Temporal IMLinUCB - a solution for Online Influence Maximization problem in Temporal Networks (based on IMLinUCB)

node2vec: Scalable Feature Learning for Networks

Online Influence Maximization under Independent Cascade Model with Semi-Bandit Feedback

Online Influence Maximization in Non-Stationary Social Networks

International Workshop on Quality of Service


Attention U-Net: Learning Where to Look for the Pancreas

Multiclass Weighted Loss for Instance Segmentation of Cluttered Cells

International Conference on Information Photonics

HA U-Net: Improved Model for Building Extraction From High Resolution Remote Sensing Imagery


The code of the AAAI-20 paper "Attractive or Faithful? Popularity-Reinforced Learning for Inspired Headline Generation".

Abstractive Text Summarization using Sequence-to-sequence RNNs and Beyond

Fast Abstractive Summarization with Reinforce-Selected Sentence Rewriting


A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.

Single-Cell Genomics of Novel Actinobacteria With the Wood–Ljungdahl Pathway Discovered in a Serpentinizing System

Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams

Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock

Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy


Code base for the EMNLP 2021 paper, "Multi-granularity Textual Adversarial Attack with Behavior Cloning".

T3: Tree-Autoencoder Constrained Adversarial Text Generation for Targeted Attack


A Matlab implementation for automatic segmentation with a graphical user interface

AutoCellSeg: robust automatic colony forming unit (CFU)/cell analysis using adaptive image segmentation and easy-to-use post-editing techniques

Principal component-based image segmentation: a new approach to outline in vitro cell colonies

A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations


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

Domain-Adversarial Training of Neural Networks

Deep Domain Confusion: Maximizing for Domain Invariance

EdgeConnect: Generative Image Inpainting with Adversarial Edge Learning

Syn2Real: Forgery Classification via Unsupervised Domain Adaptation


Code for "SCHA-VAE: Hierarchical Context Aggregation for Few-Shot Generation" @ ICML 2022

Hierarchical Few-Shot Generative Models

Diversity vs. Recognizability: Human-like generalization in one-shot
  generative models


An R package for creating mirrored Manhattan plots

Investigation of Autosomal Genetic Sex Differences in Parkinson's Disease

A unified framework identifies new links between plasma lipids and diseases from electronic medical records across large-scale cohorts

Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults

GALC variants affect galactosylceramidase enzymatic activity and risk of Parkinson’s disease

Medical data and machine learning improve power of stroke genome-wide association studies


Mastering Visual Continuous Control: Improved Data-Augmented Reinforcement Learning

Temporal Difference Learning for Model Predictive Control

Simplified Temporal Consistency Reinforcement Learning


Code for "Adversarial Over-Sensitivity and Over-Stability Strategies for Dialogue Models (CoNLL 2018)"

Get To The Point: Summarization with Pointer-Generator Networks

A Hierarchical Latent Variable Encoder-Decoder Model for Generating Dialogues

Multiresolution Recurrent Neural Networks: An Application to Dialogue Response Generation

Towards a Robust Deep Neural Network in Texts: A Survey


Tools for processing and analyzing JWST data

Discovery and properties of ultra-high redshift galaxies (9 < z < 12) in the JWST ERO SMACS 0723 Field

The JWST Hubble Sequence: The Rest-Frame Optical Evolution of Galaxy
  Structure at $1.5 < z < 8$

EPOCHS VI: The Size and Shape Evolution of Galaxies since z ~ 8 with
  JWST Observations

EPOCHS VII: Discovery of high redshift ($6.5 < z < 12$) AGN candidates
  in JWST ERO and PEARLS data

EPOCHS Paper II: The Ultraviolet Luminosity Function from 7.5<z<13.5
  using 110 square arcminutes of deep, blank-field data from the PEARLS Survey
  and Public Science Programmes

Extending the extinction law in 30 Doradus to the infrared with JWST

JEMS: A deep medium-band imaging survey in the Hubble Ultra-Deep Field
  with JWST NIRCam & NIRISS

A JWST investigation into the bar fraction at redshifts 1 < z < 3

The hierarchical formation of 30 Doradus as seen by JWST

Magellanic System Stars Identified in SMACS J0723.3-7327 James Webb Space Telescope Early Release Observations Images


EE-Net: Exploitation-Exploration Neural Networks in Contextual Bandits

Doubly High-Dimensional Contextual Bandits: An Interpretable Model for Joint Assortment-Pricing

Neural Exploitation and Exploration of Contextual Bandits

Contextual Bandits with Online Neural Regression


Fast Correlation Function Calculator

The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: 1000 multi-tracer mock catalogues with redshift evolution and systematics for galaxies and quasars of the final data release

Monthly notices of the Royal Astronomical Society

BOSS Correlation Function analysis from the Effective Field Theory of Large-Scale Structure

Updated constraints from the effective field theory analysis of the BOSS power spectrum on early dark energy

Consistency of effective field theory analyses of the BOSS power spectrum

The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: cosmological implications from multitracer BAO analysis with galaxies and voids

BOSS full-shape analysis from the EFTofLSS with exact time dependence

The DESI N-body Simulation Project – II. Suppressing sample variance with fast simulations

Zenodo (CERN European Organization for Nuclear Research)

Model BOSS & eBOSS Luminous Red Galaxies at 0.2 < z < 1.0 using SubHalo Abundance Matching with 3 parameters

Fast Correlation Function Calculator -- A high-performance pair counting
  toolkit

Cosmic void exclusion models and their impact on the distance scale
  measurements from large scale structure


Implementations in both Matlab and R of the CIMLR method. The manuscript of the method is available at: https://www.nature.com/articles/s41467-018-06921-8

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival

Evaluation and comparison of multi-omics data integration methods for cancer subtyping

SMRT: Randomized Data Transformation for Cancer Subtyping and Big Data Analysis


Rigorous free fermion entanglement renormalization from wavelet theory

Rigorous Free-Fermion Entanglement Renormalization from Wavelet Theory

Quantum Circuit Approximations and Entanglement Renormalization for the Dirac Field in 1+1 Dimensions

Communications in mathematical physics/Communications in Mathematical Physics

Bosonic entanglement renormalization circuits from wavelet theory


Code to run the ASEBO algorithm from the paper: From Complexity to Simplicity: Adaptive ES-Active Subspaces for Blackbox Optimization... please get in touch if interested!!

A Scalable Evolution Strategy with Directional Gaussian Smoothing for Blackbox Optimization.

Accelerating Reinforcement Learning with a
  Directional-Gaussian-Smoothing Evolution Strategy

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


Robust Attribution Regularization

Towards Evaluating the Robustness of Neural Networks

Robust Attribution Regularization

Smoothed Geometry for Robust Attribution


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

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

International journal of computer vision

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

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


Self-supervised Equivariant Attention Mechanism for Weakly Supervised Semantic Segmentation, CVPR 2020 (Oral)

Importance Sampling Cams For Weakly-Supervised Segmentation


RCandy:  an R package for visualising homologous recombination events in bacterial genomes

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Detection of recombination events in bacterial genomes from large population samples

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact


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

ReINTEL: A Multimodal Data Challenge for Responsible Information Identification on Social Network Sites

Investigating Monolingual and Multilingual BERTModels for Vietnamese
  Aspect Category Detection

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

ReINTEL Challenge 2020: Exploiting Transfer Learning Models for Reliable Intelligence Identification on Vietnamese Social Network Sites


Python toolbox for phenotype analysis of arrayed microbial colonies

Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens

Functional profiling of long intergenic non-coding RNAs in fission yeast

High-Throughput, High-Precision Colony Phenotyping with Pyphe.


Unofficial implementation of some fantastic shallow domain adaptation (SDA) methods.

Joint Geometrical and Statistical Alignment for Visual Domain Adaptation

Domain Invariant and Class Discriminative Feature Learning for Visual Domain Adaptation

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

Unsupervised Domain Adaptation via Structured Prediction Based Selective Pseudo-Labeling

Visual domain adaptation via transfer feature learning

Aggregating Randomized Clustering-Promoting Invariant Projections for Domain Adaptation

IEEE transactions on pattern analysis and machine intelligence

Discriminative and Geometry-Aware Unsupervised Domain Adaptation

Active Transfer Learning

IEEE transactions on circuits and systems for video technology

Discriminant Geometrical and Statistical Alignment With Density Peaks for Domain Adaptation

Maximum Mean and Covariance Discrepancy for Unsupervised Domain Adaptation

Neural processing letters/Neural Processing Letters

Joint distinct subspace learning and unsupervised transfer classification for visual domain adaptation


Design platform for creating single-chain polyhedral cages made from coiled-coil building modules

Coiled coil protein origami: from modular design principles towards biotechnological applications

Coiled-Coils: The Molecular Zippers that Self-Assemble Protein Nanostructures

International journal of molecular sciences

Designed folding pathway of modular coiled-coil-based proteins

Metal ion–regulated assembly of designed modular protein cages


Recurrent Neural Networks based Autoencoder for Time Series Anomaly Detection

LSTM-based Encoder-Decoder for Multi-sensor Anomaly Detection

Context-aware Domain Adaptation for Time Series Anomaly Detection


The PyFlow package is a Python implementation of the flow equation method for approximately diagonalising large many-body quantum systems, and simulating their non-equilibrium dynamics.

Local integrals of motion and the stability of many-body localization in Wannier-Stark potentials

Disorder-induced spin-charge separation in the 1-D Hubbard model

Unraveling long-time quantum dynamics using flow equations


Code and data of the EMNLP 2022 Main Conference paper "Reduce Catastrophic Forgetting of Dense Retrieval Training with Teleportation Negatives".

Dense Passage Retrieval for Open-Domain Question Answering

Scaling Deep Contrastive Learning Batch Size under Memory Limited Setup


Detect, classify, and track Rossby Wave Breaking (RWB) in weather and climate data.


