Adds SPICE metric to coco-caption evaluation server codes

CIDEr: Consensus-based Image Description Evaluation

Microsoft COCO Captions: Data Collection and Evaluation Server

Recurrent Fusion Network for Image Captioning

Neural Wikipedian: Generating Textual Summaries from Knowledge Base Triples

COMIC: Toward A Compact Image Captioning Model With Attention


MS-DAP: downstream analysis pipeline for quantitative proteomics

Activity-dependent translation dynamically alters the proteome of the perisynaptic astrocyte process

Age-Dependent Hippocampal Proteomics in the APP/PS1 Alzheimer Mouse Model: A Comparative Analysis with Classical SWATH/DIA and directDIA Approaches

Succinate mediates inflammation-induced adrenocortical dysfunction


Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation

基因组蛋白质组与生物信息学报

Transcriptome wide association studies: general framework and methods

QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration


Database of genomes integrated from the gut microbiome and other environments

New insights from uncultivated genomes of the global human gut microbiome

Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates

KEMET – A python tool for KEGG Module evaluation and microbial genome annotation expansion

Computational and structural biotechnology journal

Over 50000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa


Repository of "An Empirical Study of Incorporating Pseudo Data into Grammatical Error Correction" (EMNLP-IJCNLP 2019)

Frustratingly Easy System Combination for Grammatical Error Correction

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

Grammatical Error Correction with Contrastive Learning in Low Error Density Domains

Findings of the Association for Computational Linguistics: EMNLP 2021

System Combination via Quality Estimation for Grammatical Error Correction

GPT-3.5 for Grammatical Error Correction

Beyond Hard Samples: Robust and Effective Grammatical Error Correction with Cycle Self-Augmenting


A professionally curated list of awesome resources (paper, code, data, etc.) on transformers in time series.

Deep learning for time series classification: a review

Pre-trained models for natural language processing: A survey

Attention mechanisms in computer vision: A survey

Time-series forecasting with deep learning: a survey

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

Transformers in Time Series: A Survey

Deep Learning for Time Series Forecasting: A Survey

Attention, please! A survey of Neural Attention Models in Deep Learning

Time-distance vision transformers in lung cancer diagnosis from longitudinal computed tomography


This codebase is the official implementation of Test-Time Classifier Adjustment Module for Model-Agnostic Domain Generalization (NeurIPS2021, Spotlight)

In Search of Lost Domain Generalization

Improving Test-Time Adaptation via Shift-agnostic Weight Regularization and Nearest Source Prototypes

Test-Time Adaptation via Self-Training with Nearest Neighbor Information

Feature Alignment and Uniformity for Test Time Adaptation

Test-Time Model Adaptation with Only Forward Passes

Optimization-Free Test-Time Adaptation for Cross-Person Activity Recognition

Decoupled Prototype Learning for Reliable Test-Time Adaptation


Simple Implementation of Pix2Seq model for object detection in PyTorch

Attention Is All You Need

Training data-efficient image transformers & distillation through attention

Pix2seq: A Language Modeling Framework for Object Detection


Code and models from the paper "Layer Normalization"

Normalizing the Normalizers: Comparing and Extending Network Normalization Schemes

Dynamic Layer Normalization for Adaptive Neural Acoustic Modeling in Speech Recognition

Decoding Decoders: Finding Optimal Representation Spaces for Unsupervised Similarity Tasks


WebRISC-V: A Web-Based Education-Oriented RISC-V Pipeline Simulation Environment [PHP]

WebRISC-V: a Web-Based Education-Oriented RISC-V Pipeline Simulation Environment

Workshop On Computer Architecture Education


Creative Commons Attribution Share Alike 4.0 International

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

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

Reference and Document Aware Semantic Evaluation Methods for Korean Language Summarization


Segmentation and Classification models for COVID CT scans (COVID, pneumonia, normal) based on Mask R-CNN.

COVID-CT-Mask-Net: Prediction of COVID-19 from CT Scans Using Regional Features

Detection and Segmentation of Lesion Areas in Chest CT Scans For The Prediction of COVID-19

Lightweight Model For The Prediction of COVID-19 Through The Detection And Segmentation of Lesions in Chest CT Scans


Harvey Lab miniaturized mouse VR rig hardware for virtual navigation and decision-making tasks

Fos ensembles encode and shape stable spatial maps in the hippocampus

Hippocampal place codes are gated by behavioral engagement

Cognitive experience alters cortical involvement in goal-directed navigation

Cognitive experience alters cortical involvement in navigation decisions


COmmon COordinate FRAMEwork in R

HypoMap—a unified single-cell gene expression atlas of the murine hypothalamus

Mesoscale microscopy and image analysis tools for understanding the brain

Progress in biophysics and molecular biology

Mesoscale microscopy for micromammals: image analysis tools for understanding the rodent brain


A computational tool for processing and differentiating PCR duplicates from biological duplicates

RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution

Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling

UMI-Reducer: Collapsing duplicate sequencing reads via Unique Molecular Identifiers


Speech Recognition with the Caffe deep learning framework, migrating to

Deep Speech: Scaling up end-to-end speech recognition

A Clockwork RNN

An Embarrassingly Simple Approach for Trojan Attack in Deep Neural Networks

Building DNN Acoustic Models for Large Vocabulary Speech Recognition

Neural Network Laundering: Removing Black-Box Backdoor Watermarks from Deep Neural Networks


R pkg for Hierarchical Dirichlet Process

Patterns of somatic structural variation in human cancer genomes

Tobacco smoking and somatic mutations in human bronchial epithelium

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver

Classification and Personalized Prognostic Assessment on the Basis of Clinical and Genomic Features in Myelodysplastic Syndromes

Journal of clinical oncology : official journal of the American Society of Clinical Oncology

Somatic Evolution in Non-neoplastic IBD-Affected Colon

Timing the initiation of multiple myeloma

The mutational signature profile of known and suspected human carcinogens in mice

Detection of early seeding of Richter transformation in chronic lymphocytic leukemia

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

A sex-informed approach to improve the personalised decision making process in myelodysplastic syndromes: a multicentre, observational cohort study


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

DEAR: A Novel Deep Learning-based Approach for Automated Program Repair

A Survey on Automated Program Repair Techniques


code for "IFCNN: A General Image Fusion Framework Based on Convolutional Neural Network"

IFCNN: A general image fusion framework based on convolutional neural network

A Distributed Fusion Framework of Multispectral and Panchromatic Images Based on Residual Network

Multimodal medical image fusion in NSST domain with structural and spectral features enhancement

Perceptual Multi-Exposure Fusion

Efficient joint noise removal and multi exposure fusion


code for MICCAI 2019 paper 'Uncertainty-aware Self-ensembling Model for Semi-supervised 3D Left Atrium Segmentation'.

Mutual Consistency Learning for Semi-supervised Medical Image Segmentation

Inconsistency-aware Uncertainty Estimation for Semi-supervised Medical Image Segmentation

Exploring Smoothness and Class-Separation for Semi-supervised Medical Image Segmentation

Enforcing Mutual Consistency of Hard Regions for Semi-supervised Medical Image Segmentation.


ipapy is a Python module to work with International Phonetic Alphabet (IPA) strings

Deciphering Undersegmented Ancient Scripts Using Phonetic Prior

Interpreting Character Embeddings With Perceptual Representations: The Case of Shape, Sound, and Color

Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

The Hidden Folk: Linguistic Properties Encoded in Multilingual Contextual Character Representations

Proceedings of the Workshop on Computation and Written Language (CAWL 2023)


Support, annotation, evaluation, and baseline models for the imSitu dataset.

Situation Recognition: Visual Semantic Role Labeling for Image Understanding

Commonly Uncommon: Semantic Sparsity in Situation Recognition


Implicit Geometric Regularization for Learning Shapes

Shape As Points: A Differentiable Poisson Solver

Going Off-Grid: Continuous Implicit Neural Representations for 3D Vascular Modeling

p-Poisson surface reconstruction in curl-free flow from point clouds

Enhancing Surface Neural Implicits with Curvature-Guided Sampling and Uncertainty-Augmented Representations


SCANPY: large-scale single-cell gene expression data analysis

SPRING: a kinetic interface for visualizing high dimensional single-cell expression data

NGN2 induces diverse neuron types from human pluripotency

Deep Learning in Single-Cell Analysis


Diachronic Embedding for Temporal Knowledge Graph Completion

Representation Learning for Dynamic Graphs: A Survey

TimeTraveler: Reinforcement Learning for Temporal Knowledge Graph Forecasting

Temporal Knowledge Graph Forecasting with Neural ODE

xERTE: Explainable Reasoning on Temporal Knowledge Graphs for Forecasting Future Links

Few-Shot Inductive Learning on Temporal Knowledge Graphs using Concept-Aware Information

ECOLA: Enhancing Temporal Knowledge Embeddings with Contextualized Language Representations

Temporal Fact Reasoning over Hyper-Relational Knowledge Graphs


Scalable Global Optimization via Local Bayesian Optimization

Bayesian Optimization is Superior to Random Search for Machine Learning Hyperparameter Tuning: Analysis of the Black-Box Optimization Challenge 2020

High-Dimensional Bayesian Optimization with Sparse Axis-Aligned Subspaces

Learning Search Space Partition for Black-box Optimization using Monte Carlo Tree Search

Tree-Structured Parzen Estimator: Understanding Its Algorithm Components and Their Roles for Better Empirical Performance

Bayesian Optimization with a Prior for the Optimum

Monte Carlo Tree Search based Variable Selection for High Dimensional Bayesian Optimization

Cautious Bayesian Optimization for Efficient and Scalable Policy Search

c-TPE: Tree-structured Parzen Estimator with Inequality Constraints for Expensive Hyperparameter Optimization

AdaDGS: An adaptive black-box optimization method with a nonlocal directional Gaussian smoothing gradient


Reproduction of OpenAI and DeepMind's "Deep Reinforcement Learning from Human Preferences"

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

Domain Randomization for Transferring Deep Neural Networks from Simulation to the Real World

Deep reinforcement learning from human preferences

Deep Exploration via Bootstrapped DQN


This repository implements SummaryMixing, a simpler, faster and much cheaper replacement to self-attention for automatic speech recognition (see: https://arxiv.org/abs/2307.07421). The code is ready to be used with the SpeechBrain toolkit).

