for Detection and Update of Additive Changes in Road Network with GPS Trajectory Data

ISPRS international journal of geo-information

The Effect of Thermal Pressure on Collisionless Magnetic Reconnection Rate

Learning and controlling the source-filter representation of speech with a variational autoencoder

An optimization method for paleomagnetic Euler pole analysis

Numerical Simulation of a Supersonic Ejector for Vacuum Generation with Explicit and Implicit Solver in Openfoam

A Clustering Approach for the Analysis of InSAR Time Series: Application to the Bandung Basin (Indonesia)

Prediction of Olive Tree Water Requirements under Limited Soil Water Availability, Based on Sap Flow Estimations

A scheduling and control approach for an industrial furnace to minimize idle energy consumption.

Piecewise Polynomial Regression of Tame Functions via Integer Programming


SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data

Typing methods based on whole genome sequencing data

Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data

Evaluation of Salmonella Serotype Prediction With Multiplex Nanopore Sequencing

Mobilome-driven partitions of the resistome in Salmonella

Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection

Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA


Code to automatically evaluate and tune parameters for Kimera-VIO pipeline.

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

3D Dynamic Scene Graphs: Actionable Spatial Perception with Places, Objects, and Humans

Kimera: From SLAM to spatial perception with 3D dynamic scene graphs

The international journal of robotics research

Incremental Visual-Inertial 3D Mesh Generation with Structural Regularities


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

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


Program for generating load curves for residential consumers. Agentbased and extremly detailed.

LoadProfileGenerator: An Agent-Based Behavior Simulation for Generating Residential Load Profiles

The role of hydrogen in German residential buildings


2D multi-source electromagnetic simulations in frequency domain, implementing the augmented partial factorization (APF) and other methods.

Fast multi-source nanophotonic simulations using augmented partial factorization

Thickness bound for nonlocal wide-field-of-view metalenses

Transmission Efficiency Limit for Nonlocal Metalenses

Full-wave solver for massively multi-channel optics using augmented partial factorization

Fast Multichannel Inverse Design through Augmented Partial Factorization

Numerical experiments of tomographic optical imaging inside scattering media


Financial Sentiment Analysis with BERT

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

FinBERT: Financial Sentiment Analysis with Pre-trained Language Models

Evaluation of Sentiment Analysis in Finance: From Lexicons to Transformers

An Empirical Investigation of Bias in the Multimodal Analysis of Financial Earnings Calls

North American Chapter of the Association for Computational Linguistics

A Multi-Method Survey on the Use of Sentiment Analysis in Multivariate Financial Time Series Forecasting

Speech emotion recognition and text sentiment analysis for financial distress prediction

Investigating Deep Stock Market Forecasting with Sentiment Analysis

Extracting Fine-Grained Economic Events from Business News

International Conference on Computational Linguistics

FiNLP at FinCausal 2020 Task 1: Mixture of BERTs for Causal Sentence Identification in Financial Texts

Sensitivity Analysis on Transferred Neural Architectures of BERT and
  GPT-2 for Financial Sentiment Analysis


This is a record of all the Manuscript Monday links!

Evaluating the effect of 3D urban form on neighborhood land surface temperature using Google Street View and geographically weighted regression

Open land-use map: a regional land-use mapping strategy for incorporating OpenStreetMap with earth observations

Missing emissions from post-monsoon agricultural fires in northwestern India: regional limitations of MODIS burned area and active fire products

Thresholds of fire response to moisture and fuel load differ between tropical savannas and grasslands across continents

Characterizing spatial variability in coastal wetland biomass across multiple scales using UAV and satellite imagery

Remote sensing in ecology and conservation

Mapping spatial variability in shoreline change hotspots from satellite data; a case study in southeast Australia

Local-scale agricultural drought monitoring with satellite-based multi-sensor time-series

GIScience & remote sensing/GIScience and remote sensing

Using Multitemporal and Multispectral Airborne Lidar to Assess Depth of Peat Loss and Correspondence With a New Active Normalized Burn Ratio for Wildfires

Understanding 3D structural complexity of individual Scots pine trees with different management history

Big geospatial data analysis for Canada’s Air Pollutant Emissions Inventory (APEI): using google earth engine to estimate particulate matter from exposed mine disturbance areas


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

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

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

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

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

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

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


Joint 3D Face Reconstruction and Dense Alignment with Position Map Regression Network (ECCV 2018)

Appearance-based Gaze Estimation With Deep Learning: A Review and Benchmark.

Limitations and Biases in Facial Landmark Detection -- An Empirical
  Study on Older Adults with Dementia

Joint 3D facial shape reconstruction and texture completion from a single image

Beyond 3DMM: Learning to Capture High-fidelity 3D Face Shape

IEEE transactions on pattern analysis and machine intelligence

Evaluating effects of focal length and viewing angle in a comparison of recent face landmark and alignment methods

EURASIP Journal on Image and Video Processing


Application and data for analyzing and structuring portfolios for climate investing.


Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Animals : an open access journal from MDPI

TLR1 Variant H305L Associated with Protection from Pulmonary Tuberculosis

Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods


Differentiable computations for the signature-PDE-kernel on CPU and GPU.

The Signature Kernel Is the Solution of a Goursat PDE

SIAM journal on mathematics of data science

Approximate Bayesian Computation with Path Signatures

New directions in the applications of rough path theory

The Signature Kernel


Smart charging algorithms with REST API for electric vehicle fleets


A Vietnamese natural language processing toolkit (NAACL 2018)

VnCoreNLP: A Vietnamese Natural Language Processing Toolkit

Emotion Recognition for Vietnamese Social Media Text

Revisiting Back-Translation for Low-Resource Machine Translation Between Chinese and Vietnamese

From Universal Language Model to Downstream Task: Improving RoBERTa-Based Vietnamese Hate Speech Detection

Sentence Extraction-Based Machine Reading Comprehension for Vietnamese

Predicting Job Titles from Job Descriptions with Multi-label Text Classification

National Foundation for Science and Technology Development Conference on Information and Computer Science

Unsupervised Sentence Simplification via Dependency Parsing

SMTCE: A Social Media Text Classification Evaluation Benchmark and
  BERTology Models for Vietnamese

Evaluating Low-Resource Machine Translation between Chinese and Vietnamese with Back-Translation

A HYBRID MODEL USING THE PRETRAINED BERT AND DEEP NEURAL NETWORKS WITH RICH FEATURE FOR EXTRACTIVE TEXT SUMMARIZATION

Journal of Computer Science and Cybernetics (Vietnam Academy of Science and Technology)/Journal of Computer Science and Cybernetics


Official Implementation for "Encoding in Style: a StyleGAN Encoder for Image-to-Image Translation" (CVPR 2021) presenting the pixel2style2pixel (pSp) framework

Designing an Encoder for StyleGAN Image Manipulation

StyleSpace Analysis: Disentangled Controls for StyleGAN Image Generation

Diffusion Models for Adversarial Purification

3D-FM GAN: Towards 3D-Controllable Face Manipulation

Cycle Encoding of a StyleGAN Encoder for Improved Reconstruction and Editability

Transforming the Latent Space of StyleGAN for Real Face Editing

Unsupervised learning reveals interpretable latent representations for translucency perception

IA-FaceS: A Bidirectional Method for Semantic Face Editing

LSAP: Rethinking Inversion Fidelity, Perception and Editability in GAN
  Latent Space


Explains the usage of the openLCA API from Python (Jython)


Python workflow for generating benchmark datasets and machine learning models from the MIMIC-IV-ED database.

Adapting Pretrained Language Models for Solving Tabular Prediction
  Problems in the Electronic Health Record

Benchmarking Predictive Risk Models for Emergency Departments with Large Public Electronic Health Records

Benchmarking emergency department triage prediction models with machine
  learning and large public electronic health records


Evaluating NLP Models via Contrast Sets

Cold-Start Data Selection for Few-shot Language Model Fine-tuning: A
  Prompt-Based Uncertainty Propagation Approach

Detecting Local Insights from Global Labels: Supervised and Zero-Shot Sequence Labeling via a Convolutional Decomposition


Automated Algorithm Selection on Continuous Black-Box Problems by Combining Exploratory Landscape Analysis and Machine Learning

Comprehensive Feature-Based Landscape Analysis of Continuous and
  Constrained Optimization Problems Using the R-Package flacco

A Survey of Advances in Landscape Analysis for Optimisation

Trajectory-based Algorithm Selection with Warm-starting


A Library for Field-aware Factorization Machines

Deep Session Interest Network for Click-Through Rate Prediction

Product-Based Neural Networks for User Response Prediction over Multi-Field Categorical Data

Field-aware Factorization Machines in a Real-world Online Advertising System

Network On Network for Tabular Data Classification in Real-world Applications

PROCEEDINGS OF THE 43RD INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL (SIGIR '20)

AEFE: Automatic Embedded Feature Engineering for Categorical Features


Tools for producing high-quality hourly generation and emissions data for U.S. electric grids


Julia framework for energy system models with a focus on multi-period capacity expansion

Adequacy of time-series reduction for renewable energy systems

Accounting for spatiality of renewables and storage in transmission planning


This is our implementation of Probabilistic Noise2Void

Probabilistic Noise2Void: Unsupervised Content-Aware Denoising

Joint self-supervised blind denoising and noise estimation

N2V2 -- Fixing Noise2Void Checkerboard Artifacts with Modified Sampling
  Strategies and a Tweaked Network Architecture


Mesh parameterization / UV unwrapping library

GET3D: A Generative Model of High Quality 3D Textured Shapes Learned
  from Images

Latent-NeRF for Shape-Guided Generation of 3D Shapes and Textures

Extracting Triangular 3D Models, Materials, and Lighting From Images

DreamGaussian: Generative Gaussian Splatting for Efficient 3D Content
  Creation

TEXTure: Text-Guided Texturing of 3D Shapes

Text-To-4D Dynamic Scene Generation

TexFusion: Synthesizing 3D Textures with Text-Guided Image Diffusion Models

Texture Generation on 3D Meshes with Point-UV Diffusion

Flexible Isosurface Extraction for Gradient-Based Mesh Optimization

VMesh: Hybrid Volume-Mesh Representation for Efficient View Synthesis


Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study

Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer

Effectiveness of ChAdOx1-S COVID-19 booster vaccination against the Omicron and Delta variants in England

CoV2K model, a comprehensive representation of SARS-CoV-2 knowledge and data interplay

A framework for real-time monitoring, analysis and adaptive sampling of viral amplicon nanopore sequencing

Real-time monitoring and analysis of SARS-CoV-2 nanopore sequencing with minoTour


ALFRED - A Benchmark for Interpreting Grounded Instructions for Everyday Tasks

ALFRED: A Benchmark for Interpreting Grounded Instructions for Everyday Tasks

Modular Networks for Compositional Instruction Following

One Step at a Time: Long-Horizon Vision-and-Language Navigation with Milestones

Interpretable Sequence Classification via Discrete Optimization

Are We There Yet? Learning to Localize in Embodied Instruction Following

Modularity Improves Out-of-Domain Instruction Following.