Source code of CHAMELEON - A Deep Learning Meta-Architecture for News Recommender Systems

Contextual Hybrid Session-Based News Recommendation With Recurrent Neural Networks

News Session-Based Recommendations using Deep Neural Networks

PROCEEDINGS OF THE 3RD WORKSHOP ON DEEP LEARNING FOR RECOMMENDER SYSTEMS (DLRS)

CHAMELEON: A Deep Learning Meta-Architecture for News Recommender
  Systems [Phd. Thesis]

On the Importance of News Content Representation in Hybrid Neural Session-based Recommender Systems


TTC: A high-performance Compiler for Tensor Transpositions

Design of a high-performance GEMM-like Tensor-Tensor Multiplication

TTC: A Tensor Transposition Compiler for Multiple Architectures

Proceedings of the 3rd ACM SIGPLAN International Workshop on Libraries, Languages, and Compilers for Array Programming


Domain Adaptation of Neural Machine Translation by Lexicon Induction

Dictionary-based Data Augmentation for Cross-Domain Neural Machine Translation

Twist Decoding: Diverse Generators Guide Each Other


Code for the paper "RAP: Robustness-Aware Perturbations for Defending against Backdoor Attacks on NLP Models" (EMNLP 2021)

ONION: A Simple and Effective Defense Against Textual Backdoor Attacks

Backdoor Attack against NLP models with Robustness-Aware Perturbation
  defense


Variational inference and disentangled representations through unsupervised learning

Auto-Encoding Variational Bayes

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

International Conference on Learning Representations

Disentangling by Factorising

Isolating Sources of Disentanglement in Variational Autoencoders

Understanding disentangling in β-VAE

Variational Inference of Disentangled Latent Concepts from Unlabeled Observations

A Framework for the Quantitative Evaluation of Disentangled Representations

Learning Deep Disentangled Embeddings with the F-Statistic Loss


基于PaddlePaddle框架的异常检测算法复现

PaDiM: a Patch Distribution Modeling Framework for Anomaly Detection and Localization

Towards Total Recall in Industrial Anomaly Detection

Modeling the Distribution of Normal Data in Pre-Trained Deep Features for Anomaly Detection

Semi-orthogonal Embedding for Efficient Unsupervised Anomaly Segmentation


Causal Effect Inference with Deep Latent-Variable Models

Emotion-Cause Pair Extraction: A New Task to Emotion Analysis in Texts

Transfer Learning for Causal Sentence Detection

Conversational Response Re-ranking Based on Event Causality and Role Factored Tensor Event Embedding


Cohort Shapley: A local explanation method for black box prediction with only observed data

Explaining black box decisions by Shapley cohort refinement

Cohort Shapley value for algorithmic fairness

Variable importance without impossible data


Robust Multiple Kernel K-means using L21-norm

Low-rank Kernel Learning for Graph-based Clustering

Self-weighted Multiple Kernel Learning for Graph-based Clustering and Semi-supervised Classification

Twin Learning for Similarity and Clustering: A Unified Kernel Approach

Clustering with Similarity Preserving

Similarity Learning via Kernel Preserving Embedding

Discriminative Multiple Kernel Concept Factorization for Data Representation


Deep contextualized word representations

Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings

ChEMU 2020: Natural Language Processing Methods Are Effective for Information Extraction From Chemical Patents

Frontiers in research metrics and analytics

Fine-Grained Chemical Entity Typing with Multimodal Knowledge Representation


gitlinks - Git Powered Go-Links! ⛓

Adversarial Examples Are Not Bugs, They Are Features

Do Adversarially Robust ImageNet Models Transfer Better?

Unadversarial Examples: Designing Objects for Robust Vision


MASS: Multi-Attentional Semantic Segmentation ofLiDAR Data for Dense Top-View Understanding

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

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

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

MASS: Multi-Attentional Semantic Segmentation of LiDAR Data for Dense Top-View Understanding


Implement Melvin in python

Computer-inspired quantum experiments

Learning interpretable representations of entanglement in quantum optics experiments using deep generative models

QOptCraft: A Python package for the design and study of linear optical quantum systems


ICIP 2022: CTGAN : Cloud Transformer Generative Adversarial Network (Offical implementation)

Cloud Removal in Satellite Images Using Spatiotemporal Generative Networks

Cloud Removal for Remote Sensing Imagery via Spatial Attention Generative Adversarial Network


R package for Brazilian reservoirs data


Creative Commons Attribution 4.0 International

Slides, videos and other potentially useful artifacts from various presentations on responsible machine learning.

On the Art and Science of Machine Learning Explanations

Proposed Guidelines for the Responsible Use of Explainable Machine Learning

Safety design concepts for statistical machine learning components
  toward accordance with functional safety standards


A comprehensive dataset for stock movement prediction from tweets and historical stock prices.

Stock Movement Prediction from Tweets and Historical Prices

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

The Wall Street Neophyte: A Zero-Shot Analysis of ChatGPT Over
  MultiModal Stock Movement Prediction Challenges

Coupling Macro-Sector-Micro Financial Indicators for Learning Stock Representations with Less Uncertainty

THIRTY-FIFTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, THIRTY-THIRD CONFERENCE ON INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE AND THE ELEVENTH SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE

Incorporating Transformers and Attention Networks for Stock Movement Prediction


Cross Site Scripting ( XSS ) Vulnerability Payload List

GeneMiner: A Classification Approach for Detection of XSS Attacks on Web Services

Computational intelligence and neuroscience

Twenty-two years since revealing cross-site scripting attacks: a
  systematic mapping and a comprehensive survey

HALE-IoT: Hardening Legacy Internet of Things Devices by Retrofitting Defensive Firmware Modifications and Implants


Source code and data used in the papers ViQuAE (Lerner et al., SIGIR'22), Multimodal ICT (Lerner et al., ECIR'23) and Cross-modal Retrieval (Lerner et al., ECIR'24)

WIT: Wikipedia-based Image Text Dataset for Multimodal Multilingual Machine Learning

ViQuAE, a Dataset for Knowledge-based Visual Question Answering about Named Entities

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

Multimodal Inverse Cloze Task for Knowledge-based Visual Question Answering

Un jeu de données pour répondre à des questions visuelles à propos d’entités nommées en utilisant des bases de connaissances

HAL (Le Centre pour la Communication Scientifique Directe)


Source code of "IJCAI20 - Network Schema Preserving Heterogeneous Information Network Embedding"

Self-supervised Heterogeneous Graph Neural Network with Co-contrastive Learning

Hierarchical Contrastive Learning Enhanced Heterogeneous Graph Neural Network

Personalised Meta-path Generation for Heterogeneous GNNs

A Post-Training Framework for Improving Heterogeneous Graph Neural Networks


Deep Exploration Networks - Diverse Deep Generative Models for DNA, RNA and Protein Sequences

Feedback GAN for DNA optimizes protein functions

A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays


Novel hybrid firefly algorithm: an application to enhance XGBoost tuning for intrusion detection classification

A Machine Learning-Based Classification and Prediction Technique for DDoS Attacks

Classification model for accuracy and intrusion detection using machine learning approach


Preparing for the Unknown: Learning a Universal Policy with Online System Identification

Learning Fast Adaptation With Meta Strategy Optimization

Policy Transfer with Strategy Optimization


This page is for A Survey on Deep Learning of Small Sample in Biomedical Image Analysis.

Constrained-CNN losses for weakly supervised segmentation

CFEA: Collaborative Feature Ensembling Adaptation for Domain Adaptation in Unsupervised Optic Disc and Cup Segmentation


A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

Predicting effective microRNA target sites in mammalian mRNAs

GTRD: a database on gene transcription regulation—2019 update

POSTAR2: deciphering the post-transcriptional regulatory logics

Deep learning decodes the principles of differential gene expression


The MuSe 2022 Multimodal Sentiment Analysis Challenge: Humor, Emotional
  Reactions, and Stress


Social Poisson Factorization

THIRTY-FIRST AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE

Low-Rank Factorization of Determinantal Point Processes for Recommendation.


A plugin for climetlab to retrieve the Eumetnet postprocessing benchmark dataset.

The EUPPBench postprocessing benchmark dataset v1.0

The EUPPBench postprocessing benchmark


Neural Architecture Optimization

Neural Architecture Optimization

NAS evaluation is frustratingly hard

Semi-Supervised Neural Architecture Search

Understanding Neural Architecture Search Techniques

An Analysis of Super-Net Heuristics in Weight-Sharing NAS

Balanced One-shot Neural Architecture Optimization

XferNAS: Transfer Neural Architecture Search


LeCaRDv2: A Large-Scale Chinese Legal Case Retrieval Dataset

Incorporating Judgment Prediction into Legal Case Retrieval via
  Law-aware Generative Retrieval


Code and resources for evaluating cross-lingual embedding spaces

A Survey of Cross-lingual Word Embedding Models

Probing Pretrained Language Models for Lexical Semantics

How to (Properly) Evaluate Cross-Lingual Word Embeddings: On Strong Baselines, Comparative Analyses, and Some Misconceptions

Filtered Inner Product Projection for Crosslingual Embedding Alignment

Improving Bilingual Lexicon Induction with Cross-Encoder Reranking

Clustering Monolingual Vocabularies to Improve Cross-Lingual Generalization

Proceedings of the 1st Workshop on Multilingual Representation Learning


CO2SYS software for MATLAB (or octave) to compute variables of ocean CO2 system

Routine uncertainty propagation for the marine carbon dioxide system

Comparison of ten packages that compute ocean carbonate chemistry

Estimating the Absolute Salinity of Chinese offshore waters using nutrients and inorganic carbon data


First M87 EHT Results: Imaging Pipelines

Hybrid Mapping of the Black Hole Shadow in M87

The Jet and Resolved Features of the Central Supermassive Black Hole of M87 Observed with the Event Horizon Telescope (EHT)


Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.

Fast gapped-read alignment with Bowtie 2

BEDTools: a flexible suite of utilities for comparing genomic features

fastp: an ultra-fast all-in-one FASTQ preprocessor

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

A scaling normalization method for differential expression analysis of RNA-seq data

UMAP: Uniform Manifold Approximation and Projection

deepTools2: a next generation web server for deep-sequencing data analysis

MultiQC: summarize analysis results for multiple tools and samples in a single report

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

seaborn: Statistical data visualization


Perceiver-Actor: A Multi-Task Transformer for Robotic Manipulation

GNFactor: Multi-Task Real Robot Learning with Generalizable Neural
  Feature Fields


Allele-Specific Expression by Single-Cell RNA Sequencing

SCALE: modeling allele-specific gene expression by single-cell RNA sequencing

A Bayesian mixture model for the analysis of allelic expression in single cells

Semi-coordinated allelic-bursting shape dynamic random monoallelic expression in pre-gastrulation embryos


Pytorch implementation of "Revisiting ResNets: Improved Training and Scaling Strategies"(https://arxiv.org/pdf/2103.07579.pdf)

Randaugment: Practical automated data augmentation with a reduced search space

Deep Networks with Stochastic Depth


Benchmarking of Session-based Recommendation Approaches

Personalized Top-N Sequential Recommendation via Convolutional Sequence Embedding

Parallel Recurrent Neural Network Architectures for Feature-rich Session-based Recommendations

PROCEEDINGS OF THE 10TH ACM CONFERENCE ON RECOMMENDER SYSTEMS (RECSYS'16)

Evaluation of session-based recommendation algorithms

User modeling and user-adapted interaction

A Collaborative Session-based Recommendation Approach with Parallel Memory Modules

PROCEEDINGS OF THE 42ND INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL (SIGIR '19)

Inter-Session Modeling for Session-Based Recommendation

Comprehensive Empirical Evaluation of Deep Learning Approaches for
  Session-based Recommendation in E-Commerce


Code and data used in The Great Repertoire Project

Commonality despite exceptional diversity in the baseline human antibody repertoire

Landscape of Non-canonical Cysteines in Human VH Repertoire Revealed by Immunogenetic Analysis

Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals

Regulatory approved monoclonal antibodies contain framework mutations predicted from human antibody repertoires


[ISPRS Congress 2020] Lake Ice Detection from Sentinel-1 SAR with Deep Learning (Deeplabv3+, Tensorflow). The data was collected from Google Earth Engine platform.

Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation

Rethinking Atrous Convolution for Semantic Image Segmentation

Integrated monitoring of ice in selected Swiss lakes. Final project report

Recent Ice Trends in Swiss Mountain Lakes: 20-year Analysis of MODIS Imagery

Learning a Joint Embedding of Multiple Satellite Sensors: A Case Study for Lake Ice Monitoring

IEEE transactions on geoscience and remote sensing


A Windows Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data

FasParser: a package for manipulating sequence data

FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data

Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment


HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching

Identification of the Complete Chloroplast Genome of Malus zhaojiaoensis Jiang and Its Comparison and Evolutionary Analysis with Other Malus Species

The complete mitochondrial genome of Alternaria alternata (Hypocreales: Nectriaceae)

Assembly and comparative analysis of chloroplast genome of wheat K-CMS line and maintainer line

Chloroplast Genes Are Involved in The Male-Sterility of K-Type CMS in Wheat

Molecular Structure and Variation Characteristics of the Plastomes from Six Malus baccata (L.) Borkh. Individuals and Comparative Genomic Analysis with Other Malus Species


IDR

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts

YAP/TAZ drives cell proliferation and tumour growth via a polyamine-eIF5A hypusination-LSD1 axis

Machine learning sequence prioritization for cell type-specific enhancer design

AIControl: replacing matched control experiments with machine learning improves ChIP-seq peak identification

Protocol for assay of transposase accessible chromatin sequencing in non-model species

Readout of histone methylation by Trim24 locally restricts chromatin opening by p53


Download and manipulate some publicly available solar datasets


Approximate linear solution of power flow equations in power distribution networks

On the Existence and Linear Approximation of the Power Flow Solution in Power Distribution Networks

A Necessary Condition for Power Flow Insolvability in Power Distribution Systems With Distributed Generators

Hierarchical and Distributed Monitoring of Voltage Stability in Distribution Networks

Graphical Models for Optimal Power Flow

A Framework for Robust Steady-State Voltage Stability of Distribution
  Systems


Access data from Thalmic Labs' Myo Gesture Control Armband in m-code!

User-Independent Hand Gesture Recognition Classification Models Using Sensor Fusion

Adaptive Driver-Automation Shared Steering Control via Forearm Surface Electromyography Measurement

sEMG-Based Gesture Classifier for a Rehabilitation Glove

Effect of Fixed and sEMG-Based Adaptive Shared Steering Control on Distracted Driver Behavior


Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials

Learning local equivariant representations for large-scale atomistic dynamics

Scaling the Leading Accuracy of Deep Equivariant Models to Biomolecular Simulations of Realistic Size

DPA-2: Towards a universal large atomic model for molecular and material
  simulation

Spin-Dependent Graph Neural Network Potential for Magnetic Materials

Transferable Water Potentials Using Equivariant Neural Networks

Physics-Inspired Neural Graph ODE for Long-term Dynamical Simulation


Scripts and noise data for Belinkov & Bisk 2018

Synthetic and Natural Noise Both Break Neural Machine Translation

On Adversarial Examples for Character-Level Neural Machine Translation

Towards a Robust Deep Neural Network in Texts: A Survey


DeepSleepNet: A Model for Automatic Sleep Stage Scoring Based on Raw Single-Channel EEG

International Conference of the IEEE Engineering in Medicine and Biology Society

SeqSleepNet: End-to-End Hierarchical Recurrent Neural Network for Sequence-to-Sequence Automatic Sleep Staging

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


[ICML 2021] DFAC Framework: Factorizing the Value Function via Quantile Mixture for Multi-Agent Distributional Q-Learning

Rethinking Individual Global Max in Cooperative Multi-Agent
  Reinforcement Learning

RiskQ: Risk-sensitive Multi-Agent Reinforcement Learning Value
  Factorization


collection of bioinformatic scripts

Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain

Alien Domains Shaped the Modular Structure of Plant NLR Proteins

The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

Diversity of woody-host infecting Phytophthora species in public parks and botanic gardens as revealed by metabarcoding, and opportunities for mitigation through best practice

Sibbaldia: the International Journal of Botanic Garden Horticulture


Depth and Flow for Visual Odometry

Visual Odometry Revisited: What Should Be Learnt?

DF-VO: What Should Be Learnt for Visual Odometry?

Monocular Rotational Odometry with Incremental Rotation Averaging and Loop Closure

Dense Prediction Transformer for Scale Estimation in Monocular Visual Odometry


INTeractive learning via REPresentatIon Discovery

Is Q-learning Provably Efficient?

Provable Safe Reinforcement Learning with Binary Feedback


Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution

SRHiC: A Deep Learning Model to Enhance the Resolution of Hi-C Data

HiCPlus: Resolution Enhancement of Hi-C interaction heatmap


Experiment for lsat

Holistic Evaluation of Language Models

From LSAT: The Progress and Challenges of Complex Reasoning

AR-LSAT: Investigating Analytical Reasoning of Text

Analytical Reasoning of Text

Findings of the Association for Computational Linguistics: NAACL 2022


Demo code for the paper "Learning SO(3) Equivariant Representations with Spherical CNNs"

Kernel Transformer Networks for Compact Spherical Convolution


[KDD'22] Source codes of "Graph Rationalization with Environment-based Augmentations"

Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining

Graph-based Molecular Representation Learning

Data Augmentation on Graphs: A Technical Survey

Learning Invariant Molecular Representation in Latent Discrete Space


Machine Translation (MT) Preparation Scripts

Domain-Specific Text Generation for Machine Translation

Fine-tuning Large Language Models for Adaptive Machine Translation


Differential Algebra Computational Toolbox

Collision avoidance maneuver optimization with a multiple-impulse convex formulation

Data association and uncertainty pruning for tracks determined on short arcs

Celestial mechanics & dynamical astronomy/Celestial mechanics and dynamical astronomy

On the predictability and robustness of Galileo disposal orbits

Differential algebra methods applied to continuous abacus generation and bifurcation detection: application to periodic families of the Earth–Moon system

Stable sets mapping with Taylor differential algebra with application to ballistic capture orbits around Mars

Detection and estimation of spacecraft maneuvers for catalog maintenance


Official code implementation for ICDE 23 paper MAMDR: A Model Agnostic Learning Method for Multi-Domain Recommendation

Exploiting Graph Structured Cross-Domain Representation for Multi-Domain
  Recommendation

Rethinking Cross-Domain Sequential Recommendation under Open-World
  Assumptions


Temporal Predictive Coding For Model-Based Planning In Latent Space

DreamerPro: Reconstruction-Free Model-Based Reinforcement Learning with Prototypical Representations


[AAAI 2022 Oral] This is a Pytorch implementation of the AAAI 2022 paper "Cross-Domain Empirical Risk Minimization for Unbiased Long-tailed Classification"

Long-Tailed Classification by Keeping the Good and Removing the Bad Momentum Causal Effect

Long-tailed Recognition by Routing Diverse Distribution-Aware Experts

Disentangling Label Distribution for Long-tailed Visual Recognition


This repo provides four weight pruning algorithms for use in sequence-to-point energy disaggregation as well as three alternative neural network architectures.

Sequence-to-point learning with neural networks for nonintrusive load monitoring

Structured Probabilistic Pruning for Convolutional Neural Network Acceleration

Lightweight Non-Intrusive Load Monitoring Employing Pruned Sequence-to-Point Learning

Proceedings of the 5th International Workshop on Non-Intrusive Load Monitoring


Meta Learning for Semi-Supervised Few-Shot Classification

Meta-Learning for Semi-Supervised Few-Shot Classification

Few-Shot Classification with Feature Map Reconstruction Networks

Few-shot Pseudo-Labeling for Intent Detection

International Conference on Computational Linguistics


ReCO: A Large Scale Chinese Reading Comprehension Dataset on Opinion

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

RoBERTa: A Robustly Optimized BERT Pretraining Approach

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


Non official implementation of the Linear Recurrent Unit (LRU, Orvieto et al. 2023)

Efficiently Modeling Long Sequences with Structured State Spaces

Simplified State Space Layers for Sequence Modeling

Resurrecting Recurrent Neural Networks for Long Sequences

Universality of Linear Recurrences Followed by Non-linear Projections: Finite-Width Guarantees and Benefits of Complex Eigenvalues

Gated recurrent neural networks discover attention


Image Manipulation Detection by Multi-View Multi-Scale Supervision

Generate, Segment and Refine: Towards Generic Manipulation Segmentation

MVSS-Net: Multi-View Multi-Scale Supervised Networks for Image Manipulation Detection

IEEE transactions on pattern analysis and machine intelligence


Align multiple amino acid or nucleotide sequences.

