The solution of team 'grt123' in DSB2017

Evaluate the Malignancy of Pulmonary Nodules Using the 3-D Deep Leaky Noisy-OR Network

Distanced LSTM: Time-Distanced Gates in Long Short-Term Memory Models for Lung Cancer Detection

Lung Cancer Detection using Co-learning from Chest CT Images and Clinical Demographics

Coronary Calcium Detection using 3D Attention Identical Dual Deep Network Based on Weakly Supervised Learning

Deep Multi-task Prediction of Lung Cancer and Cancer-free Progression from Censored Heterogenous Clinical Imaging

Deep Multi-path Network Integrating Incomplete Biomarker and Chest CT Data for Evaluating Lung Cancer Risk

A Systematic Analysis for State-of-the-Art 3D Lung Nodule Proposals Generation


This repository contains the code for the CVPR 2021 paper "GIRAFFE: Representing Scenes as Compositional Generative Neural Feature Fields"

Convolutional Occupancy Networks

StyleNeRF: A Style-based 3D-Aware Generator for High-resolution Image Synthesis

3D-aware Image Synthesis via Learning Structural and Textural Representations

Unsupervised Discovery of Object Radiance Fields

Learning Implicit Surface Light Fields

Multi-View Consistent Generative Adversarial Networks for 3D-aware Image Synthesis

DisCoScene: Spatially Disentangled Generative Radiance Fields for Controllable 3D-aware Scene Synthesis

UrbanGIRAFFE: Representing Urban Scenes as Compositional Generative Neural Feature Fields

SinGRAV: Learning a Generative Radiance Volume from a Single Natural
  Scene


Scripts for batch rendering models using Blender. Tested with models from stanfords shapenet library.

FaceShifter: Towards High Fidelity And Occlusion Aware Face Swapping

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

Elastic-InfoGAN: Unsupervised Disentangled Representation Learning in Class-Imbalanced Data

Three-Dimensional Reconstruction from Single Image Base on Combination of CNN and Multi-Spectral Photometric Stereo

TriCoLo: Trimodal Contrastive Loss for Text to Shape Retrieval

Image Inpainting of Multi-Spectral Image with Laser Lines Based on Generative Adversarial Network


Codebase for the paper LSTM Fully Convolutional Networks for Time Series Classification

Multivariate LSTM-FCNs for Time Series Classification

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

Deep Gated Recurrent and Convolutional Network Hybrid Model for Univariate Time Series Classification

International journal of advanced computer science and applications/International journal of advanced computer science & applications

Dual Supervised Autoencoder Based Trajectory Classification Using Enhanced Spatio-Temporal Information

ML-Based Approach for NFL Defensive Pass Interference Prediction Using GPS Tracking Data

International Convention on Information and Communication Technology, Electronics and Microelectronics


R-FCN: Object Detection via Region-based Fully Convolutional Networks

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

A review: Comparison of performance metrics of pretrained models for object detection using the TensorFlow framework

IOP conference series. Materials science and engineering

Auto-Context R-CNN

Advances and Applications of Computer Vision Techniques in Vehicle Trajectory Generation and Surrogate Traffic Safety Indicators

Overhead Detection: Beyond 8-bits and RGB

A Post-processing Fusion Framework for Deep Learning Models for Crop Disease Detection


A simple Python implementation of R-PCA

L0-norm Constrained Autoencoders for Unsupervised Outlier Detection

Pacific-Asia Conference on Knowledge Discovery and Data Mining

Learning low-dimensional manifolds under the L0-norm constraint for unsupervised outlier detection


Release of CIFAR-10.1, a new test set for CIFAR-10.

Do ImageNet Classifiers Generalize to ImageNet?

Do CIFAR-10 Classifiers Generalize to CIFAR-10?

Learning Deep Kernels for Non-Parametric Two-Sample Tests

Multiobjective Evolutionary Design of Deep Convolutional Neural Networks for Image Classification

Meta Two-Sample Testing: Learning Kernels for Testing with Limited Data

Multi-Criterion Evolutionary Design of Deep Convolutional Neural Networks.

On the Strong Correlation Between Model Invariance and Generalization

How do we generalize?

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

A Kernelised Stein Statistic for Assessing Implicit Generative Models


Code for ICLR 2020 paper "VL-BERT: Pre-training of Generic Visual-Linguistic Representations".

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

FashionBERT: Text and Image Matching with Adaptive Loss for Cross-modal Retrieval

InterBERT: Vision-and-Language Interaction for Multi-modal Pretraining

Unsupervised Vision-and-Language Pre-training Without Parallel Images and Captions

Probing Contextual Language Models for Common Ground with Visual Representations

Leveraging Visual Knowledge in Language Tasks: An Empirical Study on Intermediate Pre-training for Cross-Modal Knowledge Transfer

ICAF: Iterative Contrastive Alignment Framework for Multimodal Abstractive Summarization


Enhancing the BERT training with Semi-supervised Generative Adversarial Networks

A Survey on Text Classification: From Shallow to Deep Learning

GAN-BERT: Generative Adversarial Learning for Robust Text Classification with a Bunch of Labeled Examples

Meeting of the Association for Computational Linguistics

Socratic Question Generation: A Novel Dataset, Models, and Evaluation

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

GAN-BElectra: Enhanced Multi-class Sentiment Analysis with Limited Labeled Data


LASER multilingual sentence embeddings as a pip package

Massively Multilingual Sentence Embeddings for Zero-Shot Cross-Lingual Transfer and Beyond

NewsEmbed: Modeling News through Pre-trained Document Representations

Democratizing Neural Machine Translation with OPUS-MT

Building Neural Machine Translation Systems for Multilingual Participatory Spaces


DeepSpeech based forced alignment tool

Scaling Speech Technology to 1,000+ Languages

The People's Speech: A Large-Scale Diverse English Speech Recognition
  Dataset for Commercial Usage

What shall we do with an hour of data? Speech recognition for the un-
  and under-served languages of Common Voice

A Toolbox for Construction and Analysis of Speech Datasets


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

International Conference on Information and Knowledge Management

Recommendation as Language Processing (RLP): A Unified Pretrain, Personalized Prompt & Predict Paradigm (P5)

Intent Contrastive Learning for Sequential Recommendation

Contrastive Self-supervised Sequential Recommendation with Robust Augmentation.

Sequential Recommendation via Stochastic Self-Attention

Context and Attribute-Aware Sequential Recommendation via Cross-Attention

Proceedings of the 16th ACM Conference on Recommender Systems

OpenP5: Benchmarking Foundation Models for Recommendation

Improving Transformer-based Sequential Recommenders through Preference Editing

What is Next when Sequential Prediction Meets Implicitly Hard Interaction?

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

Mutual Wasserstein Discrepancy Minimization for Sequential Recommendation


A Survey on Causal Inference

Adapting Neural Networks for the Estimation of Treatment Effects

Covariate-Balancing-Aware Interpretable Deep Learning Models for Treatment Effect Estimation

A Survey of Deep Causal Models and Their Industrial Applications


[ECCV2018] Distractor-aware Siamese Networks for Visual Object Tracking

High Performance Visual Tracking with Siamese Region Proposal Network

Towards Distraction-Robust Active Visual Tracking

A Hypergradient Approach to Robust Regression without Correspondence

Benchmarking Deep Trackers on Aerial Videos

Multi-Templates Based Robust Tracking for Robot Person-Following Tasks

SOTVerse: A User-defined Task Space of Single Object Tracking


Harvey: A Greybox Fuzzer for Smart Contracts

ContractGuard: Defend Ethereum Smart Contracts with Embedded Intrusion Detection

Targeted Greybox Fuzzing with Static Lookahead Analysis

Mutation Testing for Ethereum Smart Contract

Learning Inputs in Greybox Fuzzing


PyTorch-1.0 implementation for the adversarial training on MNIST/CIFAR-10 and visualization on robustness classifier.

Robustness May Be at Odds with Accuracy

AdamP: Slowing Down the Slowdown for Momentum Optimizers on Scale-invariant Weights

Slowing Down the Weight Norm Increase in Momentum-based Optimizers

On the Generalization Properties of Adversarial Training


Code for EvolveGCN: Evolving Graph Convolutional Networks for Dynamic Graphs

Dynamic Network Embedding Survey

Understanding graph embedding methods and their applications

A Survey on the Use of Graph Convolutional Networks for Combating Fake News

A Robust Comparative Analysis of Graph Neural Networks on Dynamic Link Prediction

DynG2G: An Efficient Stochastic Graph Embedding Method for Temporal Graphs

VStreamDRLS: Dynamic Graph Representation Learning with Self-Attention for Enterprise Distributed Video Streaming Solutions

EGAD: Evolving Graph Representation Learning with Self-Attention and Knowledge Distillation for Live Video Streaming Events

Learning to Evolve on Dynamic Graphs

Bottleneck Analysis of Dynamic Graph Neural Network Inference on CPU and GPU


Code for One-shot Relational Learning for Knowledge Graphs (EMNLP18)

One-Shot Relational Learning for Knowledge Graphs

Relational Learning with Gated and Attentive Neighbor Aggregator for Few-Shot Knowledge Graph Completion

Cognitive Knowledge Graph Reasoning for One-shot Relational Learning

Data Augmentation for Few-Shot Knowledge Graph Completion from Hierarchical Perspective

International Conference on Computational Linguistics

Learning Relation-Specific Representations for Few-shot Knowledge Graph
  Completion

A Survey On Few-shot Knowledge Graph Completion with Structural and
  Commonsense Knowledge


Code, documentation, and discussion around the MIMIC-CXR database

MIMIC-CXR: A large publicly available database of labeled chest radiographs

Generating Radiology Reports via Memory-driven Transformer

Cross-modal Memory Networks for Radiology Report Generation

Improving Factual Completeness and Consistency of Image-to-Text Radiology Report Generation

Progressive Transformer-Based Generation of Radiology Reports

Disparate Censorship & Undertesting: A Source of Label Bias in Clinical Machine Learning.