Branchformer: Parallel MLP-Attention Architectures to Capture Local and Global Context for Speech Recognition and Understanding

HyperMixer: An MLP-based Low Cost Alternative to Transformers

HyperConformer: Multi-head HyperMixer for Efficient Speech Recognition

Sumformer: A Linear-Complexity Alternative to Self-Attention for Speech Recognition

Linear-Complexity Self-Supervised Learning for Speech Processing


Package for simulating nonlinear optical spectra

Automatic Feynman diagram generation for nonlinear optical spectroscopies and application to fifth-order spectroscopy with pulse overlaps

Efficient numerical method for predicting nonlinear optical spectroscopies of open systems

QuDPy: A Python-based tool for computing ultrafast non-linear optical responses


GSimp is a Gibbs sampler-based missing value imputation approach

GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies

Missing value imputation in proximity extension assay-based targeted proteomics data


The official implementation for  ECCV22 paper: "FOSTER: Feature Boosting and  Compression for Class-Incremental Learning" in PyTorch.

Dynamic Residual Classifier for Class Incremental Learning

CL2R: Compatible Lifelong Learning Representations

ACM Transactions on Multimedia Computing, Communications, and Applications


Image segmentations of trees outside forest

Layer Normalization

Concurrent Spatial and Channel Squeeze & Excitation in Fully Convolutional Networks

Adaptive Gradient Methods with Dynamic Bound of Learning Rate

A global method to identify trees outside of closed-canopy forests with medium-resolution satellite imagery


A simulation of the true impact on climate and CO2 emissions of an electric car vs a traditional gasoline car, based on science.


An original implementation of "MetaICL Learning to Learn In Context" by Sewon Min, Mike Lewis, Luke Zettlemoyer and Hannaneh Hajishirzi

Multitask Prompted Training Enables Zero-Shot Task Generalization

UnifiedQA: Crossing Format Boundaries With a Single QA System

MetaICL: Learning to Learn In Context

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

Large Language Models Are Latent Variable Models: Explaining and Finding Good Demonstrations for In-Context Learning


pretrained BERT model for cyber security text, learned CyberSecurity Knowledge

SecureBERT: A Domain-Specific Language Model for Cybersecurity

Constructing a Knowledge Graph from Textual Descriptions of Software Vulnerabilities in the National Vulnerability Database

Semantic Ranking for Automated Adversarial Technique Annotation in
  Security Text


Bootstrapping Entity Alignment with Knowledge Graph Embedding, IJCAI 2018

SelfKG: Self-Supervised Entity Alignment in Knowledge Graphs

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

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

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

Knowledge Graph Entity Alignment with Graph Convolutional Networks: Lessons Learned

Two-Stage Entity Alignment: Combining Hybrid Knowledge Graph Embedding with Similarity-Based Relation Alignment

Pacific Rim International Conference on Artificial Intelligence

A Self-supervised Method for Entity Alignment

An Adversarial Transfer Network for Knowledge Representation Learning


C++ Implementation of the Information Bottleneck System

Novel Architectures for Unsupervised Information Bottleneck Based Speaker Diarization of Meetings

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

BERTraffic: A Robust BERT-Based Approach for Speaker Change Detection and Role Identification of Air-Traffic Communications.


Zhuang Chen, Tieyun Qian: Relation-Aware Collaborative Learning for Unified Aspect-Based Sentiment Analysis. ACL 2020: 3685-3694

Meeting of the Association for Computational Linguistics

Structured Sentiment Analysis as Dependency Graph Parsing

YASO: A Targeted Sentiment Analysis Evaluation Dataset for Open-Domain Reviews


Differentially Private Optimization for PyTorch  ♀

Deep Learning with Differential Privacy

Conference on Computer and Communications Security

A General Approach to Adding Differential Privacy to Iterative Training Procedures

Bypassing the Ambient Dimension: Private SGD with Gradient Subspace Identification

Enabling Fast Differentially Private SGD via Just-in-Time Compilation and Vectorization

Kamino: Constraint-Aware Differentially Private Data Synthesis

The Role of Adaptive Optimizers for Honest Private Hyperparameter Selection

Private Stochastic Non-Convex Optimization: Adaptive Algorithms and Tighter Generalization Bounds

Federated Quantum Machine Learning with Differential Privacy

Privacy-Preserving Models for Legal Natural Language Processing

D3p -- A Python Package for Differentially-Private Probabilistic Programming


(CVPR2022) Reflash Dropout in Image Super-Resolution

Discovering Distinctive "Semantics" in Super-Resolution Networks

Federated Learning for Blind Image Super-Resolution


Bayesian neural network package

Scalable Bayesian Optimization Using Deep Neural Networks

Bayesian Optimization with Robust Bayesian Neural Networks

How Powerful are Performance Predictors in Neural Architecture Search?

Bayesian Variational Autoencoders for Unsupervised Out-of-Distribution Detection

Neural Architecture Generator Optimization

Large Language Models to Enhance Bayesian Optimization

Detecting Misclassification Errors in Neural Networks with a Gaussian Process Model

Neural-BO: A Black-box Optimization Algorithm using Deep Neural Networks

Do Bayesian Variational Autoencoders Know What They Don't Know?

Deep Pipeline Embeddings for AutoML


An efficient way to filter duplicate lines from input, à la uniq.

BERTweetFR : Domain Adaptation of Pre-Trained Language Models for French Tweets

GreekBART: The First Pretrained Greek Sequence-to-Sequence Model

Evaluation Of Word Embeddings From Large-Scale French Web Content


BlockSim: An Extensible Simulation Tool forBlockchain Systems

BlockSim: An Extensible Simulation Tool for Blockchain Systems

Blockchain Simulators: A Systematic Mapping Study

An In-Depth Review on Blockchain Simulators for IoT Environments

Towards Practical Applications in Modeling Blockchain System


Transfer learning for time series classification

A Survey on Time-Series Pre-Trained Models

Deep learning for time series classification


An other implementation of GRU4REC using PyTorch

Session-based Recommendations with Recurrent Neural Networks

Recurrent Neural Networks with Top-k Gains for Session-based Recommendations

International Conference on Information and Knowledge Management

Learning Post-Hoc Causal Explanations for Recommendation

Rethinking Cross-Domain Sequential Recommendation under Open-World Assumptions

The Effect of Third Party Implementations on Reproducibility

Proceedings of the 17th ACM Conference on Recommender Systems

SLMRec: Empowering Small Language Models for Sequential Recommendation

Large Language Models meet Collaborative Filtering: An Efficient
  All-round LLM-based Recommender System


Snow property inversion from remote sensing (SPIReS)

Snow Property Inversion From Remote Sensing (SPIReS): A Generalized Multispectral Unmixing Approach With Examples From MODIS and Landsat 8 OLI

IEEE Transactions on Geoscience and Remote Sensing

COVID-19 lockdowns show reduced pollution on snow and ice in the Indus River Basin

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

Evaluation of E3SM land model snow simulations over the western United States


transposable element typing pipeline

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs

Molecular characterization of carbapenemase-producing Enterobacterales in a tertiary hospital in Lima, Peru


A python package to model Circular Economy policy and technological interventions in Environmentally Extended Input-Output Analysis starting from mrSUTs (EXIOBASE V3.3)


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

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

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

Distill2Vec: Dynamic Graph Representation Learning with Knowledge Distillation

Learning Representation over Dynamic Graph using Aggregation-Diffusion Mechanism


[CVPR 2023] Label-Free Liver Tumor Segmentation

Label-Free Liver Tumor Segmentation

Early Detection and Localization of Pancreatic Cancer by Label-Free Tumor Synthesis

Synthetic Tumors Make AI Segment Tumors Better

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

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


Modeling Temporal Data as Continuous Functions with Stochastic Process Diffusion

Provably Convergent Schrödinger Bridge with Applications to Probabilistic Time Series Imputation

Stochastic Optimal Control for Diffusion Bridges in Function Spaces


3D-RetinaNet a baseline models on ROAD dataset

Online Real-time Multiple Spatiotemporal Action Localisation and Prediction

ROAD: The Road Event Awareness Dataset for Autonomous Driving

ROAD-R: the autonomous driving dataset with logical requirements


Evaluating Protein Transfer Learning with TAPE

Is Transfer Learning Necessary for Protein Landscape Prediction?

Contextual Lensing of Universal Sentence Representations

Fixed-Length Protein Embeddings using Contextual Lenses


Vector-Quantized Contrastive Predictive Coding for Acoustic Unit Discovery and Voice Conversion

Representation Learning with Contrastive Predictive Coding

Neural Discrete Representation Learning

Vector-quantized neural networks for acoustic unit discovery in the ZeroSpeech 2020 challenge

Towards unsupervised phone and word segmentation using self-supervised vector-quantized neural networks


Passage Re-ranking with BERT

Question Rewriting for Conversational Question Answering

Learning-to-Rank with BERT in TF-Ranking

A Comparison of Question Rewriting Methods for Conversational Passage Retrieval

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

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

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

Explicit Query Rewriting for Conversational Dense Retrieval

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

Learning Representations and Agents for Information Retrieval


Spike sorter for electrophysiology data

Flexible timing by temporal scaling of cortical responses

The Largest Response Component in the Motor Cortex Reflects Movement Timing but Not Movement Type

Cortical preparatory activity indexes learned motor memories

Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1

Reinforcement regulates timing variability in thalamus


A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.

Uncovering new families and folds in the natural protein universe

Geometricus Represents Protein Structures as Shape-mers Derived from Moment Invariants

Fast and adaptive protein structure representations for machine learning


ICML'2022: Black-Box Tuning for Language-Model-as-a-Service & EMNLP'2022: BBTv2: Towards a Gradient-Free Future with Large Language Models


SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity detection toolkit.

Multiple wheat genomes reveal global variation in modern breeding

High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome

PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study

Database : the journal of biological databases and curation

Phylloxera and Aphids Show Distinct Features of Genome Evolution Despite Similar Reproductive Modes

bioRxiv : the preprint server for biology


[CVPR 2020] A Large-Scale Dataset for Real-World Face Forgery Detection

DeeperForensics-1.0: A Large-Scale Dataset for Real-World Face Forgery Detection

FakeAVCeleb: A Novel Audio-Video Multimodal Deepfake Dataset

Delving into Sequential Patches for Deepfake Detection

DeeperForensics Challenge 2020 on Real-World Face Forgery Detection: Methods and Results

Block shuffling learning for Deepfake Detection

Robust Deepfake On Unrestricted Media: Generation And Detection

DeepFakes Detection: the DeeperForensicsDeeperForensics Dataset and Challenge

Handbook of Digital Face Manipulation and Detection


This repository contains the data and code introduced in the paper "CrowS-Pairs: A Challenge Dataset for Measuring Social Biases in Masked Language Models" (EMNLP 2020).