A tool to identify, orient, trim and rescue full length cDNA reads

Construction of a chromosome-scale long-read reference genome assembly for potato

Single-cell RNA-seq analysis of mouse preimplantation embryos by third-generation sequencing

Single-cell multi-omics in the medicinal plant Catharanthus roseus

The Human Adenovirus 2 Transcriptome: an Amazing Complexity of Alternatively Spliced mRNAs

Detection of structural variations and fusion genes in breast cancer samples using third-generation sequencing

Chromosome-Level Genome Assembly of the Asian Red-Tail Catfish (Hemibagrus wyckioides)

Integrative Analysis of Nanopore and Illumina Sequencing Reveals Alternative Splicing Complexity in Pig Longissimus Dorsi Muscle

RUNX1 isoform disequilibrium promotes the development of trisomy 21–associated myeloid leukemia

A novel transposable element-mediated mechanism causes antiviral resistance in Drosophila through truncating the Veneno protein

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

Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages


A transition-based parser for Universal Dependencies with BiLSTM word and character representations.

82 Treebanks, 34 Models: Universal Dependency Parsing with Multi-Treebank Models

Arc-Hybrid Non-Projective Dependency Parsing with a Static-Dynamic Oracle

International Workshop/Conference on Parsing Technologies

Parser Training with Heterogeneous Treebanks

Cross-Lingual Domain Adaptation for Dependency Parsing

Proceedings of the 19th International Workshop on Treebanks and Linguistic Theories

Investigation of Transfer Languages for Parsing Latin: Italic Branch vs. Hellenic Branch

Nordic Conference of Computational Linguistics


CityGML 3.0 Conceptional Model

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

ISPRS international journal of geo-information

Building Virtual 3D City Model for Smart Cities Applications: A Case Study on Campus Area of the University of Novi Sad

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

INTEGRATION OF 3D POINT CLOUDS WITH SEMANTIC 3D CITY MODELS – PROVIDING SEMANTIC INFORMATION BEYOND CLASSIFICATION

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

A Simplified CityGML-Based 3D Indoor Space Model for Indoor Applications

COMBINED MODELLING OF MULTIPLE TRANSPORTATION INFRASTRUCTURE WITHIN 3D CITY MODELS AND ITS IMPLEMENTATION IN CITYGML 3.0


Behavior Trees Library for ROS (Robot Operating System). In C++ and python

Behavior Trees in Robotics and AI: An Introduction

A Survey of Behavior Trees in Robotics and AI

Behavior Trees in Action: A Study of Robotics Applications

Behavior Trees as a Representation for Medical Procedures

Behavior Trees and State Machines in Robotics Applications

Hidden Markov Models derived from Behavior Trees


A sybil-resilient distributed learning protocol.

Mitigating Sybils in Federated Learning Poisoning

The Limitations of Federated Learning in Sybil Settings

International Symposium on Recent Advances in Intrusion Detection

Privacy Side Channels in Machine Learning Systems


**Interspeech 2022** 《SpeechPrompt: An Exploration of Prompt Tuning on Generative Spoken Language Model for Speech Processing Tasks》Speech processing with prompting paradigm

Prefix-Tuning: Optimizing Continuous Prompts for Generation

Generative Spoken Language Modeling from Raw Audio


Reluplex: An Efficient SMT Solver for Verifying Deep Neural Networks

A Unified View of Piecewise Linear Neural Network Verification

Branch and Bound for Piecewise Linear Neural Network Verification

Verification for Machine Learning, Autonomy, and Neural Networks Survey

Piecewise Linear Neural Networks verification: A comparative study

Quantifying safety risks of deep neural networks

Towards the Quantification of Safety Risks in Deep Neural Networks


A fast and unsupervised algorithm for spike detection and sorting using wavelets and super-paramagnetic clustering

A novel and fully automatic spike-sorting implementation with variable number of features

The role of forelimb motor cortex areas in goal directed action in mice

Representation of abstract semantic knowledge in populations of human single neurons in the medial temporal lobe

Application of spike sorting algorithm to neuronal signals originated from boron doped diamond micro-electrode arrays.


Solvation model for the plane wave DFT code VASP.

High-throughput computational-experimental screening protocol for the discovery of bimetallic catalysts

Computational assessment of the efficacy of halides as shape-directing agents in nanoparticle growth

High-Performance of Electrocatalytic CO2 Reduction on Defective Graphene-Supported Cu4S2 Cluster


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

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

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

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

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

基因组蛋白质组与生物信息学报

Analysis pipelines for cancer genome sequencing in mice

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

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

Therapeutic HDAC inhibition in hypermutant diffuse intrinsic pontine glioma


Censor identifiable information in videos, in particular dashcam recordings in Germany.

aiMotive Dataset: A Multimodal Dataset for Robust Autonomous Driving
  with Long-Range Perception

CHAMP: Crowdsourced, History-Based Advisory of Mapped Pedestrians for
  Safer Driver Assistance Systems

A3CarScene: An audio-visual dataset for driving scene understanding


Code for ACL 2020 paper `A Unified MRC Framework for Named Entity Recognition`

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

Rethinking Negative Sampling for Handling Missing Entity Annotations

A Survey on Arabic Named Entity Recognition: Past, Recent Advances, and Future Trends


Source code and dataset for ACL 2019 paper "ERNIE: Enhanced Language Representation with Informative Entities"

LUKE: Deep Contextualized Entity Representations with Entity-aware Self-attention

E-BERT: Efficient-Yet-Effective Entity Embeddings for BERT

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

RICA: Evaluating Robust Inference Capabilities Based on Commonsense Axioms

Metadata Shaping: A Simple Approach for Knowledge-Enhanced Language Models

Findings of the Association for Computational Linguistics: ACL 2022

Entity Context Graph: Learning Entity Representations fromSemi-Structured Textual Sources on the Web


Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

Data-efficient and weakly supervised computational pathology on whole-slide images

Differentiable Zooming for Multiple Instance Learning on Whole-Slide Images

A General-Purpose Self-Supervised Model for Computational Pathology

Annotation-Free Deep Learning-Based Prediction of Thyroid Molecular Cancer Biomarker BRAF (V600E) from Cytological Slides

International journal of molecular sciences

Weakly Supervised Joint Whole-Slide Segmentation and Classification in
  Prostate Cancer

Multiple Instance Learning Framework with Masked Hard Instance Mining for Whole Slide Image Classification

Using less annotation workload to establish a pathological auxiliary diagnosis system for gastric cancer


A scalable SCENIC workflow for single-cell gene regulatory network analysis

Single‐cell RNA‐seq reveals clonal diversity and prognostic genes of relapsed multiple myeloma

A TCF4/BRD4-dependent regulatory network confers cross-resistance to targeted and immune checkpoint therapy in melanoma

Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors


An efficient PyTorch library for deep generative modeling.

GLEAN: Generative Latent Bank for Large-Factor Image Super-Resolution

GAN Inversion for Out-of-Range Images with Geometric Transformations

Linear Semantics in Generative Adversarial Networks

PandA: Unsupervised Learning of Parts and Appearances in the Feature Maps of GANs

GLEAN: Generative Latent Bank for Image Super-Resolution and Beyond

BEAGLE: Forensics of Deep Learning Backdoor Attack for Better Defense


See https://meta.wikimedia.org/wiki/Research:Modeling_Talk_Page_Abuse

Ex Machina: Personal Attacks Seen at Scale

Is More Data Better? Re-thinking the Importance of Efficiency in Abusive
  Language Detection with Transformers-Based Active Learning

Dis/similarities in the design and development of legal and algorithmic normative systems: the case of Perspective API

A Software Tool Aimed at Automating the Generation, Distribution, and Assessment of Social Media Messages for Health Promotion and Education Research


A visual simulator for teaching computer architecture using the RISC-V instruction set

A Survey of the RISC-V Architecture Software Support


(MOVED) Athena++ GRMHD code and adaptive mesh refinement (AMR) framework. Active repository --->

The Athena++ Adaptive Mesh Refinement Framework: Design and Magnetohydrodynamic Solvers

The Astrophysical journal. Supplement series/Astrophysical journal. Supplement series

The Event Horizon General Relativistic Magnetohydrodynamic Code Comparison Project

MHD Turbulence

Living reviews in computational astrophysics

An entropy stable nodal discontinuous Galerkin method for the resistive MHD equations. Part II: Subcell finite volume shock capturing

Technique for Separating Velocity and Density Contributions in Spectroscopic Data and Its Application to Studying Turbulence and Magnetic Fields

Thermal instability and multiphase gas in the simulated interstellar medium with conduction, viscosity, and magnetic fields

Monthly Notices of the Royal Astronomical Society

Magnetohydrodynamics with GAMER

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

Constraint Preserving Discontinuous Galerkin Method for Ideal Compressible MHD on 2-D Cartesian Grids


Learning human driver models from NGSIM data with imitation learning.