MAIRA-1: A specialised large multimodal model for radiology report
  generation

Factual Accuracy is not Enough: Planning Consistent Description Order for Radiology Report Generation

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

Significantly Improving Zero-Shot X-ray Pathology Classification via
  Fine-tuning Pre-trained Image-Text Encoders

EHRXQA: A Multi-Modal Question Answering Dataset for Electronic Health
  Records with Chest X-ray Images


semi supervised guided topic model with custom guidedLDA

Seed-Guided Topic Discovery with Out-of-Vocabulary Seeds

Context, Attention and Audio Feature Explorations for Audio Visual Scene-Aware Dialog

eTranslation’s Submissions to the WMT 2019 News Translation Task

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

eTranslation’s Submissions to the WMT 2021 News Translation Task

vONTSS: vMF based semi-supervised neural topic modeling with optimal transport


an implementation of Video Frame Interpolation via Adaptive Separable Convolution using PyTorch

ST-MFNet: A Spatio-Temporal Multi-Flow Network for Frame Interpolation

Zooming SlowMo: An Efficient One-Stage Framework for Space-Time Video Super-Resolution.

Self-supervised Light Field View Synthesis Using Cycle Consistency


Dilated CNNs for NER in TensorFlow

Fast and Accurate Entity Recognition with Iterated Dilated Convolutions

Active Bias: Training More Accurate Neural Networks by Emphasizing High Variance Samples

Using error decay prediction to overcome practical issues of deep active learning for named entity recognition

Simultaneously Linking Entities and Extracting Relations from Biomedical
  Text Without Mention-level Supervision


Discover augmentation strategies tailored for your dataset

Neural Architecture Search with Reinforcement Learning

AutoAugment: Learning Augmentation Policies from Data

Improved Regularization of Convolutional Neural Networks with Cutout


An implementation of Deep Canonical Correlation Analysis (DCCA or Deep CCA) with Keras.

MultiBench: Multiscale Benchmarks for Multimodal Representation Learning

Machine learning for multi-omics data integration in cancer

Multi-View Unsupervised User Feature Embedding for Social Media-based Substance Use Prediction

Empirical Methods in Natural Language Processing

Generalized Multiview Shared Subspace Learning Using View Bootstrapping


[ACL'19] [PyTorch] Multimodal Transformer

Multimodal Transformer for Unaligned Multimodal Language Sequences

CMU-MOSEAS: A Multimodal Language Dataset for Spanish, Portuguese, German and French

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

Analyzing Modality Robustness in Multimodal Sentiment Analysis

DialogueTRM: Exploring the Intra- and Inter-Modal Emotional Behaviors in the Conversation.

Continuous-Time Audiovisual Fusion with Recurrence vs. Attention for In-The-Wild Affect Recognition

Improving Medical Predictions by Irregular Multimodal Electronic Health
  Records Modeling

COLD Fusion: Calibrated and Ordinal Latent Distribution Fusion for Uncertainty-Aware Multimodal Emotion Recognition

StreaMulT: Streaming Multimodal Transformer for Heterogeneous and Arbitrary Long Sequential Data


BiLSTM-CNN-CRF tagger

Recurrent Neural Network Grammars

End-to-end Sequence Labeling via Bi-directional LSTM-CNNs-CRF

Neural End-to-End Learning for Computational Argumentation Mining

TARGER: Neural Argument Mining at Your Fingertips

PROCEEDINGS OF THE 57TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS: SYSTEM DEMONSTRATIONS, (ACL 2019)

Argumentation Mining on Essays at Multi Scales

Developing the Old Tibetan Treebank

Recent Advances in Natural Language Processing


Jointly Embedding Knowledge Graphs and Logical Rules

Type-Constrained Representation Learning in Knowledge Graphs

Transition-based Knowledge Graph Embedding with Relational Mapping Properties

Pacific Asia Conference on Language, Information, and Computation

Semantically Smooth Knowledge Graph Embedding

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

Composing Relationships with Translations

HAL (Le Centre pour la Communication Scientifique Directe)

KBLRN : End-to-End Learning of Knowledge Base Representations with
  Latent, Relational, and Numerical Features

Knowledge Base Completion via Coupled Path Ranking

PROCEEDINGS OF THE 54TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS, VOL 1

Combining Two And Three-Way Embeddings Models for Link Prediction in Knowledge Bases

Context-Dependent Knowledge Graph Embedding

Irreflexive and Hierarchical Relations as Translations


FreeLB: Enhanced Adversarial Training for Natural Language Understanding

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

CoDA: Contrast-enhanced and Diversity-promoting Data Augmentation for Natural Language Understanding

Token-Aware Virtual Adversarial Training in Natural Language Understanding

Exploring The Landscape of Distributional Robustness for Question Answering Models

An LLM can Fool Itself: A Prompt-Based Adversarial Attack

RoAST: Robustifying Language Models via Adversarial Perturbation with Selective Training


CVPR2022 - Deep Hierarchical Semantic Segmentation - A structured, pixel-wise description of visual scenes in terms of the class hierarchy.

Deep Hierarchical Semantic Segmentation

GMMSeg: Gaussian Mixture based Generative Semantic Segmentation Models

Semantic Hierarchy-Aware Segmentation

IEEE transactions on pattern analysis and machine intelligence


A retargetable MLIR-based machine learning compiler and runtime toolkit.

TensorIR: An Abstraction for Automatic Tensorized Program Optimization

DISC: A Dynamic Shape Compiler for Machine Learning Workloads

Union: A Unified HW-SW Co-Design Ecosystem in MLIR for Evaluating Tensor Operations on Spatial Accelerators

Automatic Creation of High-bandwidth Memory Architectures from Domain-specific Languages: The Case of Computational Fluid Dynamics

TinyIREE: An ML Execution Environment for Embedded Systems From Compilation to Deployment


Virtual-Taobao simulators with OpenAI Gym interface

Virtual-Taobao: Virtualizing Real-world Online Retail Environment for Reinforcement Learning

CIRS: Bursting Filter Bubbles by Counterfactual Interactive Recommender System

User Behavior Simulation with Large Language Model based Agents

RL4RS: A Real-World Dataset for Reinforcement Learning based Recommender System

Model-free Reinforcement Learning with Stochastic Reward Stabilization for Recommender Systems

Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval


Deep Learning with Tensor Flow for EEG MNE Epoch Objects

Deep learning-based electroencephalography analysis: a systematic review

Learning Representations from EEG with Deep Recurrent-Convolutional Neural Networks

Real-Time Sleep Staging using Deep Learning on a Smartphone for a
  Wearable EEG

An Overview of Open Source Deep Learning-Based Libraries for Neuroscience


Markov Decision Process (MDP) Toolbox for Python

Game Redesign in No-regret Game Playing

A First-Order Approach to Accelerated Value Iteration

Trust-Aware Planning: Modeling Trust Evolution in Iterated Human-Robot
  Interaction

First-Order Methods for Wasserstein Distributionally Robust MDP

Beyond discounted returns: Robust Markov decision processes with average
  and Blackwell optimality


Calculate biomass with allometric equations from the allodb package and ForestGEO data


Implementation for our paper Breaking the Cycle - Colleagues are all you need (CVPR 2020)

Multimodal Unsupervised Image-to-Image Translation

Breaking the cycle -- Colleagues are all you need

UVCGAN: UNet Vision Transformer cycle-consistent GAN for unpaired image-to-image translation


[IJCAI'18] Unsupervised Cross-Modality Domain Adaptation of ConvNets for Biomedical Image Segmentations with Adversarial Loss (code&data)

PnP-AdaNet: Plug-and-Play Adversarial Domain Adaptation Network at Unpaired Cross-Modality Cardiac Segmentation

Data Efficient Unsupervised Domain Adaptation for Cross-Modality Image Segmentation

PnP-AdaNet: Plug-and-Play Adversarial Domain Adaptation Network with a Benchmark at Cross-modality Cardiac Segmentation


ggplot extension: options for tailored facets, multiple colourscales and miscellaneous

Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

Entropy predicts sensitivity of pseudorandom seeds

Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis


SBX: Stable Baselines Jax (SB3 + Jax)

Proximal Policy Optimization Algorithms

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

Addressing Function Approximation Error in Actor-Critic Methods

Controlling Overestimation Bias with Truncated Mixture of Continuous Distributional Quantile Critics

Dropout Q-Functions for Doubly Efficient Reinforcement Learning

CrossQ: Batch Normalization in Deep Reinforcement Learning for Greater
  Sample Efficiency and Simplicity


Grey-scale Image Classification using KERAS

Rethinking the Inception Architecture for Computer Vision

Understanding How Image Quality Affects Deep Neural Networks

Why do deep convolutional networks generalize so poorly to small image transformations


R package to assess water quality trends with generalized additive models

Multi-scale trend analysis of water quality using error propagation of generalized additive models


A cold, massive, rotating disk galaxy 1.5 billion years after the Big Bang

The Kinematics of z ≳ 6 Quasar Host Galaxies

Dissecting the Local Environment of FRB 190608 in the Spiral Arm of its Host Galaxy

A Comparison of the Stellar, CO, and Dust-continuum Emission from Three Star-forming HUDF Galaxies at z similar to 2

The SUPERCOLD-CGM Survey. I. Probing the Extended CO(4–3) Emission of the Circumgalactic Medium in a Sample of 10 Enormous Lyα Nebulae at z ∼ 2


Muller diagrams excel at visualizing evolutionary dynamics of a population over time.  A common use case, and the intended use case during development, describes the abundance and succession of genotypes within a population derived from  sequencing data from samples at specified timepoints.  This provides a useful method of quickly discerning the evolutionary relationship between genotypes seen in a population and how this changes over time.