A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada

Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance

Comparative Genomic Analyses of Lactococcus garvieae Isolated from Bovine Mastitis in China


Vector Quantized Autoregressive Predictive Coding (VQ-APC)

An Unsupervised Autoregressive Model for Speech Representation Learning

Vector-Quantized Autoregressive Predictive Coding

DeCoAR 2.0: Deep Contextualized Acoustic Representations with Vector Quantization

DinoSR: Self-Distillation and Online Clustering for Self-supervised
  Speech Representation Learning

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


Online optimisation tool for wind+solar+storage systems


Code to reproduce results in "Finding Streams in Knowledge Graphs to Support Fact Checking"

Unsupervised Fact Checking by Counter-Weighted Positive and Negative Evidential Paths in A Knowledge Graph

REMOD: Relation Extraction for Modeling Online Discourse

Fact Checking via Path Embedding and Aggregation


[RSS 2023] Official code for "Goal Conditioned Imitation Learning using Score-based Diffusion Policies"

Score-Based Generative Modeling through Stochastic Differential Equations

Improved Denoising Diffusion Probabilistic Models

Elucidating the Design Space of Diffusion-Based Generative Models

Goal-Conditioned Imitation Learning using Score-based Diffusion Policies

Learning to Reach Goals via Diffusion


NovelD: A Simple yet Effective Exploration Criterion

BeBold: Exploration Beyond the Boundary of Explored Regions

Exploration via Elliptical Episodic Bonuses

LECO: Learnable Episodic Count for Task-Specific Intrinsic Reward


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

Accelerated MRI with Un-trained Neural Networks

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

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


Adapting Meta AI's Segment Anything to Downstream Tasks with Adapters and Prompts

SAM-Adapter: Adapting Segment Anything in Underperformed Scenes

2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW)

SAM Fails to Segment Anything? -- SAM-Adapter: Adapting SAM in
  Underperformed Scenes: Camouflage, Shadow, Medical Image Segmentation, and
  More

Investigating Shift Equivalence of Convolutional Neural Networks in Industrial Defect Segmentation


Implementation in MATLAB-based CVX of various convex/concave functions of matrices (matrix geometric means, quantum relative entropy, ...)

Semidefinite Approximations of the Matrix Logarithm

Foundations of computational mathematics

Improving PHY-Security of UAV-Enabled Transmission With Wireless Energy Harvesting: Robust Trajectory Design and Communications Resource Allocation

IEEE transactions on vehicular technology

Device-independent lower bounds on the conditional von Neumann entropy

Defining quantum divergences via convex optimization

Security of quantum key distribution from generalised entropy accumulation

Robust Interior Point Method for Quantum Key Distribution Rate Computation

Lieb's concavity theorem, matrix geometric means, and semidefinite optimization

Witnessing negative conditional entropy

Unpredictable Planning Under Partial Observability

Computation efficiency optimization in UAV-enabled mobile edge computing system with multi-carrier non-orthogonal multiple access

EURASIP Journal on wireless communications and networking


QC-DMET: a python implementation of density matrix embedding theory for ab initio quantum chemistry

A Practical Guide to Density Matrix Embedding Theory in Quantum Chemistry

Journal of chemical theory and computation

Multiconfigurational Self-Consistent Field Theory with Density Matrix Embedding: The Localized Active Space Self-Consistent Field Method

Can Density Matrix Embedding Theory with the Complete Activate Space Self-Consistent Field Solver Describe Single and Double Bond Breaking in Molecular Systems?


[CVPR 2022] PointCLIP: Point Cloud Understanding by CLIP

PointCLIP V2: Prompting CLIP and GPT for Powerful 3D Open-world Learning


An efficient manifold density estimator for all recommendation systems

Cleora: A Simple, Strong and Scalable Graph Embedding Scheme

Modeling Multi-Destination Trips with Sketch-Based Model


Gradient boosted decision trees for multiple outputs. Better generalization ability, faster training and inference.

GBDT-MO: Gradient-Boosted Decision Trees for Multiple Outputs

SketchBoost: Fast Gradient Boosted Decision Tree for Multioutput
  Problems


ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

3D molecular phenotyping of cleared human brain tissues with light-sheet fluorescence microscopy

High-Fidelity Imaging in Brain-Wide Structural Studies Using Light-Sheet Microscopy

Comparison of Different Tissue Clearing Methods for Three-Dimensional Reconstruction of Human Brain Cellular Anatomy Using Advanced Imaging Techniques

A Guide to Perform 3D Histology of Biological Tissues with Fluorescence Microscopy

International journal of molecular sciences

Nogo-A antibody delivery through the olfactory mucosa mitigates experimental autoimmune encephalomyelitis in the mouse CNS


Renewcast: Forecasting Renewable Electricity Generation in EU Countries.


Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.

The Mobilome-Enriched Genome of the Competence-Deficient Streptococcus pneumoniae BM6001, the Original Host of Integrative Conjugative Element Tn5253, Is Phylogenetically Distinct from Historical Pneumococcal Genomes

Phenotypic and genetic alterations of Burkholderia pseudomallei in patients during relapse and persistent infections


[WWW'2023] "DCRec: Debiased Contrastive Learning for Sequential Recommendation"

Rethinking Cross-Domain Sequential Recommendation under Open-World
  Assumptions

End-to-end Learnable Clustering for Intent Learning in Recommendation


Code, unit tests, and tutorials for running PICRUSt2

PICRUSt2: An improved and customizable approach for metagenome inference

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas

Lactobacillus plantarum PS128 alleviates neurodegenerative progression in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models of Parkinson's disease

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome

Metformin attenuated sepsis-related liver injury by modulating gut microbiota

A Korean-Style Balanced Diet Has a Potential Connection with Ruminococcaceae Enterotype and Reduction of Metabolic Syndrome Incidence in Korean Adults

Ridinilazole, a narrow spectrum antibiotic for treatment of Clostridioides difficile infection, enhances preservation of microbiota-dependent bile acids

American journal of physiology. Gastrointestinal and liver physiology/American journal of physiology: Gastrointestinal and liver physiology

Soil Microbial Diversity and Community Composition in Rice–Fish Co-Culture and Rice Monoculture Farming System

Gut Microbiota Comparison Between Intestinal Contents and Mucosa in Mice With Repeated Stress-Related Diarrhea Provides Novel Insight


Sarus implementation of classical ML models. The models are implemented using the Keras API of tensorflow 2. Vizualization are implemented and can be seen in tensorboard.

Auto-Encoding Variational Bayes

Large Scale GAN Training for High Fidelity Natural Image Synthesis

Neural Discrete Representation Learning

Pixel Recurrent Neural Networks

Conditional Image Generation with PixelCNN Decoders

PixelCNN++: Improving the PixelCNN with Discretized Logistic Mixture Likelihood and Other Modifications

Conditional Neural Processes

PixelSNAIL: An Improved Autoregressive Generative Model


Semantic Segmentation Models in Pytorch

U-Net: Convolutional Networks for Biomedical Image Segmentation

Fully Convolutional Networks for Semantic Segmentation

Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation

The One Hundred Layers Tiramisu: Fully Convolutional DenseNets for Semantic Segmentation

Practices and Applications of Convolutional Neural Network-Based Computer Vision Systems in Animal Farming: A Review


Derive the optimal cache hit ratio for Internet request traces with variable object sizes.

Practical Bounds on Optimal Caching with Variable Object Sizes

Proceedings of the ACM on measurement and analysis of computing systems

LeadCache: Regret-Optimal Caching in Networks

Online Caching with Optimal Switching Regret


Multi-view Graph Contrastive Representation Learning for Drug-drug Interaction Prediction

Multi-view Graph Contrastive Representation Learning for Drug-Drug Interaction Prediction

Conditional Graph Information Bottleneck for Molecular Relational
  Learning

Shift-Robust Molecular Relational Learning with Causal Substructure

Graph neural networks and attention-based CNN-LSTM for protein
  classification


Public Code for ICS Evasion Attack Generation

A Survey on Industrial Control System Testbeds and Datasets for Security Research

IEEE Communications surveys and tutorials/IEEE communications surveys and tutorials

Constrained Concealment Attacks against Reconstruction-based Anomaly Detectors in Industrial Control Systems

Asia-Pacific Computer Systems Architecture Conference

No Need to Know Physics: Resilience of Process-based Model-free Anomaly
  Detection for Industrial Control Systems


download Google Earth Engine datasets to tiles as geotiff arrays

Fewshot learning on global multimodal embeddings for earth observation
  tasks

Large Scale Masked Autoencoding for Reducing Label Requirements on SAR
  Data


PyTorch Implementation of DiffGAN-TTS: High-Fidelity and Efficient Text-to-Speech with Denoising Diffusion GANs

Tackling the Generative Learning Trilemma with Denoising Diffusion GANs

Grad-TTS: A Diffusion Probabilistic Model for Text-to-Speech

DiffSinger: Singing Voice Synthesis via Shallow Diffusion Mechanism

ResGrad: Residual Denoising Diffusion Probabilistic Models for Text to
  Speech

CoMoSpeech: One-Step Speech and Singing Voice Synthesis via Consistency Model

Schrodinger Bridges Beat Diffusion Models on Text-to-Speech Synthesis

Adversarial Training of Denoising Diffusion Model Using Dual
  Discriminators for High-Fidelity Multi-Speaker TTS


Adversarial Example Attacks on Policy Learners

Noisy Networks for Exploration

Challenges and Countermeasures for Adversarial Attacks on Deep Reinforcement Learning

Whatever Does Not Kill Deep Reinforcement Learning, Makes It Stronger

The Faults in Our Pi Stars: Security Issues and Open Challenges in Deep Reinforcement Learning

Mitigation of Policy Manipulation Attacks on Deep Q-Networks with Parameter-Space Noise


Multivariate functional reconstruction using finite fields and dataflow graphs.

FiniteFlow: multivariate functional reconstruction using finite fields and dataflow graphs

The Journal of high energy physics/The journal of high energy physics

AMFlow: A Mathematica package for Feynman integrals computation via auxiliary mass flow

Macaulay matrix for Feynman integrals: linear relations and intersection numbers

Restrictions of Pfaffian systems for Feynman integrals


Visual Memorability for Robotic Interestingness via Unsupervised Online Learning (TRO 2021 and ECCV 2020 Oral)

Unsupervised Online Learning for Robotic Interestingness With Visual Memory

Glimpse: A Gaze-Based Measure of Temporal Salience


NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean

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

Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean


Quick Start Guide for MARIDA (Marine Debris Archive)

MARIDA: A benchmark for Marine Debris detection from Sentinel-2 remote sensing data


Continuous Degradation Detection on the Google Earth Engine

Ongoing forest disturbance in Guatemala's protected areas

Remote sensing in ecology and conservation

Lessons Learned While Implementing a Time-Series Approach to Forest Canopy Disturbance Detection in Nepal

Project impact assessment on deforestation and forest degradation: Forest Disturbance Dataset


TIMERS: Document-level Temporal Relation Extraction

Severing the Edge Between Before and After: Neural Architectures for Temporal Ordering of Events

Easy, Reproducible and Quality-Controlled Data Collection with CROWDAQ

Temporal Relation Extraction with Joint Semantic and Syntactic Attention

Computational intelligence and neuroscience

Discriminative Reasoning with Sparse Event Representation for Document-level Event-Event Relation Extraction

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


[ICML 2020] InfoGAN-CR and ModelCentrality: Self-supervised Model Training and Selection for Disentangling GANs

InfoGAN-CR: Disentangling Generative Adversarial Networks with Contrastive Regularizers

Learning Disentangled Representation by Exploiting Pretrained Generative Models: A Contrastive Learning View

An Empirical Study on Disentanglement of Negative-free Contrastive
  Learning


The official implementation of our NAACL 2024 paper "A Wolf in Sheep’s Clothing: Generalized Nested Jailbreak Prompts can Fool Large Language Models Easily".

