Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

A review of bioinformatic pipeline frameworks

Parsl: Pervasive Parallel Programming in Python

IEEE International Symposium on High-Performance Parallel Distributed Computing

A self-driving laboratory advances the Pareto front for material properties

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

BugsInPy: a database of existing bugs in Python programs to enable controlled testing and debugging studies

PROCEEDINGS OF THE 28TH ACM JOINT MEETING ON EUROPEAN SOFTWARE ENGINEERING CONFERENCE AND SYMPOSIUM ON THE FOUNDATIONS OF SOFTWARE ENGINEERING (ESEC/FSE '20)

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes

StreamFlow: cross-breeding cloud with HPC

Software for Dataset-wide XAI: From Local Explanations to Global Insights with Zennit, CoRelAy, and ViRelAy

Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications

DALiuGE: A graph execution framework for harnessing the astronomical data deluge


Apache Commons Lang

Mining Fix Patterns for FindBugs Violations

A Closer Look at Real-World Patches

PROCEEDINGS 2018 IEEE INTERNATIONAL CONFERENCE ON SOFTWARE MAINTENANCE AND EVOLUTION (ICSME)

A comprehensive study of pseudo-tested methods

Sentinel: A Hyper-Heuristic for the Generation of Mutant Reduction Strategies

IEEE Transactions on Software Engineering

Compatible Remediation on Vulnerabilities from Third-Party Libraries for Java Projects

An approach and benchmark to detect behavioral changes of commits in continuous integration

RegMiner: Towards Constructing Large Regression Dataset from Code Evolution History

Internal Quality Evolution of Open-Source Software Systems

A Novel Refactoring and Semantic Aware Abstract Syntax Tree Differencing
  Tool and a Benchmark for Evaluating the Accuracy of Diff Tools


a language for fast, portable data-parallel computation

Learning to Perform Local Rewriting for Combinatorial Optimization

Achieving high-performance the functional way: a functional pearl on expressing high-performance optimizations as rewrite strategies

Proceedings of the ACM on Programming Languages

Rewrite Rule Inference Using Equality Saturation

ProTuner: Tuning Programs with Monte Carlo Tree Search

Schedule Synthesis for Halide Pipelines on GPUs

ACM Transactions on Architecture and Code Optimization (TACO)

Optimizing Data-Intensive Computations in Existing Libraries with Split Annotations

Verifying and improving Halide’s term rewriting system with program synthesis

A Language for Describing Optimization Strategies

Guided Optimization for Image Processing Pipelines

Model-Based Warp Overlapped Tiling for Image Processing Programs on GPUs


Open3D: A Modern Library for 3D Data Processing

SuperNOVA: Design Strategies and Opportunities for Interactive Visualization in Computational Notebooks

Initialization and Alignment for Adversarial Texture Optimization

A Multi-modal Garden Dataset and Hybrid 3D Dense Reconstruction Framework Based on Panoramic Stereo Images for a Trimming Robot

Stress-Testing Point Cloud Registration on Automotive LiDAR


Tesseract Open Source OCR Engine (main repository)

LayoutLM: Pre-training of Text and Layout for Document Image Understanding

Chargrid: Towards Understanding 2D Documents

TableBank: Table Benchmark for Image-based Table Detection and Recognition

PlotQA: Reasoning over Scientific Plots

Towards Understanding and Detecting Fake Reviews in App Stores

StructuralLM: Structural Pre-training for Form Understanding

Multimodal deep networks for text and image-based document classification

Hate Speech in Pixels: Detection of Offensive Memes towards Automatic Moderation

MMOCR: A Comprehensive Toolbox for Text Detection, Recognition and Understanding

Calamari - A High-Performance Tensorflow-based Deep Learning Package for Optical Character Recognition


Industrial-strength Natural Language Processing (NLP) in Python

Dice Loss for Data-imbalanced NLP Tasks

Scaling Up Vision-Language Pre-training for Image Captioning

Align and Prompt: Video-and-Language Pre-training with Entity Prompts

Beyond BLEU: Training Neural Machine Translation with Semantic Similarity

Content Selection in Deep Learning Models of Summarization

Training Classifiers with Natural Language Explanations

Multi-domain Clinical Natural Language Processing with MedCAT: the Medical Concept Annotation Toolkit

ASSET: A Dataset for Tuning and Evaluation of Sentence Simplification Models with Multiple Rewriting Transformations

SemStyle: Learning to Generate Stylised Image Captions using Unaligned Text

PRIMERA: Pyramid-based Masked Sentence Pre-training for Multi-document Summarization


A browser automation framework and ecosystem.

Learning Semantic Program Embeddings with Graph Interval Neural Network

Domestic violence during COVID-19 pandemic: The case for Indian women

Journal of community & applied social psychology

GooAQ: Open Question Answering with Diverse Answer Types

Leveraging Social Media Activity and Machine Learning for HIV and Substance Abuse Risk Assessment: Development and Validation Study (Preprint)

Automating Program Transformation for Java Using Semantic Patches

HAL (Le Centre pour la Communication Scientifique Directe)

What is the Commons Worth? Estimating the Value of Wikimedia Imagery by Observing Downstream Use

ESRFuzzer: an enhanced fuzzing framework for physical SOHO router devices to discover multi-Type vulnerabilities

Role of Artificial Intelligence in Detection of Hateful Speech for Hinglish Data on Social Media

MEMEX: Detecting Explanatory Evidence for Memes via Knowledge-Enriched Contextualization

Heterogeneous Value Alignment Evaluation for Large Language Models


Vowpal Wabbit is a machine learning system which pushes the frontier of machine learning with techniques such as online, hashing, allreduce, reductions, learning2search, active, and interactive learning.

Hogwild: A Lock-Free Approach to Parallelizing Stochastic Gradient Descent

Taming the Monster: A Fast and Simple Algorithm for Contextual Bandits

Stochastic Collapsed Variational Bayesian Inference for Latent Dirichlet Allocation

Dynamic Matrix Factorization with Priors on Unknown Values

Optimal and Adaptive Algorithms for Online Boosting

Evaluation Examples are not Equally Informative: How should that change NLP Leaderboards?

Meeting of the Association for Computational Linguistics

Online Gradient Boosting

Open Bandit Dataset and Pipeline: Towards Realistic and Reproducible Off-Policy Evaluation

Findings of the 2016 WMT Shared Task on Cross-lingual Pronoun Prediction

How Many Folders Do You Really Need?

International Conference on Information and Knowledge Management


An incremental parsing system for programming tools

GraphCodeBERT: Pre-training Code Representations with Data Flow

CodeBLEU: a Method for Automatic Evaluation of Code Synthesis

The Stack: 3 TB of permissively licensed source code

SynCoBERT: Syntax-Guided Multi-Modal Contrastive Pre-Training for Code Representation

Code Structure Guided Transformer for Source Code Summarization

CCTEST: Testing and Repairing Code Completion Systems

Multimodal Representation for Neural Code Search

Execution-based Code Generation using Deep Reinforcement Learning

CODE-MVP: Learning to Represent Source Code from Multiple Views with Contrastive Pre-Training

Neural Code Search Revisited: Enhancing Code Snippet Retrieval through Natural Language Intent


Streamlit — A faster way to build and share data apps.

SummVis: Interactive Visual Analysis of Models, Data, and Evaluation for Text Summarization

Stmol: A component for building interactive molecular visualizations within streamlit web-applications

Automatically evolving preference-based dispatching rules for multi-objective job shop scheduling

A sustainable infrastructure concept for improved accessibility, reusability, and archival of research software

The Botrytis cinerea Gene Expression Browser

AMGPT: A large language model for contextual querying in additive manufacturing

Using Open-Source Software for Business, Urban, and Other Applications of Deep Neural Networks, Machine Learning, and Data Analytics Tools

International Journal of Artificial Intelligence and Machine Learning

RouteExplainer: An Explanation Framework for Vehicle Routing Problem

CMULAB: An Open-Source Framework for Training and Deployment of Natural
  Language Processing Models


Qiskit is an open-source SDK for working with quantum computers at the level of extended quantum circuits, operators, and primitives.

Quantum Chemistry in the Age of Quantum Computing

Quantum information processing with superconducting circuits: a review

Reports on progress in physics. Physical Society (Great Britain)

An Efficient Methodology for Mapping Quantum Circuits to the IBM QX Architectures

Software Mitigation of Crosstalk on Noisy Intermediate-Scale Quantum Computers

TWENTY-FIFTH INTERNATIONAL CONFERENCE ON ARCHITECTURAL SUPPORT FOR PROGRAMMING LANGUAGES AND OPERATING SYSTEMS (ASPLOS XXV)

Mapping Quantum Circuits to IBM QX Architectures Using the Minimal Number of SWAP and H Operations

Overview and Comparison of Gate Level Quantum Software Platforms

Challenges and Opportunities of Near-Term Quantum Computing Systems

Qiskit Backend Specifications for OpenQASM and OpenPulse Experiments

Compiling SU(4) Quantum Circuits to IBM QX Architectures

A verified optimizer for Quantum circuits

Symposium on Principles of Programming Languages


Language, engine, and tooling for expressing, testing, and evaluating composable language rules on input strings.

Dark Web Marketplaces and COVID-19: before the vaccine

MTab: Matching Tabular Data to Knowledge Graph using Probability Models

DisBot: A Portuguese Disaster Support Dynamic Knowledge Chatbot

Upon Improving the Performance of Localized Healthcare Virtual Assistants

TabEAno: Table to Knowledge Graph Entity Annotation

Jaco: An Offline Running Privacy-aware Voice Assistant

Flowstorm: Open-Source Platform with Hybrid Dialogue Architecture

Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: System Demonstrations


Graph Neural Network Library for PyTorch

Inductive Representation Learning on Large Graphs

Translating Embeddings for Modeling Multi-relational Data

Graph Neural Networks: A Review of Methods and Applications

Fast Graph Representation Learning with PyTorch Geometric

Complex Embeddings for Simple Link Prediction

Embedding Entities and Relations for Learning and Inference in Knowledge Bases

PointCNN: Convolution On ��-Transformed Points

RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space

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

Order Matters: Sequence to sequence for sets


Official repository for Spyder - The Scientific Python Development Environment

Consciousness & Brain Functional Complexity in Propofol Anaesthesia

An image-based data-driven analysis of cellular architecture in a developing tissue

Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology

Pydna: a simulation and documentation tool for DNA assembly strategies using python

Vis-Eval Metric Viewer: A Visualisation Tool for Inspecting and Evaluating Metric Scores of Machine Translation Output

North American Chapter of the Association for Computational Linguistics

Fractal Dimension of Cortical Functional Connectivity Networks Predicts Severity in Disorders of Consciousness

Natural Language Processing with Pandas DataFrames

Proceedings of the Python in Science Conferences

WA-Continuum: Visualising Word Alignments across Multiple Parallel Sentences Simultaneously

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

PYESSENCE - Generalised Coupled Quintessence Linear Perturbation Python Code - User Guide


Aggregate results from bioinformatics analyses across many samples into a single report.

Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs

Best practices for bioinformatic characterization of neoantigens for clinical utility

Th17 reprogramming of T cells in systemic juvenile idiopathic arthritis

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers

Analysis pipelines for cancer genome sequencing in mice

The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles

An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim

Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome

International journal of molecular sciences

FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs


PyTorch implementation of "Lip to Speech Synthesis in the Wild with Multi-task Learning" (ICASSP2023)

SVTS: Scalable Video-to-Speech Synthesis

Lip-to-Speech Synthesis in the Wild with Multi-task Learning

Towards Accurate Lip-to-Speech Synthesis in-the-Wild

Proceedings of the 31st ACM International Conference on Multimedia


New Insights on Reducing Abrupt Representation Change in Online Continual Learning

Schedule-Robust Online Continual Learning

Orchestrate Latent Expertise: Advancing Online Continual Learning with
  Multi-Level Supervision and Reverse Self-Distillation


| Real Time Head Pose Estimation: Accurate head pose estimation using ResNet 18/34/50 and MobileNet V2/V3 models. Evaluate yaw, pitch, and roll with pre-trained weights for quick integration.

Deep Residual Learning for Image Recognition

MobileNetV2: Inverted Residuals and Linear Bottlenecks

Searching for MobileNetV3

Fine-Grained Head Pose Estimation Without Keypoints

6D Rotation Representation For Unconstrained Head Pose Estimation

Sample and Computation Redistribution for Efficient Face Detection

Towards Robust and Unconstrained Full Range of Rotation Head Pose Estimation


This project is a tensorflow implement of our work, ECM.

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

Low-Resource Response Generation with Template Prior

Empirical Methods in Natural Language Processing

EmoKbGAN: Emotion controlled response generation using Generative Adversarial Network for knowledge grounded conversation


[NeurIPS 2024] Can LLMs Learn by Teaching for Better Reasoning? A Preliminary Study

Direct Preference Optimization: Your Language Model is Secretly a Reward Model

Reflexion: Language Agents with Verbal Reinforcement Learning


A Survey on Multi-Task Learning

Self-Paced Multi-Task Clustering

Model-Protected Multi-Task Learning


ANDES has been transferred to the CURENT organization account. Please post questions to https://github.com/curent/andes. Maintenance and development will continue. Python toolbox / library for power system transient dynamics simulation with symbolic modeling and numerical analysis

Hybrid Symbolic-Numeric Framework for Power System Modeling and Analysis

Tools for modelling and simulating the Smart Grid

Control and limit enforcements for VSC multi-terminal HVDC in newton power flow

Power and Energy Society General Meeting

Hybrid Symbolic-Numeric Library for Power System Modeling and Analysis


Official PyTorch implementation of "Learning with Memory-based Virtual Classes for Deep Metric Learning" (ICCV 2021)

SoftTriple Loss: Deep Metric Learning Without Triplet Sampling

Proxy Synthesis: Learning with Synthetic Classes for Deep Metric Learning


Invariance Principle Meets Information Bottleneck for Out-of-Distribution Generalization

Conditional entropy minimization principle for learning domain invariant representation features

Which Invariance Should We Transfer? A Causal Minimax Learning Approach

Counterfactual Supervision-based Information Bottleneck for Out-of-Distribution Generalization

Invariant-Feature Subspace Recovery: A New Class of Provable Domain Generalization Algorithms


A CSV formatted file using data from the Yelp Academic Dataset.

Regularized Submodular Maximization at Scale

Streaming Submodular Maximization under a k-Set System Constraint

Submodular Maximization Through Barrier Functions


Atomic Line Spectral Estimation Toolbox

Variational Bayesian Inference of Line Spectra

Superfast Line Spectral Estimation

A Fast Interior Point Method for Atomic Norm Soft Thresholding


The repo consists of a Python package that works with functional data. In particular, it includes two distinct methodologies: Functional Feature Selection and Functional Graph Convolutional Networks.  funGCN has been developed as part of the Horizon 2020 SEURO Project under grant agreement No. 945449.

FAStEN: An Efficient Adaptive Method for Feature Selection and Estimation in High-Dimensional Functional Regressions

Feature Selection for Functional Data Classification

Functional Graph Convolutional Networks: A unified multi-task and
  multi-modal learning framework to facilitate health and social-care insights


Map-Elites based on Evolution Strategies

Robots that can adapt like animals

Scaling MAP-Elites to Deep Neuroevolution

Genetic and Evolutionary Computation Conference

Empirical analysis of PGA-MAP-Elites for Neuroevolution in Uncertain Domains

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


torchange - A Unified Change Representation Learning Benchmark Library

Change is Everywhere: Single-Temporal Supervised Object Change Detection in Remote Sensing Imagery

Scalable Multi-Temporal Remote Sensing Change Data Generation via Simulating Stochastic Change Process

Segment Any Change

Changen2: Multi-Temporal Remote Sensing Generative Change Foundation Model

Single-Temporal Supervised Learning for Universal Remote Sensing Change Detection

International Journal of Computer Vision


Practical Deep Reinforcement Learning Approach for Stock Trading

FinRL: A Deep Reinforcement Learning Library for Automated Stock Trading in Quantitative Finance

Multi-Agent Deep Reinforcement Learning for Liquidation Strategy Analysis


YOLOv3: An Incremental Improvement

EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks

EfficientDet: Scalable and Efficient Object Detection


Source code for MICRODEM, open source GIS program for 64 bit Windows

Novel approach for ranking DEMs: Copernicus DEM improves one arc second open global topography


Classification and Gradient-based Localization of Chest Radiographs using PyTorch.

Deep Residual Learning for Image Recognition

Very Deep Convolutional Networks for Large-Scale Image Recognition

Densely Connected Convolutional Networks

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


Graph revised convolutional network (ECML-PKDD 2020)

Revisiting Semi-Supervised Learning with Graph Embeddings

Graph-Revised Convolutional Network

A Comparative Study on Robust Graph Neural Networks to Structural Noises

Latent Graph Inference with Limited Supervision


Gyrochronology via interpolation of open cluster rotation sequences.

The Empirical Limits of Gyrochronology

Wide binaries demonstrate the consistency of rotational evolution between open cluster and field stars

How Gaia sheds light on the Milky Way star cluster population


Code of the paper 'Neural Transformation Learning for Anomaly Detection' published in ICML 2021

Neural Transformation Learning for Deep Anomaly Detection Beyond Images

Unsupervised Anomaly Detection for Auditing Data and Impact of Categorical Encodings


98.8 solution for german sign classifing problem, done as p2 for Udacity's Self-driving car nano degree

Robust Physical-World Attacks on Deep Learning Models

A Survey on Automated Driving System Testing: Landscapes and Trends

Traffic Sign Classification Using Deep Inception Based Convolutional Networks

Adversarial Patch Attacks and Defences in Vision-Based Tasks: A Survey

Adversarial Attacks on Traffic Sign Recognition: A Survey

Robust Classification using Robust Feature Augmentation


Implementation for NAT.

DARTS: Differentiable Architecture Search

Efficient Neural Architecture Search via Parameter Sharing

NAT: Neural Architecture Transformer for Accurate and Compact Architectures

Towards Accurate and Compact Architectures via Neural Architecture Transformer


Implementation of Graph Convolutional Networks in TensorFlow

Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning

Deep Learning on Graphs: A Survey

Toward Robust Graph Semi-Supervised Learning Against Extreme Data Scarcity

A Systematic Review of Deep Graph Neural Networks: Challenges, Classification, Architectures, Applications & Potential Utility in Bioinformatics


Code for the paper, "Learning Human Objectives by Evaluating Hypothetical Behavior"

Reward learning from human preferences and demonstrations in Atari

Scalable agent alignment via reward modeling: a research direction


Matlab scripts that extract single subject grey matter networks from grey matter segmented T1 weighted images

Gray Matter Network Disruptions and Regional Amyloid Beta in Cognitively Normal Adults

Brain Structural Network Compensation Is Associated With Cognitive Impairment and Alzheimer’s Disease Pathology

Age and Sex-Related Effects on Single-Subject Gray Matter Networks in Healthy Participants

Gray matter structural networks related to 18F-THK5351 retention in cognitively normal older adults and Alzheimer's disease patients


A ML-ready curated data set for a wide range of seismic signals from Pacific Northwest

Curated Pacific Northwest AI-ready Seismic Dataset

SeisCLIP: A Seismology Foundation Model Pre-Trained by Multimodal Data for Multipurpose Seismic Feature Extraction

SeisT: A foundational deep learning model for earthquake monitoring tasks


Challenge on Textual Inference and Question Entailment in the Medical Domain https://sites.google.com/view/mediqa2019

Overview of the MEDIQA 2019 Shared Task on Textual Inference, Question Entailment and Question Answering

SIGBIOMED WORKSHOP ON BIOMEDICAL NATURAL LANGUAGE PROCESSING (BIONLP 2019)

BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing

DUT-NLP at MEDIQA 2019: An Adversarial Multi-Task Network to Jointly Model Recognizing Question Entailment and Question Answering

DUT-BIM at MEDIQA 2019: Utilizing Transformer Network and Medical Domain-Specific Contextualized Representations for Question Answering


[KDD 2023] code for "Test accuracy vs. generalization gap: model selection in NLP without accessing training or testing data" https://arxiv.org/pdf/2202.02842.pdf

Attention Is All You Need

Fantastic Generalization Measures and Where to Find Them

Evaluating natural language processing models with generalization metrics that do not need access to any training or testing data


Parse NCBI taxonomy and accessions to find taxonomic assignments

Genomic dissection of an extended phenotype: Oak galling by a cynipid gall wasp

Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival

Mycorrhizal benefits on plant growth and protection againstSpodoptera exiguadepend on N availability

A Novel Primer Mixture for GH48 Genes: Quantification and Identification of Truly Cellulolytic Bacteria in Biogas Fermenters

LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins


data and scripts for the shared task "Task 1: Paraphrase and Semantic Similarity in Twitter (PIT)" at SemEval 2015

A multi-cascaded model with data augmentation for enhanced paraphrase detection in short texts

A Paraphrase and Semantic Similarity Detection System for User Generated Short-Text Content on Microblogs

International Conference on Computational Linguistics


An empirical analysis of Earth's annual-average surface reflectivity potential


The implementation for DropMessage.