Generative Adversarial Imitation Learning

InfoGAIL: Interpretable Imitation Learning from Visual Demonstrations

Multi-Agent Imitation Learning for Driving Simulation

Simulating Emergent Properties of Human Driving Behavior Using Multi-Agent Reward Augmented Imitation Learning

Online Parameter Estimation for Human Driver Behavior Prediction

A Hybrid Rule-Based and Data-Driven Approach to Driver Modeling Through Particle Filtering


Mpox 2022 repository

Monkeypox: A clinical update for paediatricians

Travel-Related Monkeypox Outbreaks in the Era of COVID-19 Pandemic: Are We Prepared?

Atypical and Unique Transmission of Monkeypox Virus during the 2022 Outbreak: An Overview of the Current State of Knowledge

Projecting the impact of testing and vaccination on the transmission dynamics of the 2022 monkeypox outbreak in the USA

Voluntary vaccination may not stop monkeypox outbreak: A game-theoretic model

Monkeypox outbreaks in the context of the COVID-19 pandemic: Network and clustering analyses of global risks and modified SEIR prediction of epidemic trends


LUKE -- Language Understanding with Knowledge-based Embeddings

Attention Is All You Need

LUKE: Deep Contextualized Entity Representations with Entity-aware Self-attention

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

Global Entity Disambiguation with BERT

mLUKE: The Power of Entity Representations in Multilingual Pretrained Language Models

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

Generative Prompt Tuning for Relation Classification

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

Beyond modeling: NLP Pipeline for efficient environmental policy
  analysis

LUKE-Graph: A Transformer-based Approach with Gated Relational Graph Attention for Cloze-style Reading Comprehension


Connectome Workbench

A massive 7T fMRI dataset to bridge cognitive neuroscience and artificial intelligence

Determining the Hierarchical Architecture of the Human Brain Using Subject-Level Clustering of Functional Networks

Diffusion Tensor Model links to Neurite Orientation Dispersion and Density Imaging at high b-value in Cerebral Cortical Gray Matter

A massive 7T fMRI dataset to bridge cognitive and computational neuroscience

Local and long-distance organization of prefrontal cortex circuits in the marmoset brain

Development of visual cortex in human neonates is selectively modified by postnatal experience

Mapping the macrostructure and microstructure of the in vivo human hippocampus using diffusion MRI

The Interaction of Glycemia with Anxiety and Depression Is Related to Altered Cerebellar and Cerebral Functional Correlations

Adolescents at clinical high risk for psychosis show qualitatively altered patterns of activation during rule learning


[CVPR2021] UAV-Human: A Large Benchmark for Human Behavior Understanding with Unmanned Aerial Vehicles

MSST-RT: Multi-Stream Spatial-Temporal Relative Transformer for Skeleton-Based Action Recognition

Skeleton-Based Mutually Assisted Interacted Object Localization and Human Action Recognition


:scissors: :zap: Rapid haploid variant calling and core genome alignment

Multidrug-Resistant Enterobacter cloacae Complex Emerging as a Global, Diversifying Threat

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

Discovery of MRSA active antibiotics using primary sequence from the human microbiome

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation

Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation

bioRxiv : the preprint server for biology

Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution


Multi-modality pre-training

Pixel-BERT: Aligning Image Pixels with Text by Deep Multi-Modal Transformers

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

Advancing High-Resolution Video-Language Representation with Large-Scale Video Transcriptions

CLIP-ViP: Adapting Pre-trained Image-Text Model to Video-Language
  Representation Alignment

Long-Form Video-Language Pre-Training with Multimodal Temporal
  Contrastive Learning


Implementation of TabTransformer, attention network for tabular data, in Pytorch

Revisiting Deep Learning Models for Tabular Data

TabTransformer: Tabular Data Modeling Using Contextual Embeddings

SAINT: Improved Neural Networks for Tabular Data via Row Attention and Contrastive Pre-Training

TransTab: Learning Transferable Tabular Transformers Across Tables

Transfer Learning with Deep Tabular Models

MambaTab: A Simple Yet Effective Approach for Handling Tabular Data

UniTabE: A Universal Pretraining Protocol for Tabular Foundation Model in Data Science

Tabular Few-Shot Generalization Across Heterogeneous Feature Spaces


Deep generative models of 3D grids for structure-based drug discovery

Generating 3D molecules conditional on receptor binding sites with deep generative models

Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models.

Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models

Docking-based generative approaches in the search for new drug candidates

Learning Subpocket Prototypes for Generalizable Structure-based Drug
  Design


Home of StarCoder: fine-tuning & inference!

Finetuned Language Models Are Zero-Shot Learners

StarCoder: may the source be with you!

Is Your Code Generated by ChatGPT Really Correct? Rigorous Evaluation of
  Large Language Models for Code Generation

SantaCoder: don't reach for the stars!

Data Quality in Imitation Learning

A Survey on Large Language Models for Software Engineering

An HCI-Centric Survey and Taxonomy of Human-Generative-AI Interactions


Official repository for the "Big Transfer (BiT): General Visual Representation Learning" paper.

Exploring the Limits of Out-of-Distribution Detection

Knowledge distillation: A good teacher is patient and consistent

On the Importance of Gradients for Detecting Distributional Shifts in the Wild

DICE: Leveraging Sparsification for Out-of-Distribution Detection

The Deep Bootstrap Framework: Good Online Learners are Good Offline Generalizers

Supervised Transfer Learning at Scale for Medical Imaging

Robust and Efficient Medical Imaging with Self-Supervision

Active Learning Helps Pretrained Models Learn the Intended Task

Deep learning models for histologic grading of breast cancer and association with disease prognosis


Circular and Rectangular Manhattan Plot

The origin of domestication genes in goats

The Trans-omics Landscape of COVID-19

Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance

A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

BnaMPK3 Is a Key Regulator of Defense Responses to the Devastating Plant Pathogen Sclerotinia sclerotiorum in Oilseed Rape

Improving Genomic Selection With Quantitative Trait Loci and Nonadditive Effects Revealed by Empirical Evidence in Maize

Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan)


Comparing many FRP implementations by reimplementing the same toy app in each.

The 5th Reactive Synthesis Competition (SYNTCOMP 2018): Benchmarks,
  Participants & Results

Temporal Stream Logic: Synthesis beyond the Bools

Synthesizing Functional Reactive Programs


MELD: A Multimodal Multi-Party Dataset for Emotion Recognition in Conversation

DialogueCRN: Contextual Reasoning Networks for Emotion Recognition in Conversations

Real-Time Emotion Recognition via Attention Gated Hierarchical Memory Network

Topic-Driven and Knowledge-Aware Transformer for Dialogue Emotion Detection

A Preliminary Study on Realizing Human–Robot Mental Comforting Dialogue via Sharing Experience Emotionally

A Facial Expression-Aware Multimodal Multi-task Learning Framework for Emotion Recognition in Multi-party Conversations

Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

Whose emotion matters? Speaking activity localisation without prior knowledge

An Assessment of In-the-Wild Datasets for Multimodal Emotion Recognition

A Dual-Stream Recurrence-Attention Network With Global-Local Awareness
  for Emotion Recognition in Textual Dialog


A collection of tools for Hi-C data analysis

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

HiGlass: web-based visual exploration and analysis of genome interaction maps

Condensin-driven remodelling of X chromosome topology during dosage compensation


This repo contains source code and materials for the TEmporally COherent GAN SIGGRAPH project.

Learning temporal coherence via self-supervision for GAN-based video generation

Video Super Resolution Based on Deep Learning: A Comprehensive Survey

Temporally Coherent GANs for Video Super-Resolution (TecoGAN).


ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

ProtTrans: Towards Cracking the Language of Life's Code Through
  Self-Supervised Deep Learning and High Performance Computing

Controllable protein design with language models

Pre-trained Language Models in Biomedical Domain: A Systematic Survey

Pretraining model for biological sequence data

LMPred: predicting antimicrobial peptides using pre-trained language models and deep learning

DeepSTABp: A Deep Learning Approach for the Prediction of Thermal Protein Stability

DTI-BERT: Identifying Drug-Target Interactions in Cellular Networking Based on BERT and Deep Learning Method

PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models

Fine-tuning protein language models boosts predictions across diverse tasks

Multi-level Protein Representation Learning for Blind Mutational Effect
  Prediction


Data on energy by Our World in Data

PyPSA-Earth. A new global open energy system optimization model demonstrated in Africa


Relax! Flux is the ML library that doesn't make you tensor

PyTorch: An Imperative Style, High-Performance Deep Learning Library

Surgical Data Science -- from Concepts toward Clinical Translation

Fashionable Modelling with Flux

Deep learning in electron microscopy

Machine learning: science and technology

Julia Language in Machine Learning: Algorithms, Applications, and Open Issues

Learning with Combinatorial Optimization Layers: a Probabilistic Approach

Automatic Full Compilation of Julia Programs and ML Models to Cloud TPUs

Using scientific machine learning for experimental bifurcation analysis of dynamic systems

AbstractDifferentiation.jl: Backend-Agnostic Differentiable Programming in Julia

Automatic Differentiation using Constraint Handling Rules in Prolog


Square’s meticulous HTTP client for the JVM, Android, and GraalVM.

What Makes a Good Commit Message?