Universal and Transferable Adversarial Attacks on Aligned Language
  Models

AutoDAN: Generating Stealthy Jailbreak Prompts on Aligned Large Language
  Models

A Wolf in Sheep's Clothing: Generalized Nested Jailbreak Prompts can
  Fool Large Language Models Easily


exBAKE: Automatic Fake News Detection Model Based on Bidirectional Encoder Representations from Transformers (BERT)

From Clickbait to Fake News Detection: An Approach based on Detecting the Stance of Headlines to Articles

Empirical Methods in Natural Language Processing

From Stances' Imbalance to Their HierarchicalRepresentation and Detection

WEB CONFERENCE 2019: PROCEEDINGS OF THE WORLD WIDE WEB CONFERENCE (WWW 2019)

Investigating Rumor News Using Agreement-Aware Search

International Conference on Information and Knowledge Management

Variational Self-attention Model for Sentence Representation

University of Copenhagen Participation in TREC Health Misinformation Track 2020

A survey on rumor detection and prevention in social media using deep learning

News Monitor: A Framework for Exploring News in Real-Time

International Conference on Data Technologies and Applications

Danish Stance Classification and Rumour Resolution

Human-in-the-Loop Disinformation Detection: Stance, Sentiment, or Something Else?


Deeply Supervised, Layer-wise Prediction-aware (DSLP) Transformer for Non-autoregressive Neural Machine Translation

A Survey on Non-Autoregressive Generation for Neural Machine Translation and Beyond

Non-Autoregressive Translation with Layer-Wise Prediction and Deep
  Supervision

DePA: Improving Non-autoregressive Machine Translation with
  Dependency-Aware Decoder


2 Dimensional Kolmogorov-Smirnov test for goodness-of-fit

The Gaia-Kepler Stellar Properties Catalog. II. Planet Radius Demographics as a Function of Stellar Mass and Age

Mimicking the halo–galaxy connection using machine learning

Monthly notices of the Royal Astronomical Society

An observational correlation between magnetic field, angular momentum and fragmentation in the envelopes of Class 0 protostars?

Cosmological coupling of nonsingular black holes

Statistical analysis of cavitation erosion impacts in a vibratory apparatus with copulas

IOP conference series. Earth and environmental science


Universal and Transferable Adversarial Attacks on Aligned Language
  Models

SmoothLLM: Defending Large Language Models Against Jailbreaking Attacks

How Johnny Can Persuade LLMs to Jailbreak Them: Rethinking Persuasion to
  Challenge AI Safety by Humanizing LLMs


Bayesian hierarchical model for complex trait analysis

Improved polygenic prediction by Bayesian multiple regression on summary statistics

Performance of risk prediction for inflammatory bowel disease based on genotyping platform and genomic risk score method

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

Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data

Accuracies of genomic predictions for disease resistance of striped catfish to Edwardsiella ictaluri using artificial intelligence algorithms

An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction

An Integrative Genomic Prediction Approach for Predicting Buffalo Milk Traits by Incorporating Related Cattle QTLs

SLEMM: million-scale genomic predictions with window-based SNP weighting


Mobile App Tasks with Iterative Feedback (MoTIF): Addressing Task Feasibility in Interactive Visual Environments

A Dataset for Interactive Vision-Language Navigation with Unknown Command Feasibility

Reinforced UI Instruction Grounding: Towards a Generic UI Task
  Automation API


Software Language Processing Suite

Guided Grammar Convergence. Full Case Study Report. Generated by converge::Guided

Guided Grammar Convergence.


Official implementation for Likelihood Regret: An Out-of-Distribution Detection Score For Variational Auto-encoder at NeurIPS 2020

Likelihood Ratios for Out-of-Distribution Detection

Unsupervised Out-of-Distribution Detection with Diffusion Inpainting

Robust Out-of-Distribution Detection on Deep Probabilistic Generative Models


Filter SAM file for soft and hard clipped alignments

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

Nanopore sequencing of RNA and cDNA molecules in Escherichia coli

Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome

A single unidirectional piRNA cluster similar to the flamenco locus is the major source of EVE-derived transcription and small RNAs in Aedes aegypti mosquitoes

Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood

Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems

A whole-genome worldwide molecular epidemiology approach for contagious caprine pleuropneumonia


(3DV 2021 oral) PyTorch implementation of paper "PoseContrast: Class-Agnostic Object Viewpoint Estimation in the Wild with Pose-Aware Contrastive Learning"

Few-Shot Object Detection and Viewpoint Estimation for Objects in the Wild

Pose from Shape: Deep Pose Estimation for Arbitrary 3D Objects


A light-weight tool for converting CAD drawings into the GDML format.

Internal alignment and position resolution of the silicon tracker of DAMPE determined with orbit data

Nuclear instruments and methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment/Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment

Efficient determination of HPGe γ-ray efficiencies at high energies with ready-to-use simulation software

Reconstruction software of the silicon tracker of DAMPE mission

A deep learning method for the trajectory reconstruction of cosmic rays with the DAMPE mission


Brain Tomur Classification Using Pre-trained Models

Deep Residual Learning for Image Recognition


Graph Neural Network for Traffic Forecasting: A Survey

Coupled Layer-wise Graph Convolution for Transportation Demand Prediction

Bike sharing usage prediction with deep learning: a survey


NASA Cleaned Defect Datasets

Software Defect Prediction Using Variant based Ensemble Learning and Feature Selection Techniques

International journal of modern education and computer science

Software defect prediction using Binary Particle Swarm Optimization with Binary Cross Entropy as the fitness function

Dimensional Reduction on Cross Project Defect Prediction

Tackling Imbalanced Class on Cross-Project Defect Prediction Using Ensemble SMOTE

IOP conference series. Materials science and engineering

Ensemble Undersampling to Handle Unbalanced Class on Cross-Project Defect Prediction

The Integrity of Machine Learning Algorithms against Software Defect
  Prediction

Penerapan PSO Over Sampling Dan Adaboost Random Forest Untuk Memprediksi Cacat Software

Indonesian Journal on Software Engineering (IJSE)/IJSE (Indonesian Journal on Software Engineering)


StyleSpace Analysis: Disentangled Controls for StyleGAN Image Generation

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

Principled Knowledge Extrapolation with GANs

Fantastic Style Channels and Where to Find Them: A Submodular Framework for Discovering Diverse Directions in GANs


This project is special for SemEval2020 task4 Commonsense Validation and Explanantion

Does It Make Sense? And Why? A Pilot Study for Sense Making and Explanation

SemEval-2020 Task 4: Commonsense Validation and Explanation

A Benchmark Arabic Dataset for Commonsense Explanation

HR@JUST Team at SemEval-2020 Task 4: The Impact of RoBERTa Transformer for Evaluation Common Sense Understanding

International Workshop on Semantic Evaluation

Is this sentence valid? An Arabic Dataset for Commonsense Validation

NLP@JUST at SemEval-2020 Task 4: Ensemble Technique for BERT and Roberta to Evaluate Commonsense Validation


Knowledge Graph Embedding with Iterative Guidance from Soft Rules

Improving Knowledge Graph Embedding Using Simple Constraints


Parameter sets for the WOFOST crop simulation model implemented in YAML

Forecasting future crop suitability with microclimate data

Modelling Gas Exchange and Biomass Production in West
African Sahelian and Sudanian Ecological Zones

Modeling gas exchange and biomass production in West African Sahelian and Sudanian ecological zones


PIC: Permutation Invariant Critic for Multi-Agent Deep Reinforcement Learning

Agent-Temporal Attention for Reward Redistribution in Episodic
  Multi-Agent Reinforcement Learning


Neural network toolkit for sentence pair modeling.

Neural Network Models for Paraphrase Identification, Semantic Textual Similarity, Natural Language Inference, and Question Answering

Character-based Neural Networks for Sentence Pair Modeling

Knowledge-Guided Paraphrase Identification

Findings of the Association for Computational Linguistics: EMNLP 2021


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

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

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


NIPS2017 challenge

Learning to Run challenge solutions: Adapting reinforcement learning
  methods for neuromusculoskeletal environments

The Springer series on challenges in machine learning

Learning to Run Challenge: Synthesizing Physiologically Accurate Motion Using Deep Reinforcement Learning

Learning to Run with Actor-Critic Ensemble


A dataset containing story plots from Wikipedia (books, movies, etc.) and the code for the extractor.

PlotMachines: Outline-Conditioned Generation with Dynamic Plot State Tracking

Transformer-based Conditional Variational Autoencoder for Controllable Story Generation.

Tip of the Tongue Known-Item Retrieval: A Case Study in Movie Identification

DiscoDVT: Generating Long Text with Discourse-Aware Discrete Variational Transformer

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

Outline to Story: Fine-grained Controllable Story Generation from Cascaded Events

Towards Coherent and Consistent Use of Entities in Narrative Generation

Synopses of Movie Narratives: a Video-Language Dataset for Story
  Understanding

StoryDB: Broad Multi-language Narrative Dataset

Generating Coherent Narratives by Learning Dynamic and Discrete Entity States with a Contrastive Framework


AI agent using GPT-4V(ision) capable of using a mouse/keyboard to interact with web UI

Set-of-Mark Prompting Unleashes Extraordinary Visual Grounding in GPT-4V

WebVoyager: Building an End-to-End Web Agent with Large Multimodal
  Models


Implementations of various published works on self-supervised learning approaches to biosignal feature extraction.