Improving neural networks by preventing co-adaptation of feature detectors

DropEdge: Towards Deep Graph Convolutional Networks on Node Classification

Graph Random Neural Networks for Semi-Supervised Learning on Graphs

DropMessage: Unifying Random Dropping for Graph Neural Networks


iPEPS ground- and excited-state implementation based on Automatic Differentiation

Automatic differentiation applied to excitations with projected entangled pair states

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

YASTN: Yet another symmetric tensor networks; A Python library for
  abelian symmetric tensor network calculations


Gromov-Wasserstein Learning for Graph Matching and Node Embedding

Scalable Gromov-Wasserstein Learning for Graph Partitioning and Matching

Fast and Robust Comparison of Probability Measures in Heterogeneous Spaces

Unsupervised Manifold Alignment with Joint Multidimensional Scaling

Adaptive Softassign via Hadamard-Equipped Sinkhorn


Removes shot noise from astronomical images using adaptive kernels

Close encounters: How stellar flybys shape planet-forming discs

The SPHERE view of three interacting twin disc systems in polarized light

Monthly Notices of the Royal Astronomical Society


[NeurIPS 2022] DreamShard: Generalizable Embedding Table Placement for Recommender Systems

Data-centric Artificial Intelligence: A Survey

Pre-train and Search: Efficient Embedding Table Sharding with Pre-trained Neural Cost Models


Matlab package for Tensor decompositions

Multi-Way Analysis Coupled with Near-Infrared Spectroscopy in Food Industry: Models and Applications

CP decomposition for tensors via alternating least squares with QR decomposition

A Fast Implementation for the Canonical Polyadic Decomposition

Tensor decompositions and algorithms, with applications to tensor learning


ARAE-Tensorflow for Discrete Sequences (Adversarially Regularized Autoencoder)

Adversarially Regularized Autoencoders

TextKD-GAN: Text Generation using KnowledgeDistillation and Generative Adversarial Networks

Latent Code and Text-based Generative Adversarial Networks for Soft-text Generation


Continual Learning for Visual Search with Backward Consistent Feature Embedding, CVPR 2022 https://openaccess.thecvf.com/content/CVPR2022/papers/Wan_Continual_Learning_for_Visual_Search_With_Backward_Consistent_Feature_Embedding_CVPR_2022_paper.pdf

Learning without Forgetting

Towards Backward-Compatible Representation Learning

On the Exploration of Incremental Learning for Fine-grained Image Retrieval


Recent Trends in the Use of Statistical Tests for Comparing Swarm and Evolutionary Computing Algorithms: Practical Guidelines and a Critical Review

Benchmarking in Optimization: Best Practice and Open Issues

Learning Adaptive Differential Evolution Algorithm From Optimization Experiences by Policy Gradient

How Does the Number of Objective Function Evaluations Impact Our Understanding of Metaheuristics Behavior?

Reinforcement Learning-assisted Evolutionary Algorithm: A Survey and Research Opportunities

A novel meta-heuristic optimization algorithm based on cell division: Cell Division Optimizer

On the performance of deep learning for numerical optimization: an application to protein structure prediction


Development of Antibody-Based PROTACs for the Degradation of the Cell-Surface Immune Checkpoint Protein PD-L1

Journal of the American Chemical Society

Deep Generative Models for 3D Linker Design

Journal of chemical information and modeling

TF-PROTACs Enable Targeted Degradation of Transcription Factors

RNA‐PROTACs: Degraders of RNA‐Binding Proteins

Proteolysis‐targeting chimeras in drug development: A safety perspective

In Silico Modeling of PROTAC-Mediated Ternary Complexes: Validation and Application

Prey for the Proteasome: Targeted Protein Degradation-A Medicinal Chemist's Perspective

PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes

Covalently Engineered Nanobody Chimeras for Targeted Membrane Protein Degradation

DCAF11 Supports Targeted Protein Degradation by Electrophilic Proteolysis-Targeting Chimeras


Self-Adaptive Training: beyond Empirical Risk Minimization

Deep Gamblers: Learning to Abstain with Portfolio Theory

Selective Classification via One-Sided Prediction

Self-Adaptive Training: Bridging Supervised and Self-Supervised Learning

Towards Better Selective Classification


Label Informed Attributed Network Embedding, WSDM 2017

Network Together: Node Classification via Cross-Network Deep Network Embedding

IEEE transactions on neural networks and learning systems

AGNN: Alternating Graph-Regularized Neural Networks to Alleviate Over-Smoothing

Effective and Scalable Clustering on Massive Attributed Graphs

Simplification of Graph Convolutional Networks: A Matrix Factorization-based Perspective

Joint Use of Node Attributes and Proximity for Semi-Supervised Classification on Graphs


[ACL'24, Outstanding Paper] Emulated Disalignment: Safety Alignment for Large Language Models May Backfire!

An Emulator for Fine-Tuning Large Language Models using Small Language Models

Tuning Language Models by Proxy


An up-to-date list of papers and code relating to progress in the burgeoning field of AI-Drug Discovery

Extended-Connectivity Fingerprints

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

Molecular graph convolutions: moving beyond fingerprints

Journal of computer-aided molecular design

Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks

Deep Neural Nets as a Method for Quantitative Structure-Activity Relationships

Molecular Transformer – A Model for Uncertainty-Calibrated Chemical Reaction Prediction

Deep Learning for Computational Chemistry

GuacaMol: Benchmarking Models for De Novo Molecular Design

Machine learning prediction errors better than DFT accuracy

Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction


scRNAseq analysis notes from Ming Tang

The arcsine is asinine: the analysis of proportions in ecology

Current best practices in single‐cell RNA‐seq analysis: a tutorial

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

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

Design and computational analysis of single-cell RNA-sequencing experiments

Single sample scoring of molecular phenotypes

Proportionality: A Valid Alternative to Correlation for Relative Data

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database


In-Network Volumetric DDoS Victim Identification Using Programmable Commodity Switches

IEEE Transactions on Network and Service Management

P-IOTA: A Cloud-Based Geographically Distributed Threat Alert System That Leverages P4 and IOTA

Unleashing Dynamic Pipeline Reconfiguration of P4 Switches for Efficient Network Monitoring


Pretrained models on CIFAR10/100 in PyTorch

Continual Learning in Deep Networks: an Analysis of the Last Layer

T-Cal: An optimal test for the calibration of predictive models

Imperceptible Adversarial Attack via Invertible Neural Networks

Learning from Multiple Annotator Noisy Labels via Sample-wise Label Fusion

Free Fine-tuning: A Plug-and-Play Watermarking Scheme for Deep Neural Networks

Confidence and Dispersity Speak: Characterising Prediction Matrix for Unsupervised Accuracy Estimation

Continual Feature Selection: Spurious Features in Continual Learning

A Bag-of-Prototypes Representation for Dataset-Level Applications

Energy-based Automated Model Evaluation

K-means Clustering Based Feature Consistency Alignment for Label-free Model Evaluation


On the Role of Sparsity and DAG Constraints for Learning Linear DAGs

Beware of the Simulated DAG! Causal Discovery Benchmarks May Be Easy To Game

BCD Nets: Scalable Variational Approaches for Bayesian Causal Discovery

DAGMA: Learning DAGs via M-matrices and a Log-Determinant Acyclicity Characterization

On the Convergence of Continuous Constrained Optimization for Structure Learning

MissDAG: Causal Discovery in the Presence of Missing Data with Continuous Additive Noise Models

Optimizing NOTEARS Objectives via Topological Swaps

Learning DAGs from Data with Few Root Causes

On the Role of Entropy-based Loss for Learning Causal Structures with Continuous Optimization


*UNOFFICIAL, UNMAINTAINED and OUTDATED*: This was an unofficial archive of GMAP-GSNAP releases.  Please use the original website for current versions of the source code.

A mosaic monoploid reference sequence for the highly complex genome of sugarcane

Technology dictates algorithms: Recent developments in read alignment

Early Life Exposure to Environmentally Relevant Levels of Endocrine Disruptors Drive Multigenerational and Transgenerational Epigenetic Changes in a Fish Model

Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression

Transcript Complexity and New Insights of Restorer Line in CMS-D8 Cotton Through Full-Length Transcriptomic Analysis

Single-Molecule Real-Time Sequencing for Identifying Sexual-Dimorphism-Related Transcriptomes and Genes in the Chinese Soft-Shelled Turtle (Pelodiscus sinensis)

Animals : an open access journal from MDPI


This is the official code repository for "Graph Neural Networks are Inherently Good Generalizers: Insights by Bridging GNNs and MLPs", which is accepted to ICLR 2023.

DropEdge: Towards Deep Graph Convolutional Networks on Node Classification

MLPInit: Embarrassingly Simple GNN Training Acceleration with MLP Initialization

Geometric Knowledge Distillation: Topology Compression for Graph Neural Networks


Creative Commons Attribution 4.0 International

Overview of the TREC 2019 deep learning track

Overview of the TREC 2020 deep learning track

ORCAS: 18 Million Clicked Query-Document Pairs for Analyzing Search

TREC Deep Learning Track: Reusable Test Collections in the Large Data Regime

Conformer-Kernel with Query Term Independence for Document Retrieval

Conformer-Kernel with Query Term Independence at TREC 2020 Deep Learning Track


Long short-term memory Spiking Neural Networks

Long short-term memory and learning-to-learn in networks of spiking neurons

Deep Rewiring: Training very sparse deep networks

Biologically inspired alternatives to backpropagation through time for learning in recurrent neural nets


The DevNet project on github stores the PacBio DevNet website.

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Fast and accurate de novo genome assembly from long uncorrected reads

MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome

Illuminating the dark side of the human transcriptome with long read transcript sequencing

Inferring synteny between genome assemblies: a systematic evaluation

A comparative evaluation of hybrid error correction methods for error-prone long reads

Completing bacterial genome assemblies: strategy and performance comparisons

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles


X-ray absorption re-emission scattering - Monte Carlo simulator for X-ray obscurers

X-ray spectral and eclipsing model of the clumpy obscurer in active galactic nuclei

Physically motivated X-ray obscurer models

X-ray radiative transfer in full 3D with SKIRT

The High-Energy X-ray Probe (HEX-P): the circum-nuclear environment of growing supermassive black holes

A hard look at the X-ray spectral variability of NGC 7582

Investigating Model Dependencies for Obscured Active Galactic Nuclei: A Case Study of NGC 3982


A feasible method for optimization with orthogonality constraints

Riemannian Optimization on the Symplectic Stiefel Manifold

Multipliers Correction Methods for Optimization Problems over the Stiefel Manifold

Error bound and exact penalty method for optimization problems with nonnegative orthogonal constraint

An alternate gradient method for optimization problems with orthogonality constraints

Numerical Algebra, Control and Optimization


Code for "M. Zhang, Z. Cui, M. Neumann, and Y. Chen, An End-to-End Deep Learning Architecture for Graph Classification, AAAI-18".