Bias and Fairness in Large Language Models: A Survey

Measuring Fairness with Biased Rulers: A Comparative Study on Bias Metrics for Pre-trained Language Models

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

Measuring Fairness with Biased Rulers: A Survey on Quantifying Biases in Pretrained Language Models

Tackling Bias in Pre-trained Language Models: Current Trends and Under-represented Societies

An Efficient Multilingual Language Model Compression through Vocabulary Trimming

Robust Evaluation Measures for Evaluating Social Biases in Masked Language Models


Randomized online matrix factorization

Dictionary Learning for Massive Matrix Factorization

Learning Neural Representations of Human Cognition across Many fMRI Studies

Stochastic Subsampling for Factorizing Huge Matrices

Subsampled online matrix factorization with convergence guarantees


finetune with keras

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

Distilling the Knowledge in a Neural Network

DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter

TinyBERT: Distilling BERT for Natural Language Understanding


A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles

Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction

Genome-wide association study of problematic opioid prescription use in 132,113 23andMe research participants of European ancestry

Cell type-specific and cross-population polygenic risk score analyses of MIR137 gene pathway in schizophrenia

3D genome organization links non-coding disease-associated variants to genes

Frontiers in cell and developmental biology

Connecting gene regulatory relationships to neurobiological mechanisms of brain disorders

Limited Association between Schizophrenia Genetic Risk Factors and Transcriptomic Features

Neurogenetic and multi-omic sources of overlap among sensation seeking, alcohol consumption, and alcohol use disorder

medRxiv : the preprint server for health sciences

MULTI-ANCESTRY META-ANALYSIS OF TOBACCO USE DISORDERS PRIORITIZES NOVEL CANDIDATE RISK GENES AND REVEALS ASSOCIATIONS WITH NUMEROUS HEALTH OUTCOMES


Marching cubes (and related tools) for Python

Generative Multiplane Images: Making a 2D GAN 3D-Aware

NeRFMeshing: Distilling Neural Radiance Fields into Geometrically-Accurate 3D Meshes

3D generation on ImageNet

Occupancy Planes for Single-view RGB-D Human Reconstruction

Learning Neural Radiance Fields from Multi-View Geometry

A cyber-physical system to design 3D models using mixed reality technologies and deep learning for additive manufacturing


A systematic review of homomorphic encryption and its contributions in healthcare industry

A Review of Homomorphic Encryption for Privacy-Preserving Biometrics

FHEBench: Benchmarking Fully Homomorphic Encryption Schemes

k-Anonymously Private Search over Encrypted Data


Statistical NLG for spoken dialogue systems

Why We Need New Evaluation Metrics for NLG

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

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

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

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

Semantic Noise Matters for Neural Natural Language Generation

Findings of the E2E NLG Challenge

A Context-aware Natural Language Generator for Dialogue Systems

Annual Meeting of the Special Interest Group on Discourse and Dialogue

Controlling Personality-Based Stylistic Variation with Neural Natural Language Generators

Training a Natural Language Generator From Unaligned Data

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

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


[CVPR2019] The Perfect Match: 3D Point Cloud Matching with Smoothed Densities

End-to-End Learning Local Multi-view Descriptors for 3D Point Clouds

ARCS: Accurate Rotation and Correspondence Search


Creating quantum circuit diagrams in TikZ

Expressibility and Entangling Capability of Parameterized Quantum Circuits for Hybrid Quantum‐Classical Algorithms

Quantum Error Correction: An Introductory Guide

Factoring with qutrits: Shor's algorithm on ternary and metaplectic quantum architectures

Evaluation of Parameterized Quantum Circuits: on the relation between classification accuracy, expressibility and entangling capability

Protecting quantum memories using coherent parity check codes

Hybrid Quantum Classical Graph Neural Networks for Particle Track Reconstruction

Logic Synthesis for Quantum Computing

Quantum-accelerated constraint programming

Performance of Particle Tracking Using a Quantum Graph Neural Network

Simulating Majorana zero modes on a noisy quantum processor


Reusable BatchBALD implementation

BatchBALD: Efficient and Diverse Batch Acquisition for Deep Bayesian Active Learning

Advancing Deep Active Learning & Data Subset Selection: Unifying Principles with Information-Theory Intuitions


Paxos protocol framework

WPaxos: Wide Area Network Flexible Consensus

Bottlenecks in Blockchain Consensus Protocols

BigBFT: A Multileader Byzantine Fault Tolerance Protocol for High Throughput

Multilayer Environment and Toolchain for Holistic NetwOrk Design and Analysis

BunchBFT: Across-Cluster Consensus Protocol


Python package for calculating reference/potential evapotranspiration (ETo).

Robust Vegetation Parameterization for Green Roofs in the EPA Stormwater Management Model (SWMM)


This repository contains the SpeechBrain Benchmarks

Speech Self-Supervised Representations Benchmarking: A Case for Larger Probing Heads

CL-MASR: A Continual Learning Benchmark for Multilingual ASR

DASB -- Discrete Audio and Speech Benchmark

How Should We Extract Discrete Audio Tokens from Self-Supervised Models?


Preliminary DRAGON2 with the various cross section options

Implications of current nuclear cross sections on secondary cosmic rays with the upcoming DRAGON2 code

Journal of Cosmology and Astroparticle Physics

Combined analyses of the antiproton production from cosmic-ray interactions and its possible dark matter origin

FLUKA cross sections for cosmic-ray interactions with the DRAGON2 code

New Markov-Chain Monte Carlo analyses for the evaluation of the antiproton background

Cosmic-ray propagation and production of secondary particles in the Galaxy

Multimessenger search for electrophilic feebly interacting particles from supernovae

Robust constraints on feebly interacting particles using XMM-Newton

Antiproton bounds on dark matter annihilation from a combined analysis using the DRAGON2 code

Cosmic-Ray Propagation Models Elucidate the Prospects for Antinuclei
  Detection

On the origin of the spectral features observed in the cosmic ray spectrum


the hierfstat package

Using Genomic Selection to Leverage Resources among Breeding Programs: Consortium-Based Breeding

Systematics of the Stripetail Darter, Etheostoma kennicotti (Putnam), and the Distinctiveness of the Upper Cumberland Endemic Etheostoma cumberlandicum Jordan and Swain

Population genetic structure of the maize weevil, Sitophilus zeamais, in southern Mexico

Genetic diversity in the IZUMO1-JUNO protein-receptor pair involved in human reproduction

Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size


Easy access to NOAA Integrated Surface Database (ISD) surface meteorological observations

Spring Festival and COVID‐19 Lockdown: Disentangling PM Sources in Major Chinese Cities

Visibility as a proxy for air quality in East Africa

Changing supersites: assessing the impact of the southern UK EMEP supersite relocation on measured atmospheric composition

Meteorological Normalisation Using Boosted Regression Trees to Estimate the Impact of COVID-19 Restrictions on Air Quality Levels

International journal of environmental research and public health

Variation of pollution sources and health effects on air pollution before and during COVID-19 pandemic in Linfen, Fenwei Plain


MAW: a suite on the computation and application of Minimal Absent Words

Linear-time Computation of Minimal Absent Words Using Suffix Array

Alignment-free sequence comparison using absent words

Linear-Time Sequence Comparison Using Minimal Absent Words & Applications

emMAW: computing minimal absent words in external memory

Bacteria classification using minimal absent words


Statistical comparison of multiple algorithms

MrSQM: Fast Time Series Classification with Symbolic Representations

Scalable classifier-agnostic channel selection for multivariate time series classification

Improving Accuracy of Interpretability Measures in Hyperparameter Optimization via Bayesian Algorithm Execution

Barrakuda: A Hybrid Evolutionary Algorithm for Minimum Capacitated Dominating Set Problem

Evolving Neural Networks in Reinforcement Learning by means of UMDAc

New Characterizations and Efficient Local Search for General Integer Linear Programming

Pattern recognition in data as a diagnosis tool


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

An Information Theory-Based Feature Selection Framework for Big Data Under Apache Spark

IEEE Transactions on Systems, Man, and Cybernetics: Systems

A greedy feature selection algorithm for Big Data of high dimensionality

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

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


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


Simod is a tool for automated BPS model discovery

Automated discovery of business process simulation models from event logs

Discovering Generative Models from Event Logs: Data-driven Simulation vs Deep Learning

Discovering Business Process Simulation Models in the Presence of Multitasking


Learning to detect an animal sound from five examples

Few-shot bioacoustic event detection at the DCASE 2022 challenge

Surrey System for DCASE 2022 Task 5: Few-shot Bioacoustic Event Detection with Segment-level Metric Learning

Few-shot bioacoustic event detection at the DCASE 2023 challenge

Mind the Domain Gap: a Systematic Analysis on Bioacoustic Sound Event
  Detection


A neural gym for training deep learning models to carry out geoscientific image segmentation. Works best with labels generated using https://github.com/Doodleverse/dash_doodler

A 1.2 Billion Pixel Human-Labeled Dataset for Data-Driven Classification of Coastal Environments

Segmentation Zoo Res-UNet models for Landsat-8 satellite imagery, Coast Train v1 Landsat-8 4-class subset.

Zenodo (CERN European Organization for Nuclear Research)

Segmentation Zoo UNet models for Landsat-8 satellite imagery, Coast Train v1 Landsat-8 4-class subset.


The R climate package: an interface for downloading in-situ meteorological (and hydrological) dataset


Python meteor physics library developed by the Western Meteor Physics Group.