Uncovering the structure of clinical EEG signals with self-supervised learning

Subject-Aware Contrastive Learning for Biosignals

Boosting Generalization in Bio-Signal Classification by Learning the Phase-Amplitude Coupling


Source codes for "Improved Few-Shot Visual Classification" (CVPR 2020), "Enhancing Few-Shot Image Classification with Unlabelled Examples" (WACV 2022), and "Beyond Simple Meta-Learning: Multi-Purpose Models for Multi-Domain, Active and Continual Few-Shot Learning" (Neural Networks 2022 - in submission)

Meta-Dataset: A Dataset of Datasets for Learning to Learn from Few Examples

Improved Few-Shot Visual Classification

Improving Few-Shot Visual Classification with Unlabelled Examples

On Label-Eﬀicient Computer Vision: Building Fast and Effective Few-Shot Image Classifiers


Transformers: State-of-the-Art Natural Language Processing

Longformer: The Long-Document Transformer

PEGASUS: Pre-training with Extracted Gap-sentences for Abstractive Summarization


weedNet: Dense semantic weed classification using multispectral images and MAV for smart farming

weedNet: Dense Semantic Weed Classification Using Multispectral Images and MAV for Smart Farming

A Survey of Deep Learning Techniques for Weed Detection from Images

Deep learning techniques to classify agricultural crops through UAV imagery: a review

Deep learning techniques for in-crop weed recognition in large-scale grain production systems: a review


Biological Age Calculations Using Several Biomarker Algorithms

DunedinPACE, a DNA methylation biomarker of the pace of aging

A toolkit for quantification of biological age from blood chemistry and organ function test data: BioAge

Accelerated biological aging and risk of depression and anxiety: evidence from 424,299 UK Biobank participants

Effect of dietary inflammatory potential on the aging acceleration for cardiometabolic disease: A population-based study


A heuristic solver for the set cover problem

The Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: Large-scale structure catalogues for cosmological analysis

Monthly Notices of the Royal Astronomical Society

What's The Latest? A Question-driven News Chatbot

Meeting of the Association for Computational Linguistics

Performance of the Quasar Spectral Templates for the Dark Energy Spectroscopic Instrument

A New View of Classification in Astronomy with the Archetype Technique: An Astronomical Case of the NP-complete Set Cover Problem

Modeling the Spectral Diversity of Quasars in the Sixteenth Data Release from the Sloan Digital Sky Survey


Annocript is a pipeline for the annotation of de-novo generated  transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts. Like our facebook page to be always updated: https://www.facebook.com/annocript

Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs

Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi

mRNA Expression and Biomarker Responses in Perch at a Biomonitoring Site in the Baltic Sea – Possible Influence of Natural Brominated Chemicals


SpCas9 activity prediction by DeepSpCas9, a deep learning–based model with high generalization performance

C-RNNCrispr: Prediction of CRISPR/Cas9 sgRNA activity using convolutional and recurrent neural networks

Computational and structural biotechnology journal

A Novel Hybrid CNN-SVR for CRISPR/Cas9 Guide RNA Activity Prediction

A method for characterizing Cas9 variants via a one-million target sequence library of self-targeting sgRNAs


A full pipeline to finetune Alpaca LLM with LoRA and RLHF on consumer hardware. Implementation of RLHF (Reinforcement Learning with Human Feedback) on top of the Alpaca architecture. Basically ChatGPT but with Alpaca

LoRA: Low-Rank Adaptation of Large Language Models

Fine-Tuning Language Models from Human Preferences

Efficient and Effective Text Encoding for Chinese LLaMA and Alpaca

LLM-Adapters: An Adapter Family for Parameter-Efficient Fine-Tuning of Large Language Models


Handwritten Kazakh and Russian (HKR) database for text recognition

Attention-Based Fully Gated CNN-BGRU for Russian Handwritten Text

Classification of Handwritten Names of Cities and Handwritten Text Recognition using Various Deep Learning Models

Advances in science, technology and engineering systems journal


Code for the collection and analysis of the MTNT dataset

MTNT: A Testbed for Machine Translation of Noisy Text

Shifts: A Dataset of Real Distributional Shift Across Multiple Large-Scale Tasks

Synthesizing Parallel Data of User-Generated Texts with Zero-Shot Neural Machine Translation

Transactions of the Association for Computational Linguistics

Learning Neural Models for Natural Language Processing in the Face of Distributional Shift


This repo contains the code for our paper "EditNTS: An Neural Programmer-Interpreter Model for Sentence Simplification through Explicit Editing" accepted at ACL 2019.

Neural CRF Model for Sentence Alignment in Text Simplification

Controllable Text Simplification with Explicit Paraphrasing


Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.

A Roadmap for Genome-Based Phage Taxonomy

INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes

INfrastructure for a PHAge REference Database: Identification of large-scale biases in the current collection of phage genomes

Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

Genomic Characterization and Annotation of Two Novel Bacteriophages Isolated from a Wastewater Treatment Plant in Qatar

Predicting stop codon reassignment improves functional annotation of bacteriophages

bioRxiv : the preprint server for biology

Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick


This is the Github repository for SemEval-2018 Task 3

SemEval-2018 Task 3: Irony Detection in English Tweets

North American Chapter of the Association for Computational Linguistics

THU_NGN at SemEval-2018 Task 3: Tweet Irony Detection with Densely connected LSTM and Multi-task Learning

A Dual-Channel Framework for Sarcasm Recognition by Detecting Sentiment Conflict

HashCount at SemEval-2018 Task 3: Concatenative Featurization of Tweet and Hashtags for Irony Detection

Enhancing the Generalization for Text Classification through Fusion of Backward Features

Prompt Tuning with Contradictory Intentions for Sarcasm Recognition

Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics

Computational Sarcasm Analysis on Social Media: A Systematic Review


A flexible ML framework built to simplify medical image reconstruction and analysis experimentation.

VORTEX: Physics-Driven Data Augmentations Using Consistency Training for
  Robust Accelerated MRI Reconstruction

Developing and deploying deep learning models in brain MRI: a review

Scale-Equivariant Unrolled Neural Networks for Data-Efficient Accelerated MRI Reconstruction

Noise2Recon: Enabling Joint MRI Reconstruction and Denoising with
  Semi-Supervised and Self-Supervised Learning


Universal and Transferable Attacks on Aligned Language Models

Universal and Transferable Adversarial Attacks on Aligned Language
  Models

Fine-tuning Aligned Language Models Compromises Safety, Even When Users
  Do Not Intend To!

Baseline Defenses for Adversarial Attacks Against Aligned Language
  Models

SmoothLLM: Defending Large Language Models Against Jailbreaking Attacks

Red-Teaming Large Language Models using Chain of Utterances for
  Safety-Alignment

AutoDAN: Generating Stealthy Jailbreak Prompts on Aligned Large Language
  Models

How Johnny Can Persuade LLMs to Jailbreak Them: Rethinking Persuasion to
  Challenge AI Safety by Humanizing LLMs

Analyzing the Inherent Response Tendency of LLMs: Real-World
  Instructions-Driven Jailbreak

On Prompt-Driven Safeguarding for Large Language Models

Gradient Cuff: Detecting Jailbreak Attacks on Large Language Models by Exploring Refusal Loss Landscapes


Certified Removal from Machine Learning Models

Certified Data Removal from Machine Learning Models

A Survey of Machine Unlearning

Certifiable Machine Unlearning for Linear Models

Efficiently Forgetting What You Have Learned in Graph Representation
  Learning via Projection


A micro-benchmark suite to assess the effectiveness of tools designed for IoT apps

TAPInspector: Safety and Liveness Verification of Concurrent Trigger-Action IoT Systems

HSAS-MD Analyzer: A Hybrid Security Analysis System Using Model-Checking Technique and Deep Learning for Malware Detection in IoT Apps

A Mutation Framework for Evaluating Security Analysis Tools in IoT Applications

VISCR: Intuitive & Conflict-free Automation for Securing the Dynamic Consumer IoT Infrastructures.


[ECCV '22] Intrinsic Neural Fields: Learning Functions on Manifolds

Sign and Basis Invariant Networks for Spectral Graph Representation
  Learning

Generalised Implicit Neural Representations

Δ-PINNs: Physics-informed neural networks on complex geometries


Creating Anime Faces using Generative Adversarial Networks (GAN) techniques such as: DCGAN, WGAN, StyleGAN, StyleGAN2 and StyleGAN3. Top repos on GitHub for AnimeFace GAN Generative AI Models

Unsupervised Representation Learning with Deep Convolutional Generative Adversarial Networks

Wasserstein GAN

A Style-Based Generator Architecture for Generative Adversarial Networks

Towards the Automatic Anime Characters Creation with Generative Adversarial Networks


DTVNet: Dynamic Time-lapse Video Generation via Single Still Image, ECCV'20 Spotlight.

Learning to Generate Time-Lapse Videos Using Multi-Stage Dynamic Generative Adversarial Networks

Stochastic Image-to-Video Synthesis using cINNs


Solver for Large-Scale Rank-One Semidefinite Relaxations

A Quaternion-based Certifiably Optimal Solution to the Wahba Problem with Outliers

Certifiably Optimal Outlier-Robust Geometric Perception: Semidefinite Relaxations and Scalable Global Optimization

An inexact projected gradient method with rounding and lifting by nonlinear programming for solving rank-one semidefinite relaxation of polynomial optimization


Implementation of "DiffFit: Unlocking Transferability of Large Diffusion Models via Simple Parameter-Efficient Fine-Tuning"

BitFit: Simple Parameter-efficient Fine-tuning for Transformer-based Masked Language-models

Large Convolutional Model Tuning via Filter Subspace


Data and analysis scripts for our Embryo Timecourse paper.

Stalled developmental programs at the root of pediatric brain tumors

Defining totipotency using criteria of increasing stringency

A single-cell time-lapse of mouse prenatal development from gastrula to birth


Implementation of the paper: Replay and Synthetic Speech Detection with Res2Net architecture (ICASSP 2021) https://arxiv.org/abs/2010.15006

ASVspoof 2019: Future Horizons in Spoofed and Fake Audio Detection

Replay and Synthetic Speech Detection with Res2net Architecture

Channel-wise Gated Res2Net: Towards Robust Detection of Synthetic Speech Attacks

Audio Deepfake Detection: A Survey


Are we building on the rock? on the importance of data preprocessing for code summarization

Multi-branch Attentive Transformer

MMF3: Neural Code Summarization Based on Multi-Modal Fine-Grained Feature Fusion

RefBERT: A Two-Stage Pre-trained Framework for Automatic Rename Refactoring


NeurIPS 2017 best paper. An interpretable linear-time kernel goodness-of-fit test.

A Linear-Time Kernel Goodness-of-Fit Test

Informative Features for Model Comparison

Denoising Score Matching with Random Fourier Features


Tensorflow implementations of Relational Networks and a VQA dataset named Sort-of-CLEVR proposed by DeepMind.