Proceedings of the 44th International Conference on Software Engineering

Refactoring Graphs: Assessing Refactoring over Time

Security Header Fields in HTTP Clients

Verifying Semantic Conflict-Freedom in Three-Way Program Merges.

Device-centric Federated Analytics At Ease

Relationships between design problem agglomerations and concerns having types and domains of software as transverse dimensions


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

Conditionally Elicitable Dynamic Risk Measures for Deep Reinforcement Learning

AI and Wargaming

Deep Learning for General Game Playing with Ludii and Polygames

Efficient Reasoning in Regular Boardgames


A stochastic agent-based model for predicting raptor movements during updraft-subsidized directional flights


This is the documentation repository for ongoing releases to the NDA collection 3165.  Please add GitHub Issues here for requests or feedback.

Reproducible brain-wide association studies require thousands of individuals

Adolescent Brain Cognitive Development (ABCD) Community MRI Collection and Utilities

Accounting for Temporal Variability in Functional Magnetic Resonance
  Imaging Improves Prediction of Intelligence

Functional connectome through the human life span


Pytorch implementation of HighRes-net, a neural network for multi-frame super-resolution, trained and tested on the European Space Agency’s Kelvin competition. This is a ServiceNow Research project that was started at Element AI.

HighRes-net: Recursive Fusion for Multi-Frame Super-Resolution of Satellite Imagery

HighRes-net: Multi-Frame Super-Resolution by Recursive Fusion

Single-Frame Super-Resolution of Solar Magnetograms: Investigating
  Physics-Based Metrics & Losses


SemEval 2024 Task 1 : Textual Semantic Relatedness

SemRel2024: A Collection of Semantic Textual Relatedness Datasets for 14 Languages


A fresh approach to deep learning written in MATLAB

Stable Architectures for Deep Neural Networks

Reversible Architectures for Arbitrarily Deep Residual Neural Networks

Learning across scales - A multiscale method for Convolution Neural Networks

slimTrain -- A Stochastic Approximation Method for Training Separable
  Deep Neural Networks


A framework for nonlinear continuous-time regression

A large-scale study of the effects of word frequency and predictability in naturalistic reading

North American Chapter of the Association for Computational Linguistics

Comparison of Structural Parsers and Neural Language Models as Surprisal Estimators

Deconvolutional Time Series Regression: A Technique for Modeling Temporally Diffuse Effects

Empirical Methods in Natural Language Processing

CDRNN: Discovering Complex Dynamics in Human Language Processing

Meeting of the Association for Computational Linguistics

A Deep Learning Approach to Analyzing Continuous-Time Systems

Word Frequency and Predictability Dissociate in Naturalistic Reading

A Deep Learning Approach to Analyzing Continuous-Time Cognitive Processes


A Python implementation of the brain connectivity toolbox. **Not actively maintained.**

Time-resolved structure-function coupling in brain networks

Network topology of the marmoset connectome

Whole-brain modeling explains the context-dependent effects of cholinergic neuromodulation


Bamboo: a morphing smart contract language

The Art of The Scam: Demystifying Honeypots in Ethereum Smart Contracts

Resource-Aware Session Types for Digital Contracts

Smart Contract Security: a Practitioners' Perspective

The State of Ethereum Smart Contracts Security: Vulnerabilities, Countermeasures, and Tool Support

Elysium: Context-Aware Bytecode-Level Patching to Automatically Heal Vulnerable Smart Contracts


:books: :microscope: :unlock:  :mag: A curated list of resources, data, tools, scholarship related to Open Access, Data and Open Science :books: :microscope: :unlock:  :mag:

Data from Investigating Variation in Replicability: A “Many Labs” Replication Project

Ten Simple Rules for Reproducible Computational Research

What Drives Academic Data Sharing

The data paper: a mechanism to incentivize data publishing in biodiversity science

Public Data Archiving in Ecology and Evolution: How Well Are We Doing?

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

Open Data as Open Educational Resources: Towards transversal skills and global citizenship


higher is a pytorch library allowing users to obtain higher order gradients over losses spanning training loops rather than individual training steps.

Generalized Inner Loop Meta-Learning

CrossFit: A Few-shot Learning Challenge for Cross-task Generalization in NLP

Meta-Learning via Learned Loss

Zero-Shot Cross-Lingual Transfer with Meta Learning

Meta-Learning Symmetries by Reparameterization

Taming GANs with Lookahead-Minmax

Tailoring: encoding inductive biases by optimizing unsupervised objectives at prediction time

Global Convergence and Induced Kernels of Gradient-Based Meta-Learning with Neural Nets.

Global Convergence and Generalization Bound of Gradient-Based Meta-Learning with Deep Neural Nets

Meta Self-Refinement for Robust Learning with Weak Supervision


Annotation helper tool for the manual curation of transposable element consensus sequences

Duplication and Specialization of NUDX1 in Rosaceae Led to Geraniol Production in Rose Petals

Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Transposable Element Interactions Shape the Ecology of the Deer Mouse Genome


openMINDS comprises a set of metadata models for research products in the field of neuroscience.

Brain simulation as a cloud service: The Virtual Brain on EBRAINS

International data governance for neuroscience

Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

Brain Modelling as a Service: The Virtual Brain on EBRAINS

AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures


Deep mutational scanning of the receptor-binding domain of SARS-CoV-2 Spike

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

Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies

Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes

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

Predicting the antigenic evolution of SARS-COV-2 with deep learning

Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants


Deep Reinforcement Learning for Resource Constrained Multiclass Scheduling in Wireless Networks

Deep Reinforcement Learning for Wireless Resource Allocation Using Buffer State Information


Modern implementation of the hybrid genetic search (HGS) algorithm specialized to the capacitated vehicle routing problem (CVRP). This code also includes an additional neighborhood called SWAP*.

Hybrid Genetic Search for the CVRP: Open-Source Implementation and SWAP* Neighborhood

Deep Policy Dynamic Programming for Vehicle Routing Problems

Learning to Delegate for Large-scale Vehicle Routing

Towards Omni-generalizable Neural Methods for Vehicle Routing Problems


Python package for Sentential Decision Diagrams (SDD)

Three Modern Roles for Logic in AI

Symposium on Principles of Database Systems

Semantic Probabilistic Layers for Neuro-Symbolic Learning

Tractable Explanations for d-DNNF Classifiers

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

Feature Necessity & Relevancy in ML Classifier Explanations

Efficient Explanations for Knowledge Compilation Languages

A-NeSI: A Scalable Approximate Method for Probabilistic Neurosymbolic
  Inference

Tractable Inference in Credal Sentential Decision Diagrams

Tractable Boolean and Arithmetic Circuits

Efficient Computation of Shap Explanation Scores for Neural Network Classifiers via Knowledge Compilation

Semantic Strengthening of Neuro-Symbolic Learning


Scalable Time Series Data Analytics

Fast and Accurate Time Series Classification with WEASEL

International Conference on Information and Knowledge Management

TapNet: Multivariate Time Series Classification with Attentional Prototypical Network

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

Multivariate Time Series Classification with WEASEL+MUSE

TEASER: early and accurate time series classification

A Distributed Multi-Sensor Machine Learning Approach to Earthquake Early Warning

XEM: An explainable-by-design ensemble method for multivariate time series classification

Dataset: Rare Event Classification in Multivariate Time Series

Local Cascade Ensemble for Multivariate Data Classification.


Generate 3D objects conditioned on text or images

Shap-E: Generating Conditional 3D Implicit Functions

Next Steps for Human-Centered Generative AI: A Technical Perspective

iNVS: Repurposing Diffusion Inpainters for Novel View Synthesis

HexaGen3D: StableDiffusion is just one step away from Fast and Diverse
  Text-to-3D Generation

3DTopia: Large Text-to-3D Generation Model with Hybrid Diffusion Priors

BoostDream: Efficient Refining for High-Quality Text-to-3D Generation from Multi-View Diffusion


Rule-based facts extraction for Russian language

Question Embeddings Based on Shannon Entropy: Solving intent classification task in goal-oriented dialogue system


python Circos

A panoramic view of the genomic landscape of the genus Streptomyces

Analysis of Genome-Wide Mutational Dependence in Naturally Evolving Mycobacterium tuberculosis Populations


Pytorch implementation of HorizonNet: Learning Room Layout with 1D Representation and Pano Stretch Data Augmentation.

Structured3D: A Large Photo-realistic Dataset for Structured 3D Modeling

HoHoNet: 360 Indoor Holistic Understanding with Latent Horizontal Features

3D Manhattan Room Layout Reconstruction from a Single 360 Image

LGT-Net: Indoor Panoramic Room Layout Estimation with Geometry-Aware Transformer Network

360-MLC: Multi-view Layout Consistency for Self-training and
  Hyper-parameter Tuning


Tutorials on implementing a few sequence-to-sequence (seq2seq) models with PyTorch and TorchText.

Neural Machine Translation by Jointly Learning to Align and Translate

Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation

Sequence to Sequence Learning with Neural Networks

Mixed-Level Neural Machine Translation

Computational intelligence and neuroscience

A Minimalist Dataset for Systematic Generalization of Perception,
  Syntax, and Semantics

Would You Ask it that Way?

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

An End-to-End Khmer Optical Character Recognition using
  Sequence-to-Sequence with Attention


Online and batch-based concept and data drift detection algorithms to monitor and maintain ML performance.