A Comprehensive Survey on Graph Neural Networks

THIRTY-SECOND AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE / THIRTIETH INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE / EIGHTH AAAI SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE

Deep Learning on Graphs: A Survey

Physically-interpretable classification of biological network dynamics for complex collective motions

Leveraging Ferroelectric Stochasticity and In-Memory Computing for DNN IP Obfuscation

IEEE Journal on Exploratory Solid-State Computational Devices and Circuits

Resting-state based prediction of task-related activation in patients with disorders of consciousness

A Systematic Review of Deep Graph Neural Networks: Challenges, Classification, Architectures, Applications & Potential Utility in Bioinformatics


Microglia morphology quantification tool

Automated Morphological Analysis of Microglia After Stroke

Active poly-GA vaccination prevents microglia activation and motor deficits in a C9orf72 mouse model

The NKCC1 ion transporter modulates microglial phenotype and inflammatory response to brain injury in a cell-autonomous manner

Microglial morphometric analysis: so many options, so little consistency

LRRC8A is dispensable for a variety of microglial functions and response to acute stroke

Microglia undergo rapid phenotypic transformation in acute brain slices but remain essential for neuronal synchrony


Code for the RL method MATD3 described in the paper "Reducing Overestimation Bias in Multi-Agent Domains Using Double Centralized Critics"

Addressing Function Approximation Error in Actor-Critic Methods

Multi-Agent Actor-Critic for Mixed Cooperative-Competitive Environments


Defeasible Natural Language Inference

A large annotated corpus for learning natural language inference

ATOMIC: An Atlas of Machine Commonsense for If-Then Reasoning

Social Chemistry 101: Learning to Reason about Social and Moral Norms

Thinking Like a Skeptic: Defeasible Inference in Natural Language

Think about it! Improving defeasible reasoning by first modeling the question scenario.

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

Could you give me a hint? Generating inference graphs for defeasible reasoning


Data and papers related to epigenetic clocks predicting age

DNA methylation-based biomarkers and the epigenetic clock theory of ageing

An epigenetic biomarker of aging for lifespan and healthspan

Epigenetic Predictor of Age

Aging of blood can be tracked by DNA methylation changes at just three CpG sites

DNA Methylation Clocks in Aging: Categories, Causes, and Consequences

Multi-tissue DNA methylation age predictor in mouse

Glycans Are a Novel Biomarker of Chronological and Biological Ages

The journals of gerontology. Series A, Biological sciences and medical sciences

Using DNA Methylation Profiling to Evaluate Biological Age and Longevity Interventions

Deep biomarkers of human aging: Application of deep neural networks to biomarker development

A new aging measure captures morbidity and mortality risk across diverse subpopulations from NHANES IV: A cohort study


Unsupervised Anomaly Localization using Variational Auto-Encoders

Reversing the Abnormal: Pseudo-Healthy Generative Networks for Anomaly Detection

What do we learn? Debunking the Myth of Unsupervised Outlier Detection

Learning to leverage salient regions in neuro-oncology using Deep Learning


DeepLocalize: Fault Localization for Deep NeuralNetworks

DeepLocalize: Fault Localization for Deep Neural Networks

DeepDiagnosis: Automatically Diagnosing Faults and Recommending Actionable Fixes in Deep Learning Programs

An Effective Data-Driven Approach for Localizing Deep Learning Faults


Quantum Operators from SYmmetry

Numerical Evidence for Many-Body Localization in Two and Three Dimensions.

Engineering topological models with a general-purpose symmetry-to-Hamiltonian approach

Operator Growth and Symmetry-Resolved Coefficient Entropy in Quantum Maps


The official implementation of NeMo: Neural Mesh Models of Contrastive Features for Robust 3D Pose Estimation [ICLR-2021].  https://arxiv.org/pdf/2101.12378.pdf

OOD-CV: A Benchmark for Robustness to Out-of-Distribution Shifts of Individual Nuisances in Natural Images

OOD-CV-v2: An extended Benchmark for Robustness to Out-of-Distribution Shifts of Individual Nuisances in Natural Images


[SemEval-2024 Task 3] Multimodal Emotion Cause Analysis in Conversations

SemEval-2024 Task 3: Multimodal Emotion Cause Analysis in Conversations

PetKaz at SemEval-2024 Task 3: Advancing Emotion Classification with an
  LLM for Emotion-Cause Pair Extraction in Conversations

LyS at SemEval-2024 Task 3: An Early Prototype for End-to-End Multimodal Emotion Linking as Graph-Based Parsing

UIC NLP GRADS at SemEval-2024 Task 3: Two-Step Disjoint Modeling for Emotion-Cause Pair Extraction

International Workshop on Semantic Evaluation


R package for estimating copula entropy (mutual information), transfer entropy (conditional mutual information), and the statistic for multivariate normality test and two-sample test

Estimating Transfer Entropy via Copula Entropy

Variable Selection with Copula Entropy

Discovering Association with Copula Entropy

Predicting TUG score from gait characteristics with video analysis and machine learning

copent: Estimating Copula Entropy in R.

Predicting MMSE Score from Finger-Tapping Measurement

copent: Estimating Copula Entropy and Transfer Entropy in R

Associations between finger tapping, gait and fall risk with application to fall risk assessment


This is the PyTorch code + data repository for paper "Hierarchical Multi-head Attentive Network for Evidence-aware Fake News Detection", EACL 2021

Integrating Pattern- and Fact-based Fake News Detection via Model Preference Learning

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

Adversarial Contrastive Learning for Evidence-aware Fake News Detection with Graph Neural Networks

MUSER: A MUlti-Step Evidence Retrieval Enhancement Framework for Fake News Detection

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


deep learning for math

DeepMath - Deep Sequence Models for Premise Selection

Reinforcement Learning of Theorem Proving

Improving Graph Neural Network Representations of Logical Formulae with Subgraph Pooling

A Deep Reinforcement Learning Approach to First-Order Logic Theorem Proving

Prolog Technology Reinforcement Learning Prover

Learning to Guide a Saturation-Based Theorem Prover

Premise selection with neural networks and distributed representation of features

The Role of Entropy in Guiding a Connection Prover

An Experimental Study of Formula Embeddings for Automated Theorem Proving in First-Order Logic


The tRNA adaptation index

Variation and selection on codon usage bias across an entire subphylum

Biased Mutation and Selection in RNA Viruses

An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria

Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation

ΦX174 Attenuation by Whole-Genome Codon Deoptimization

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi

Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5ʹ End of ORFeomes

Codon usage bias in prokaryotic genomes and environmental adaptation


Quantitative prediction of enhancer-promoter interactions

Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

Computational and structural biotechnology journal

EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions

Local Epigenomic Data are more Informative than Local Genome Sequence Data in Predicting Enhancer-Promoter Interactions Using Neural Networks

CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps

CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction

Latent representation of the human pan-celltype epigenome through a deep recurrent neural network

Enhancer/gene relationships: Need for more reliable genome-wide reference sets

Machine and deep learning methods for predicting 3D genome organization

Hi-C-LSTM: Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of 3D genome conformation


Traffic prediction is the task of predicting future traffic measurements (e.g. volume, speed, etc.) in a road network (graph), using historical data (timeseries).

DeepMove: Predicting Human Mobility with Attentional Recurrent Networks

WEB CONFERENCE 2018: PROCEEDINGS OF THE WORLD WIDE WEB CONFERENCE (WWW2018)

Urban Traffic Prediction from Spatio-Temporal Data Using Deep Meta Learning

Traffic Flow Prediction via Spatial Temporal Graph Neural Network

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

On the Modeling of Traffic and Crowds: A Survey of Models, Speculations, and Perspectives

Traffic transformer: Capturing the continuity and periodicity of time series for traffic forecasting

Deep Sequence Learning with Auxiliary Information for Traffic Prediction

Spatiotemporal Adaptive Gated Graph Convolution Network for Urban Traffic Flow Forecasting

International Conference on Information and Knowledge Management

Hybrid Spatio-Temporal Graph Convolutional Network: Improving Traffic Prediction with Navigation Data

Graph Convolutional Networks with Kalman Filtering for Traffic Prediction

Advances in Geographic Information Systems

BusTr: Predicting Bus Travel Times from Real-Time Traffic


Paper list of federated learning: About system design

Federated Machine Learning: Concept and Applications

Practical Secure Aggregation for Privacy-Preserving Machine Learning

Spark SQL

SIGMOD'15: PROCEEDINGS OF THE 2015 ACM SIGMOD INTERNATIONAL CONFERENCE ON MANAGEMENT OF DATA

A Survey on Distributed Machine Learning

A Comprehensive Survey of Privacy-preserving Federated Learning: A Taxonomy, Review, and Future Directions

A generic communication scheduler for distributed DNN training acceleration

Symposium on Operating Systems Principles

TiFL: A Tier-based Federated Learning System

CHET: an optimizing compiler for fully-homomorphic neural-network inferencing

Programming Language Design and Implementation

F1: A Fast and Programmable Accelerator for Fully Homomorphic Encryption

PROCEEDINGS OF 54TH ANNUAL IEEE/ACM INTERNATIONAL SYMPOSIUM ON MICROARCHITECTURE, MICRO 2021

FedAT: A High-Performance and Communication-Efficient Federated Learning System with Asynchronous Tiers


Implementation of "Sample-Efficient Deep Reinforcement Learning via Episodic Backward Update", NeurIPS 2019.

Learning to Play in a Day: Faster Deep Reinforcement Learning by Optimality Tightening

Topological Experience Replay


The implementation of "End-to-End Multi-Task Learning with Attention" [CVPR 2019].

RotoGrad: Gradient Homogenization in Multitask Learning

AdaTask: A Task-aware Adaptive Learning Rate Approach to Multi-task Learning

Learning Multiple Dense Prediction Tasks from Partially Annotated Data

Maximum Roaming Multi-Task Learning

Proceedings of the AAAI Conference on Artificial Intelligence

Measuring and Harnessing Transference in Multi-Task Learning

Multi-Task Learning with Multi-Task Optimization


Plot maps of Sri Lanka


PyTorch implementation of the classical image steganalysis networks, compatible with both grayscale and color images, and supporting multiple image sizes.

Deep Residual Network for Steganalysis of Digital Images

IEEE Transactions on Information Forensics and Security

Deep Learning Hierarchical Representations for Image Steganalysis

Structural Design of Convolutional Neural Networks for Steganalysis

A Siamese CNN for Image Steganalysis

Fast and Effective Global Covariance Pooling Network for Image Steganalysis

Information Hiding and Multimedia Security Workshop


Convolutional Neural Tangent Kernel

On Exact Computation with an Infinitely Wide Neural Net

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


Official Implementation of Graph Mixer Networks

Principal Neighbourhood Aggregation for Graph Nets

A Generalization of ViT/MLP-Mixer to Graphs


Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes

Draft Genome Sequences of 59 Endospore-Forming Gram-Positive Bacteria Associated with Crop Plants Grown in Vietnam

Novel Plant-Associated Brevibacillus and Lysinibacillus Genomospecies Harbor a Rich Biosynthetic Potential of Antimicrobial Compounds

Genetic diversity of Leptospira isolates in Lao PDR and genome analysis of an outbreak strain

Genome sequence data of Bacillus velezensis BP1.2A and BT2.4

Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds


Sliced Score Matching: A Scalable Approach to Density and Score Estimation

Learning Energy-Based Models in High-Dimensional Spaces with Multiscale Denoising-Score Matching

Variational Noise-Contrastive Estimation

Bi-level Score Matching for Learning Energy-based Latent Variable Models


Joint text classification on multiple levels with multiple labels, using a multi-head attention mechanism to wire two prediction tasks together.