Parallel Evolution of Tobramycin Resistance across Species and Environments

On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis

Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance

Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis

Species and condition shape the mutational spectrum in experimentally evolved biofilms

Parallel genetic adaptation of Bacillus subtilis to different plant species

Following the Trail of One Million Genomes: Footprints of SARS-CoV-2 Adaptation to Humans


A Python module that implements NAFF Algorithm

Identification and characterization of high order incoherent space charge driven structure resonances in the CERN Proton Synchrotron

Refined betatron tune measurements by mixing beam position data

Resonance identification studies at the CERN PS

Coupling and Space Charge studies at the CERN PSB

Frequency analysis and dynamic aperture studies in a low energy antiproton ring with realistic 3D magnetic fields


Create and manipulate stellar light curves!

Hot planets around cool stars -- two short-period mini-Neptunes
  transiting the late K-dwarf TOI-1260

Monthly Notices of the Royal Astronomical Society

TOI-2196 b: Rare planet in the hot Neptune desert transiting a G-type star


这是一个YoloV4-pytorch的源码，可以用于训练自己的模型。

YOLOv4: Optimal Speed and Accuracy of Object Detection

A Detection Model of the Complex Dynamic Traffic Environment for Unmanned Vehicles

Multifeature Semantic Complementation Network for Marine Oil Spill Localization and Segmentation Based on SAR Images

IEEE journal of selected topics in applied earth observations and remote sensing


Readers and converters for ESA CCI Soil Moisture image and time series data. Written in Python.


Code for pmVAE model, seen in ICML CompBio '21

Learning interpretable latent autoencoder representations with annotations of feature sets

pmVAE: Learning Interpretable Single-Cell Representations with Pathway Modules

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

基因组蛋白质组与生物信息学报


CREST - Classification Resources for Environmnetal Sequence Tags, is a collection of software and databases for taxonomic classification of environmental marker genes from sequencing-based community profiling studies.

Benthic eDNA metabarcoding provides accurate assessments of impact from oil extraction, and ecological insights

Planctomycetes as a Vital Constituent of the Microbial Communities Inhabiting Different Layers of the Meromictic Lake Sælenvannet (Norway)

Grab what you can—an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

‘Is it Justice, or Just Us?’: Examining how radical media and the news framed an Aboriginal death in police custody’


Compute mean telomere length from Whole Genome Sequencing data.

Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data

Telomere Length Maintenance and Its Transcriptional Regulation in Lynch Syndrome and Sporadic Colorectal Carcinoma


Building Radial Density Profiles for Interstellar Filaments

Filamentary Accretion Flows in the Infrared Dark Cloud G14.225–0.506 Revealed by ALMA

Dense gas kinematics and a narrow filament in the Orion A OMC1 region using NH_3

Like a spider in its web: a study of the large-scale structure around the Coma cluster

ALMA Observations of NGC 6334S. II. Subsonic and Transonic Narrow Filaments in a High-mass Star Formation Cloud

OGHReS: Large-scale filaments in the outer Galaxy

ALMA Uncovers Highly Filamentary Structure toward the Sgr E Region


GDSC Single Molecule Light Microscopy ImageJ Plugins

The speed of GTP hydrolysis determines GTP cap size and controls microtubule stability

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers

Performance Boost of Organic Light-Emitting Diodes with Plasmonic Nanostars

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

PCNA ubiquitylation ensures timely completion of unperturbed DNA replication in fission yeast

GDSC SMLM: Single-molecule localisation microscopy software for ImageJ


Code and videos accompanying the paper "Flickering Adversarial Attacks against Video Recognition Networks"

Quo Vadis, Action Recognition? A New Model and the Kinetics Dataset

A Closer Look at Spatiotemporal Convolutions for Action Recognition

Sparse Adversarial Perturbations for Videos

Over-the-Air Adversarial Flickering Attacks against Video Recognition Networks


Access and Analyze eBird Status and Trends Data


[Re] Can gradient clipping mitigate label noise? (ML Reproducibility Challenge 2020)

Deep Residual Learning for Image Recognition

Generalized Cross Entropy Loss for Training Deep Neural Networks with Noisy Labels

Learning from Noisy Labels with Deep Neural Networks: A Survey

Learning with Symmetric Label Noise: The Importance of Being Unhinged

International Conference on Learning Representations


Mitigating Data Heterogeneity in Federated Learning with Data
  Augmentation

Proportional Fairness in Federated Learning

Understanding Hessian Alignment for Domain Generalization

Normalization Is All You Need: Understanding Layer-Normalized Federated
  Learning under Extreme Label Shift


This project is a collection of tools for bioinformatic processing of ancient DNA data at the Harvard Medical School Reich Lab.

The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean

Ancient DNA and deep population structure in sub-Saharan African foragers

A minimally destructive protocol for DNA extraction from ancient teeth

The Anglo-Saxon migration and the formation of the early English gene pool

An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

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

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

A genetic history of the Balkans from Roman frontier to Slavic migrations


Repository for Doctor AI project

Doctor AI: Predicting Clinical Events via Recurrent Neural Networks

Inferring multimodal latent topics from electronic health records

A Survey on Principles, Models and Methods for Learning from Irregularly Sampled Time Series: From Discretization to Attention and Invariance.

CATNet: Cross-event Attention-based Time-aware Network for Medical Event Prediction


Scripts to run several protocols to process and analyze Next-Generation Sequencing data

Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans

Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths

A Glimpse into the Satellite DNA Library in Characidae Fish (Teleostei, Characiformes)

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes

In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus

A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed

Biology and Genomics of an Historic Therapeutic Escherichia coli Bacteriophage Collection

The complete mitochondrial genome sequence of Astyanax paranae(Teleostei: characiformes)

The Satellite DNA Catalogues of Two Serrasalmidae (Teleostei, Characiformes): Conservation of General satDNA Features over 30 Million Years


Learning Spatiotemporal Features with 3D Convolutional Networks

Quo Vadis, Action Recognition? A New Model and the Kinetics Dataset

End-to-End Dense Video Captioning with Parallel Decoding

Negative Sample Matters: A Renaissance of Metric Learning for Temporal Grounding


ICON Lab @ Bilkent University

Progressively Volumetrized Deep Generative Models for Data-Efficient Contextual Learning of MR Image Recovery

Projection onto Epigraph Sets for Rapid Self-Tuning Compressed Sensing MRI

Reconstruction by calibration over tensors for multi‐coil multi‐acquisition balanced SSFP imaging

Semi-Supervised Learning of Mutually Accelerated MRI Synthesis without Fully-Sampled Ground Truths

Constrained Ellipse Fitting for Efficient Parameter Mapping With Phase-Cycled bSSFP MRI

Automated Parameter Selection for Accelerated MRI Reconstruction via Low-Rank Modeling of Local k-Space Neighborhoods


Causal inference is a critical task in various fields such as healthcare,economics, marketing and education. Recently, there have beensignificant advances through the application of machine learningtechniques, especially deep neural networks. Unfortunately, to-datemany of the proposed methods are evaluated on different (data,software/hardware, hyperparameter) setups and consequently it isnearly impossible to compare the efficacy of the available methodsor reproduce results presented in original research manuscripts.In this paper, we propose a causal inference toolbox (CauseBox)that addresses the aforementioned problems. At the time of thewriting, the toolbox includes seven state of the art causal inferencemethods and two benchmark datasets. By providing convenientcommand-line and GUI-based interfaces, theCauseBoxtoolboxhelps researchers fairly compare the state of the art methods intheir chosen application context against benchmark datasets.

Evaluation Methods and Measures for Causal Learning Algorithms

CauseBox: A Causal Inference Toolbox for Benchmarking Treatment Effect Estimators with Machine Learning Methods

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


A python library for studying Calabi-Yau metrics

Learning Size and Shape of Calabi-Yau Spaces

Numerical metrics for complete intersection and Kreuzer–Skarke Calabi–Yau manifolds

Machine Learned Calabi-Yau Metrics and Curvature


A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation

Predicting Functional Associations using Flanking Genes (FlaGs)


Kuzushiji Recognition Kaggle 2019. Build a DL model to transcribe ancient Kuzushiji into contemporary Japanese characters. Opening the door to a thousand years of Japanese culture.