On the Reliable Detection of Concept Drift from Streaming Unlabeled Data

Hellinger distance based drift detection for nonstationary environments

IEEE Symposium on Computational Intelligence in Dynamic and Uncertain Environments

Concept Drift Detection for Streaming Data

A PCA-Based Change Detection Framework for Multidimensional Data Streams

Drift detection using uncertainty distribution divergence

Frouros: A Python library for drift detection in machine learning
  systems


SKA Radio Telescope Simulator

A Simplified, Lossless Reanalysis of PAPER-64

Comparing foreground removal techniques for recovery of the LOFAR-EoR 21 cm power spectrum

A Comparative Analysis to Deal with Missing Spectral Information Caused by RFI in Cosmological H i 21 cm Observations

Separating the EoR signal with a convolutional denoising autoencoder: a deep-learning-based method

Monthly notices of the Royal Astronomical Society

A unified calibration framework for 21 cm cosmology

Studying the morphology of reionization with the triangle correlation function of phases

The bispectrum and 21-cm foregrounds during the Epoch of Reionization

Monthly Notices of the Royal Astronomical Society

Contribution of Radio Halos to the Foreground for SKA EoR Experiments

First look at the multiphase interstellar medium using synthetic observations from low-frequency Faraday tomography

Contribution of Galactic free–free emission to the foreground for EoR signal in SKA experiments


All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")

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

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth

Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland

FEMS microbiology ecology/FEMS microbiology, ecology

Undocumented potential for primary productivity in a globally-distributed bacterial photoautotroph

Phylogenetically and metabolically diverse autotrophs in the world’s deepest blue hole


Pairwise multilevel comparison using adonis

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

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

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

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

International journal of environmental research and public health

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

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

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

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

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

Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization


A Python 3 package to efficiently compute non-Markovian open quantum systems.

Non-Markovian quantum processes: Complete framework and efficient characterization

Efficient non-Markovian quantum dynamics using time-evolving matrix product operators

Advanced Photonic Sciences

Efficient Exploration of Hamiltonian Parameter Space for Optimal Control of Non-Markovian Open Quantum Systems

Efficient real-time path integrals for non-Markovian spin-boson models


Code for neural network parameterization project

Deep learning to represent sub-grid processes in climate models

Could Machine Learning Break the Convection Parameterization Deadlock?

Enforcing Analytic Constraints in Neural Networks Emulating Physical Systems.

Towards Physically-consistent, Data-driven Models of Convection

Climate-Invariant Machine Learning

raspstephan/CBRAIN-CAM

Sample SPCAM dataset

Zenodo (CERN European Organization for Nuclear Research)

Improving Atmospheric Processes in Earth System Models with Deep
  Learning Ensembles and Stochastic Parameterizations


Harmonization tools for multi-site neuroimaging analysis. Implemented as a python package. Harmonization of MRI, sMRI, dMRI, fMRI variables with support for NIFTI images. Complements the work in Neuroimage by Pomponio et al. (2019).

Site effects how-to and when: An overview of retrospective techniques to accommodate site effects in multi-site neuroimaging analyses

A comparison of methods to harmonize cortical thickness measurements across scanners and sites

The impact of harmonization on radiomic features in Parkinson’s disease and healthy controls: A multicenter study

Functional connectome through the human life span

bioRxiv : the preprint server for biology

Multi-site benchmark classification of major depressive disorder using machine learning on cortical and subcortical measures

Efficacy of MRI data harmonization in the age of machine learning: a multicenter study across 36 datasets

Depressive symptoms moderate functional connectivity within the emotional brain in chronic pain


Pure Python, MIT-licensed implementation of nested sampling algorithms for evaluating Bayesian evidence.

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

TauREx 3: A Fast, Dynamic, and Extendable Framework for Retrievals

Forward Modeling and Retrievals with PLATON, a Fast Open-source Tool

Publications of the Astronomical Society of the Pacific

Reconstructing the Last Major Merger of the Milky Way with the H3 Survey

Collaborative Nested Sampling: Big Data vs. complex physical models

Nested sampling methods

Sub-Chandrasekhar progenitors favoured for Type Ia supernovae: evidence from late-time spectroscopy

Nested sampling for physical scientists

A search for a surviving companion in SN 1006

Evidence for the volatile-rich composition of a 1.5-Earth-radius planet


A Python wrapper for the NOAA CO-OPS Tides & Currents Data and Metadata APIs.


An accurate and efficient deep learning method for single-cell RNA-seq data imputation

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data

Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review

基因组蛋白质组与生物信息学报

An Overview of Algorithms and Associated Applications for Single Cell RNA-Seq Data Imputation


Inf-Net: Automatic COVID-19 Lung Infection Segmentation from CT Images, IEEE TMI 2020.

Label-Free Segmentation of COVID-19 Lesions in Lung CT

COVID TV-UNet: Segmenting COVID-19 Chest CT Images Using Connectivity Imposed U-Net

Video Polyp Segmentation: A Deep Learning Perspective

Comparative study of deep learning methods for the automatic segmentation of lung, lesion and lesion type in CT scans of COVID-19 patients

CHS-Net: A Deep learning approach for hierarchical segmentation of COVID-19 infected CT images

CARes‐UNet: Content‐aware residual UNet for lesion segmentation of COVID‐19 from chest CT images

Medical physics on CD-ROM/Medical physics

A convolutional neural network with pixel-wise sparse graph reasoning for COVID-19 lesion segmentation in CT images

D2A U-Net: Automatic Segmentation of COVID-19 Lesions from CT Slices with Dilated Convolution and Dual Attention Mechanism

Volume-of-Interest Aware Deep Neural Networks for Rapid Chest CT-Based COVID-19 Patient Risk Assessment


Extract and Visualize the Results of Multivariate Data Analyses

GDSL-domain proteins have key roles in suberin polymerization and degradation

SCHENGEN receptor module drives localized ROS production and lignification in plant roots

FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells

The global dissemination of hospital clones of Enterococcus faecium

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

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

Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective

International journal of molecular sciences

Comparative transcriptome and metabolome analysis reveal key regulatory defense networks and genes involved in enhanced salt tolerance of Actinidia (kiwifruit)

Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle

Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken


StyleFlow: Attribute-conditioned Exploration of StyleGAN-generated Images using  Conditional Continuous Normalizing Flows (ACM TOG 2021)

PointFlow: 3D Point Cloud Generation with Continuous Normalizing Flows

StyleFlow: Attribute-conditioned Exploration of StyleGAN-Generated Images using Conditional Continuous Normalizing Flows

Controllable and Compositional Generation with Latent-Space Energy-Based Models

Improving the Fairness of Deep Generative Models without Retraining

FairStyle: Debiasing StyleGAN2 with Style Channel Manipulations

GANravel: User-Driven Direction Disentanglement in Generative Adversarial Networks

Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems


Accurately generate all possible forms of an English word e.g "election" --> "elect", "electoral", "electorate" etc.

A Lightweight Constrained Generation Alternative for Query-focused Summarization

Data Augmentation of Incorporating Real Error Patterns and Linguistic Knowledge for Grammatical Error Correction

Proceedings of the 25th Conference on Computational Natural Language Learning

An Extended Sequence Tagging Vocabulary for Grammatical Error Correction


This is the community-maintained issue tracker for uBlock Origin

The CNAME of the Game: Large-scale Analysis of DNS-based Tracking Evasion

SOK: On the Analysis of Web Browser Security


SimXNS is a research project for information retrieval. This repo contains official implementations by MSRA NLC team.

SimANS: Simple Ambiguous Negatives Sampling for Dense Text Retrieval

PROD: Progressive Distillation for Dense Retrieval

MASTER: Multi-task Pre-trained Bottlenecked Masked Autoencoders are
  Better Dense Retrievers

LEAD: Liberal Feature-based Distillation for Dense Retrieval

CAPSTONE: Curriculum Sampling for Dense Retrieval with Document Expansion

Allies: Prompting Large Language Model with Beam Search


Haplotype based scans for selection

selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

The evolutionary history and genomics of European blackcap migration

Identifying the favored mutation in a positive selective sweep

Prioritizing natural-selection signals from the deep-sequencing genomic data suggests multi-variant adaptation in Tibetan highlanders

Genomic data as the “hitchhiker's guide” to cattle adaptation: tracking the milestones of past selection in the bovine genome

selscan 2.0: scanning for sweeps in unphased data

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Animals : an open access journal from MDPI

Population-specific, recent positive directional selection suggests adaptation of human male reproductive genes to different environmental conditions

Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis

Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries


Deep learning software for colorizing black and white images with a few clicks.

Real-Time User-Guided Image Colorization with Learned Deep Priors

Image Colorization: A Survey and Dataset

GIMP-ML: Python Plugins for using Computer Vision Models in GIMP


A learning rate range test implementation in PyTorch

Cyclical Learning Rates for Training Neural Networks

Primordial non-Gaussianity from the completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey - I: Catalogue preparation and systematic mitigation

Backtracking gradient descent method for general C^1 functions, with applications to Deep Learning

Instance-based Label Smoothing For Better Calibrated Classification Networks


Natural language detection library for Go

Understanding Longitudinal Behaviors of Toxic Accounts on Reddit

Sub-Standards and Mal-Practices: Misinformation's Role in Insular,
  Polarized, and Toxic Interactions

Twits, Toxic Tweets, and Tribal Tendencies: Trends in Politically
  Polarized Posts on Twitter


Training neural networks in TensorFlow 2.0 with 5x less memory

Checkmate: Breaking the Memory Wall with Optimal Tensor Rematerialization

Survey on Large Scale Neural Network Training

Winner-Take-All Column Row Sampling for Memory Efficient Adaptation of
  Language Model

Tempo: Accelerating Transformer-Based Model Training through Memory
  Footprint Reduction


Adversarial Natural Language Inference Benchmark

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

RoBERTa: A Robustly Optimized BERT Pretraining Approach

XLNet: Generalized Autoregressive Pretraining for Language Understanding

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

Adversarial NLI: A New Benchmark for Natural Language Understanding

Adversarial Training for Large Neural Language Models

Adversarial GLUE: A Multi-Task Benchmark for Robustness Evaluation of Language Models

InfoBERT: Improving Robustness of Language Models from An Information Theoretic Perspective

VALSE: A Task-Independent Benchmark for Vision and Language Models Centered on Linguistic Phenomena

ANLIzing the Adversarial Natural Language Inference Dataset


This package contains a generic implementation of greedy Information Theoretic Feature Selection (FS) methods. The implementation is based on the common theoretic framework presented by Gavin Brown. Implementations of mRMR, InfoGain, JMI and other commonly used FS filters are provided.