Attention Is All You Need

Semi-supervised Multitask Learning for Sequence Labeling

Jointly Learning to Label Sentences and Tokens

Seeing Both the Forest and the Trees: Multi-head Attention for Joint Classification on Different Compositional Levels


[AAAI2022] Code Release of Attacking Video Recognition Models with Bullet-Screen Comments

Show, Attend and Tell: Neural Image Caption Generation with Visual Attention

PatchAttack: A Black-box Texture-based Attack with Reinforcement Learning


Socially Aware Motion Planning with Deep Reinforcement Learning

Motion Planning Among Dynamic, Decision-Making Agents with Deep Reinforcement Learning

Collision Avoidance in Pedestrian-Rich Environments With Deep Reinforcement Learning


Methods for mapping proteomics data on 3D protein structure.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

Binder 2.0 - Reproducible, interactive, sharable environments for science at scale

Proceedings of the Python in Science Conferences

3Dmol.js: molecular visualization with WebGL

A Curated Resource for Phosphosite-specific Signature Analysis

Chemical proteomics reveals new targets of cysteine sulfinic acid reductase

Diverse Redoxome Reactivity Profiles of Carbon Nucleophiles

Journal of the American Chemical Society

Towards an efficient compression of 3D coordinates of macromolecular structures

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank


Data Parameters: A New Family of Parameters for Learning a Differentiable Curriculum

Dynamic curriculum learning via data parameters for noise robust keyword spotting

DiscrimLoss: A Universal Loss for Hard Samples and Incorrect Samples Discrimination


Source code for figure generation and analysis of the ENGAGE netzero scenario analysis

Cost and attainability of meeting stringent climate targets without overshoot

ENGAGE Global Scenarios

Zenodo (CERN European Organization for Nuclear Research)


(Intended) Nationally Determined Contributions as provided in the UNFCCC registries, containing only the main document and using the English version if multiple are available.


This is the development fork - Stable code has been moved to ==>

Lollipops in the Clinic: Information Dense Mutation Plots for Precision Medicine

Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus

Morphologic and molecular study of lung cancers associated with idiopathic pulmonary fibrosis and other pulmonary fibroses

γ2 GABAAR Trafficking and the Consequences of Human Genetic Variation

The Saccharomyces Genome Database Variant Viewer

Development of a rapid functional assay that predicts GLUT1 disease severity

Novel Missense CNTNAP2 Variant Identified in Two Consanguineous Pakistani Families With Developmental Delay, Epilepsy, Intellectual Disability, and Aggressive Behavior

Profiling lung adenocarcinoma by liquid biopsy: can one size fit all?

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


This repository contains JSON decision models for analyzed disability-claim decisions issued by the Board of Veterans' Appeals of the U.S. Department of Veterans Affairs.

Sentence Embeddings and High-Speed Similarity Search for Fast Computer Assisted Annotation of Legal Documents

The unreasonable effectiveness of large language models in zero-shot semantic annotation of legal texts

Cross-Domain Generalization and Knowledge Transfer in Transformers Trained on Legal Data

Extractive Summarization of Legal Decisions using Multi-task Learning and Maximal Marginal Relevance

Data-Centric Machine Learning: Improving Model Performance and Understanding Through Dataset Analysis

Data-Centric Machine Learning in the Legal Domain


Plug-and-play Algorithms for Large-scale Snapshot Compressive Imaging (CVPR 2020, Oral)

Snapshot Compressive Imaging: Theory, Algorithms, and Applications

Plug-and-Play Algorithms for Large-scale Snapshot Compressive Imaging

Plug-and-Play Algorithms for Video Snapshot Compressive Imaging


ACL 2023 paper "A Critical Evaluation of Evaluations for Long-form Question Answering"

WebGPT: Browser-assisted question-answering with human feedback

Hurdles to Progress in Long-form Question Answering


CoSQL: A Conversational Text-to-SQL Challenge Towards Cross-Domain Natural Language Interfaces to Databases

SParC: Cross-Domain Semantic Parsing in Context

Editing-Based SQL Query Generation for Cross-Domain Context-Dependent Questions


Industrial datasets - datasets for evaluating industrial intrusion detection systems on IPAL.

A Hardware-in-the-Loop Water Distribution Testbed Dataset for Cyber-Physical Security Testing

Timing-Based Anomaly Detection in SCADA Networks

Process Control Cyber-Attacks and Labelled Datasets on S7Comm Critical Infrastructure

Intrusion Detection for Sequence-Based Attacks with Reduced Traffic Models

Messung, Modellierung und Bewertung von Rechen- und Kommunikationssystemen

Cybersecurity Research and Training for Power Distribution Grids -- A Blueprint

Conference on Computer and Communications Security


Efficient Object Localization Using Convolutional Networks

Averaging Weights Leads to Wider Optima and Better Generalization

Renofeation: A Simple Transfer Learning Method for Improved Adversarial Robustness

Improving the Adversarial Robustness of Transfer Learning via Noisy Feature Distillation


Code and data related to the meta-analysis of fat distribution in UK Biobank and GIANT

Meta-analysis of genome-wide association studies for body fat distribution in 694 649 individuals of European ancestry

Sexual differences in genetic architecture in UK Biobank

Obesity, Fat Distribution and Risk of Cancer in Women and Men: A Mendelian Randomisation Study

Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits


modified aa.bst with clickable url link in the bibliography

Polarimetric investigation of selected cloud compositions in exoplanetary atmospheres

The impact of the presence of water ice on the analysis of debris disk observations

Using debris disk observations to infer substellar companions orbiting within or outside a parent planetesimal belt

How much large dust could be present in hot exozodiacal dust systems?


Code for Global Convergence of Block Coordinate Descent in Deep Learning (ICML 2019)

Personalized On-Device E-Health Analytics With Decentralized Block Coordinate Descent

Learning DNN networks using un-rectifying ReLU with compressed sensing application


Mixture-of-Adapters

LoRA: Low-Rank Adaptation of Large Language Models

Parameter-efficient Model Adaptation for Vision Transformers

Sparse Mixture-of-Experts are Domain Generalizable Learners

Domain Generalization Using Large Pretrained Models with Mixture-of-Adapters


An interpretable framework for inferring nonlinear multivariate Granger causality based on self-explaining neural networks.

Interpretable Models for Granger Causality Using Self-explaining Neural Networks

A Survey on Causal Discovery Methods for I.I.D. and Time Series Data

Bayesian Spillover Graphs for Dynamic Networks


Official PyTorch Implementation of Learning Affordance Grounding from Exocentric Images, CVPR 2022

Phrase-Based Affordance Detection via Cyclic Bilateral Interaction

Grounded Affordance from Exocentric View


[ICLR 2022] Official repository for "Robust Unlearnable Examples: Protecting Data Against Adversarial Learning"

Image Shortcut Squeezing: Countering Perturbative Availability Poisons with Compression

Learning the Unlearnable: Adversarial Augmentations Suppress Unlearnable Example Attacks

The Devil's Advocate: Shattering the Illusion of Unexploitable Data using Diffusion Models


Code for paper "Improving Generalizability of Graph Anomaly Detection Models via Data Augmentation" (TKDE 2023)

Out-Of-Distribution Generalization on Graphs: A Survey

Beyond Generalization: A Survey of Out-Of-Distribution Adaptation on
  Graphs


Code for "Restricted Boltzmann Machine Flows and The Critical Temperature of Ising models"

A high-bias, low-variance introduction to Machine Learning for physicists

An exact mapping between the Variational Renormalization Group and Deep Learning

Scale-invariant feature extraction of neural network and renormalization group flow


List of software packages for multi-trait / multiple-trait / multivariate / high-dimensional GWAS

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS

A Unified Framework for Association Analysis with Multiple Related Phenotypes

A Multi-Trait, Meta-analysis for Detecting Pleiotropic Polymorphisms for Stature, Fatness and Reproduction in Beef Cattle

TATES: Efficient Multivariate Genotype-Phenotype Analysis for Genome-Wide Association Studies

GPA: A Statistical Approach to Prioritizing GWAS Results by Integrating Pleiotropy and Annotation

A Comparison of Multivariate Genome-Wide Association Methods

Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis

Analyze multivariate phenotypes in genetic association studies by combining univariate association tests


Code for "Can We Scale Transformers to Predict Parameters of Diverse ImageNet Models?" [ICML 2023]

ResNet strikes back: An improved training procedure in timm


Code for the paper "Neural Question Generation from Text: A Preliminary Study"

A Survey of Knowledge-enhanced Text Generation

Answer-driven Deep Question Generation based on Reinforcement Learning

International Conference on Computational Linguistics

Neural Question Generation with Answer Pivot

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

Multi-Lingual Question Generation with Language Agnostic Language Model

Meeting of the Association for Computational Linguistics

On Generating Fact-Infused Question Variations

Recent Advances in Natural Language Processing


[CVPR 2023] 3D Representation Learning via Foreground Aware Feature Contrast

PointRCNN: 3D Object Proposal Generation and Detection from Point Cloud

PV-RCNN: Point-Voxel Feature Set Abstraction for 3D Object Detection

From Points to Parts: 3D Object Detection from Point Cloud with Part-aware and Part-aggregation Network

Voxel R-CNN: Towards High Performance Voxel-based 3D Object Detection

Generalized 3D Self-supervised Learning Framework via Prompted Foreground-Aware Feature Contrast


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

Soft Actor-Critic Algorithms and Applications

Distributional Soft Actor-Critic: Off-Policy Reinforcement Learning for Addressing Value Estimation Errors

IEEE transactions on neural networks and learning systems

Boosting Soft Actor-Critic: Emphasizing Recent Experience without Forgetting the Past


A collection of scripts for analyzing the data from the Gaia satellite

Gaia EDR3 view on galactic globular clusters

Monthly notices of the Royal Astronomical Society

UOCS - III. UVIT catalogue of open clusters with machine learning-based membership using Gaia EDR3 astrometry

Monthly Notices of the Royal Astronomical Society

AstroSat Study of the Globular Cluster NGC 2298: Probable Evolutionary Scenarios of Hot Horizontal Branch Stars

UOCS-IX. AstroSat/UVIT Study of the Open Cluster NGC 2818: Blue Stragglers, Yellow Stragglers, Planetary Nebula, and their Membership

ED-2: A cold but not so narrow stellar stream crossing the solar neighbourhood

Discovery of the shell structure via break radii in the outer halo of the Milky Way

Tracing Milky Way substructure with an RR Lyrae hierarchical clustering forest

Multiple stellar populations found outside the tidal radius of NGC 1851 via Gaia DR3 XP spectra

Using Gaia for studying Milky Way star clusters

Proceedings of the International Astronomical Union


Dynamic and static models for real-time facial emotion recognition

Deep Residual Learning for Image Recognition

VGGFace2: A dataset for recognising faces across pose and age

When Does Label Smoothing Help?