Estimating trajectories of meteors: an observational Monte Carlo approach – I. Theory

Monthly notices of the Royal Astronomical Society

Estimating trajectories of meteors: an observational Monte Carlo approach – II. Results

The Winchcombe fireball—That lucky survivor

A dynamical analysis of the Taurid Complex: evidence for past orbital convergences

Monthly Notices of the Royal Astronomical Society

Computing optical meteor flux using global meteor network data

Direct measurement of decimetre-sized rocky material in the Oort cloud

Iron Rain: measuring the occurrence rate and origin of small iron meteoroids at Earth

τ Herculid meteor shower in the night of 30/31 May 2022 and the meteoroid properties

Comparing the dynamics of Jupiter-family Comets and comet-like fireballs


These scripts create daily survey station daily temperature and anomaly plots as the ships work their way through the Bering Sea. These ships are conducting NOAA Fisheries' Alaska Fisheries Science Center's fisheries independent surveys in the Eastern Bering Sea. Scripts pull temperatures from google drive, entered by FPCs at sea, create daily maps and composite gifs, and then push the maps to google drive for the communications team.


A survey on data plane programming with P4: Fundamentals, advances, and applied research

Automating In-Network Machine Learning

P4Testgen: An Extensible Test Oracle For P4

Open Source Compiling for V1Model RMT Switch: Making Data Center Networking Innovation Accessible


Continuum modelling for electrochemical devices.


A modest Feature Finder (moFF) to extract  MS1 intensities from Thermo raw file

The Salivary Protein Repertoire of the Polyphagous Spider Mite Tetranychus urticae: A Quest for Effectors

Understanding Cervical Cancer through Proteomics

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform

Update on the moFF Algorithm for Label-Free Quantitative Proteomics.


RANDAO: A DAO working as RNG of Ethereum

A scalable verification solution for blockchains

Astraea: A Decentralized Blockchain Oracle

Probabilistic Smart Contracts: Secure Randomness on the Blockchain

Detecting nondeterministic payment bugs in Ethereum smart contracts

Proceedings of the ACM on Programming Languages

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

Blockchain Vulnerabilities in Practice

Cryptocurrency Smart Contracts for Distributed Consensus of Public Randomness

Verifiable Computing Applications in Blockchain

Trustless and Bias-resistant Game-theoretic Distributed Randomness

Committee selection in DAG distributed ledgers and applications


Pure Numpy Implementation of the Coherent Point Drift Algorithm

Scalable Gromov-Wasserstein Learning for Graph Partitioning and Matching

Decoding locomotion from population neural activity in moving C. elegans

3DeeCellTracker, a deep learning-based pipeline for segmenting and tracking cells in 3D time lapse images

Parallel visual circuitry in a basal chordate

Fast and Accurate Point Cloud Registration using Trees of Gaussian Mixtures

Robust recognition and exploratory analysis of crystal structures via Bayesian deep learning

Direct Fitting of Gaussian Mixture Models

Enumerating Calabi‐Yau Manifolds: Placing Bounds on the Number of Diffeomorphism Classes in the Kreuzer‐Skarke List

Partial Transport for Point-Cloud Registration


Holistic Evaluation of Language Models

Investigating BERT's Knowledge of Language: Five Analysis Methods with NPIs

Are Natural Language Inference Models IMPPRESsive? Learning IMPlicature and PRESupposition

BLiMP: The Benchmark of Linguistic Minimal Pairs for English

ViLMA: A Zero-Shot Benchmark for Linguistic and Temporal Grounding in Video-Language Models


[GSOC] Greek language support for spacy.io python NLP software

GREEK-BERT: The Greeks visiting Sesame Street

Hellenic Conference on Artificial Intelligence

Upon Improving the Performance of Localized Healthcare Virtual Assistants

AthPPA: A Data Visualization Tool for Identifying Political Popularity over Twitter

A Review of Greek NLP Technologies for Chatbot Development

Proceedings of the 27th Pan-Hellenic Conference on Progress in Computing and Informatics


June is a framework for agent based modelling in an epidemiological and geographical context.

June: open-source individual-based epidemiology simulation

Bayesian emulation and history matching of JUNE

A Mixed-Method Approach to Determining Contact Matrices in the Cox's Bazar Refugee Settlement


Apache Commons Codec

Extracting Concise Bug-Fixing Patches from Human-Written Patches in Version Control Systems

A comprehensive study of pseudo-tested methods

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

IEEE Transactions on Software Engineering

DSpot: Test Amplification for Automatic Assessment of Computational Diversity

Predicting Crash Fault Residence via Simplified Deep Forest Based on A Reduced Feature Set

Automatic Diversity in the Software Supply Chain


Experimental GitHub read-only mirror of ns-3 development repository, will be kept in sync with original Mercurial repository; pull requests not accepted at the moment. http://www.nsnam.org/

Scalability analysis of large-scale LoRaWAN networks in ns-3

LR-FHSS-Sim: A Discrete-Event Simulator for LR-FHSS Networks


Optimizing inference proxy for LLMs

Self-Consistency Improves Chain of Thought Reasoning in Language Models

Chain-of-Thought Reasoning Without Prompting

Mixture-of-Agents Enhances Large Language Model Capabilities

Monte Carlo Tree Search Boosts Reasoning via Iterative Preference
  Learning

In-Context Principle Learning from Mistakes

Re-Reading Improves Reasoning in Large Language Models

Mutual Reasoning Makes Smaller LLMs Stronger Problem-Solvers

Unsupervised Evaluation of Code LLMs with Round-Trip Correctness

Prover-Verifier Games improve legibility of LLM outputs

Entropy-Based Decoding for Retrieval-Augmented Large Language Models


Unsupervised Statistical Machine Translation

An Effective Approach to Unsupervised Machine Translation

When Does Unsupervised Machine Translation Work?

Bilingual Lexicon Induction through Unsupervised Machine Translation

(Almost) Unsupervised Grammatical Error Correction using Synthetic Comparable Corpus

Workshop on Innovative Use of NLP for Building Educational Applications

CUNI Systems for the Unsupervised News Translation Task in WMT 2019

Towards Unsupervised Grammatical Error Correction using Statistical Machine Translation with Synthetic Comparable Corpus


GlossBERT: BERT for Word Sense Disambiguation with Gloss Knowledge (EMNLP 2019)

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

WiC-TSV: An Evaluation Benchmark for Target Sense Verification of Words in Context


Code for the paper "Adversarial Generator-Encoder Networks"

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

Variational Approaches for Auto-Encoding Generative Adversarial Networks

It Takes (Only) Two: Adversarial Generator-Encoder Networks

Pioneer Networks: Progressively Growing Generative Autoencoder

Semi-supervised image attribute editing using generative adversarial networks

Pairwise Augmented GANs with Adversarial Reconstruction Loss


Context-Aware Attentive Knowledge Tracing

Enhancing Knowledge Tracing via Adversarial Training

MonaCoBERT: Monotonic attention based ConvBERT for Knowledge Tracing

Deep knowledge tracing with learning curves

Difficulty-Focused Contrastive Learning for Knowledge Tracing with a Large Language Model-Based Difficulty Prediction

Deep Knowledge Tracing with Learning Curves


Code of the paper: Cross-lingual Knowledge Graph Alignment via Graph Convolutional Networks.

Relational Reflection Entity Alignment

International Conference on Information and Knowledge Management

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

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

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

Knowledge Graph Entity Alignment with Graph Convolutional Networks: Lessons Learned

Dependency-aware Self-training for Entity Alignment


A python module for English lemmatization and inflection.

It’s Morphin’ Time! Combating Linguistic Discrimination with Inflectional Perturbations

Meeting of the Association for Computational Linguistics

Video2Commonsense: Generating Commonsense Descriptions to Enrich Video Captioning

Temporal Reasoning in Natural Language Inference

Mind Your Inflections! Improving NLP for Non-Standard Englishes with Base-Inflection Encoding

Tractable Control for Autoregressive Language Generation

Decrypting Cryptic Crosswords: Semantically Complex Wordplay Puzzles as a Target for NLP

On the Robustness of Intent Classification and Slot Labeling in Goal-oriented Dialog Systems to Real-world Noise

Mobile-Env: Building Qualified Evaluation Benchmarks for LLM-GUI Interaction

An Extended Sequence Tagging Vocabulary for Grammatical Error Correction

Robustness of Explanation Methods for NLP Models


PyTorch implementation of over 30 realtime semantic segmentations models, e.g. BiSeNetv1, BiSeNetv2, CGNet, ContextNet, DABNet, DDRNet, EDANet, ENet, ERFNet, ESPNet, ESPNetv2, FastSCNN, ICNet, LEDNet, LinkNet, PP-LiteSeg, SegNet, ShelfNet, STDC, SwiftNet, and support knowledge distillation, distributed training etc.

Distilling the Knowledge in a Neural Network

BiSeNet: Bilateral Segmentation Network for Real-time Semantic Segmentation

ENet: A Deep Neural Network Architecture for Real-Time Semantic Segmentation

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

LinkNet: Exploiting Encoder Representations for Efficient Semantic Segmentation

Visual Communications and Image Processing

BiSeNet V2: Bilateral Network with Guided Aggregation for Real-Time Semantic Segmentation

ESPNet: Efficient Spatial Pyramid of Dilated Convolutions for Semantic Segmentation

Rethinking BiSeNet For Real-time Semantic Segmentation

CGNet: A Light-weight Context Guided Network for Semantic Segmentation

ESPNetv2: A Light-weight, Power Efficient, and General Purpose Convolutional Neural Network


Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028  See also http://www.ioexplorer.org for interactive visuallization

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

Targeting TMEM176B Enhances Antitumor Immunity and Augments the Efficacy of Immune Checkpoint Blockers by Unleashing Inflammasome Activation

Identification of 15 lncRNAs Signature for Predicting Survival Benefit of Advanced Melanoma Patients Treated with Anti-PD-1 Monotherapy

Identification and Validation in a Novel Quantification System of Ferroptosis Patterns for the Prediction of Prognosis and Immunotherapy Response in Left- and Right-Sided Colon Cancer

Multi-modal molecular programs regulate melanoma cell state

Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab


Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

A Reference Genome Assembly of American Bison, Bison bison bison

The clove (Syzygium aromaticum) genome provides insights into the eugenol biosynthesis pathway

Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata

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

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

bioRxiv : the preprint server for biology

A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii

De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica

A chromosome-level genome assembly for the dugong (Dugong dugon)

A chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting

Chromosome-scale assemblies of S. malaccense, S. aqueum, S. jambos, and S. syzygioides provide insights into the evolution of Syzygium genomes


Code for 'Dynamics-Aware Unsupervised Discovery of Skills' (DADS). Enables skill discovery without supervision, which can be combined with model-based control.