A greedy feature selection algorithm for Big Data of high dimensionality

A scalable and effective rough set theory-based approach for big data pre-processing

A Detailed Study of the Distributed Rough Set Based Locality Sensitive Hashing Feature Selection Technique


Deep End-to-end Causal Inference

Simultaneous Missing Value Imputation and Structure Learning with Groups

Causal Reasoning in the Presence of Latent Confounders via Neural ADMG
  Learning

NeurIPS Competition Instructions and Guide: Causal Insights for Learning
  Paths in Education


TensorFlow Implementation of Neural Attentive Item Similarity Model for Recommendation on TKDE 2018

NAIS: Neural Attentive Item Similarity Model for Recommendation

IEEE transactions on knowledge and data engineering

Deep Item-based Collaborative Filtering for Top-N Recommendation

Simultaneous Learning of the Inputs and Parameters in Neural
  Collaborative Filtering


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

Do Deep Learning Models Really Outperform Traditional Approaches in
  Molecular Docking?

Modeling Molecular Structures with Intrinsic Diffusion Models

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


PraNet: Parallel Reverse Attention Network for Polyp Segmentation, MICCAI 2020 (Oral). Code using Jittor Framework is available.

Polyp-PVT: Polyp Segmentation with Pyramid Vision Transformers

Medical Image Segmentation Using Squeeze-and-Expansion Transformers

FCN-Transformer Feature Fusion for Polyp Segmentation

Medical Image Understanding and Analysis

Video Polyp Segmentation: A Deep Learning Perspective

NeoUNet: Towards accurate colon polyp segmentation and neoplasm detection

Double Encoder-Decoder Networks for Gastrointestinal Polyp Segmentation


A semantic segmentation toolbox based on PyTorch

U-Net: Convolutional Networks for Biomedical Image Segmentation

DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs

Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation

Pyramid Scene Parsing Network

Rethinking Atrous Convolution for Semantic Image Segmentation

Bag of Tricks for Image Classification with Convolutional Neural Networks


Python command line tool for Multi-Trait Analysis of GWAS (MTAG)

Genome-wide meta-analysis of problematic alcohol use in 435,563 individuals yields insights into biology and relationships with other traits

Multiomics study of nonalcoholic fatty liver disease

Investigating the shared genetic architecture between multiple sclerosis and inflammatory bowel diseases

A regulatory variant at 3q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density

Multi-trait genome-wide association study identifies new loci associated with optic disc parameters

Enhancing Discovery of Genetic Variants for Posttraumatic Stress Disorder Through Integration of Quantitative Phenotypes and Trauma Exposure Information

Shared genetic etiology and causality between body fat percentage and cardiovascular diseases: a large-scale genome-wide cross-trait analysis

Multitrait genome-wide analyses identify new susceptibility loci and candidate drugs to primary sclerosing cholangitis

Genomic Overlap between Platelet Parameters Variability and Age at Onset of Parkinson Disease

Genome-wide association study of social relationship satisfaction: significant loci and correlations with psychiatric conditions


Creative Commons Attribution Share Alike 4.0 International

Repository for Kuzushiji-MNIST, Kuzushiji-49, and Kuzushiji-Kanji

Deep Learning for Classical Japanese Literature

Do We Need Zero Training Loss After Achieving Zero Training Error?

Provably Consistent Partial-Label Learning

Complementary-Label Learning for Arbitrary Losses and Models

Learning with Multiple Complementary Labels

Debiasing Graph Neural Networks via Learning Disentangled Causal
  Substructure

Pointwise Binary Classification with Pairwise Confidence Comparisons

Bridging Ordinary-Label Learning and Complementary-Label Learning

Learning from Similarity-Confidence Data

Gated information bottleneck for generalization in sequential environments


pathfindR: Enrichment Analysis Utilizing Active Subnetworks

pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks

pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks

Deep proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of naïve mice


:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Plastic-degrading potential across the global microbiome correlates with recent pollution trends

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

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

The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis


Adaptive Skip-gram implementation in Julia

Breaking Sticks and Ambiguities with Adaptive Skip-gram

Conditional Generators of Words Definitions

Unsupervised Does Not Mean Uninterpretable: The Case for Word Sense Induction and Disambiguation

Conference of the European Chapter of the Association for Computational Linguistics

Improving Document Classification with Multi-Sense Embeddings

Improving Neural Sequence Labelling using Additional Linguistic Information

Evaluating a Multi-sense Definition Generation Model for Multiple Languages


An Efficient Lexical Analyzer for Chinese

SECaps: A Sequence Enhanced Capsule Model for Charge Prediction

VCWE: Visual Character-Enhanced Word Embeddings

NE–LP: Normalized entropy- and loss prediction-based sampling for active learning in Chinese word segmentation on EHRs

Recurrent Attention for Neural Machine Translation

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

Discussion on Bilingual Cognition in International Exchange Activities

Constructing Uyghur Name Entity Recognition System using Neural Machine Translation Tag Projection


Canonical Correlation Analysis Zoo: A collection of Regularized, Deep Learning based, Kernel, and Probabilistic methods in a scikit-learn style framework

Tensor Canonical Correlation Analysis for Multi-view Dimension Reduction

Deep Generalized Canonical Correlation Analysis

An iterative penalized least squares approach to sparse canonical correlation analysis

Deep Tensor CCA for Multi-view Learning

Learning Representations without Compositional Assumptions


NicheNet: predict active ligand-target links between interacting cells

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

Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches

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

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

The Journal of experimental medicine/The journal of experimental medicine

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

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


Water Detect Algorithm


CUDA-accelerated Fully Homomorphic Encryption Library

HEAX: An Architecture for Computing on Encrypted Data

SoK: Fully Homomorphic Encryption Compilers

ARK: Fully Homomorphic Encryption Accelerator with Runtime Data Generation and Inter-Operation Key Reuse

Non-Interactive Private Decision Tree Evaluation

Accelerating Encrypted Computing on Intel GPUs

Virtual Secure Platform: A Five-Stage Pipeline Processor over TFHE

HAAC: A Hardware-Software Co-Design to Accelerate Garbled Circuits

SoK: Fully Homomorphic Encryption Accelerators


Implementation of "Lifting from the Deep: Convolutional 3D Pose Estimation from a Single Image"

Recent Advances of Monocular 2D and 3D Human Pose Estimation: A Deep Learning Perspective

3D Human Pose Estimation in Vietnamese Traditional Martial Art Videos

Journal of Advanced Engineering and Computation


[ICCV21] Self-Calibrating Neural Radiance Fields

BARF: Bundle-Adjusting Neural Radiance Fields

NeRF--: Neural Radiance Fields Without Known Camera Parameters

Self-Calibrating Neural Radiance Fields


Self-Supervision for Named Entity Disambiguation at the Tail

Bootleg: Chasing the Tail with Self-Supervised Named Entity Disambiguation

TABi: Type-Aware Bi-Encoders for Open-Domain Entity Retrieval

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


A Simple Multi-Modality Transfer Learning Baseline for Sign Language Translation

Two-Stream Network for Sign Language Recognition and Translation

Natural Language-Assisted Sign Language Recognition

CiCo: Domain-Aware Sign Language Retrieval via Cross-Lingual Contrastive Learning


Official Implementation of OCR-free Document Understanding Transformer (Donut) and Synthetic Document Generator (SynthDoG), ECCV 2022

LMDX: Language Model-based Document Information Extraction and
  Localization

On Text Localization in End-to-End OCR-Free Document Understanding Transformer Without Text Localization Supervision

PHD: Pixel-Based Language Modeling of Historical Documents


Fast and differentiable MS-SSIM and SSIM for pytorch.

Image sensing with multilayer nonlinear optical neural networks

Heterogeneous Face Recognition via Face Synthesis With Identity-Attribute Disentanglement

IEEE transactions on information forensics and security

Improving Adversarial Attacks on Latent Diffusion Model

HyperHyperNetworks for the Design of Antenna Arrays

BAA-NGP: Bundle-Adjusting Accelerated Neural Graphics Primitives

What You Hear Is What You See: Audio Quality Metrics From Image Quality
  Metrics


The Levenshtein Python C extension module contains functions for fast computation of Levenshtein distance and string similarity

Dialect and Variant Identification as a Multi-Label Classification Task: A Proposal Based on Near-Duplicate Analysis

Workshop on NLP for Similar Languages, Varieties and Dialects


A Keras implementation of YOLOv3 (Tensorflow backend)

YOLOv3: An Incremental Improvement

Assessment of CNN-Based Methods for Individual Tree Detection on Images Captured by RGB Cameras Attached to UAVs

Poly-YOLO: higher speed, more precise detection and instance segmentation for YOLOv3

A deep learning based automatic defect analysis framework for In-situ TEM ion irradiations

Archaeologic Machine Learning for Shipwreck Detection Using Lidar and Sonar

Application of a Model that Combines the YOLOv3 Object Detection Algorithm and Canny Edge Detection Algorithm to Detect Highway Accidents

Fast eyes detection in thermal images

FastPathology: An Open-Source Platform for Deep Learning-Based Research and Decision Support in Digital Pathology