AffectNet: A Database for Facial Expression, Valence, and Arousal Computing in the Wild

IEEE Transactions on Affective Computing

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

CREMA-D: Crowd-Sourced Emotional Multimodal Actors Dataset

IEEE transactions on affective computing

Aff-Wild2: Extending the Aff-Wild Database for Affect Recognition

In search of a robust facial expressions recognition model: A large-scale visual cross-corpus study

RAMAS: Russian Multimodal Corpus of Dyadic Interaction for Affective Computing


Exploring the use of machine learning to convert a Digital Surface Model (e.g. SRTM) to a Digital Terrain Model

Mapping forest canopy height globally with spaceborne lidar

Journal of Geophysical Research Atmospheres

A high‐accuracy map of global terrain elevations

A Comparison of Machine Learning Approaches to Improve Free Topography Data for Flood Modelling


Code for Diagnosing Bottlenecks in Deep Q-learning. Contains implementations of tabular environments plus solvers.

Diagnosing Bottlenecks in Deep Q-learning Algorithms

DisCor: Corrective Feedback in Reinforcement Learning via Distribution Correction

Offline RL With Realistic Datasets: Heteroskedasticity and Support Constraints


Panoramic localization library containing PyTorch implementations of various panoramic localization algorithms including PICCOLO (ICCV 2021), CPO (ECCV 2022), LDL (ICCV 2023) and FGPL (CVPR 2024).

PICCOLO: Point Cloud-Centric Omnidirectional Localization

CPO: Change Robust Panorama to Point Cloud Localization

Fully Geometric Panoramic Localization

LDL: Line Distance Functions for Panoramic Localization


Image Splicing Localization using a Multi-task Fully Convolutional Network (MFCN)

Journal of Visual Communication and Image Representation

Scene Classification Based on Multiscale Convolutional Neural Network

PROCEEDINGS OF THE 6TH ACM WORKSHOP ON INFORMATION HIDING AND MULTIMEDIA SECURITY (IH&MMSEC'18)

Image forgery detection using steerable pyramid transform and local binary pattern

Detection and Localization of Image Forgeries using Resampling Features and Deep Learning

Double JPEG compression forensics based on a convolutional neural network


Survey on Emotional Body Gesture Recognition

ARBEE: Towards Automated Recognition of Bodily Expression of Emotion in the Wild

International journal of computer vision

Affect2MM: Affective Analysis of Multimedia Content Using Emotion Causality


Multiplicative Normalizing Flow (MNF) posteriors for variational Bayesian neural networks

Multiplicative Normalizing Flows for Variational Bayesian Neural Networks

Uncertainty-Aware Deep Classifiers using Generative Models

Projected BNNs: Avoiding weight-space pathologies by learning latent representations of neural network weights

Bayesian deep learning for cosmic volumes with modified gravity


CompILE: Compositional Imitation Learning and Execution (ICML 2019)

Unsupervised Learning of Temporal Abstractions With Slot-Based Transformers

Learning Task Decomposition with Ordered Memory Policy Network


The information sieve for discrete variables.

Discovering Structure in High-Dimensional Data Through Correlation Explanation

Maximally Informative Hierarchical Representations of High-Dimensional Data

The Information Sieve


Implementation of our paper "Meta Reinforcement Learning with Task Embedding and Shared Policy"

Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks

Meta-SGD: Learning to Learn Quickly for Few-Shot Learning

Meta-Reinforcement Learning of Structured Exploration Strategies


A Frank-Wolfe Framework for Efficient and Effective Adversarial Attacks (AAAI'20)

Rethinking the Inception Architecture for Computer Vision

Identity Mappings in Deep Residual Networks

An empirical study of derivative-free-optimization algorithms for targeted black-box attacks in deep neural networks


A Novel Multitask Learning Empowered Codebook Design for Downlink SCMA Networks

A Design of Low-Projection SCMA Codebooks for Ultra-Low Decoding Complexity in Downlink IoT Networks

Enhancing Signal Space Diversity for SCMA Over Rayleigh Fading Channels


Liquid Prep offers an end-to-end solution for farmers looking to optimize their water usage, especially during times of drought.


Official PyTorch implementation of BigVGAN (ICLR 2023)

High-Fidelity Audio Compression with Improved RVQGAN

BigVGAN: A Universal Neural Vocoder with Large-Scale Training

Vocos: Closing the gap between time-domain and Fourier-based neural vocoders for high-quality audio synthesis

CLIPSonic: Text-to-Audio Synthesis with Unlabeled Videos and Pretrained Language-Vision Models

BigVSAN: Enhancing GAN-based Neural Vocoders with Slicing Adversarial Network

Autoregressive Diffusion Transformer for Text-to-Speech Synthesis

Integrating Paralinguistics in Speech-Empowered Large Language Models for Natural Conversation

HiFTNet: A Fast High-Quality Neural Vocoder with Harmonic-plus-Noise Filter and Inverse Short Time Fourier Transform

Towards generalizing deep-audio fake detection networks

PeriodWave: Multi-Period Flow Matching for High-Fidelity Waveform
  Generation


Official PyTorch repository for Hypercomplex Image-to-Image Transaltion

PHNNs: Lightweight Neural Networks via Parameterized Hypercomplex Convolutions

Quaternion Generative Adversarial Networks

A Quaternion-Valued Variational Autoencoder

Hypercomplex Image-to-Image Translation

IEEE International Joint Conference on Neural Network


The Norm Must Go On: Dynamic Unsupervised Domain Adaptation by Normalization (CVPR 2022)

AugMix: A Simple Data Processing Method to Improve Robustness and Uncertainty

An Efficient Domain-Incremental Learning Approach to Drive in All Weather Conditions

Neuro-Modulated Hebbian Learning for Fully Test-Time Adaptation

ActMAD: Activation Matching to Align Distributions for Test-Time-Training

Each Test Image Deserves A Specific Prompt: Continual Test-Time Adaptation for 2D Medical Image Segmentation

Test-Time Poisoning Attacks Against Test-Time Adaptation Models


ODE2VAE: Deep generative second order ODEs with Bayesian neural networks

ODE^2VAE: Deep generative second order ODEs with Bayesian neural networks

The Neural Process Family: Survey, Applications and Perspectives

Contrastive Conditional Neural Processes

Equivariant Neural Simulators for Stochastic Spatiotemporal Dynamics

Adversarially Contrastive Estimation of Conditional Neural Processes


Improving Anatomical Plausibility in Medical Image Segmentation via Hybrid Graph Neural Networks: Applications to Chest X-Ray Analysis

Hybrid graph convolutional neural networks for landmark-based anatomical segmentation

Multi-Center Anatomical Segmentation with Heterogeneous Labels Via Landmark-Based Models

Unsupervised bias discovery in medical image segmentation


Low-complexity neural image & video codec.

COOL-CHIC: Coordinate-based Low Complexity Hierarchical Image Codec

C3: High-performance and low-complexity neural compression from a single image or video

Low-complexity Overfitted Neural Image Codec

Cool-chic video: Learned video coding with 800 parameters

Cool-Chic: Perceptually Tuned Low Complexity Overfitted Image Coder


The public repository about our joint FINN research project

Convolutional LSTM Network: A Machine Learning Approach for Precipitation Nowcasting

Weight Uncertainty in Neural Networks

Fourier Neural Operator for Parametric Partial Differential Equations

Disentangling Physical Dynamics from Unknown Factors for Unsupervised Video Prediction

Augmenting physical models with deep networks for complex dynamics forecasting

Skillful Twelve Hour Precipitation Forecasts using Large Context Neural Networks

Composing Partial Differential Equations with Physics-Aware Neural Networks

A Distributed Neural Network Architecture for Robust Non-Linear Spatio-Temporal Prediction


PyTorch implementation of cvpr2019 paper "Spherical Regression: Learning Viewpoints, Surface Normals and 3D Rotations on n-Spheres".

Implicit-PDF: Non-Parametric Representation of Probability Distributions on the Rotation Manifold

Image to Sphere: Learning Equivariant Features for Efficient Pose Prediction

Neural Fourier Transform: A General Approach to Equivariant Representation Learning


EAD: Elastic-Net Attacks to Deep Neural Networks via Adversarial Examples

On the Limitation of Local Intrinsic Dimensionality for Characterizing the Subspaces of Adversarial Examples

On the Limitation of MagNet Defense against L_1-based Adversarial Examples

On The Utility of Conditional Generation Based Mutual Information for Characterizing Adversarial Subspaces


Representation Learning in RL

Hybrid RL: Using Both Offline and Online Data Can Make RL Efficient

Efficient Reinforcement Learning in Block MDPs: A Model-free Representation Learning Approach

Provable Benefits of Representational Transfer in Reinforcement Learning

Representation Learning for General-sum Low-rank Markov Games


An open-source framework to benchmark and assess safety specifications of Reinforcement Learning problems.

Safe Deep Reinforcement Learning by Verifying Task-Level Properties

SafeRL-Kit: Evaluating Efficient Reinforcement Learning Methods for Safe Autonomous Driving


Code for "From Pixel to Patch: Synthesize Context-aware Features for Zero-shot Semantic Segmentation".

Zero-Shot Semantic Segmentation

Context-aware Feature Generation for Zero-shot Semantic Segmentation

MM '20: PROCEEDINGS OF THE 28TH ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA


PyKNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for high-throughput image annotation of 3D electron microscopy stacks of brain tissue. https://www.ariadne.ai

Whitening of odor representations by the wiring diagram of the olfactory bulb

Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain

3-dimensional electron microscopic imaging of the zebrafish olfactory bulb and dense reconstruction of neurons

Methods for Mapping Neuronal Activity to Synaptic Connectivity: Lessons From Larval Zebrafish

Dense skeleton reconstructions of neurons in the larval zebrafish olfactory bulb

Zenodo (CERN European Organization for Nuclear Research)


Toolbox for parameter estimation of the Standard Model of diffusion in white matter

NODDI: Practical in vivo neurite orientation dispersion and density imaging of the human brain

White matter characterization with diffusional kurtosis imaging

Quantifying brain microstructure with diffusion MRI: Theory and parameter estimation

Multi-compartment microscopic diffusion imaging

Degeneracy in model parameter estimation for multi‐compartmental diffusion in neuronal tissue

Rotationally-invariant mapping of scalar and orientational metrics of neuronal microstructure with diffusion MRI

TE dependent Diffusion Imaging (TEdDI) distinguishes between compartmental T2 relaxation times

Disentangling micro from mesostructure by diffusion MRI: A Bayesian approach

Ball and rackets: Inferring fiber fanning from diffusion-weighted MRI

Fiber ball imaging


Few-Shot Learning with Localization in Realistic Settings

Joint Distribution Matters: Deep Brownian Distance Covariance for Few-Shot Classification

Learning from Few Samples: A Survey


Generic Neural Architecture Search via Regression

Extensible and Efficient Proxy for Neural Architecture Search

IEEE International Conference on Computer Vision

Extensible Proxy for Efficient NAS


PyTorch implementation of the Deep SLDA method from our CVPRW-2020 paper "Lifelong Machine Learning with Deep Streaming Linear Discriminant Analysis"

Cold Start Streaming Learning for Deep Networks


A framework for financial systemic risk valuation and analysis.