Emergent Real-World Robotic Skills via Unsupervised Off-Policy Reinforcement Learning

Continual Learning of Control Primitives: Skill Discovery via Reset-Games

Dynamics-Aware Unsupervised Skill Discovery

International Conference on Learning Representations

Meta-Learning Parameterized Skills


transform-average-concatenate (TAC) method for end-to-end microphone permutation and number invariant ad-hoc beamforming.

Dual-path RNN: efficient long sequence modeling for time-domain single-channel speech separation

End-to-end Microphone Permutation and Number Invariant Multi-channel Speech Separation

FaSNet: Low-latency Adaptive Beamforming for Multi-microphone Audio Processing

L3DAS21 Challenge: Machine Learning for 3D Audio Signal Processing

Group Communication With Context Codec for Lightweight Source Separation

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

DESNet: A Multi-channel Network for Simultaneous Speech Dereverberation, Enhancement and Separation

SpatialNet: Extensively Learning Spatial Information for Multichannel Joint Speech Separation, Denoising and Dereverberation

A Time-Domain Real-Valued Generalized Wiener Filter for Multi-Channel Neural Separation Systems

Microphone Array Generalization for Multichannel Narrowband Deep Speech Enhancement

Implicit Filter-and-sum Network for Multi-channel Speech Separation


Calibration of Convolutional Neural Networks

Intra Order-preserving Functions for Calibration of Multi-Class Neural Networks

Better Uncertainty Calibration via Proper Scores for Classification and Beyond

Introspective Learning : A Two-Stage Approach for Inference in Neural Networks

Post-hoc Calibration of Neural Networks by g-Layers

The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera

Scaling of Class-wise Training Losses for Post-hoc Calibration


Collaborative text editor written in Elixir/Phoenix, running at alchemy.digitalfreepen.com

Real Differences between OT and CRDT in Correctness and Complexity for Consistency Maintenance in Co-Editors

Proceedings of the ACM on Human-Computer Interaction

Real Differences between OT and CRDT in Building Co-Editing Systems and Real World Applications

Real Differences between OT and CRDT for Co-Editors


Code for "RayNet: Learning Volumetric 3D Reconstruction with Ray Potentials", CVPR 2018

SurfaceNet: An End-to-end 3D Neural Network for Multiview Stereopsis

International Conference on Computer Vision

Learned Multi-Patch Similarity


An attempt at replicating the Matching Networks for One Shot Learning in Tensorflow - Paper URL: https://arxiv.org/pdf/1606.04080.pdf

Matching Networks for One Shot Learning

Discriminative k-shot learning using probabilistic models

Learning from Few Samples: A Survey


利用bert预训练的中文模型进行文本分类  数据集中文情感分析语料chnsenticorp

Attention Is All You Need

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

Semi-supervised Sequence Learning

NEZHA: Neural Contextualized Representation for Chinese Language Understanding

WeLM: A Well-Read Pre-trained Language Model for Chinese

A Fine-grained Interpretability Evaluation Benchmark for Neural NLP

ERNIE-Tiny : A Progressive Distillation Framework for Pretrained Transformer Compression

SeqGPT: An Out-of-the-box Large Language Model for Open Domain Sequence Understanding

Exploiting Word Semantics to Enrich Character Representations of Chinese Pre-trained Models

Evaluation on ChatGPT for Chinese Language Understanding


Zero-Resource Knowledge-Grounded Dialogue Generation

Learning to Express in Knowledge-Grounded Conversation

Contextual Knowledge Learning for Dialogue Generation


VCTK multi-speaker tacotron for ICASSP 2020

Zero-Shot Multi-Speaker Text-To-Speech with State-of-the-art Neural Speaker Embeddings

Can Speaker Augmentation Improve Multi-Speaker End-to-End TTS?


ISSAFE: Improving Semantic Segmentation in Accidents by Fusing Event-based Data

Exploring Event-driven Dynamic Context for Accident Scene Segmentation

Vision-Based Traffic Accident Detection and Anticipation: A Survey


[NeurIPS 2023] OV-PARTS: Towards Open-Vocabulary Part Segmentation

Image Segmentation Using Text and Image Prompts

A Simple Baseline for Open-Vocabulary Semantic Segmentation with Pre-trained Vision-language Model

CAT-Seg: Cost Aggregation for Open-Vocabulary Semantic Segmentation


Contains code for the NeurIPS 2019 paper "Practical Deep Learning with Bayesian Principles"

Bayesian Deep Learning via Subnetwork Inference

Structured Dropout Variational Inference for Bayesian Neural Networks


Code for ACL 2022 paper "CONTaiNER: Few-Shot Named Entity Recognition via Contrastive Learning"

Few-NERD: A Few-Shot Named Entity Recognition Dataset

Type-Aware Decomposed Framework for Few-Shot Named Entity Recognition

Language Model Pre-Training with Sparse Latent Typing


Workshop and Challenge on  Perceptual Image Restoration  and Manipulation

Photo-Realistic Single Image Super-Resolution Using a Generative Adversarial Network

The Perception-Distortion Tradeoff

Progressive Perception-Oriented Network for Single Image Super-Resolution

Journey Towards Tiny Perceptual Super-Resolution

RankSRGAN: Super Resolution Generative Adversarial Networks With Learning to Rank

Tarsier: Evolving Noise Injection in Super-Resolution GANs

Kernelized Back-Projection Networks for Blind Super Resolution

Unsupervised Denoising for Super-Resolution (UDSR) of Real-World Images


Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms

Present Scenario of Circular RNAs (circRNAs) in Plants

Circular RNAs: Methodological challenges and perspectives in cardiovascular diseases

Journal of cellular and molecular medicine

Circ-camk4 involved in cerebral ischemia/reperfusion induced neuronal injury

Circular RNAs in the cardiovascular system

Advances in circular RNAs and their role in glioma (Review)

Disease-Associated Circular RNAs: From Biology to Computational Identification

Computational approaches for circRNAs prediction and in silico characterization

Novel Identified Circular Transcript of RCAN2, circ-RCAN2, Shows Deviated Expression Pattern in Pig Reperfused Infarcted Myocardium and Hypoxic Porcine Cardiac Progenitor Cells In Vitro

International journal of molecular sciences


MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry

Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer–Giedion syndrome and Cornelia de Lange syndrome-4

Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells

Biallelic structural variations within FGF12 detected by long-read sequencing in epilepsy

Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing


WikiDiverse: A Multimodal Entity Linking Dataset with Diversified Contextual Topics and Entity Types

Named Entity and Relation Extraction with Multi-Modal Retrieval

Benchmarking Diverse-Modal Entity Linking with Generative Models


This tool is used for generating Manufacture Usage Description(MUD) from Device Traffic Trace(PCAP)

Clear as MUD: Generating, Validating and Applying IoT Behavioral Profiles

Verifying and Monitoring IoTs Network Behavior using MUD Profiles

Enforcing Behavioral Profiles through Software-Defined Networks in the Industrial Internet of Things

SoK: Beyond IoT MUD Deployments -- Challenges and Future Directions


Towards increasing stability of neural networks for continual learning: https://arxiv.org/abs/2006.06958.pdf (NeurIPS'20)

Understanding the Role of Training Regimes in Continual Learning

Generalisation Guarantees for Continual Learning with Orthogonal Gradient Descent

Dropout as an Implicit Gating Mechanism For Continual Learning


A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

Exploring Chemical Space with Score-based Out-of-distribution Generation

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

Learning Subpocket Prototypes for Generalizable Structure-based Drug Design

Benchmarking structure-based three-dimensional molecular generative
  models using GenBench3D: ligand conformation quality matters


Report processing and protein quantification for MS-based proteomics

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

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

Pan-cancer proteomic map of 949 human cell lines

The proteomic landscape of genome-wide genetic perturbations

Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics

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

Proteome Remodeling of the Eye Lens at 50 Years Identified With Data-Independent Acquisition

The bigger picture: global analysis of solubilization performance of classical detergents versus new synthetic polymers utilizing shotgun proteomics

DIAgui: a Shiny application to process the output from DIA-NN


the Zurich Atmosphere Purge. Sky subtraction for MUSE.

MusE GAs FLOw and Wind (MEGAFLOW) II. A study of gas accretion around z approximate to 1 star-forming galaxies with background quasars

Monthly Notices of the Royal Astronomical Society

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

The Astrophysical Journal Supplement Series

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


PyTorch implementation of the end-to-end coreference resolution model with different higher-order inference methods.

Revealing the Myth of Higher-Order Inference in Coreference Resolution

A Structured Span Selector

Parallel Data Helps Neural Entity Coreference Resolution

The Role of Common Ground for Referential Expressions in Social Dialogues


Fre-GAN: Adversarial Frequency-consistent Audio Synthesis

KaraTuner: Towards end to end natural pitch correction for singing voice in karaoke


An Implementation of Poptrie IP Routing Table Lookup Algorithm

Fast Longest Prefix Matching by Exploiting SIMD Instructions

Surgical DDoS Filtering With Fast LPM


Plotly dataset-visualization pairs, feature extraction scripts, and model training code for VizML (CHI 2019)

VizML: A Machine Learning Approach to Visualization Recommendation

Table2Charts: Recommending Charts by Learning Shared Table Representations

Agnostic Visual Recommendation Systems: Open Challenges and Future Directions


A k-mer based program for the identification of known plasmids from whole-genome sequencing reads

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads

The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria

The Emergence of the Tetrathionate Reductase Operon in the Escherichia coli/Shigella Pan-genome.

Insights into the genetic contexts of sulfonamide resistance among early clinical isolates of Acinetobacter baumannii.