A simple neural network module for relational reasoning

Interaction Networks for Learning about Objects, Relations and Physics

Visual Interaction Networks: Learning a Physics Simulator from Video

State of the Art and Potentialities of Graph-level Learning


Benchmarks for semi-supervised domain generalization.

Arbitrary Style Transfer in Real-time with Adaptive Instance Normalization

FixMatch: Simplifying Semi-Supervised Learning with Consistency and Confidence

Semi-Supervised Domain Generalization with Stochastic StyleMatch

MixStyle Neural Networks for Domain Generalization and Adaptation


A Survey on Gradient Inversion: Attacks, Defenses and Future Directions

Making sense of sensory input

Evaluating the Apperception Engine


Filteraugment: An Acoustic Environmental Data Augmentation Method

Frequency Dynamic Convolution: Frequency-Adaptive Pattern Recognition for Sound Event Detection


Text Summarization for Research Papers

Text Summarization with Pretrained Encoders

A Supervised Approach to Extractive Summarisation of Scientific Papers

Data-driven Summarization of Scientific Articles


A PyTorch implementation of state of the art video captioning models from 2015-2019 on MSVD and MSRVTT datasets.

Sequence to Sequence -- Video to Text

Describing Videos by Exploiting Temporal Structure

Translating Videos to Natural Language Using Deep Recurrent Neural Networks

Reconstruction Network for Video Captioning

Memory-Attended Recurrent Network for Video Captioning


Code accompanying the paper "Better Exploration with Optimistic Actor Critic" (NeurIPS 2019)

Better Exploration with Optimistic Actor-Critic

Task-Agnostic Exploration via Policy Gradient of a Non-Parametric State Entropy Estimate

A Policy Gradient Method for Task-Agnostic Exploration


CVPR2022 (Oral) - Rethinking Semantic Segmentation: A Prototype View

Exploring Cross-Image Pixel Contrast for Semantic Segmentation

Deep Hierarchical Semantic Segmentation


Speech Recognition with the Caffe deep learning framework, migrating to

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

A Clockwork RNN

Building DNN Acoustic Models for Large Vocabulary Speech Recognition

An Embarrassingly Simple Approach for Trojan Attack in Deep Neural Networks

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


Official git for "CTAB-GAN: Effective Table Data Synthesizing"

CTAB-GAN+: Enhancing Tabular Data Synthesis

Generative Modeling of Complex Data

ConvGeN: Convex space learning improves deep-generative oversampling for
  tabular imbalanced classification on smaller datasets

TabuLa: Harnessing Language Models for Tabular Data Synthesis


An object-aware diffusion model for generating chemical reactions

Equivariant Diffusion for Molecule Generation in 3D

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

Structure-based Drug Design with Equivariant Diffusion Models

Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model


Code for paper "Attention on Attention for Image Captioning". ICCV 2019

Self-critical Sequence Training for Image Captioning

Image Captioning through Image Transformer

Show, Edit and Tell: A Framework for Editing Image Captions

Towards Unique and Informative Captioning of Images

Text Augmentation Using BERT for Image Captioning

Multi-Modal Image Captioning for the Visually Impaired

The Curious Layperson: Fine-Grained Image Recognition Without Expert Labels

B-SCST: Bayesian Self-Critical Sequence Training for Image Captioning


My collection of light bioinformatics analysis pipelines for specific tasks

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

Evolution and Expression of Tandem Duplicated Maize Flavonol Synthase Genes

A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance

Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

Comprehensive analysis of bZIP transcription factors uncovers their roles during dimorphic floret differentiation and stress response in Cleistogenes songorica

Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)

A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus (JUJUNCAO) provides insights into its evolution and C4 photosynthesis

Expression Patterns of MYB (V-myb Myeloblastosis Viral Oncogene Homolog) Gene Family in Resistant and Susceptible Tung Trees Responding to Fusarium Wilt Disease

Muntjac chromosome evolution and architecture


AMR Parsing via Graph-Sequence Iterative Inference

Ensembling Graph Predictions for AMR Parsing

HIT-SCIR at MRP 2020: Transition-based Parser and Iterative Inference Parser

Proceedings of the CoNLL 2020 Shared Task: Cross-Framework Meaning Representation Parsing

Improving Neural Machine Translation with the Abstract Meaning Representation by Combining Graph and Sequence Transformers

Proceedings of the 2nd Workshop on Deep Learning on Graphs for Natural Language Processing (DLG4NLP 2022)

Referenceless Parsing-Based Evaluation of AMR-to-English Generation

Proceedings of the 2nd Workshop on Evaluation and Comparison of NLP Systems


Code for CIKM2020 "S3-Rec: Self-Supervised Learning for Sequential Recommendation with Mutual Information Maximization"

International Conference on Information and Knowledge Management

Memory Augmented Multi-Instance Contrastive Predictive Coding for Sequential Recommendation

Recommender Systems with Generative Retrieval

Improving Sequential Recommendation Models with an Enhanced Loss
  Function


Pipeline for processing inDrops sequencing data

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

Population snapshots predict early haematopoietic and erythroid hierarchies

Cholinergic regulation of vascular endothelial function by human ChAT+ T cells

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

Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis

Molecular and anatomical organization of the dorsal raphe nucleus

In vitro characterization of the human segmentation clock

Systematic comparative analysis of single cell RNA-sequencing methods

A scalable platform for the development of cell-type-specific viral drivers

Complex Autoinflammatory Syndrome Unveils Fundamental Principles of JAK1 Kinase Transcriptional and Biochemical Function

A method for the generation of human stem cell-derived alpha cells


[ICCV 2023] The official PyTorch code for Group Pose: A Simple Baseline for End-to-End Multi-person Pose Estimation

Explicit Box Detection Unifies End-to-End Multi-Person Pose Estimation

QueryPose: Sparse Multi-Person Pose Regression via Spatial-Aware
  Part-Level Query


Transformer based Turkish language models

Impact of Tokenization on Language Models: An Analysis for Turkish

Auto-tagging of Short Conversational Sentences using Transformer Methods

A Twitter Corpus for Named Entity Recognition in Turkish

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION

Ad Text Classification with Transformer-Based Natural Language Processing Methods


Pytorch notebook with One Cycle Policy implementation (https://arxiv.org/abs/1803.09820)

Cyclical Learning Rates for Training Neural Networks

A disciplined approach to neural network hyper-parameters: Part 1 -- learning rate, batch size, momentum, and weight decay

Wide-minima Density Hypothesis and the Explore-Exploit Learning Rate Schedule


A bounded multi-producer multi-consumer concurrent queue written in C++11

An Initial Study of Two Approaches to Eliminating Out-of-Thin-Air Results

Proceedings of the ACM on programming languages

Toward high-throughput algorithms on many-core architectures

High Performance Embedded Architectures and Compilers

Performance evaluation of interthread communicationmechanisms on multicore/multithreaded architectures

IEEE International Symposium on High-Performance Parallel Distributed Computing

Formal verification of a concurrent bounded queue in a weak memory model


Block Sparse movement pruning

Q8BERT: Quantized 8Bit BERT

Movement Pruning: Adaptive Sparsity by Fine-Tuning

Training with Quantization Noise for Extreme Model Compression

And the Bit Goes Down: Revisiting the Quantization of Neural Networks

BERMo: What can BERT learn from ELMo?


MOsaic CHromosomal Alterations (MoChA) caller

Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations

Chromosomal alterations among age-related haematopoietic clones in Japan

Rawcopy: Improved copy number analysis with Affymetrix arrays

Large mosaic copy number variations confer autism risk

Mosaic chromosome Y loss is associated with alterations in blood cell counts in UK Biobank men

Hematopoietic mosaic chromosomal alterations and risk for infection among 767,891 individuals without blood cancer

medRxiv : the preprint server for health sciences

Biological insights from the whole genome analysis of human embryonic stem cells

Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology

MONTAGE: a new tool for high-throughput detection of mosaic copy number variation


Code for NeurIPS'19 "Layer-Dependent Importance Sampling for Training Deep and Large Graph Convolutional Networks"

Scalable Graph Neural Networks via Bidirectional Propagation

Sampling Methods for Efficient Training of Graph Convolutional Networks: A Survey

IGLU: Efficient GCN Training via Lazy Updates


Codes for papers: 1. Graph Convolutional Network for Recommendation with Low-pass Collaborative Filters (ICML). 2. Less is More: Exploring Simple and Powerful Low-pass Graph Convolutional Network for Recommendation. 3. Self-propagation Graph Neural Network for Recommendation (TKDE).

Self-Propagation Graph Neural Network for Recommendation

IEEE transactions on knowledge and data engineering

Low-Pass Graph Convolutional Network for Recommendation

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


A versatile sequenced read processor for nanopore direct RNA sequencing

Nanopore sequencing and its application to the study of microbial communities

Computational and structural biotechnology journal

Exploring differential exon usage via short- and long-read RNA sequencing strategies

RIPpore: A Novel Host-Derived Method for the Identification of Ricin Intoxication through Oxford Nanopore Direct RNA Sequencing

Antisense lncRNA CHROMR is linked to glioma patient survival


Extrapolating Beyond Suboptimal Demonstrations via Inverse Reinforcement Learning from Observations

Safe Imitation Learning via Fast Bayesian Reward Inference from Preferences

Deep Bayesian Reward Learning from Preferences


Playing Text-Adventure Games with Graph-Based Deep Reinforcement Learning

Transfer in Deep Reinforcement Learning using Knowledge Graphs

Reinforcement Learning on Graphs: A Survey


DeepHawkes: Popularity Prediction of Information Cascades

DeepHawkes: Bridging the Gap between Prediction and Understanding of Information Cascades

A Survey of Information Cascade Analysis: Models, Predictions, and Recent Advances

CCGL: Contrastive Cascade Graph Learning

CasCIFF: A Cross-Domain Information Fusion Framework Tailored for
  Cascade Prediction in Social Networks


Source code to reproduce the results in the ACL 2019 paper "Syntactically Supervised Transformers for Faster Neural Machine Translation"

Hard-Coded Gaussian Attention for Neural Machine Translation

Meeting of the Association for Computational Linguistics

A Survey on Non-Autoregressive Generation for Neural Machine Translation and Beyond


JavaScript library for Augmented Reality applications

Web Apps Come of Age for Molecular Sciences

Low-Cost Fiducial-based 6-Axis Force-Torque Sensor


Official code for: Conformal prediction interval for dynamic time-series (conference, ICML 21 Long Presentation) AND Conformal prediction for time-series (journal, IEEE TPAMI)

Conformal Anomaly Detection on Spatio-Temporal Observations with Missing Data

Conformal prediction for time series

Conformal prediction set for time-series


LPD-Net: 3D Point Cloud Learning for Large-Scale Place Recognition and Environment Analysis, ICCV 2019, Seoul, Korea

BVMatch: Lidar-Based Place Recognition Using Bird's-Eye View Images

International Conference on Robotics and Automation

PSE-Match: A Viewpoint-Free Place Recognition Method With Parallel Semantic Embedding


PSCC-Net: Progressive Spatio-Channel Correlation Network for Image Manipulation Detection and Localization

AutoSplice: A Text-prompt Manipulated Image Dataset for Media Forensics

Rethinking Image Forgery Detection via Contrastive Learning and
  Unsupervised Clustering


Code for WSDM 2022 paper, Contrastive Learning for Representation Degeneration Problem in Sequential Recommendation.