Better to Give than to Receive: Predictive Directional Measurement of Volatility Spillovers

Reprint of: On the network topology of variance decompositions: Measuring the connectedness of financial firms

Econometric Measures of Connectedness and Systemic Risk in the Finance and Insurance Sectors

Measuring Systemic Risk

SRISK: A Conditional Capital Shortfall Measure of Systemic Risk

Does Systemic Risk in the Financial Sector Predict Future Economic Downturns?

Principal Components as a Measure of Systemic Risk

VAR for VaR: Measuring Tail Dependence Using Multivariate Regression Quantiles

Systemic risk: The impact of COVID-19

Skulls, Financial Turbulence, and Risk Management


Evaluating the Mamba architecture on the Othello game

Emergent World Representations: Exploring a Sequence Model Trained on a Synthetic Task

Emergent Linear Representations in World Models of Self-Supervised Sequence Models

Linear Latent World Models in Simple Transformers: A Case Study on Othello-GPT


This repository provides the AJIVE software in Matlab and all related Matlab scripts to reproduce the results in the paper Angle-basied Joint And Individual Variation Explained (Feng et.al., 2018). Please refer to README.md for instruction.

Angle-based joint and individual variation explained

Integrative, multi-omics, analysis of blood samples improves model predictions: applications to cancer


Optimised estimates of reproduction numbers over time, which extract more information from an incidence curve than many conventional approaches

Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves

Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges

Deciphering early-warning signals of SARS-CoV-2 elimination and resurgence from limited data at multiple scales


The Combined Anomalous Object Segmentation (CAOS) Benchmark

Scaling Out-of-Distribution Detection for Real-World Settings

A Benchmark for Anomaly Segmentation.

Perception Datasets for Anomaly Detection in Autonomous Driving: A Survey

Towards Robustness of Neural Networks


remef: Remove Partial Effects

The eye-voice span during reading aloud

Linked linear mixed models: A joint analysis of fixation locations and fixation durations in natural reading

Speed-Accuracy Tradeoffs in Brain and Behavior: Testing the Independence of P300 and N400 Related Processes in Behavioral Responses to Sentence Categorization

Positive Psychology Broadens Readers’ Attentional Scope During L2 Reading: Evidence From Eye Movements

Human and computer estimations of Predictability of words in written language

Cross-Linguistic Word Recognition Development Among Chinese Children: A Multilevel Linear Mixed-Effects Modeling Approach

Predictive pre-activation of orthographic and lexical-semantic representations facilitates visual word recognition

Predicting Known Sentences: Neural Basis of Proverb Reading Using Non-parametric Statistical Testing and Mixed-Effects Models

Object Properties Influence Visual Guidance of Motor Actions


Official Code for Local Search GFlowNets (ICLR 2024 Spotlight)

Local Search GFlowNets

Bifurcated Generative Flow Networks

Rectifying Reinforcement Learning for Reward Matching


Acoustic mosquito detection code with Bayesian Neural Networks

Learning to detect an animal sound from five examples

HumBugDB: A Large-scale Acoustic Mosquito Dataset

Few-shot bioacoustic event detection at the DCASE 2022 challenge


Tree House Explorer (THEx) is a novel genome browser for exploring phylogenetic and genomic data in one succinct place.

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments

Radiation with reticulation marks the origin of a major malaria vector

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

Tree House Explorer: A Novel Genome Browser for Phylogenomics


TabTransformer: Tabular Data Modeling Using Contextual Embeddings

Neural Additive Models for Location Scale and Shape: A Framework for Interpretable Neural Regression Beyond the Mean

Structural Neural Additive Models: Enhanced Interpretable Machine Learning


Vision

Deeper Depth Prediction with Fully Convolutional Residual Networks

Benchmarking Single-Image Dehazing and Beyond

O-HAZE: a dehazing benchmark with real hazy and haze-free outdoor images

I-HAZE: a dehazing benchmark with real hazy and haze-free indoor images


Proximal Policy Optimization Algorithms

Continuous control with deep reinforcement learning

Image quality assessment for machine learning tasks using meta-reinforcement learning

Adaptable image quality assessment using meta-reinforcement learning of task amenability

Image quality assessment by overlapping task-specific and task-agnostic measures: application to prostate multiparametric MR images for cancer segmentation


ImageJ plugin detecting and colocalizing particles of given size (vesicles, dots, etc on biological microscopy images)

Complement C1q-dependent excitatory and inhibitory synapse elimination by astrocytes and microglia in Alzheimer’s disease mouse models

The HAUS Complex Is a Key Regulator of Non-centrosomal Microtubule Organization during Neuronal Development

Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments

Kinesin-4 KIF21B is a potent microtubule pausing factor

Pyrrole Hemithioindigo Antimitotics with Near-Quantitative Bidirectional Photoswitching Photocontrol Cellular Microtubule Dynamics with Single-Cell Precision

Meiotic cohesins mediate initial loading of HORMAD1 to the chromosomes and coordinate SC formation during meiotic prophase

Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy

Designing a chemical inhibitor for the AAA protein spastin using active site mutations

Modular antibodies reveal DNA damage-induced mono-ADP-ribosylation as a second wave of PARP1 signaling

Integrin Binding Dynamics Modulate Ligand-Specific Mechanosensing in Mammary Gland Fibroblasts


PyTorch implementation of Spatially Transformed Adversarial Examples

Imperceptible Adversarial Examples by Spatial Chroma-Shift

Adversarial image generation by spatial transformation in perceptual colorspaces


This is Pytorch Implementation of Google's Non-attentive Tacotron.

wav2vec 2.0: A Framework for Self-Supervised Learning of Speech Representations

Non-Attentive Tacotron: Robust and Controllable Neural TTS Synthesis Including Unsupervised Duration Modeling

K-Wav2vec 2.0: Automatic Speech Recognition based on Joint Decoding of Graphemes and Syllables


A Guide to Reconstructing Dynamical Systems from Neural Measurements Using Recurrent Neural Networks

Generalized Teacher Forcing for Learning Chaotic Dynamics

Integrating Multimodal Data for Joint Generative Modeling of Complex Dynamics

Inferring stochastic low-rank recurrent neural networks from neural data


Asynchronous Methods for Deep Reinforcement Learning

Effective Approaches to Attention-based Neural Machine Translation

Reinforcement Learning for Bandit Neural Machine Translation with Simulated Human Feedback


List of datasets and papers in X-ray security images (Computer vision/Machine Learning)

Prohibited Item Detection in Airport X-Ray Security Images via Attention Mechanism Based CNN

PATTERN RECOGNITION AND COMPUTER VISION, PT II

Semantic Segmentation for Prohibited Items in Baggage Inspection

Sino-foreign-interchange Workshop on Intelligent Science and Intelligent Data Engineering

Threat Objects Detection in X-ray Images Using an Active Vision Approach

A GAN-Based Image Generation Method for X-Ray Security Prohibited Items

PATTERN RECOGNITION AND COMPUTER VISION (PRCV 2018), PT I

Handgun Detection in Single-Spectrum Multiple X-ray Views Based on 3D Object Recognition

Deep Learning-Based X-Ray Baggage Hazardous Object Detection – An FPGA Implementation

Graph clustering and variational image segmentation for automated firearm detection in X-ray images

Modified Adaptive Implicit Shape Model for Object Detection

NEURAL INFORMATION PROCESSING, ICONIP 2019, PT V

Application of Machine Learning Methods for Material Classification with Multi-energy X-Ray Transmission Images


Poisson Identifiable VAE  (pi-VAE)

Learnable latent embeddings for joint behavioural and neural analysis

Learning identifiable and interpretable latent models of high-dimensional neural activity using pi-VAE


Code for TEDVAE, a VAE-based treatment effect estimation algorithm.

Treatment effect estimation with disentangled latent factors

A Unified Survey of Treatment Effect Heterogeneity Modelling and Uplift Modelling

Targeted VAE: Variational and Targeted Learning for Causal Inference

A unified survey of treatment effect heterogeneity modeling and uplift modeling

Causal Inference with Conditional Instruments using Deep Generative Models

Disentangled Representation for Causal Mediation Analysis

Learning Conditional Instrumental Variable Representation for Causal Effect Estimation


This repository contains EmoBank, a large-scale text corpus manually annotated with emotion according to the psychological Valence-Arousal-Dominance scheme.

EmoBank: Studying the Impact of Annotation Perspective and Representation Format on Dimensional Emotion Analysis

Readers vs. Writers vs. Texts: Coping with Different Perspectives of Text Understanding in Emotion Annotation

Modelling the interplay of metaphor and emotion through multitask learning

Empirical Methods in Natural Language Processing

Adversarial Attention Modeling for Multi-dimensional Emotion Regression

Meeting of the Association for Computational Linguistics

WRIME: A New Dataset for Emotional Intensity Estimation with Subjective and Objective Annotations

North American Chapter of the Association for Computational Linguistics

Dimensional Emotion Detection from Categorical Emotion

Learning Word Ratings for Empathy and Distress from Document-Level User Responses

Computational Storytelling and Emotions: A Survey


Classifying Forged vs Authentic using Domain Adaptation across in new domains in unsupervised settings

Domain-Adversarial Training of Neural Networks

Deep Domain Confusion: Maximizing for Domain Invariance

EdgeConnect: Generative Image Inpainting with Adversarial Edge Learning

Syn2Real: Forgery Classification via Unsupervised Domain Adaptation


Differentially Private Federated Learning on Heterogeneous Data

Federated Optimization in Heterogeneous Networks

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


UniAudio: An Audio Foundation Model Toward Universal Audio Generation

Neural Target Speech Extraction: An overview

Listen only to me! How well can target speech extraction handle false alarms?

Target Speech Extraction with Conditional Diffusion Model

Target Speech Extraction with Pre-trained Self-supervised Learning
  Models

Typing to Listen at the Cocktail Party: Text-Guided Target Speaker Extraction

Weakly-Supervised Speech Pre-training: A Case Study on Target Speech Recognition

Beamformer-Guided Target Speaker Extraction

Analysis of impact of emotions on target speech extraction and speech separation

Speaker-Aware Mixture of Mixtures Training for Weakly Supervised Speaker Extraction


DALL-E for Detection: Language-driven Compositional Image Synthesis for Object Detection

Cut, Paste and Learn: Surprisingly Easy Synthesis for Instance Detection

Beyond Generation: Harnessing Text to Image Models for Object Detection and Segmentation

EM-Paste: EM-guided Cut-Paste with DALL-E Augmentation for Image-level Weakly Supervised Instance Segmentation


FuSeBMC is a novel Energy-Efficient Test Generator that exploits fuzzing and BMC engines to detect security vulnerabilities in real-world C programs.