Kidney Recognition in CT Using YOLOv3

Object Detection During Newborn Resuscitation Activities

IEEE journal of biomedical and health informatics


Converts an xyz file to an RDKit mol object

GEOM: Energy-annotated molecular conformations for property prediction and molecular generation

A Generative Model for Molecular Distance Geometry

Machine learning based energy-free structure predictions of molecules, transition states, and solids

Symmetry-Aware Actor-Critic for 3D Molecular Design

Scalable Fragment-Based 3D Molecular Design with Reinforcement Learning

Fast and Automated Identification of Reactions with Low Barriers: The Decomposition of 3-Hydroperoxypropanal

Fast and automated identification of reactions with low barriers using meta-MD simulations

CONFPASS: fast DFT re-optimizations of structures from conformation searches

Journal of chemical information and modeling

Evolutionary Monte Carlo of QM Properties in Chemical Space: Electrolyte Design

Journal of chemical theory and computation

Navigating chemical reaction space with a steering wheel


SPECTER: Document-level Representation Learning using Citation-informed Transformers

Neighborhood Contrastive Learning for Scientific Document Representations with Citation Embeddings

The Semantic Scholar Open Data Platform

Improving BERT-based Query-by-Document Retrieval with Multi-Task
  Optimization

Heterogeneous Graph Neural Networks for Keyphrase Generation

A dataset of mentorship in bioscience with semantic and demographic estimations

DORIS-MAE: Scientific Document Retrieval using Multi-level Aspect-based
  Queries

ULTRA: A Data-driven Approach for Recommending Team Formation in Response to Proposal Calls


ColabFold on your local PC

ColabFold - Making protein folding accessible to all

Discovery and structure of a widespread bacterial ABC transporter specific for ergothioneine

Solubility-Aware Protein Binding Peptide Design Using AlphaFold

Stepwise emergence of the neuronal gene expression program in early animal evolution

Seasonal effects decouple SARS-CoV-2 haplotypes worldwide

DNA-binding mechanism and evolution of Replication Protein A

Design of Cyclic Peptides Targeting Protein-Protein Interactions using AlphaFold

Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops

Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

bioRxiv : the preprint server for biology


RDF2Vec: RDF graph embeddings and their applications

Semantic similarity and machine learning with ontologies

OWL2Vec*: Embedding of OWL Ontologies

pyRDF2Vec: A Python Implementation and Extension of RDF2Vec

The Microsoft Academic Knowledge Graph enhanced: Author name disambiguation, publication classification, and embeddings

Walk Extraction Strategies for Node Embeddings with RDF2Vec in Knowledge Graphs

More is not Always Better: The Negative Impact of A-box Materialization on RDF2vec Knowledge Graph Embeddings

Supervised Biomedical Semantic Similarity

Empowering machine learning models with contextual knowledge for enhancing the detection of eating disorders in social media posts


Beyond the Imitation Game collaborative benchmark for measuring and extrapolating the capabilities of language models

PaLM: Scaling Language Modeling with Pathways

Chain-of-Thought Prompting Elicits Reasoning in Large Language Models

On the Opportunities and Risks of Foundation Models

Self-Consistency Improves Chain of Thought Reasoning in Language Models

Multitask Prompted Training Enables Zero-Shot Task Generalization

Training Compute-Optimal Large Language Models

Beyond the Imitation Game: Quantifying and extrapolating the
  capabilities of language models

Scaling Language Models: Methods, Analysis & Insights from Training
  Gopher

Training a Helpful and Harmless Assistant with Reinforcement Learning
  from Human Feedback

Program Synthesis with Large Language Models


A distributed, fault-tolerant graph database

Demystifying Graph Databases: Analysis and Taxonomy of Data Organization, System Designs, and Graph Queries

Graph Databases: Their Power and Limitations

An introduction to Graph Data Management

Graph Analytics using the Vertica Relational Database

Open source libraries and frameworks for biological data visualisation: A guide for developers

GRAPHiQL: A graph intuitive query language for relational databases

Cybersecurity knowledge graphs

Certified Graph View Maintenance with Regular Datalog

Timed Epistemic Knowledge Bases for Social Networks (Extended Version).

biggy: An Implementation of Unified Framework for Big Data Management System


Automated deep learning algorithms implemented in PyTorch.

DARTS: Differentiable Architecture Search

Searching for A Robust Neural Architecture in Four GPU Hours

NAS-Bench-102: Extending the Scope of Reproducible Neural Architecture Search

Auto-ReID: Searching for a Part-Aware ConvNet for Person Re-Identification

Network Pruning via Transformable Architecture Search

One-Shot Neural Architecture Search via Self-Evaluated Template Network

International Conference on Computer Vision

NATS-Bench: Benchmarking NAS Algorithms for Architecture Topology and Size

IEEE transactions on pattern analysis and machine intelligence

Subspace Attack: Exploiting Promising Subspaces for Query-Efficient Black-box Attacks

A Comprehensive Survey on Hardware-Aware Neural Architecture Search

Yet Another Intermediate-Level Attack


DEPRECATED. See Talk-Api.

PLANET HUNTERS: A TRANSITING CIRCUMBINARY PLANET IN A QUADRUPLE STAR SYSTEM

The Milky Way Project First Data Release: a bubblier Galactic disc

Monthly Notices of the Royal Astronomical Society

PLANET HUNTERS. V. A CONFIRMED JUPITER-SIZE PLANET IN THE HABITABLE ZONE AND 42 PLANET CANDIDATES FROM THE KEPLER ARCHIVE DATA

Planet Hunters: Assessing the Kepler Inventory of Short Period Planets

Planet Hunters: New Kepler planet candidates from analysis of quarter 2

Citizen Science: Contributions to Astronomy Research


Snow and ice albedo modelling in Python

Glacier algae accelerate melt rates on the south-western Greenland Ice Sheet

Neither dust nor black carbon causing apparent albedo decline in Greenland's dry snow zone: Implications for MODIS C5 surface reflectance

SNICAR-ADv3: a community tool for modeling spectral snow albedo

A flexible parameterization for shortwave optical properties of ice crystals

Intercomparison and improvement of two-stream shortwave radiative transfer schemes in Earth system models for a unified treatment of cryospheric surfaces

Quantifying bioalbedo: A new physically-based model and critique of empirical
methods for characterizing biological influence on ice and snow albedo

Glacier algae accelerate melt rates on the western Greenland Ice Sheet


small mammals brain MRI

Sammba-MRI: A Library for Processing SmAll-MaMmal BrAin MRI Data in Python

Broad Influence of Mutant Ataxin-3 on the Proteome of the Adult Brain, Young Neurons, and Axons Reveals Central Molecular Processes and Biomarkers in SCA3/MJD Using Knock-In Mouse Model

Building Domain-Specific Machine Learning Workflows: A Conceptual Framework for the State-of-the-Practice

SCA7 mice recapitulate CNS, PNS and retina pathologies and show a transcriptional signature of Purkinje cell dysfunction prevailing in SCA1 and SCA2 mice.


Fast cosmological perturbation theory

Beyond linear galaxy alignments

FAST-PT: a novel algorithm to calculate convolution integrals in cosmological perturbation theory

Journal of Cosmology and Astroparticle Physics

FAST-PT II: an algorithm to calculate convolution integrals of general tensor quantities in cosmological perturbation theory

Hyper Suprime-Cam Year 3 results: Cosmology from cosmic shear two-point correlation functions

Cosmology with 6 parameters in the Stage-IV era: efficient
  marginalisation over nuisance parameters

Modeling intrinsic galaxy alignment in the MICE simulation

An empirical approach to model selection: weak lensing and intrinsic
  alignments

Modified gravity and massive neutrinos: constraints from the full shape analysis of BOSS galaxies and forecasts for Stage IV surveys


CREPE: A Convolutional REpresentation for Pitch Estimation -- pre-trained model (ICASSP 2018)

CREPE: A Convolutional Representation for Pitch Estimation

Traditional Machine Learning for Pitch Detection

Addressing the confounds of accompaniments in singer identification

Score and Lyrics-Free Singing Voice Generation

Cross-domain Neural Pitch and Periodicity Estimation

The Efficacy of Self-Supervised Speech Models for Audio Representations

F0 analysis of Ghanaian pop singing reveals progressive alignment with equal temperament over the past three decades: a case study


A Haskell library for Approximating Exact Real Numbers (AERN) based on interval computation. (aern2 is a rewrite of aern.)

Parametrised second-order complexity theory with applications to the study of interval computation

Foundation of Computer (Algebra) ANALYSIS Systems: Semantics, Logic, Programming, Verification

Auto-Active Verification of Floating-Point Programs via Nonlinear Real Provers


Python package for handling and analyzing PSRFITS files

A Second Chromatic Timing Event of Interstellar Origin toward PSR J1713+0747

THE NANOGRAV NINE-YEAR DATA SET: NOISE BUDGET FOR PULSAR ARRIVAL TIMES ON INTRADAY TIMESCALES

Upgraded antennas for pulsar observations in the Argentine Institute of Radio astronomy

VLA Observations of Single Pulses from the Galactic Center Magnetar

PSR J0437-4715: The Argentine Institute of Radioastronomy 2019–2020 Observational Campaign

Analysis of Multi-hour Continuous Observations of Seven Millisecond Pulsars

A Study in Frequency-dependent Effects on Precision Pulsar Timing Parameters with the Pulsar Signal Simulator

A broad survey of spectro-temporal properties from FRB 20121102A

Evaluating Low-frequency Pulsar Observations to Monitor Dispersion with the Giant Metrewave Radio Telescope


Julia Package for Generating Scenario Trees and Scenario Lattices for Multistage Stochastic Optimization

A Distance For Multistage Stochastic Optimization Models

Dynamic generation of scenario trees

Computational optimization and applications

From Empirical Observations to Tree Models for Stochastic Optimization: Convergence Properties

ScenTrees.jl: A Julia Package for Generating Scenario Trees and Scenario Lattices for Multistage Stochastic Programming

New Algorithms And Fast Implementations To Approximate Stochastic Processes


Public repository of the META-SHARE software

The META-SHARE Language Resources Sharing Infrastructure: Principles, Challenges, Solutions

The META-SHARE Metadata Schema for the Description of Language Resources

RDF Representation of Licenses for Language Resources

Proceedings of the 4th Workshop on Linked Data in Linguistics: Resources and Applications

META-SHARE: One year after

META-SHARE v2: An Open Network of Repositories for Language Resources including Data and Tools

A Data Sharing and Annotation Service Infrastructure

PROCEEDINGS OF THE 53RD ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS AND THE 7TH INTERNATIONAL JOINT CONFERENCE ON NATURAL LANGUAGE PROCESSING (ACL-IJCNLP 2015): SYSTEM DEMONSTRATIONS


Download and visualize single or multiple classes from the huge Open Images v4 dataset

Knockoff Nets: Stealing Functionality of Black-Box Models

We don't need no bounding-boxes: Training object class detectors using only human verification

SLAM-OR: Simultaneous Localization, Mapping and Object Recognition Using Video Sensors Data in Open Environments from the Sparse Points Cloud


Java based tools for bulk downloading read/analysis files from ENA via FTP or Aspera.