Contrastive Learning for Sequential Recommendation

Memory Augmented Multi-Instance Contrastive Predictive Coding for Sequential Recommendation

Mutual Wasserstein Discrepancy Minimization for Sequential Recommendation

Self-Supervised Multi-Modal Sequential Recommendation

Improving Micro-video Recommendation by Controlling Position Bias

A multi-intent based multi-policy relay contrastive learning for sequential recommendation


Hierarchical Attention Transfer Network for Cross-domain Sentiment Classification (AAAI'18)

Hierarchical Attention Transfer Network for Cross-Domain Sentiment Classification

THIRTY-THIRD AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE / THIRTY-FIRST INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE / NINTH AAAI SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE

PERL: Pivot-based Domain Adaptation for Pre-trained Deep Contextualized Embedding Models

Diversity-Based Generalization for Unsupervised Text Classification under Domain Shift

Unsupervised and Interpretable Domain Adaptation to Rapidly Filter Tweets for Emergency Services

Unsupervised and Interpretable Domain Adaptation to Rapidly Filter Social Web Data for Emergency Services


Encoding in Style: a StyleGAN Encoder for Image-to-Image Translation

A Style-Based GAN Encoder for High Fidelity Reconstruction of Images and Videos

Feature-Style Encoder for Style-Based GAN Inversion


Global phylogenies of SARS-CoV-2 sequences

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike

Virological characteristics of the SARS-CoV-2 Omicron BA.2.75 variant

Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2

bioRxiv : the preprint server for biology

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

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

Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

Early and ongoing importations of SARS-CoV-2 in Canada

Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA


pysster: Learning Sequence And Structure Motifs In Biological Sequences Using Convolutional Neural Networks

pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks

Learning the Regulatory Code of Gene Expression

DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery


Deep Reinforcement Learning: An Overview

Learning to Evade Static PE Machine Learning Malware Models via Reinforcement Learning

Deep Reinforcement Learning


This is outdated -- New version: https://github.com/boyangumn/DCN-New

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

Temporal Phenotyping using Deep Predictive Clustering of Disease Progression

Hierarchically Clustered Representation Learning

A Transfer Learning based Feature-Weak-Relevant Method for Image Clustering.


Code for the paper "VistaNet: Visual Aspect Attention Network for Multimodal Sentiment Analysis", AAAI'19

Cross-Modal Sentiment Sensing with Visual-Augmented Representation and Diverse Decision Fusion

VisdaNet: Visual Distillation and Attention Network for Multimodal Sentiment Classification

UsbVisdaNet: User Behavior Visual Distillation and Attention Network for Multimodal Sentiment Classification


communication-efficient distributed coordinate ascent

CoCoA: A General Framework for Communication-Efficient Distributed Optimization

Adding vs. Averaging in Distributed Primal-Dual Optimization

Pursuits in Structured Non-Convex Matrix Factorizations

DUAL-LOCO: Distributing Statistical Estimation Using Random Projections

LOCO: Distributing Ridge Regression with Random Projections

SCOPE: Scalable Composite Optimization for Learning on Spark


Implementation for <Large-Margin Softmax Loss for Convolutional Neural Networks> in ICML'16.

OLE: Orthogonal Low-rank Embedding, A Plug and Play Geometric Loss for Deep Learning

Ensemble Soft-Margin Softmax Loss for Image Classification


VQMT: Video Quality Measurement Tool. Fast implementations of the following objective image quality metrics: PSNR, SSIM,  MS-SSIM, VIFp, PSNR-HVS and PSNR-HVS-M.

Assessment of QoE for Video and Audio in WebRTC Applications Using Full-Reference Models

Practical Evaluation of VMAF Perceptual Video Quality for WebRTC Applications

Datasheet for Subjective and Objective Quality Assessment Datasets


Certified defense to adversarial examples using CROWN and IBP. Also includes GPU implementation of CROWN verification algorithm (in PyTorch).

Efficient Neural Network Robustness Certification with General Activation Functions

Towards Stable and Efficient Training of Verifiably Robust Neural Networks

Automatic Perturbation Analysis for Scalable Certified Robustness and Beyond

Certifiable Robustness to Adversarial State Uncertainty in Deep Reinforcement Learning

Training Provably Robust Models by Polyhedral Envelope Regularization

REaaS: Enabling Adversarially Robust Downstream Classifiers via Robust Encoder as a Service


An optimizer that trains as fast as Adam and as good as SGD.

Adaptive Gradient Methods with Dynamic Bound of Learning Rate

AdaBelief Optimizer: Adapting Stepsizes by the Belief in Observed Gradients

On the Convergence of AdaBound and its Connection to SGD

Adaptive Hierarchical Hyper-gradient Descent

CProp: Adaptive Learning Rate Scaling from Past Gradient Conformity


Code and model for "Peeking into the Future: Predicting Future Person Activities and Locations in Videos", Liang et al, CVPR 2019

Peeking Into the Future: Predicting Future Person Activities and Locations in Videos

Deep Learning for Vision-based Prediction: A Survey


kNN-based next-basket recommendation

A Survey on Session-based Recommender Systems

Modeling Personalized Item Frequency Information for Next-basket Recommendation

A Systematical Evaluation for Next-Basket Recommendation Algorithms

A New Method Combining Pattern Prediction and Preference Prediction for Next Basket Recommendation


:boom: Quickly calculate and visualize sequence coverage in alignment files

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (Trapa spp., Lythraceae)

Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

DeepMicrobeFinder Sorts Metagenomes into Prokaryotes, Eukaryotes and Viruses, with Marine Applications

Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics


A machine learning-based model for survival prediction in COVID patients

An interpretable mortality prediction model for COVID-19 patients

Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy

A Comprehensive Benchmark for COVID-19 Predictive Modeling Using
  Electronic Health Records in Intensive Care


Generating and Imputing Tabular Data via Diffusion and Flow XGBoost Models

Your Diffusion Model is Secretly a Zero-Shot Classifier

Intriguing properties of generative classifiers

Generating and Imputing Tabular Data via Diffusion and Flow-based
  Gradient-Boosted Trees


Forecast the US demand for electricity


MoVQGAN - model for the image encoding and reconstruction

Vector-quantized Image Modeling with Improved VQGAN

Autoregressive Image Generation using Residual Quantization

MoVQ: Modulating Quantized Vectors for High-Fidelity Image Generation

Kandinsky: an Improved Text-to-Image Synthesis with Image Prior and
  Latent Diffusion


Dataset for JSB Chorales at different temporal resolutions, with train, validation, test split from Boulanger-Lewandowski (2012).

Music Transformer

Counterpoint by Convolution

Music Deep Learning: Deep Learning Methods for Music Signal Processing—A Review of the State-of-the-Art

Improving Polyphonic Music Models with Feature-Rich Encoding

Generating Music with a Self-Correcting Non-Chronological Autoregressive Model


Student Classroom Behavior dataset

SCB-dataset: A Dataset for Detecting Student Classroom Behavior

Student Classroom Behavior Detection based on YOLOv7-BRA and Multi-Model
  Fusion

Student Classroom Behavior Detection based on Improved YOLOv7

SCB-Dataset3: A Benchmark for Detecting Student Classroom Behavior


An official reimplementation of the method described in the INTERSPEECH 2021 paper - Speech Resynthesis from Discrete Disentangled Self-Supervised Representations.

DDDM-VC: Decoupled Denoising Diffusion Models with Disentangled
  Representation and Prior Mixup for Verified Robust Voice Conversion

RepCodec: A Speech Representation Codec for Speech Tokenization

Textless Low-Resource Speech-to-Speech Translation With Unit Language Models


FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation

Improving and generalizing flow-based generative models with minibatch
  optimal transport

Flow Matching on General Geometries


ULIP: Learning a Unified Representation of Language, Images, and Point Clouds for 3D Understanding

ULIP-2: Towards Scalable Multimodal Pre-training for 3D Understanding


Code for paper "CrossFit :weight_lifting:: A Few-shot Learning Challenge for Cross-task Generalization in NLP" (https://arxiv.org/abs/2104.08835)

MetaICL: Learning to Learn In Context

OPT-IML: Scaling Language Model Instruction Meta Learning through the
  Lens of Generalization

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


Automatic Data-Regularized Actor-Critic (Auto-DrAC)

Automatic Data Augmentation for Generalization in Deep Reinforcement Learning

Automatic Data Augmentation for Generalization in Reinforcement Learning

Tuning Mixed Input Hyperparameters on the Fly for Efficient Population Based AutoRL

Rethinking Value Function Learning for Generalization in Reinforcement
  Learning

Tackling Visual Control via Multi-View Exploration Maximization

Automatic Intrinsic Reward Shaping for Exploration in Deep Reinforcement
  Learning


LightningFSL: Pytorch-Lightning implementations of Few-Shot Learning models.

Rectifying the Shortcut Learning of Background for Few-Shot Learning

EASY: Ensemble Augmented-Shot Y-shaped Learning: State-Of-The-Art
  Few-Shot Classification with Simple Ingredients

Boosting Few-Shot Classification with View-Learnable Contrastive Learning


Inception Score for GANs in Pytorch

Improved Techniques for Training GANs

A Note on the Inception Score

Exposing flaws of generative model evaluation metrics and their unfair
  treatment of diffusion models

An Empirical Study of Batch Normalization and Group Normalization in
  Conditional Computation

Leveraging Visual Question Answering to Improve Text-to-Image Synthesis


[ICLR'22] [KDD'22] [IJCAI'24] Implementation of "Graph Condensation for Graph Neural Networks"

Condensing Graphs via One-Step Gradient Matching

Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining

A Comprehensive Survey on Graph Reduction: Sparsification, Coarsening,
  and Condensation