CenterNet: Keypoint Triplets for Object Detection

Albumentations: fast and flexible image augmentations

Deep Learning for Classical Japanese Literature

Survey on Deep Learning-based Kuzushiji Recognition


Dutch coreference resolution & dialogue analysis using deterministic rules

A Dutch coreference resolution system with an evaluation on literary fiction

Computational Linguistics in the Netherlands

A Benchmark of Rule-Based and Neural Coreference Resolution in Dutch Novels and News

A Hybrid Rule-Based and Neural Coreference Resolution System with an Evaluation on Dutch Literature

Proceedings of the Fourth Workshop on Computational Models of Reference, Anaphora and Coreference


Practical Federated Gradient Boosting Decision Trees

Privacy-Preserving Gradient Boosting Decision Trees

The OARF Benchmark Suite: Characterization and Implications for Federated Learning Systems


Word Mover's Distance from Matthew J Kusner's paper "From Word Embeddings to Document Distances"

Re-evaluating Automatic Metrics for Image Captioning

Re-evaluating Word Mover's Distance

Speeding up Word Mover's Distance and its variants via properties of distances between embeddings

Supervised Tree-Wasserstein Distance

Unbalanced Optimal Transport meets Sliced-Wasserstein

Unsupervised Sentence-embeddings by Manifold Approximation and Projection

Word Tour: One-dimensional Word Embeddings via the Traveling Salesman Problem

Model Comparison for Semantic Grouping

Moving Other Way: Exploring Word Mover Distance Extensions


⚡ FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies

Antimicrobial resistance and population genomics of multidrug-resistant Escherichia coli in pig farms in mainland China

FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies

Intra-species diversity of Clostridium perfringens: A diverse genetic repertoire reveals its pathogenic potential


World Mortality Dataset: international data on all-cause mortality.

Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset

Preliminary Analysis of Excess Mortality in India During the COVID-19 Pandemic

The American journal of tropical medicine and hygiene

Disparities in excess deaths from the COVID-19 pandemic among migrant workers in Kuwait

A framework for reconstructing SARS-CoV-2 transmission dynamics using excess mortality data

International Completeness of Death Registration 2015-2019


PyORBIT: a code for exoplanet orbital parameters and stellar activity.

An Ultra-short Period Rocky Super-Earth with a Secondary Eclipse and a Neptune-like Companion around K2-141

The GAPS programme with HARPS-N at TNG XI. Pr~0211 in M~44: the first multi-planet system in an open cluster

The Kepler-19 System: A Thick-envelope Super-Earth with Two Neptune-mass Companions Characterized Using Radial Velocities and Transit Timing Variations

A PSF-based Approach to TESS High quality data Of Stellar clusters (PATHOS) -- II. Search for exoplanets in open clusters of the southern ecliptic hemisphere and their frequency

The GAPS Programme at TNG XXI -- A GIARPS case-study of known young planetary candidates: confirmation of HD 285507 b and refutation of AD Leo b

An unusually low density ultra-short period super-Earth and three mini-Neptunes around the old star TOI-561

Monthly notices of the Royal Astronomical Society

The GAPS Programme with HARPS-N at TNG XVII. Line profile indicators and kernel regression as diagnostics of radial-velocity variations due to stellar activity in solar-like stars

The GAPS Programme at TNG XXVIII -- A pair of hot-Neptunes orbiting the young star TOI-942

A PSF-based Approach to TESS High quality data Of Stellar clusters (PATHOS) - III. Exploring the properties of young associations through their variables, dippers, and candidate exoplanets

A PSF-based Approach to TESS High quality data Of Stellar clusters (PATHOS) – IV. Candidate exoplanets around stars in open clusters: frequency and age–planetary radius distribution


FAMIE: A Fast Active Learning Framework for Multilingual Information Extraction

Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds

Deep Active Learning for Named Entity Recognition


An open science effort to benchmark legal reasoning in foundation models

On the Opportunities and Risks of Foundation Models

LegalBench: A Collaboratively Built Benchmark for Measuring Legal
  Reasoning in Large Language Models

LegalBench: Prototyping a Collaborative Benchmark for Legal Reasoning


Several models for POS Tagging

Attention Is All You Need

Recurrent Neural Network Grammars

Bidirectional LSTM-CRF Models for Sequence Tagging

The Best of Both Worlds: Combining Recent Advances in Neural Machine Translation

Empower Sequence Labeling with Task-Aware Neural Language Model


a "minimal buy-in" FITS library and utility package for astronomical data analysis

The HIX galaxy survey I: Study of the most gas rich galaxies from HIPASS

X-Ray Variability from the Ultraluminous Black Hole Candidate X-Ray Binary in the Globular Cluster RZ 2109

A Multi-band Study of the Remarkable Jet in Quasar 4C+19.44

Centaurus A: constraints on the nature of the giant lobe filaments from XMM-Newton observations

Optical and X-ray follow-up to a globular cluster ultraluminous X-ray source in NGC 4472


[NeurIPS 2023] Assessor360: Multi-sequence Network for Blind Omnidirectional Image Quality Assessment

MANIQA: Multi-dimension Attention Network for No-Reference Image Quality Assessment


Distributed semi-constrained microphone arrays

DNN-Based Mask Estimation for Distributed Speech Enhancement in Spatially Unconstrained Microphone Arrays

Distributed speech separation in spatially unconstrained microphone
  arrays

Attention-based distributed speech enhancement for unconstrained microphone arrays with varying number of nodes


DFOIL: Introgression Testing for Five Taxa

The rice paradox: Multiple origins but single domestication in Asian rice

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

Genetic homogenization of the nuclear ITS loci across two morphologically distinct gentians in their overlapping distributions in the Qinghai-Tibet Plateau

Selection and gene flow define polygenic barriers between incipient butterfly species

Speciation in sympatry with ongoing secondary gene flow and an olfactory trigger in a radiation of Cameroon cichlids


PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics

SHR4z, a novel decoy effector from the haustorium of the parasitic weed Striga gesnerioides, suppresses host plant immunity

Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes

Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

PlantTribes2: Tools for comparative gene family analysis in plant genomics


Overcooked human-AI experiment platform

Collaborating with Humans without Human Data

Maximum Entropy Population-Based Training for Zero-Shot Human-AI
  Coordination

ProAgent: Building Proactive Cooperative AI with Large Language Models

Cooperative Open-ended Learning Framework for Zero-shot Coordination

Tackling Cooperative Incompatibility for Zero-Shot Human-AI Coordination


SAASBO: a package for high-dimensional bayesian optimization

High-Dimensional Bayesian Optimization with Sparse Axis-Aligned Subspaces

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

Comparison of High-Dimensional Bayesian Optimization Algorithms on BBOB


Functions for compositional analysis of high throughput sequencing

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics

Strong succession in arbuscular mycorrhizal fungal communities

A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease

Diverse viruses have restricted biogeography in deep-sea hydrothermal vent fluids

A reproducible effect size is more useful than an irreproducible hypothesis test to analyze high throughput sequencing datasets

Processing human urine and ureteral stents for 16S rRNA amplicon sequencing


Graph Clustering Merger

MAGUS: Multiple sequence Alignment using Graph clUStering

Recursive MAGUS: scalable and accurate multiple sequence alignment

MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences

UPP2: fast and accurate alignment of datasets with fragmentary sequences

The Maximum Weight Trace Alignment Merging Problem

HMMerge: an ensemble method for multiple sequence alignment

Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem

IEEE/ACM transactions on computational biology and bioinformatics


An easy-to-use federated learning platform

Performance Optimization of Federated Person Re-identification via Benchmark Analysis

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

Collaborative Unsupervised Visual Representation Learning from Decentralized Data

Divergence-aware Federated Self-Supervised Learning

Joint Optimization in Edge-Cloud Continuum for Federated Unsupervised Person Re-identification

EasyFL: A Low-Code Federated Learning Platform for Dummies

Optimizing Performance of Federated Person Re-identification: Benchmarking and Analysis

ACM transactions on multimedia computing, communications and applications/ACM transactions on multimedia computing communications and applications

MAS: Towards Resource-Efficient Federated Multiple-Task Learning


Public Kerr metric polarized ray tracing radiative transfer code

Detection of orbital motions near the last stable circular orbit of the massive black hole SgrA*

A public code for general relativistic, polarised radiative transfer around spinning black holes

Faraday rotation in GRMHD simulations of the jet launching zone of M87

Ab Initio Horizon-scale Simulations of Magnetically Arrested Accretion in Sagittarius A* Fed by Stellar Winds

Sgr A* near-infrared flares from reconnection events in a magnetically arrested disc

The impact of Faraday effects on polarized black hole images of Sagittarius A

Evolving non-thermal electrons in simulations of black hole accretion

General Purpose Ray Tracing and Polarized Radiative Transfer in General Relativity

The impact of non-thermal electrons on event horizon scale images and spectra of Sgr A

Radiative Transfer with POLARIS. II. Modeling of Synthetic Galactic Synchrotron Observations


Generative Forests in Python

Joints in Random Forests


A unified framework for event-based video. Encoder/transcoder/decoder for ADΔER (Address, Decimation, Δt Event Representation) video streams.

An Asynchronous Intensity Representation for Framed and Event Video Sources

Accelerated Event-Based Feature Detection and Compression for
  Surveillance Video Systems


A toolkit for performing set operations - union, intersection and complement - on k-mer lists.