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases


Absorption Line Fitter

The stellar metallicities of massive quiescent galaxies at 1.0 < z < 1.3 from KMOS+VANDELS

The Assembly History of M87 through Radial Variations in Chemical Abundances of Its Field Star and Globular Cluster Populations

Initial mass function variability from the integrated light of diverse stellar systems


WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies

Gapless genome assembly of East Asian finless porpoise

Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations

Chromosome-Level Genome Assembly of the Rare and Endangered Tropical Plant Speranskia yunnanensis (Euphorbiaceae)


Repo for ShenNong-TCM-LLM (“神农”大模型，首个中医药中文大模型)

PromptCBLUE: A Chinese Prompt Tuning Benchmark for the Medical Domain

Datasets for Large Language Models: A Comprehensive Survey

IvyGPT: InteractiVe Chinese pathwaY language model in medical domain


A hybrid DNN–LSTM model for detecting phishing URLs

Detecting Phishing Sites -- An Overview

Mitigating Adversarial Gray-Box Attacks Against Phishing Detectors

IEEE Transactions on Dependable and Secure Computing

Recent Advancements in Machine Learning for Cybercrime Prediction


The Dynamic Agroforestry Coffee Crop Model


source code of our paper presents in EMNLP 2019. https://www.aclweb.org/anthology/D19-1345/

Text Level Graph Neural Network for Text Classification

Graph Classification by Mixture of Diverse Experts

Text Classification: A Review, Empirical, and Experimental Evaluation

Connecting the Dots: What Graph-Based Text Representations Work Best for Text Classification Using Graph Neural Networks?


GndNet: Fast ground plane estimation and point cloud segmentation for autonomous vehicles using deep neural networks.

GndNet: Fast Ground Plane Estimation and Point Cloud Segmentation for Autonomous Vehicles

Ground estimation and point cloud segmentation using SpatioTemporal Conditional Random Field

GroundGrid: LiDAR Point Cloud Ground Segmentation and Terrain Estimation


Learning node representation using edge semantics

edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

UniNet: Scalable Network Representation Learning with Metropolis-Hastings Sampling

A Comprehensive Analytical Survey on Unsupervised and Semi-Supervised Graph Representation Learning Methods


Scene Graph Generation by Iterative Message Passing

Neural Motifs: Scene Graph Parsing with Global Context

Mapping Images to Scene Graphs with Permutation-Invariant Structured Prediction


Cleaned up version of the PlotMachines code

PlotMachines: Outline-Conditioned Generation with Dynamic Plot State Tracking

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

LongStory: Coherent, Complete and Length Controlled Long story Generation


Unsorted scripts for bioinformatics

Sequencing abasic sites in DNA at single-nucleotide resolution

ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs

DNA sequence-dependent formation of heterochromatin nanodomains

Epigenetic and Genetic Differentiation Between Coregonus Species Pairs.


A parallel, open-source geothermal flow simulator


Official repository for the paper "Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval"

ProGen2: Exploring the Boundaries of Protein Language Models

Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval

RITA: a Study on Scaling Up Generative Protein Sequence Models

Accurate and Definite Mutational Effect Prediction with Lightweight Equivariant Graph Neural Networks

Ensemble Learning with Supervised Methods Based on Large-Scale Protein Language Models for Protein Mutation Effects Prediction

Multi-level Protein Representation Learning for Blind Mutational Effect Prediction


Analysis of EBOV genome sequence from Guinea, Sierra Leone and Liberia from 2014-2016

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models

From viral evolution to spatial contagion: a biologically modulated Hawkes model

Identifying spatio-temporal dynamics of Ebola in Sierra Leone using virus genomes

Fitting stochastic epidemic models to gene genealogies using linear noise approximation

On the importance of assessing topological convergence in Bayesian phylogenetic inference


This is a implementation of SDNE (Structural Deep Network embedding)

A Comprehensive Survey on Graph Neural Networks

IEEE transactions on neural networks and learning systems

Graph Neural Networks: A Review of Methods and Applications

Structural Deep Network Embedding

Deep Learning on Graphs: A Survey

Network Representation Learning: A Survey

Graph-based Semi-supervised Learning: A Comprehensive Review

Billion-scale Network Embedding with Iterative Random Projection

Seven-Layer Model in Complex Networks Link Prediction: A Survey

Empirical Comparison of Graph Embeddings for Trust-Based Collaborative Filtering

Search Efficient Binary Network Embedding


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

Somatic inflammatory gene mutations in human ulcerative colitis epithelium

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

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

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

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

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency

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

Zenodo (CERN European Organization for Nuclear Research)


Meta-Learning with Differentiable Convex Optimization

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

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

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


Implementation of seq2seq model for Visual Storytelling Challenge (VIST) http://visionandlanguage.net/VIST/index.html

Effective Approaches to Attention-based Neural Machine Translation

Visual Storytelling

Stories for Images-in-Sequence by using Visual and Narrative Components

International Conference on Telecommunications


Improving the Transformer translation model with document-level context

Attention Is All You Need

Neural Machine Translation by Jointly Learning to Align and Translate

Improving the Transformer Translation Model with Document-Level Context

THUMT: An Open Source Toolkit for Neural Machine Translation

Can Your Context-Aware MT System Pass the DiP Benchmark Tests? : Evaluation Benchmarks for Discourse Phenomena in Machine Translation


Fast Approximate Membership Filters (C++)

Xor Filters: Faster and Smaller Than Bloom and Cuckoo Filters

ACM Journal of Experimental Algorithmics

Binary Fuse Filters: Fast and Smaller Than Xor Filters

Prefix Filter: Practically and Theoretically Better Than Bloom


Steven C. Y. Hung, Cheng-Hao Tu, Cheng-En Wu, Chien-Hung Chen, Yi-Ming Chan, and Chu-Song Chen, "Compacting, Picking and Growing for Unforgetting Continual Learning," Thirty-third Conference on Neural Information Processing Systems, NeurIPS 2019

Increasingly Packing Multiple Facial-Informatics Modules in A Unified Deep-Learning Model via Lifelong Learning

International Conference on Multimedia Retrieval

Canonical Saliency Maps: Decoding Deep Face Models


CP-JKU submission to DCASE 20

The Receptive Field as a Regularizer in Deep Convolutional Neural Networks for Acoustic Scene Classification

Receptive Field Regularization Techniques for Audio Classification and Tagging With Deep Convolutional Neural Networks

Receptive-field-regularized CNN variants for acoustic scene classification

Low-Complexity Models for Acoustic Scene Classification Based on Receptive Field Regularization and Frequency Damping


Large-scale multi-document summarization dataset and code

Multi-News: a Large-Scale Multi-Document Summarization Dataset and Abstractive Hierarchical Model

A Comprehensive Survey on Process-Oriented Automatic Text Summarization
  with Exploration of LLM-Based Methods

Leveraging Locality in Abstractive Text Summarization

A comprehensive review of automatic text summarization techniques: method, data, evaluation and coding

A Spectral Method for Unsupervised Multi-Document Summarization

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

PoBRL: Optimizing Multi-Document Summarization by Blending Reinforcement Learning Policies

Chunk, Align, Select: A Simple Long-sequence Processing Method for Transformers

Incorporating Linguistic Knowledge for Abstractive Multi-document Summarization

SEAM: A Stochastic Benchmark for Multi-Document Tasks

Multi-doc Hybrid Summarization via Salient Representation Learning

Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 5: Industry Track)


Transition-based dependency parser based on stack LSTMs

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

DyNet: The Dynamic Neural Network Toolkit

Improved Transition-Based Parsing by Modeling Characters instead of Words with LSTMs

Distilling an Ensemble of Greedy Dependency Parsers into One MST Parser

Greedy, Joint Syntactic-Semantic Parsing with Stack LSTMs

Parsing as Pretraining

DeepCx: A transition-based approach for shallow semantic parsing with complex constructional triggers

Empirical Methods in Natural Language Processing

Greedy Transition-Based Dependency Parsing with Stack LSTMs

International Conference on Computational Logic

Differentia compositionem facit. A Slower-Paced and Reliable Parser for Latin


Work for the tree sequence inference paper.

Inferring whole-genome histories in large population datasets

Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits

Inferring the ancestry of everyone


Python library for fast time-series analysis on CUDA GPUs

An 8.8 Minute Orbital Period Eclipsing Detached Double White Dwarf Binary

Exploring the dependence of hot Jupiter occurrence rates on stellar mass with TESS

Discovery and characterization of five new eclipsing AM CVn systems

Monthly notices of the Royal Astronomical Society

The ZTF Source Classification Project. I. Methods and Infrastructure

Magnetic braking saturates: evidence from the orbital period distribution of low-mass detached eclipsing binaries from ZTF

The ZTF Source Classification Project - II. Periodicity and variability processing metrics

A Systematic Search for Short-period Close White Dwarf Binary Candidates Based on Gaia EDR3 Catalog and Zwicky Transient Facility Data

GPU-Accelerated Periodic Source Identification in Large-Scale Surveys:
  Measuring P and Ṗ

CoRoT-TESS eclipsing binaries with light-travel-time effect

Variable stars in the residual light curves of OGLE-IV eclipsing binaries towards the Galactic Bulge


Image classification for imaging flow cytometry.

CellProfiler 3.0: Next-generation image processing for biology

Label‐Free Identification of White Blood Cells Using Machine Learning

Cytometry. Part A : the journal of the International Society for Analytical Cytology

Objective assessment of stored blood quality by deep learning

Label‐Free Leukemia Monitoring by Computer Vision

Label-free assessment of red blood cell storage lesions by deep learning


EfficientDet: Scalable and Efficient Object Detection

A ConvNet for the 2020s

YOLOX: Exceeding YOLO Series in 2021

MLP-Mixer: An all-MLP Architecture for Vision

BEiT: BERT Pre-Training of Image Transformers

ResNeSt: Split-Attention Networks

Designing Network Design Spaces

DINOv2: Learning Robust Visual Features without Supervision

Swin Transformer V2: Scaling Up Capacity and Resolution

PVT v2: Improved baselines with Pyramid Vision Transformer


V2X simulator

Performance Analysis of Sidelink 5G-V2X Mode 2 Through an Open-Source Simulator

Adaptive Repetition Strategies in IEEE 802.11bd V2X Networks

Performance analysis of IEEE 802.11p preamble insertion in C-V2X sidelink signals for co-channel coexistence

A Methodology for Abstracting the Physical Layer of Direct V2X Communications Technologies

Analysis of Co-Channel Coexistence Mitigation Methods Applied to IEEE 802.11p and 5G NR-V2X Sidelink


Source code for the Last Millennium Reanalysis (LMR) project

Last Millennium Reanalysis with an expanded proxy database and seasonal proxy modeling

Greenland temperature and precipitation over the last 20 000 years using data assimilation

cfr (v2024.1.26): a Python package for climate field reconstruction


An R Package for downloading, preprocessing, and statistical downscaling of the European Centre for Medium-range Weather Forecasts ReAnalysis 5 (ERA5) family provided by the European Centre for Medium‐Range Weather Forecasts (ECMWF).