The COMPARE Data Hubs

Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole genome sequences

The European Nucleotide Archive in 2023


Statistical estimation of a clear sky signal from PV system power data

Signal Processing on PV Time-Series Data: Robust Degradation Analysis Without Physical Models

Statistical Clear Sky Fitting Algorithm


Workflow for SARS-CoV-2 genome Assembly at FioCruz/IAM

Unusual SARS-CoV-2 intra-host diversity reveals lineages superinfection

ViralFlow: an automated workflow for SARS-CoV-2 genome assembly, lineage assignment, mutations and intrahost variants detection


NRG Ljubljana is a numerical renormalization group implementation for solving quantum impurity problems in theoretical physics

Iron phthalocyanine on Au(111) is a "non-Landau" Fermi liquid

Topological quantum phase transition of nickelocene on Cu(100)


Qclib is a quantum computing library implemented using qiskit. The focus of qclib is on preparing quantum states, but it is not limited to that.

A divide-and-conquer algorithm for quantum state preparation

Linear-depth quantum circuits for multiqubit controlled gates

Double sparse quantum state preparation

Low-Rank Quantum State Preparation

Decomposition of Multi-controlled Special Unitary Single-Qubit Gates

Linear decomposition of approximate multi-controlled single qubit gates


Code for "LoFTR: Detector-Free Local Feature Matching with Transformers", CVPR 2021, T-PAMI 2022

SuperGlue: Learning Feature Matching with Graph Neural Networks


GUI for OPEM library

OPEM : Open Source PEM Cell Simulation Tool


A Python package to learn the Koopman operator.

Learning Dynamical Systems via Koopman Operator Regression in
  Reproducing Kernel Hilbert Spaces

Sharp Spectral Rates for Koopman Operator Learning

Koopman Kernel Regression


An implementation of Hoare and He's Unifying Theories of Programming in Isabelle

Unifying theories of reactive design contracts

Automating Verification of State Machines with Reactive Designs and Isabelle/UTP

Unifying semantic foundations for automated verification tools in Isabelle/UTP

Unifying theories of time with generalised reactive processes

Towards Deductive Verification of Control Algorithms for Autonomous Marine Vehicles

International Conference on Engineering of Complex Computer Systems

Calculational Verification of Reactive Programs with Reactive Relations and Kleene Algebra

A Unary Semigroup Trace Algebra

Relational and Algebraic Methods in Computer Science


A Python module for preprocessing and evaluating aerodynamic airfoil data---primarily for wind turbine applications.


An R package  making it easy to query, preview, download and preprocess multiple kinds of spatial data  via R. All beta.

Mammals adjust diel activity across gradients of urbanization

A Machine Learning Based Downscaling Approach to Produce High Spatio-Temporal Resolution Land Surface Temperature of the Antarctic Dry Valleys from MODIS Data


Deep Visual-Semantic Alignments for Generating Image Descriptions

CIDEr: Consensus-based Image Description Evaluation

Microsoft COCO Captions: Data Collection and Evaluation Server

SCA-CNN: Spatial and Channel-wise Attention in Convolutional Networks for Image Captioning

Conceptual Captions: A Cleaned, Hypernymed, Image Alt-text Dataset For Automatic Image Captioning

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

Image Captioning with Semantic Attention

SPICE: Semantic Propositional Image Caption Evaluation

Sequence to Sequence -- Video to Text

Exploring Visual Relationship for Image Captioning

Attention on Attention for Image Captioning


A quasi-deterministic (Q-D) channel implementation in MATLAB software

Simplified Ray Tracing for the Millimeter Wave Channel: A Performance Evaluation

Information Theory and Applications Workshop

Accuracy vs. Complexity for mmWave Ray-Tracing: A Full Stack Perspective

On the Real Experimentation and Simulation Models for Millimeter-Wave

A Full-Stack Open-Source Framework for Antenna and Beamforming Evaluation in mmWave 5G NR


CodeT: Code Generation with Generated Tests

Large Language Models Meet NL2Code: A Survey

RepoCoder: Repository-Level Code Completion Through Iterative Retrieval and Generation

ALGO: Synthesizing Algorithmic Programs with LLM-Generated Oracle
  Verifiers


A robust web archive analytics toolkit

OpenWebMath: An Open Dataset of High-Quality Mathematical Web Text

FastWARC: Optimizing Large-Scale Web Archive Analytics


rFIA

rFIA: An R package for estimation of forest attributes with the US Forest Inventory and Analysis database


TensorFI is a fault injection framework for injecting both hardware and software faults into applications written using the TensorFlow framework. You can find more information about TensorFI in the paper below.

TensorFI: A Flexible Fault Injection Framework for TensorFlow Applications

A Low-cost Fault Corrector for Deep Neural Networks through Range Restriction

Ranger: Boosting Error Resilience of Deep Neural Networks through Range Restriction.


Improving XGBoost survival analysis with embeddings and debiased estimators

Effective Ways to Build and Evaluate Individual Survival Distributions

Tree Space Prototypes: Another Look at Making Tree Ensembles Interpretable

The Brier Score under Administrative Censoring: Problems and Solutions


Geometric loss functions between point clouds, images and volumes

Deep Generalized Schrödinger Bridge

A Neural Tangent Kernel Perspective of GANs

On Leveraging the Visual Modality for Neural Machine Translation

Knowledge Distillation for 6D Pose Estimation by Aligning Distributions of Local Predictions

Estimating Regression Predictive Distributions with Sample Networks

Mirror Diffusion Models for Constrained and Watermarked Generation

KNOT: Knowledge Distillation using Optimal Transport for Solving NLP
  Tasks


This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir

On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data

Recycler: an algorithm for detecting plasmids from de novo assembly graphs

Plasmids of the urinary microbiota


Official Implementation for "StyleCLIP: Text-Driven Manipulation of StyleGAN Imagery" (ICCV 2021 Oral)

Designing an Encoder for StyleGAN Image Manipulation

StyleSpace Analysis: Disentangled Controls for StyleGAN Image Generation

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

An Image is Worth More Than a Thousand Words: Towards Disentanglement in the Wild


Download geospatial data from GISCO API - Eurostat


ValueNet: A Neural Text-to-SQL Architecture Incorporating Values

Towards Complex Text-to-SQL in Cross-Domain Database with Intermediate Representation

ValueNet: A Natural Language-to-SQL System that Learns from Database Information


Trinotate source code

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes

Venomic, Transcriptomic, and Bioactivity Analyses of Pamphobeteus verdolaga Venom Reveal Complex Disulfide-Rich Peptides That Modulate Calcium Channels

Interleukin-1 Ligands and Receptors in Lumpfish (Cyclopterus lumpus L.): Molecular Characterization, Phylogeny, Gene Expression, and Transcriptome Analyses

De novo assembly and transcriptome characterization: Novel insights into the mechanisms of primary ovarian cancer in Microtus fortis

Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes

A first draft genome of holm oak (Quercus ilex subsp. ballota), the most representative species of the Mediterranean forest and the Spanish agrosylvopastoral ecosystem “dehesa”

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plantNepenthes gracilis

Integrating Metabolomics and Transcriptomics to Unveil Atisine Biosynthesis in Aconitum gymnandrum Maxim

International journal of molecular sciences

Comparative Characterization of Immune Response in Sheep with Caseous Lymphadenitis through Analysis of the Whole Blood Transcriptome

Animals : an open access journal from MDPI

Gene expression shifts in Emperor penguin adaptation to the extreme Antarctic environment


The Eldarica model checker

Competition Report: CHC-COMP-20

Exploring interpolants

Solving non-linear Horn clauses using a linear Horn clause solver

CHC-COMP 2022: Competition Report

Tree dimension in verification of constrained Horn clauses

Interpolating bit-vector formulas using uninterpreted predicates and Presburger arithmetic

A Theory of Heap for Constrained Horn Clauses (Extended Technical Report).

Commutativity Simplifies Proofs of Parameterized Programs

An encoding of array verification problems into array-free Horn clauses


Compute SHAP values for your tree-based models using the TreeSHAP algorithm

Fast TreeSHAP: Accelerating SHAP Value Computation for Trees

Graph-guided random forest for gene set selection

Landscape of R packages for eXplainable Artificial Intelligence

Digital Biomarkers for Personalized Nutrition: Predicting Meal Moments and Interstitial Glucose with Non-Invasive, Wearable Technologies