FuSeBMC: A White-Box Fuzzer for Finding Security Vulnerabilities in C Programs (Competition Contribution)

FuSeBMC v.4: Smart Seed Generation for Hybrid Fuzzing

FuSeBMC v4: Improving code coverage with smart seeds via BMC, fuzzing and static analysis


This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.

Automated high throughput animal CO1 metabarcode classification

DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness

Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments

Automated high throughput animal DNA metabarcode classification

Unveiling invasive insect threats to plant biodiversity: Leveraging eDNA metabarcoding and saturated salt trap solutions for biosurveillance

taxalogue: a toolkit to create comprehensive CO1 reference databases


An un-trained neural network with a potential application in accelerated MRI

Accelerated MRI with Un-trained Neural Networks

K-UNN: k-Space Interpolation With Untrained Neural Network

Can Un-trained Neural Networks Compete with Trained Neural Networks at Image Reconstruction?


Generating with Confidence: Uncertainty Quantification for Black-box Large Language Models

Large Language Model Confidence Estimation via Black-Box Access


codes for the paper "Simulation-guided Beam Search for Neural Combinatorial Optimization"

Neural Combinatorial Optimization with Heavy Decoder: Toward Large Scale Generalization

Routing Arena: A Benchmark Suite for Neural Routing Solvers


Scattering GCN: overcoming oversmoothness in graph convolutional networks

Graph-based Semi-supervised Learning: A Comprehensive Review

Scattering GCN: Overcoming Oversmoothness in Graph Convolutional Networks

Overcoming Oversmoothness in Graph Convolutional Networks via Hybrid Scattering Networks


A short library for calculating the state transitions Perturbational Complexity Index (PCIst)

Local sleep-like cortical reactivity in the awake brain after focal injury

Cortico-thalamo-cortical interactions modulate electrically evoked EEG responses in mice

Capacity for consciousness under ketamine anaesthesia is selectively associated with activity in posteromedial cortex in rats

Assessing awareness in severe Alzheimer’s disease

Laminar evoked responses in mouse somatosensory cortex suggest a special role for deep layers in cortical complexity


The AUTOmated Photometry Of Transients (AutoPhOT) is a novel automated pipeline that is designed for rapid, publication-quality photometry of transients.

The Automated Photometry of Transients pipeline (AutoPhOT)

A shock flash breaking out of a dusty red supergiant

Photometric and spectroscopic evolution of the interacting transient at 2016jbu(Gaia16cfr)

Monthly notices of the Royal Astronomical Society

A long life of excess: The interacting transient SN 2017hcc

SN 2018bsz: significant dust formation in a nearby superluminous supernova

Optical polarization and spectral properties of the hydrogen-poor superluminous supernovae SN 2021bnw and SN 2021fpl

Photometric study of the late-time near-infrared plateau in Type Ia supernovae

Rapidly Evolving Transients in Archival ZTF Public Alerts


Repo for my Master Thesis at ULiège in 2019 (Machine learning under resource constraints)

NetAdapt: Platform-Aware Neural Network Adaptation for Mobile Applications

MorphNet: Fast & Simple Resource-Constrained Structure Learning of Deep Networks

A Closer Look at Structured Pruning for Neural Network Compression


ViterbiNet: A Deep Learning Based Viterbi Algorithm for Symbol Detection

DeepSIC: Deep Soft Interference Cancellation for Multiuser MIMO Detection

Online Meta-Learning for Hybrid Model-Based Deep Receivers


Code and checkpoints of compressed networks for the paper titled "HYDRA: Pruning Adversarially Robust Neural Networks" (NeurIPS 2020) (https://arxiv.org/abs/2002.10509).

On Pruning Adversarially Robust Neural Networks

Deadwooding: Robust Global Pruning for Deep Neural Networks

Model-Agnostic Meta-Attack: Towards Reliable Evaluation of Adversarial Robustness


Dictionary of obscene words for Ukrainian language

MultiParaDetox: Extending Text Detoxification with Parallel Data to New
  Languages


Repository for the CODAH dataset

Common Sense Beyond English: Evaluating and Improving Multilingual Language Models for Commonsense Reasoning

CODAH: An adversarially-authored question answering dataset for common sense

Workshop on Evaluating Vector-Space Representations for NLP

Vera: A General-Purpose Plausibility Estimation Model for Commonsense Statements

Crystal: Introspective Reasoners Reinforced with Self-Feedback

CODAH: An Adversarially Authored Question-Answer Dataset for Common Sense


BNNs (XNOR, BNN and DoReFa) implementation for PyTorch 1.0+

XNOR-Net: ImageNet Classification Using Binary Convolutional Neural Networks

DoReFa-Net: Training Low Bitwidth Convolutional Neural Networks with Low Bitwidth Gradients

CoopNet: Cooperative Convolutional Neural Network for Low-Power MCUs

International Conference on Electronics, Circuits, and Systems

TentacleNet: A Pseudo-Ensemble Template for Accurate Binary Convolutional Neural Networks


ACL'2022: Prompt for Extraction? PAIE: Prompting Argument Interaction for Event Argument Extraction

Learning How to Ask: Querying LMs with Mixtures of Soft Prompts

Large Language Model Is Not a Good Few-shot Information Extractor, but a Good Reranker for Hard Samples!

AMPERE: AMR-Aware Prefix for Generation-Based Event Argument Extraction Model

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

TextEE: Benchmark, Reevaluation, Reflections, and Future Challenges in Event Extraction


Simple Techniques for Enhancing Sentence Embeddings in Generative Language Models

CoT-BERT: Enhancing Unsupervised Sentence Representation through Chain-of-Thought

Advancing Semantic Textual Similarity Modeling: A Regression Framework
  with Translated ReLU and Smooth K2 Loss


Order-N orbital-free density-functional calculations with machine learning of functional derivatives for semiconductors and metals

Unfolding energy spectra of multi-periodicity materials

Structural stability and energy levels of carbon-related defects in amorphous SiO2 and its interface with SiC

Microscopic Mechanisms of Initial Formation Process of Graphene on SiC(0001) Surfaces: Selective Si Desorption from Step Edges

Mechanisms of initial oxidation of 4H-SiC (0001) and (0001̅) surfaces unraveled by first-principles calculations

Analysis of single and composite structural defects in pure amorphous silicon: A first-principles study

First-Principles Prediction of Densities of Amorphous Materials: The Case of Amorphous Silicon

Journal of the Physical Society of Japan

A precaution for the hybrid density functional calculation of open-shell systems


Library for working with 3D rotations in C++

Fused Angles: A Representation of Body Orientation for Balance

Fused Angles and the Deficiencies of Euler Angles

Bipedal Walking with Corrective Actions in the Tilt Phase Space

Tilt Rotations and the Tilt Phase Space


Variational inference and disentangled representations through unsupervised learning

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

International Conference on Learning Representations

Auto-Encoding Variational Bayes

Disentangling by Factorising

Isolating Sources of Disentanglement in Variational Autoencoders

Understanding disentangling in β-VAE

Variational Inference of Disentangled Latent Concepts from Unlabeled Observations

A Framework for the Quantitative Evaluation of Disentangled Representations

Learning Deep Disentangled Embeddings with the F-Statistic Loss


NIST_FRVT Top 1 Face Recognition, Liveness Detection(Face Anti-Spoof), Face Attribute Analysis Linux Server SDK Demo ☑ Face Recognition ☑ Face Liveness Detection ☑ Face Attribute Analysis

MesoNet: a Compact Facial Video Forgery Detection Network

International Workshop on Information Forensics and Security

Celeb-DF: A Large-scale Challenging Dataset for DeepFake Forensics

A Light CNN for Deep Face Representation With Noisy Labels

DeepID3: Face Recognition with Very Deep Neural Networks

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

The DeepFake Detection Challenge (DFDC) Dataset

DeepFakes: a New Threat to Face Recognition? Assessment and Detection

Biometric Face Presentation Attack Detection With Multi-Channel Convolutional Neural Network

IEEE Transactions on Information Forensics and Security

Unmasking DeepFakes with simple Features

M2TR: Multi-modal Multi-scale Transformers for Deepfake Detection


Python software that uses emcee to fit parametric models to interferometric observations of astronomical sources, appropriately accounting for gravitational lensing as needed.

HerMES: ALMA IMAGING OF HERSCHEL-SELECTED DUSTY STAR-FORMING GALAXIES*

(Sub)millimetre interferometric imaging of a sample of COSMOS/AzTEC submillimetre galaxies

ALMA Resolves the Molecular Gas in a Young Low-metallicity Starburst Galaxy at z = 1.7


Repository for the project "DeepShadows: Separating LSBGs from artifacts using Deep Learning"

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

International Journal of Computer Vision

DeepShadows: Separating Low Surface Brightness Galaxies from Artifacts using Deep Learning

Dwarfs from the Dark (Energy Survey): a machine learning approach to classify dwarf galaxies from multi-band images

Shedding light on low-surface-brightness galaxies in dark energy surveys with transformer models


This project develops the program FORGE. It allows to calculate gene p-values from Genome-Wide Association Data using multivariate methods. The gene-level statistics can be used for pathway or other system biology analyses (check out sister project for additional on pathway analysis with GWAS data: https://github.com/inti/GeneSetAnalysis/wiki). Check our Wiki for more details

Reduced Anxiety and Depression-Like Behaviours in the Circadian Period Mutant Mouse Afterhours

FORGE: multivariate calculation of gene-wide p-values from Genome-Wide Association Studies


Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation

Extensive genomic rearrangements mediated by repetitive sequences in plastomes of Medicago and its relatives

Plastome Structural Conservation and Evolution in the Clusioid Clade of Malpighiales

The Loss of the Inverted Repeat in the Putranjivoid Clade of Malpighiales

Does IR-loss promote plastome structural variation and sequence evolution?

Plastid Phylogenomics and Plastomic Diversity of the Extant Lycophytes

Plastid phylogenomics provides new insights into the systematics, diversification, and biogeography of Cymbidium (Orchidaceae)

A DNA barcode library for woody plants in tropical and subtropical China

Complete plastid genome structure of 13 Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses


Diagnosing failures of fairness transfer across distribution shift in real-world medical settings

Concept-based model explanations for electronic health records

Proceedings of the Conference on Health, Inference, and Learning

Multitask prediction of organ dysfunction in the intensive care unit using sequential subnetwork routing

Journal of the American Medical Informatics Association : JAMIA

Boosting the interpretability of clinical risk scores with intervention predictions


A Kotlin DSL for probabilistic programming.

Summingbird

Quantitative Information Flow with Monads in Haskell

Foundations of Probabilistic Programming

Fast Concurrent Data Sketches

Uncertainty Propagation in Data Processing Systems

Smooth estimates of multiple quantiles in dynamically varying data streams