Data and code for Shen, Horikawa, Majima, and Kamitani (2019) Deep image reconstruction from human brain activity. PLoS Comput. Biol. http://dx.doi.org/10.1371/journal.pcbi.1006633.

Generating Images with Perceptual Similarity Metrics based on Deep Networks

Reconstructing visual illusory experiences from human brain activity

Mental image reconstruction from human brain activity: Neural decoding of mental imagery via deep neural network-based Bayesian estimation

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

Inter-individual deep image reconstruction via hierarchical neural code conversion

Sound reconstruction from human brain activity via a generative model with brain-like auditory features

Attentionally modulated subjective images reconstructed from brain activity


BeamformIt acoustic beamforming software

Far-Field Automatic Speech Recognition

Automated evaluation of psychotherapy skills using speech and language technologies

Multi-Channel Automatic Speech Recognition Using Deep Complex Unet

Multichannel AV-wav2vec2: A Framework for Learning Multichannel Multi-Modal Speech Representation


Score-based Generative Models (Diffusion Models) for Speech Enhancement and Dereverberation

Speech Enhancement and Dereverberation With Diffusion-Based Generative Models

Speech Enhancement with Score-Based Generative Models in the Complex STFT Domain

StoRM: A Diffusion-Based Stochastic Regeneration Model for Speech Enhancement and Dereverberation

Analysing Diffusion-based Generative Approaches Versus Discriminative Approaches for Speech Restoration

Reducing the Prior Mismatch of Stochastic Differential Equations for Diffusion-based Speech Enhancement

Target Speech Extraction with Conditional Diffusion Model

Diffusion-Based Speech Enhancement with Joint Generative and Predictive Decoders

Noise-aware Speech Enhancement using Diffusion Probabilistic Model

The PESQetarian: On the Relevance of Goodhart's Law for Speech Enhancement

Unsupervised speech enhancement with diffusion-based generative models


Code for the CVPR2021 paper "Patch-NetVLAD: Multi-Scale Fusion of Locally-Global Descriptors for Place Recognition"

StructVPR: Distill Structural Knowledge with Weighting Samples for Visual Place Recognition

Towards Seamless Adaptation of Pre-trained Models for Visual Place
  Recognition

CricaVPR: Cross-image Correlation-aware Representation Learning for
  Visual Place Recognition


Explainable AI framework for data scientists. Explain & debug any blackbox machine learning model with a single line of code. We are looking for co-authors to take this project forward. Reach out @ ms8909@nyu.edu


A suite of tools to explore protein structures with Protein Blocks :snake:

Protein flexibility in the light of structural alphabets

Extension of the classical classification of β-turns

PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins

Database : the journal of biological databases and curation

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

Global analysis of VHHs framework regions with a structural alphabet

Investigation of the impact of PTMs on the protein backbone conformation

Data set of intrinsically disordered proteins analysed at a local protein conformation level

Evaluation of the Potential Impact of In Silico Humanization on VHH Dynamics

International journal of molecular sciences


LibSA4Py: Light-weight static analysis for extracting type hints and features

Type4Py: Practical Deep Similarity Learning-Based Type Inference for Python

Proceedings of the 44th International Conference on Software Engineering

ManyTypes4Py: A Benchmark Python Dataset for Machine Learning-based Type Inference

Cross-Domain Evaluation of a Deep Learning-Based Type Inference System


A Multilingual and Multilevel Representation Learning Toolkit for NLP

Distributed Representations of Sentences and Documents

BilBOWA: Fast Bilingual Distributed Representations without Word Alignments

UsingWord Embedding for Cross-Language Plagiarism Detection

MultiVec: a Multilingual and Multilevel Representation Learning Toolkit for NLP

CompiLIG at SemEval-2017 Task 1: Cross-Language Plagiarism Detection Methods for Semantic Textual Similarity

Bilingual Embeddings and Word Alignments for Translation Quality Estimation

Proceedings of the First Conference on Machine Translation: Volume 2,
          Shared Task Papers

Discovering Light Verb Constructions and their Translations from Parallel Corpora without Word Alignment

Proceedings of the 13th Workshop on Multiword Expressions (MWE 2017)


Sequence-to-sequence TTS based on Kyubyong's dc_tts

Efficiently Trainable Text-to-Speech System Based on Deep Convolutional Networks with Guided Attention

International Conference on Acoustics, Speech, and Signal Processing

Confidence through Attention

Laughter Synthesis: Combining Seq2seq modeling with Transfer Learning

Speaker verification-derived loss and data augmentation for DNN-based multispeaker speech synthesis

Location, Location: Enhancing the Evaluation of Text-to-Speech Synthesis Using the Rapid Prosody Transcription Paradigm


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


Molecular Property Prediction: A Multilevel Quantum Interactions Modeling Perspective

Alchemy: A Quantum Chemistry Dataset for Benchmarking AI Models

Deep Learning for Optoelectronic Properties of Organic Semiconductors


Translation models for 22 scheduled languages of India

IndicTrans2: Towards High-Quality and Accessible Machine Translation Models for all 22 Scheduled Indian Languages

MEGAVERSE: Benchmarking Large Language Models Across Languages, Modalities, Models and Tasks

Assessing Translation capabilities of Large Language Models involving English and Indian Languages

INDIC QA BENCHMARK: A Multilingual Benchmark to Evaluate Question Answering capability of LLMs for Indic Languages


A community repository for benchmarking Bayesian methods

Gaussian Processes for Big Data

Inference in Deep Gaussian Processes using Stochastic Gradient Hamiltonian Monte Carlo

Differentiable Compositional Kernel Learning for Gaussian Processes

Structured Variational Learning of Bayesian Neural Networks with Horseshoe Priors

Gaussian Process Conditional Density Estimation

Bayesian Model Selection, the Marginal Likelihood, and Generalization

Orthogonally Decoupled Variational Gaussian Processes

Additive Gaussian Processes Revisited

Tighter Bounds on the Log Marginal Likelihood of Gaussian Process Regression Using Conjugate Gradients

Guided Deep Kernel Learning


Tree edit distance using the Zhang Shasha algorithm

Does String-Based Neural MT Learn Source Syntax?

Generating Sentences from Disentangled Syntactic and Semantic Spaces

A Multi-Task Approach for Disentangling Syntax and Semantics in Sentence Representations

Cost-effective End-to-end Information Extraction for Semi-structured Document Images

Automated Clustering and Program Repair for Introductory Programming Assignments

Role of persistent cascades in diffusion.

Leveraging Natural Supervision for Language Representation Learning and Generation

MEEL: Multi-Modal Event Evolution Learning


Provides a function to measure the energy usage of another function.

Energy and Policy Considerations for Deep Learning in NLP

Energy Usage Reports: Environmental awareness as part of algorithmic accountability


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

A Distance For Multistage Stochastic Optimization Models

Dynamic generation of scenario trees

Computational optimization and applications

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

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

New Algorithms And Fast Implementations To Approximate Stochastic Processes


Kinship (genetic relatedness) using GBS (genotyping-by-sequencing) with Depth adjustment

Developing Successful Breeding Programs for New Zealand Aquaculture: A Perspective on Progress and Future Genomic Opportunities

Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō

Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data

Divergent Genomic Selection for Herbage Accumulation and Days-To-Heading in Perennial Ryegrass

Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus)

Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls (Larus bulleri)

Using genotyping‐by‐sequencing to predict gender in animals


Framework for testing models with AI2 leaderboards

Do Fine-tuned Commonsense Language Models Really Generalize?

Understanding Prior Bias and Choice Paralysis in Transformer-based Language Representation Models through Four Experimental Probes

A Formalism and Approach for Improving Robustness of Large Language Models Using Risk-Adjusted Confidence Scores


Access ZTF data from Python

ZTF J185139.81+171430.3 = ZTF18abnbzvx: the second white dwarf pulsar?

Orbital and spin periods of the candidate white dwarf pulsar ASASSN-V J205543.90+240033.5

New candidates for AM Canum Venaticorum stars among ASAS-SN transients

Publications of the Astronomical Society of Japan

BC Cassiopeiae: First detection of IW Andromedae-type phenomenon among post-eruption novae

Gaia22ayj: outburst from a deeply eclipsing 9.36-min binary?

Growth-rate measurement with type-Ia supernovae using ZTF survey simulations

Z Cam star PY Per in SU UMa state?

ASASSN-V J205543.90+240033.5: another white dwarf pulsar?

Emerging ordinary superhumps as the standard candle for WZ Sge stars

Romanov V48: unusual intermediate polar in the period gap


Main package


Density Estimation Likelihood-Free Inference with neural density estimators and adaptive acquisition of simulations

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

SBI -- A toolkit for simulation-based inference

Fast likelihood-free cosmology with neural density estimators and active learning

Benchmarking Simulation-Based Inference

Likelihood-free inference with emulator networks

Nuisance hardened data compression for fast likelihood-free inference

Simulation-based Inference of Reionization Parameters from 3D Tomographic 21 cm Light-cone Images

Solving high-dimensional parameter inference: marginal posterior densities & Moment Networks

Cosmic shear: Inference from forward models

Sum of the masses of the Milky Way and M31: A likelihood-free inference approach


Python version of Barycorr

Python Leap Second Management and Implementation of Precise Barycentric Correction (barycorrpy)

Radial Velocity Measurements of HR 8799 b and c with Medium Resolution Spectroscopy

Medium-resolution spectrum of the exoplanet HIP 65426 b

The CARMENES search for exoplanets around M dwarfs. Guaranteed time observations Data Release 1 (2016-2020)

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

TOI-1759 b: A transiting sub-Neptune around a low mass star characterized with SPIRou and TESS

The SPIRou Legacy Survey Rotation period of quiet M dwarfs from circular polarization in near-infrared spectral lines: I. The SPIRou APERO analysis

Constraints on accretion disk size in the massive type 1 quasar PG 2308+098 from optical continuum reverberation lags

Optical and near-infrared stellar activity characterization of the early M dwarf Gl 205 with SOPHIE and SPIRou

Discovery of a proto-white dwarf with a massive unseen companion


Repository with code for MaChAmp: https://aclanthology.org/2021.eacl-demos.22/

Massive Choice, Ample Tasks (MaChAmp): A Toolkit for Multi-task Learning in NLP

Experimental Standards for Deep Learning in Natural Language Processing Research

EventNet-ITA: Italian Frame Parsing for Events


This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

PCSF: An R-package for network-based interpretation of high-throughput data

Clinical protein science in translational medicine targeting malignant melanoma

Computational Analysis of Phosphoproteomics Data in Multi‐Omics Cancer Studies

Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data

Methods in molecular biology (Clifton, N.J.)