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads

AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

Estimation of genome size using k-mer frequencies from corrected long reads


BOND: BERT-Assisted Open-Domain Name Entity Recognition with Distant Supervision

BOND: BERT-Assisted Open-Domain Named Entity Recognition with Distant Supervision

Template-free Prompt Tuning for Few-shot NER

Distantly-Supervised Named Entity Recognition with Noise-Robust Learning and Language Model Augmented Self-Training

Named Entity Recognition with Small Strongly Labeled and Large Weakly Labeled Data

Distantly Supervised Named Entity Recognition via Confidence-Based Multi-Class Positive and Unlabeled Learning

ChemNER: Fine-Grained Chemistry Named Entity Recognition with Ontology-Guided Distant Supervision

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

MetaTS: Meta Teacher-Student Network for Multilingual Sequence Labeling with Minimal Supervision

Simple Questions Generate Named Entity Recognition Datasets


Unsupervised Language Modeling at scale for robust sentiment classification

Attention Is All You Need

Mining Dual Emotion for Fake News Detection

Generating Sentiment-Preserving Fake Online Reviews Using Neural Language Models and Their Human- and Machine-based Detection

Practical Text Classification With Large Pre-Trained Language Models

Large Scale Language Modeling: Converging on 40GB of Text in Four Hours

Multimodal dual emotion with fusion of visual sentiment for rumor detection


Spitfire is a Python/C++ library for constructing tabulated chemistry models and solving differential equations.

Cost function for low-dimensional manifold topology assessment

Local manifold learning and its link to domain-based physics knowledge


[ACL-IJCNLP 2021] Automated Concatenation of Embeddings for Structured Prediction

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

PHEE: A Dataset for Pharmacovigilance Event Extraction from Text

Enhanced Universal Dependency Parsing with Automated Concatenation of Embeddings

Beyond modeling: NLP Pipeline for efficient environmental policy
  analysis


LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

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

Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet

Chromosome Level Genome Assembly of Andrographis paniculata

Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

Allele-aware chromosome-level genome assembly of the autohexaploid Diospyros kaki Thunb

Decoupling subgenomes within hybrid lavandin provide new insights into speciation and monoterpenoid diversification of Lavandula

Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility


serious constellations of reoccurring phylogenetically-independent origin

The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

Context-specific emergence and growth of the SARS-CoV-2 Delta variant

medRxiv : the preprint server for health sciences

Genomics-informed outbreak investigations of SARS-CoV-2 using civet

Comparison of different sequencing techniques for identification of SARS-CoV-2 variants of concern with multiplex real-time PCR

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Assessment of Inter-Laboratory Differences in SARS-CoV-2 Consensus Genome Assemblies between Public Health Laboratories in Australia

Modeling the impact of the Omicron infection wave in Germany

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method

Systematic Guidelines for Effective Utilization of COVID-19 Databases in Genomic, Epidemiologic, and Clinical Research


A practical guide to linking brain-wide gene expression and neuroimaging data

Cortical structural differences in major depressive disorder correlate with cell type-specific transcriptional signatures

Regional brain iron and gene expression provide insights into neurodegeneration in Parkinson’s disease

Differences in network controllability and regional gene expression underlie hallucinations in Parkinson’s disease

Relating quantitative 7T MRI across cortical depths to cytoarchitectonics, gene expression and connectomics: a framework for tracking neurodegenerative disease

Functional hierarchy of the angular gyrus and its underlying genetic architecture

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders

Distinct Genetic Signatures of Cortical and Subcortical Regions Associated with Human Memory

Transcriptomic and Macroscopic Architectures of Multimodal Covariance Network Reveal Molecular-Structural-Functional Co-alterations

Transcriptional and Cellular Signatures of Morphometric Similarity Remodeling in Major Depressive Disorder


A neural network emulator to transform field data

AI-assisted superresolution cosmological simulations – II. Halo substructures, velocities, and higher order statistics

Field-level Neural Network Emulator for Cosmological N-body Simulations

Simple lessons from complex learning: what a neural network model learns about cosmic structure formation

Super-resolving Dark Matter Halos using Generative Deep Learning


Repository for our NeurIPS 2022 paper "Concept Embedding Models: Beyond the Accuracy-Explainability Trade-Off" and our NeurIPS 2023 paper "Learning to Receive Help: Intervention-Aware Concept Embedding Models"

Concept Bottleneck Models

Probabilistic Concept Bottleneck Models


see README

A Comparative Study on Recent Neural Spoofing Countermeasures for Synthetic Speech Detection

Investigating self-supervised front ends for speech spoofing countermeasures

Spoofed Training Data for Speech Spoofing Countermeasure Can Be Efficiently Created Using Neural Vocoders

Improving LPCNet-based Text-to-Speech with Linear Prediction-structured Mixture Density Network

Investigating Active-Learning-Based Training Data Selection for Speech Spoofing Countermeasure

A Practical Guide to Logical Access Voice Presentation Attack Detection

Period VITS: Variational Inference with Explicit Pitch Modeling for End-To-End Emotional Speech Synthesis

Estimating the confidence of speech spoofing countermeasure

One-class learning towards generalized voice spoofing detection.


Microbial Populations as Clusters Of Gene Transfer

Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology

Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria


MaskFusion: Real-Time Recognition, Tracking and Reconstruction of Multiple Moving Objects

BundleTrack: 6D Pose Tracking for Novel Objects without Instance or Category-Level 3D Models

RGB-D Odometry and SLAM

Evaluating the Impact of Semantic Segmentation and Pose Estimation on Dense Semantic SLAM


Code for "NODE-GAM: Neural Generalized Additive Model for Interpretable Deep Learning"

How Interpretable and Trustworthy are GAMs?

Interpretability with full complexity by constraining feature
  information


Livox horizon porting for loam

FAST-LIO: A Fast, Robust LiDAR-Inertial Odometry Package by Tightly-Coupled Iterated Kalman Filter

CamVox: A Low-cost and Accurate Lidar-assisted Visual SLAM System

A SLAM System with Direct Velocity Estimation for Mechanical and Solid-State LiDARs

RailLoMer: Rail Vehicle Localization and Mapping with
  LiDAR-IMU-Odometer-GNSS Data Fusion


2 ~ 6 sets venn diagram for python

Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN

Genetic and phylogenetic analysis of dissimilatory iodate-reducing bacteria identifies potential niches across the world’s oceans

Toll-like Interleukin 1 Receptor Regulator Is an Important Modulator of Inflammation Responsive Genes

Metamorphic Testing for Quality Assurance of Protein Function Prediction Tools

Efficient and accurate detection of viral sequences at single-cell resolution reveals novel viruses perturbing host gene expression

bioRxiv : the preprint server for biology

Establishing comprehensive quaternary structural proteomes from genome sequence


Anonymized dataset of COVID-19 cases with a focus on radiological imaging. This includes images (x-ray / ct) with extensive metadata, such as admission-, ICU-, laboratory-, and patient master-data.

COVID-CXNet: Detecting COVID-19 in frontal chest X-ray images using deep learning

COVID-19 Infection Map Generation and Detection from Chest X-Ray Images

Chest X-ray Classification for the Detection of COVID-19 Using Deep Learning Techniques

Public Covid-19 X-ray datasets and their impact on model bias – A systematic review of a significant problem

A deep learning architecture for multi-class lung diseases classification using chest X-ray (CXR) images

Alexandria Engineering Journal /Alexandria Engineering Journal

Label-Efficient Self-Supervised Federated Learning for Tackling Data Heterogeneity in Medical Imaging

COVID-19 Classification on Chest X-ray Images Using Deep Learning Methods

International journal of environmental research and public health

On the Composition and Limitations of Publicly Available COVID-19 X-Ray Imaging Datasets

Detection of various lung diseases including COVID-19 using extreme learning machine algorithm based on the features extracted from a lightweight CNN architecture

Biocybernetics and Biomedical Engineering

Detection of COVID-19 in X-ray Images Using Densely Connected Squeeze Convolutional Neural Network (DCSCNN): Focusing on Interpretability and Explainability of the Black Box Model


Speaking the Same Language: Matching Machine to Human Captions by Adversarial Training

Object Hallucination in Image Captioning

Mitigating Gender Bias in Captioning Systems

Looking for Confirmations: An Effective and Human-Like Visual Dialogue Strategy


GLAC Net: GLocal Attention Cascading Network for the Visual Storytelling Challenge

GLAC Net: GLocal Attention Cascading Networks for Multi-image Cued Story Generation

The Steep Road to Happily Ever After: An Analysis of Current Visual Storytelling Models

Vision Transformer Based Model for Describing a Set of Images as a Story

Visual Transformation Telling


Using RLLib and PycoLab to explore intelligent cooperative behavior in sequential social dilemmas

Multi-agent Reinforcement Learning in Sequential Social Dilemmas

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

Inequity aversion improves cooperation in intertemporal social dilemmas


Repository containing code for "How to Train BERT with an Academic Budget" paper

ExtremeBERT: A Toolkit for Accelerating Pretraining of Customized BERT


release version

De novo annotation and characterization of the translatome with ribosome profiling data

LncRNA-Encoded Peptide: Functions and Predicting Methods

Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases


Benchmarking continual learning techniques for Human Activity Recognition data. We offer interesting insights on how the performance techniques vary with a domain other than images.