Functional stratification of cancer drugs through integrated network similarity


List of major cities of the world as a datapackage

Global Syntactic Variation in Seven Languages: Toward a Computational Dialectology

Mapping Languages and Demographics with Georeferenced Corpora

Towards Sentence Level Inference Attack Against Pre-trained Language Models

Proceedings on Privacy Enhancing Technologies

KG-FRUS: a Novel Graph-based Dataset of 127 Years of US Diplomatic Relations

Low-resource neural machine translation with morphological modeling


a bash pipeline for RAD sequencing

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

Signatures of selection underpinning rapid coral adaptation to the world’s warmest reefs

A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination

Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies

Zenodo (CERN European Organization for Nuclear Research)

Genetic patterns in peripheral marine populations of the fusilier fish Caesio cuning within the Kuroshio Current

Location and Species Matters: Variable Influence of the Environment on the Gene Flow of Imperiled, Native and Invasive Cottontails

Weak Genetic Isolation and Putative Phenotypic Selection in the Wild Carnation Dianthus virgineus (Caryophyllaceae)


Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

Do Transformers Really Perform Bad for Graph Representation?

DeeperGCN: All You Need to Train Deeper GCNs

Vision GNN: An Image is Worth Graph of Nodes

Training Graph Neural Networks with 1000 Layers

Node Feature Extraction by Self-Supervised Multi-scale Neighborhood Prediction

Graph Sparsification via Mixture of Graphs


The Renewable Energy Potential(V) eXchange Tool: reVX


A benchmark environment for fully cooperative human-AI performance.

On the Utility of Learning about Humans for Human-AI Coordination

Heterogeneous Multi-agent Zero-Shot Coordination by Coevolution

A Hierarchical Approach to Population Training for Human-AI Collaboration

Quantifying Zero-shot Coordination Capability with Behavior Preferring Partners

Select to Perfect: Imitating desired behavior from large multi-agent data

Explaining the Behaviour of Reinforcement Learning Agents in a Multi-Agent Cooperative Environment Using Policy Graphs


The Ludii general game system, developed as part of the ERC-funded Digital Ludeme Project.

General Board Game Concepts

Ludii Game Logic Guide

General Board Geometry

Extracting tactics learned from self-play in general games

The Ludii Game Description Language is Universal

Spatial State-Action Features for General Games

Optimised Playout Implementations for the Ludii General Game System


SmartBugs: A Framework to Analyze Ethereum Smart Contracts

Empirical Review of Automated Analysis Tools on 47,587 Ethereum Smart Contracts

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

Symbolic value-flow static analysis: deep, precise, complete modeling of Ethereum smart contracts

Proceedings of the ACM on Programming Languages

Source Code Obfuscation for Smart Contracts

Asia-Pacific Software Engineering Conference

SmartBugs 2.0: An Execution Framework for Weakness Detection in Ethereum Smart Contracts

Evolution of automated weakness detection in Ethereum bytecode: a comprehensive study

Smart Contract Upgradeability on the Ethereum Blockchain Platform: An Exploratory Study

AutoMESC: Automatic Framework for Mining and Classifying Ethereum Smart Contract Vulnerabilities and Their Fixes

VOLCANO: Detecting Vulnerabilities of Ethereum Smart Contracts Using Code Clone Analysis

Soley: Identification and Automated Detection of Logic Vulnerabilities
  in Ethereum Smart Contracts Using Large Language Models


One Class Splitting Criteria for Random Forests

Revisiting randomized choices in isolation forests

A meta-level analysis of online anomaly detectors


Galactic Dynamics in python

galpy: A python LIBRARY FOR GALACTIC DYNAMICS

The Astrophysical Journal Supplement Series

Vertical waves in Gaia DR2

Chemodynamics of the Milky Way. I. The first year of APOGEE data

HAL (Le Centre pour la Communication Scientifique Directe)

Confirming chemical clocks: asteroseismic age dissection of the Milky Way disc(s)

Monthly Notices of the Royal Astronomical Society

Universality of free fall from the orbital motion of a pulsar in a stellar triple system

Evidence from APOGEE for the presence of a major building block of the halo buried in the inner Galaxy

Monthly notices of the Royal Astronomical Society

Apocenter Pile-up: Origin of the Stellar Halo Density Break

A time-resolved picture of our Milky Way’s early formation history

Linear perturbation theory for tidal streams and the small-scale CDM power spectrum

DYNAMICAL MODELING OF TIDAL STREAMS


USB: Universal-Scale Object Detection Benchmark (BMVC 2022)

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

MMDetection: Open MMLab Detection Toolbox and Benchmark

Swin Transformer V2: Scaling Up Capacity and Resolution

PVT v2: Improved baselines with Pyramid Vision Transformer

MetaFormer is Actually What You Need for Vision

ResNet strikes back: An improved training procedure in timm

Generalized Focal Loss V2: Learning Reliable Localization Quality Estimation for Dense Object Detection

Focal Modulation Networks

CBNet: A Composite Backbone Network Architecture for Object Detection

Scale-Equalizing Pyramid Convolution for Object Detection


Hooks for VCOCO

Visual Semantic Role Labeling

Detecting Visual Relationships Using Box Attention

Weakly-supervised HOI Detection via Prior-guided Bi-level Representation Learning

Classifying All Interacting Pairs in a Single Shot


Example of using revealed "Spectre" exploit (CVE-2017-5753 and CVE-2017-5715)

SpecuSym: Speculative Symbolic Execution for Cache Timing Leak Detection

Fight Hardware with Hardware: Systemwide Detection and Mitigation of Side-channel Attacks Using Performance Counters

RT-Sniper: A Low-Overhead Defense Mechanism Pinpointing Cache Side-Channel Attacks


Phenome Exome Association and Correlation Of Key phenotypes

Rare variant contribution to human disease in 281,104 UK Biobank exomes

Rare variant associations with plasma protein levels in the UK Biobank

Human genetics uncovers MAP3K15 as an obesity-independent therapeutic target for diabetes

Disease prediction with multi-omics and biomarkers empowers case–control genetic discoveries in the UK Biobank


PyTorch implementation of Audio Flamingo: A Novel Audio Language Model with Few-Shot Learning and Dialogue Abilities.

Listen, Think, and Understand

LLark: A Multimodal Foundation Model for Music

Improving Text-To-Audio Models with Synthetic Captions


MobileNetV2: Inverted Residuals and Linear Bottlenecks

Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation

Rethinking Atrous Convolution for Semantic Image Segmentation


An R-shiny app that provides backsplice and canonical splicing analysis for both circular RNA (circRNA) and parental transcripts

Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing

Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants

Ularcirc: Visualisation and enhanced analysis of circular RNAs via back and canonical forward splicing


Create pgm map from Gazebo world file for ROS localization

iRotate: Active Visual SLAM for Omnidirectional Robots

Active Visual SLAM with Independently Rotating Camera

Design and Implementation of a Modular UUV Simulation Platform

Integration of 4D BIM and Robot Task Planning: Creation and Flow of
  Construction-Related Information for Action-Level Simulation of Indoor Wall
  Frame Installation


A new adversarial purification method that uses the forward and reverse processes of diffusion models to remove adversarial perturbations.

Diffusion Models for Adversarial Purification

Adversarial Example Does Good: Preventing Painting Imitation from Diffusion Models via Adversarial Examples

On the Limitations of Stochastic Pre-processing Defenses

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

Can Protective Perturbation Safeguard Personal Data from Being Exploited by Stable Diffusion?

Instruct2Attack: Language-Guided Semantic Adversarial Attacks

Unifying Gradients to Improve Real-World Robustness for Deep Networks

Classifier Guidance Enhances Diffusion-based Adversarial Purification by
  Preserving Predictive Information


Pretrained GANs in PyTorch: StyleGAN2, BigGAN, BigBiGAN, SAGAN, SNGAN, SelfCondGAN, and more

Representation Topology Divergence: A Method for Comparing Neural Network Representations

DreamTeacher: Pretraining Image Backbones with Deep Generative Models


marineHeatWaves is a module for python which implements the Marine Heatwave (MHW)  definition of Hobday et al. (2016, Prog Ocean).

Longer and more frequent marine heatwaves over the past century

Projected Marine Heatwaves in the 21st Century and the Potential for Ecological Impact

Insights into projected changes in marine heatwaves from a high-resolution ocean circulation model

Threat by marine heatwaves to adaptive large marine ecosystems in an eddy-resolving model

Subseasonal prediction of the 2020 Great Barrier Reef and Coral Sea marine heatwave

Marine Heatwaves and Their Depth Structures on the Northeast U.S. Continental Shelf

Assessing Outcomes in Stratospheric Aerosol Injection Scenarios Shortly After Deployment

Tropical western and central Pacific marine heatwave data calculated from gridded sea surface temperature observations and CMIP6

Southern Europe and Western Asia Marine Heat Waves (SEWA-MHWs): a dataset based on macro events

The rapid rise of severe marine heat wave systems


Mechanical Turk on your own machine.

Large Language Models and Simple, Stupid Bugs

Can machine learning improve patient selection for cardiac resynchronization therapy?

Text Extraction and Retrieval from Smartphone Screenshots: Building a Repository for Life in Media

Advancing Data for Street-level Flood Vulnerability: Extraction of Variables from Google Street View in Quito, Ecuador


XL-mHG: A Semiparametric Test for Enrichment in Ranked Lists.

GO-PCA: An Unsupervised Method to Explore Gene Expression Data Using Prior Knowledge

The XL-mHG test for gene set enrichment

The XL-mHG Test For Enrichment: A Technical Report

The XL-mHG test for enrichment: Algorithms, bounds, and power


U-Time: A Fully Convolutional Network for Time Series Segmentation Applied to Sleep Staging

U-Sleep's resilience to AASM guidelines

Quantifying the Impact of Data Characteristics on the Transferability of Sleep Stage Scoring Models