Overcoming catastrophic forgetting in neural networks

Memory Aware Synapses: Learning what (not) to forget

Rotate your Networks: Better Weight Consolidation and Less Catastrophic Forgetting

Continual learning in sensor-based human activity recognition: An empirical benchmark analysis

Continual Learning in Human Activity Recognition: an Empirical Analysis of Regularization

Greedy Frank-Wolfe Algorithm for Exemplar Selection


Download Datasets and Ground Truths:  https://github.com/TuSimple/tusimple-benchmark/issues/3

RESA: Recurrent Feature-Shift Aggregator for Lane Detection

PersFormer: 3D Lane Detection via Perspective Transformer and the OpenLane Benchmark

Deflating Dataset Bias Using Synthetic Data Augmentation

Physical Backdoor Attacks to Lane Detection Systems in Autonomous Driving

A Fast and Robust Lane Detection Method Based on Semantic Segmentation and Optical Flow Estimation

High-Definition Map Generation Technologies For Autonomous Driving

OpenLane-V2: A Topology Reasoning Benchmark for Unified 3D HD Mapping

Enabling Retrain-free Deep Neural Network Pruning Using Surrogate Lagrangian Relaxation

Open-sourced Data Ecosystem in Autonomous Driving: the Present and
  Future

Foggy Lane Dataset Synthesized from Monocular Images for Lane Detection Algorithms


The released code of Neurify in NIPS 2018

Formal Security Analysis of Neural Networks using Symbolic Intervals

Efficient Formal Safety Analysis of Neural Networks

A Review of Formal Methods applied to Machine Learning

Debona: Decoupled Boundary Network Analysis for Tighter Bounds and Faster Adversarial Robustness Proofs.


Easy MDPs and grid worlds with accessible transition dynamics to do exact calculations

Understanding the impact of entropy on policy optimization

Marginalized State Distribution Entropy Regularization in Policy Optimization

VFunc: a Deep Generative Model for Functions


Webpage for the DSTC8 - NOESIS II: Predicting Responses

On the Calibration and Uncertainty of Neural Learning to Rank Models for Conversational Search

Conference of the European Chapter of the Association for Computational Linguistics

On the Calibration and Uncertainty of Neural Learning to Rank Models.

Do the Findings of Document and Passage Retrieval Generalize to the Retrieval of Responses for Dialogues?


R Package for Single-Cell Dataset Processing and Visualization

Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted murine heart

Expression and regulatory characteristics of peripheral blood immune cells in primary Sjögren’s syndrome patients using single-cell transcriptomic

Single-cell evaluation reveals shifts in the tumor-immune niches that shape and maintain aggressive lesions in the breast

An integrative analysis of single-cell and bulk transcriptome and bidirectional mendelian randomization analysis identified C1Q as a novel stimulated risk gene for Atherosclerosis


Official code for  "InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization" (ICLR 2020, spotlight)

Contrastive Learning with Hard Negative Samples

Graph Self-Supervised Learning: A Survey

A Comprehensive Survey on Pretrained Foundation Models: A History from
  BERT to ChatGPT

Self-Supervised Learning on Graphs: Contrastive, Generative, or Predictive

Graph-based Semi-supervised Learning: A Comprehensive Review

Deep Graph-level Anomaly Detection by Glocal Knowledge Distillation

Augmentations in Graph Contrastive Learning: Current Methodological Flaws & Towards Better Practices

Graph-based Molecular Representation Learning

Imbalanced Graph Classification via Graph-of-Graph Neural Networks


Easy to use, state-of-the-art Neural Machine Translation for 100+ languages

Beyond English-Centric Multilingual Machine Translation

Multilingual Translation with Extensible Multilingual Pretraining and
  Finetuning

Collecting a Large-Scale Gender Bias Dataset for Coreference Resolution and Machine Translation

The Effect of Domain and Diacritics in Yoruba–English Neural Machine Translation

Translate, then Parse! A strong baseline for Cross-Lingual AMR Parsing

Towards Explainable Evaluation Metrics for Natural Language Generation

Findings of the The RuATD Shared Task 2022 on Artificial Text Detection in Russian

An Empirical Study on Cross-X Transfer for Legal Judgment Prediction

RuCoLA: Russian Corpus of Linguistic Acceptability

The Eval4NLP 2023 Shared Task on Prompting Large Language Models as
  Explainable Metrics


Open source person re-identification library in python

Bag of Tricks and A Strong Baseline for Deep Person Re-identification

Progressive Pose Attention Transfer for Person Image Generation

Torchreid: A Library for Deep Learning Person Re-Identification in Pytorch

KeepAugment: A Simple Information-Preserving Data Augmentation Approach

DeepSportradar-v1: Computer Vision Dataset for Sports Understanding with High Quality Annotations

Proceedings of the 5th International ACM Workshop on Multimedia Content Analysis in Sports

Progressive and Aligned Pose Attention Transfer for Person Image Generation

Progressive Transfer Learning

Taking A Closer Look at Synthesis: Fine-Grained Attribute Analysis for Person Re-Identification

Progressive Transfer Learning for Person Re-identification

PROCEEDINGS OF THE TWENTY-EIGHTH INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE

Improved Hard Example Mining by Discovering Attribute-based Hard Person Identity


HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells

Association of an IGHV3-66 gene variant with Kawasaki disease

T Cell Receptor Profiling in Type 1 Diabetes

A current and future perspective on T cell receptor repertoire profiling


PyDeep is a machine learning / deep learning library with focus on unsupervised learning. The library has a modular design, is well documented and purely written in Python/Numpy. This allows you to understand, use, modify, and debug the code easily. Furthermore, its extensive use of unittests assures a high level of reliability and correctness.

Gaussian-binary restricted Boltzmann machines for modeling natural image statistics

How to Center Binary Deep Boltzmann Machines

A Hippocampus Model for Online One-Shot Storage of Pattern Sequences


:package: Non-parametric Causal Effects Based on Modified Treatment Policies :crystal_ball:

Nonparametric Causal Effects Based on Longitudinal Modified Treatment Policies

When effects cannot be estimated: redefining estimands to understand the
  effects of naloxone access laws

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

Effect of Sepsis on Death as Modified by Solid Organ Transplantation


Utility to greatly simplify downloading, converting, viewing and extracting annotations from the Digital Database for Screening Mammography (DDSM) database available here: http://marathon.csee.usf.edu/Mammography/Database.html

Crossbar-Net: A Novel Convolutional Network for Kidney Tumor Segmentation in CT Images

Evaluation of Feature Selection Methods for Mammographic Breast Cancer Diagnosis in a Unified Framework

A Sneak Attack on Segmentation of Medical Images Using Deep Neural Network Classifiers


Tools to analyze Dip-C (or other 3C/Hi-C) data

Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization

Determining the 3D genome structure of a single mammalian cell with Dip-C

Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice

RNA-mediated symmetry breaking enables singular olfactory receptor choice


The net:cal calibration framework is a Python 3 library for measuring and mitigating miscalibration of uncertainty estimates, e.g., by a neural network.

Multivariate Confidence Calibration for Object Detection

Introducing Intermediate Domains for Effective Self-Training during
  Test-Time

Parametric and Multivariate Uncertainty Calibration for Regression and Object Detection

Bayesian Confidence Calibration for Epistemic Uncertainty Modelling


Neural CRF Model for Sentence Alignment in Text Simplification

Text Revision by On-the-Fly Representation Optimization

Cognitive Simplification Operations Improve Text Simplification

Gauging the Gap Between Human and Machine Text Simplification Through Analytical Evaluation of Simplification Strategies and Errors

Findings of the Association for Computational Linguistics: EACL 2023


DSMIL: Dual-stream multiple instance learning networks for tumor detection in Whole Slide Image

Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning

MixUp-MIL: Novel Data Augmentation for Multiple Instance Learning and a Study on Thyroid Cancer Diagnosis

Scalable Set Encoding with Universal Mini-Batch Consistency and Unbiased
  Full Set Gradient Approximation


An R client for broads firehose pipeline, providing TCGA data sets

The role of markets in sovereign debt crisis detection, prevention and resolution

A novel CDC25A/DYRK2 regulatory switch modulates cell cycle and survival

A Transcriptomic Analysis of Head and Neck Squamous Cell Carcinomas for Prognostic Indications


A tensorflow implementation of RippleNet

RippleNet: Propagating User Preferences on the Knowledge Graph for Recommender Systems

International Conference on Information and Knowledge Management

Jointly Learning Explainable Rules for Recommendation with Knowledge Graph

An End-to-End Neighborhood-based Interaction Model for Knowledge-enhanced Recommendation

User Response Prediction in Online Advertising

FairSR: Fairness-aware Sequential Recommendation through Multi-Task Learning with Preference Graph Embeddings

ACM transactions on intelligent systems and technology


Official Pytorch Implementation for “Plug-and-Play Diffusion Features for Text-Driven Image-to-Image Translation” (CVPR 2023)

MAG-Edit: Localized Image Editing in Complex Scenarios via Mask-Based Attention-Adjusted Guidance


An R package for computing the Standardized Precipitation-Evapotranspiration Index (SPEI), Penman-Monteith and other reference evapotranspiration, SPI, etc.


Taskonomy: Disentangling Task Transfer Learning [Best Paper, CVPR2018]

Efficiently Identifying Task Groupings for Multi-Task Learning

Representation Similarity Analysis for Efficient Task taxonomy & Transfer Learning

Deep Model Transferability from Attribution Maps

Multitask Learning Strengthens Adversarial Robustness

Unveiling functions of the visual cortex using task-specific deep neural networks

Task-specific vision models explain task-specific areas of visual cortex

Smart Multi-tenant Federated Learning


Out-of-Distribution Generalization via Risk Extrapolation (REx)

Accounting for Unobserved Confounding in Domain Generalization

Environment-Aware Dynamic Graph Learning for Out-of-Distribution
  Generalization


Learning diverse image-to-image translation from unpaired data

Diverse Image-to-Image Translation via Disentangled Representations

Mode Seeking Generative Adversarial Networks for Diverse Image Synthesis

Reusing Discriminators for Encoding: Towards Unsupervised Image-to-Image Translation

Positional Normalization

Memory-guided Unsupervised Image-to-image Translation

MCL-GAN: Generative Adversarial Networks with Multiple Specialized Discriminators


Learning from Synthetic Humans, CVPR 2017

Learning from Synthetic Humans


Circle plot with bundled edges

Prognostic Ability of Enhancer RNAs in Metastasis of Non-Small Cell Lung Cancer


Shiny apps for NGS etc based on reusable components created using Shiny modules

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data

iDEP: An integrated web application for differential expression and pathway analysis

WIlsON: Web-based Interactive Omics VisualizatioN

Establishment of the TALE-code reveals aberrantly activated homeobox gene PBX1 in Hodgkin lymphoma

Aberrant expression of NKL homeobox genes HMX2 and HMX3 interferes with cell differentiation in acute myeloid leukemia

Genomic Aberrations Generate Fusion Gene FOXK2::TP63 and Activate NFKB1 in Cutaneous T-Cell Lymphoma


Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)

ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees

Phylogenomic Coalescent Analyses of Avian Retroelements Infer Zero-Length Branches at the Base of Neoaves, Emergent Support for Controversial Clades, and Ancient Introgressive Hybridization in Afroaves

Phylogenomic branch length estimation using quartets


FastSpeech: Fast, Robust and Controllable Text to Speech

VRAIN-UPV MLLP's system for the Blizzard Challenge 2021


Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks

SSD: Single Shot MultiBox Detector

YOLOv3: An Incremental Improvement

End-to-End Object Detection with Transformers

Unmanned Aerial Vehicle Visual Detection and Tracking using Deep Neural Networks: A Performance Benchmark


Open source Li-ion data management and modelling software


FarsTail: a Persian natural language inference dataset

FarsTail: A Persian Natural Language Inference Dataset

Contradiction Detection in Persian Text


[CADL'22, ECCVW] Official repository of paper titled "EdgeNeXt: Efficiently Amalgamated CNN-Transformer Architecture for Mobile Vision Applications".

MobileViT: Light-weight, General-purpose, and Mobile-friendly Vision Transformer

SwiftFormer: Efficient Additive Attention for Transformer-based Real-time Mobile Vision Applications

Solving ImageNet: a Unified Scheme for Training any Backbone to Top
  Results


Official Git repository of R package meta

Progression-Free Survival and Overall Survival of CDK 4/6 Inhibitors Plus Endocrine Therapy in Metastatic Breast Cancer: A Systematic Review and Meta-Analysis

Occupational Lead Exposure and Brain Tumors: Systematic Review and Meta-Analysis

Assessing the causal role of epigenetic clocks in the development of multiple cancers: a Mendelian randomization study

Alaskan carbon-climate feedbacks will be weaker than inferred from short-term experiments

The Use of Tocilizumab in Patients with COVID-19: A Systematic Review, Meta-Analysis and Trial Sequential Analysis of Randomized Controlled Studies

Impact of differences in acute respiratory distress syndrome randomised controlled trial inclusion and exclusion criteria: systematic review and meta-analysis

Clinical and radiographic outcomes of upper thoracic versus lower thoracic upper instrumented vertebrae for adult scoliosis: a meta-analysis

Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas

Effect of the COVID-19 pandemic on the proportion of physically active children and adults worldwide: A systematic review and meta-analysis

Higher versus lower dose corticosteroids for severe to critical COVID-19: A systematic review and dose-response meta-analysis

Direct Oral Anticoagulants as the First Choice of Anticoagulation for Patients with Peripheral Artery Disease to Prevent Adverse Vascular Events: A Systematic Review and Meta-Analysis

Journal of cardiovascular development and disease


Asynchronous Methods for Deep Reinforcement Learning

Pre-training with non-expert human demonstration for deep reinforcement learning

Jointly Pre-training with Supervised, Autoencoder, and Value Losses for
  Deep Reinforcement Learning

Vision-based deep execution monitoring


LeViT a Vision Transformer in ConvNet's Clothing for Faster Inference

LeViT: a Vision Transformer in ConvNet's Clothing for Faster Inference

Transformers in computational visual media: A survey


Convex potential flows

Masked Autoregressive Flow for Density Estimation

Sylvester Normalizing Flows for Variational Inference

Convex Potential Flows: Universal Probability Distributions with Optimal Transport and Convex Optimization

Turning Normalizing Flows into Monge Maps with Geodesic Gaussian
  Preserving Flows

ELF: Exact-Lipschitz Based Universal Density Approximator Flow

Learning with Stochastic Orders


Graph-linked unified embedding for single-cell multi-omics data integration

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

Deep Learning in Single-Cell Analysis

Multi-omics integration and regulatory inference for unpaired single-cell data with a graph-linked unified embedding framework


Uninformed Students: Student-Teacher Anomaly Detection with Discriminative Latent Embeddings

Do Deep Generative Models Know What They Don't Know?

Improving Unsupervised Defect Segmentation by Applying Structural Similarity to Autoencoders


A suite of MiniZinc benchmarks.

Google vs IBM: A Constraint Solving Challenge on the Job-Shop Scheduling Problem

Modelling and Solving Online Optimisation Problems

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

Learning Objective Boundaries for Constraint Optimization Problems


Spatial mapping of cell types by integration of transcriptomics data

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data

Spatial omics: Navigating to the golden era of cancer research

A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

Zenodo (CERN European Organization for Nuclear Research)

Benchmarking and integration of methods for deconvoluting spatial transcriptomic data

SPROUT: spectral sparsification helps restore the spatial structure at single-cell resolution


A PyTorch implementation of ACM SIGKDD 2019 paper "Predicting Dynamic Embedding Trajectory in Temporal Interaction Networks"

Intensity-Free Learning of Temporal Point Processes

TCL: Transformer-based Dynamic Graph Modelling via Contrastive Learning

UNIPoint: Universally Approximating Point Processes Intensities

Spectral Transform Forms Scalable Transformer

Efficient Dynamic Graph Representation Learning at Scale

From Static to Dynamic Node Embeddings

Modeling Inter-Dependence Between Time and Mark in Multivariate Temporal Point Processes

Proceedings of the 31st ACM International Conference on Information & Knowledge Management

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


Model Agnostic Counterfactual Explanations

Algorithmic Recourse: from Counterfactual Explanations to Interventions

Model-Agnostic Counterfactual Explanations for Consequential Decisions

Counterfactuals and Causability in Explainable Artificial Intelligence: Theory, Algorithms, and Applications

Optimal Counterfactual Explanations in Tree Ensembles

NICE: An Algorithm for Nearest Instance Counterfactual Explanations


This is the data repository for the Imperial College London YouGov Covid 19 Behaviour Tracker Data Hub.

Estimating marine plastic pollution from COVID-19 face masks in coastal regions

Recent Smell Loss Is the Best Predictor of COVID-19 Among Individuals With Recent Respiratory Symptoms

The psychosocial impact of the COVID-19 pandemic on changes in smoking behavior: Evidence from a nationwide survey in the UK

The best COVID-19 predictor is recent smell loss: a cross-sectional study

Modelling the impact of vaccine hesitancy in prolonging the need for Non-Pharmaceutical Interventions to control the COVID-19 pandemic

Inequality-Related Health and Social Factors and Their Impact on Well-Being during the COVID-19 Pandemic: Findings from a National Survey in the UK

Associations Between Compliance With Non-pharmaceutical Interventions and Social-distancing Policies in Korea During the COVID-19 Pandemic

Journal of preventive medicine and public health = Yebang Uihakhoe chi

Improving vaccination intent among skeptics through confidence in governments' handling of the COVID-19 pandemic

A cross-national study of multilevel determinants on public fully vaccination against COVID-19

Health and place/Health & place (Online)

Lessons from COVID-19 for rescalable data collection


Papers and code related to 'Less Than One'-Shot (LO-Shot) Learning

'Less Than One'-Shot Learning: Learning N Classes From M<N Samples

One Line To Rule Them All: Generating LO-Shot Soft-Label Prototypes

Optimal 1-NN prototypes for pathological geometries


Code and data of the ACL 2020 paper "Word-level Textual Adversarial Attacking as Combinatorial Optimization"

Towards a Robust Deep Neural Network in Texts: A Survey

Survival of the Most Influential Prompts: Efficient Black-Box Prompt Search via Clustering and Pruning


Whole Genome Simulator for Next-Generation Sequencing

Evaluating the Information Content of Shallow Shotgun Metagenomics

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population

Interactive analysis and assessment of single-cell copy-number variations

Exploring genome characteristics and sequence quality without a reference

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

Spaced seeds improve k-mer-based metagenomic classification

NanoVar: Accurate Characterization of Patients’ Genomic Structural Variants Using Low-Depth Nanopore Sequencing

QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data


Marathi NLP - is a repository dedicated to development of tools and resources for Marathi language.

L3Cube-MahaCorpus and MahaBERT: Marathi Monolingual Corpus, Marathi BERT
  Language Models, and Resources

L3Cube-HindBERT and DevBERT: Pre-Trained BERT Transformer models for
  Devanagari based Hindi and Marathi Languages

L3CubeMahaSent: A Marathi Tweet-based Sentiment Analysis Dataset

L3Cube-MahaHate: A Tweet-based Marathi Hate Speech Detection Dataset and
  BERT models

L3Cube-MahaNER: A Marathi Named Entity Recognition Dataset and BERT models

L3Cube-MahaNLP: Marathi Natural Language Processing Datasets, Models,
  and Library

L3Cube-MahaSBERT and HindSBERT: Sentence BERT Models and Benchmarking BERT Sentence Representations for Hindi and Marathi

Spread Love Not Hate: Undermining the Importance of Hateful Pre-training
  for Hate Speech Detection

My Boli: Code-mixed Marathi-English Corpora, Pretrained Language Models
  and Evaluation Benchmarks

L3Cube-MahaSent-MD: A Multi-domain Marathi Sentiment Analysis Dataset
  and Transformer Models


A simple and accurate method to fool deep neural networks

DeepFool: a simple and accurate method to fool deep neural networks

Detecting Adversarial Image Examples in Deep Neural Networks with Adaptive Noise Reduction

IEEE Transactions on Dependable and Secure Computing/IEEE transactions on dependable and secure computing

Deep Defense: Training DNNs with Improved Adversarial Robustness

EdgeFool: An Adversarial Image Enhancement Filter

Robustness via Deep Low-Rank Representations

Harmonic Adversarial Attack Method

Employing Deep Ensemble Learning for Improving the Security of Computer Networks Against Adversarial Attacks

Defending against Adversarial Attacks through Resilient Feature Regeneration.

Unraveling Attacks in Machine Learning-based IoT Ecosystems: A Survey and the Open Libraries Behind Them


An open information extraction system that provides compact extractions

MinIE: Minimizing Facts in Open Information Extraction

Empirical Methods in Natural Language Processing

OPIEC: An Open Information Extraction Corpus

On Generating Fact-Infused Question Variations

Recent Advances in Natural Language Processing

IELM: An Open Information Extraction Benchmark for Pre-Trained Language Models


ShortStack: Comprehensive annotation and quantification of small RNA genes

Improved Placement of Multi-mapping Small RNAs

Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici)

Environmental and epigenetic regulation of Rider retrotransposons in tomato

TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs

Integrated Analysis of Small RNA, Transcriptome and Degradome Sequencing Provides New Insights into Floral Development and Abscission in Yellow Lupine (Lupinus luteus L.)

International journal of molecular sciences

Butter: High-precision genomic alignment of small RNA-seq data

A role for MIR828 in pineapple fruit development

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


AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

The Human Cell Atlas bone marrow single-cell interactive web portal

Mouse models of neutropenia reveal progenitor-stage-specific defects

cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes

Nasal microbiota dominated by Moraxella spp. is associated with respiratory health in the elderly population: a case control study

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes


Benchmarking the Spectrum of Agent Capabilities

TransDreamer: Reinforcement Learning with Transformer World Models

GriddlyJS: A Web IDE for Reinforcement Learning


[NeurIPS 2022] Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphs

Variational Graph Auto-Encoders

Pareto Invariant Risk Minimization: Towards Mitigating the Optimization
  Dilemma in Out-of-Distribution Generalization

Learning Invariant Molecular Representation in Latent Discrete Space


MSE5540/6640 Materials Informatics course at the University of Utah

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

Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals

Self-referencing embedded strings (SELFIES): A 100% robust molecular string representation

Machine Learning for Materials Scientists: An Introductory Guide Towards Best Practices

Machine Learning Directed Search for Ultraincompressible, Superhard Materials

Journal of the American Chemical Society

Benchmarking materials property prediction methods: the Matbench test set and Automatminer reference algorithm

Predicting materials properties without crystal structure: deep representation learning from stoichiometry

Can machine learning identify the next high-temperature superconductor? Examining extrapolation performance for materials discovery

Machine Learning and Energy Minimization Approaches for Crystal Structure Predictions: A Review and New Horizons

Compositionally restricted attention-based network for materials property predictions


A generalized Louvain method for community detection implemented in MATLAB

Network analysis of particles and grains

Muscle Synergies and Coherence Networks Reflect Different Modes of Coordination During Walking

Topological Data Analysis of Task-Based fMRI Data from Experiments on Schizophrenia

Sectorization for Water Distribution Systems with Multiple Sources: A Performance Indices Comparison

Graph Clustering in All Parameter Regimes

Acute Effect of Betel Quid Chewing on Brain Network Dynamics: A Resting-State Functional Magnetic Resonance Imaging Study

Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System

Mapping robust multiscale communities in chromosome contact networks

Multilayer Modularity Belief Propagation to Assess Detectability of Community Structure

SIAM journal on mathematics of data science

Mapping the semi-nested community structure of 3D chromosome contact networks


A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution

Chlorogenic Acid Alleviates Colon Mucosal Damage Induced by a High-Fat Diet via Gut Microflora Adjustment to Increase Short-Chain Fatty Acid Accumulation in Rats

Oxidative medicine and cellular longevity

Spatial control of potato tuberization by the TCP transcription factor BRANCHED1b

De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar ‘Tieguanyin’ compared with cultivar ‘Benshan’

Adipose tissue-derived neurotrophic factor 3 regulates sympathetic innervation and thermogenesis in adipose tissue

A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data

Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

Chromosome-Scale Assembly of the Dendrobium nobile Genome Provides Insights Into the Molecular Mechanism of the Biosynthesis of the Medicinal Active Ingredient of Dendrobium

Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation


Official implementation of HARL algorithms based on PyTorch.

Heterogeneous-Agent Reinforcement Learning

Byzantine Robust Cooperative Multi-Agent Reinforcement Learning as a
  Bayesian Game


Unofficial implementation of Palette: Image-to-Image Diffusion Models by Pytorch

Denoising Diffusion Probabilistic Models

Diffusion Models Beat GANs on Image Synthesis

Conffusion: Confidence Intervals for Diffusion Models

Ensemble flow reconstruction in the atmospheric boundary layer from spatially limited measurements through latent diffusion models

Gradpaint: Gradient-Guided Inpainting with Diffusion Models


Simple, extendable, easy to understand Glow implementation in PyTorch

Glow: Generative Flow with Invertible 1x1 Convolutions

Do Deep Generative Models Know What They Don't Know?

Your Classifier is Secretly an Energy Based Model and You Should Treat it Like One

Understanding and mitigating exploding inverses in invertible neural networks

Understanding Anomaly Detection with Deep Invertible Networks through Hierarchies of Distributions and Features.

Refining Deep Generative Models via Discriminator Gradient Flow

Denoising diffusion models for out-of-distribution detection

Out-of-Distribution Detection with Distance Guarantee in Deep Generative Models

RockFlow: Fast Generation of Synthetic Source Rock Images Using Generative Flow Models

Normalizing flows for random fields in cosmology


Disentangled and Controllable Face Image Generation via 3D Imitative-Contrastive Learning (CVPR 2020 Oral)

Deep Learning for Deepfakes Creation and Detection: A Survey

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

A Review of Image Processing Techniques for Deepfakes


An SDK for multi-agent collaborative perception.

V2VNet: Vehicle-to-Vehicle Communication for Joint Perception and Prediction

When2com: Multi-Agent Perception via Communication Graph Grouping

Learning Distilled Collaboration Graph for Multi-Agent Perception

Who2com: Collaborative Perception via Learnable Handshake Communication

Towards Vehicle-to-everything Autonomous Driving: A Survey on
  Collaborative Perception


[ICCV 2023] Consistent Image Synthesis and Editing

MasaCtrl: Tuning-Free Mutual Self-Attention Control for Consistent Image Synthesis and Editing

CycleNet: Rethinking Cycle Consistency in Text-Guided Diffusion for
  Image Manipulation


Generating faces with deconvolution networks

Learning to Generate Chairs, Tables and Cars with Convolutional Networks

k-Same-Net: k-Anonymity with Generative Deep Neural Networks for Face Deidentification

Face deidentification with generative deep neural networks


Transition-based tree-to-graph AMR Parser

A Transition-based Algorithm for AMR Parsing

North American Chapter of the Association for Computational Linguistics

An Incremental Parser for Abstract Meaning Representation

SemEval-2017 Task 9: Abstract Meaning Representation Parsing and Generation

Meeting of the Association for Computational Linguistics

RIGA at SemEval-2016 Task 8: Impact of Smatch Extensions and Character-Level Neural Translation on AMR Parsing Accuracy

Semi-supervised New Event Type Induction and Event Detection

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

SemBleu: A Robust Metric for AMR Parsing Evaluation

Augmenting Abstract Meaning Representation for Human-Robot Dialogue

Proceedings of the First International Workshop on Designing Meaning Representations

Parsing Meaning Representations: Is Easier Always Better?

AMR Normalization for Fairer Evaluation


VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Review article: the human intestinal virome in health and disease

Application of Machine Learning in Microbiology

Machine Learning Advances in Microbiology: A Review of Methods and Applications

Bioinformatic approaches for studying the microbiome of fermented food

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models

Seasonal Regime Shift in the Viral Communities of a Permafrost Thaw Lake

Current trends in RNA virus detection through metatranscriptome sequencing data

A Tale of Two Seasons: Distinct Seasonal Viral Communities in a Thermokarst Lake


[ICML2020] Normalized Loss Functions for Deep Learning with Noisy Labels

Learning from Noisy Labels with Deep Neural Networks: A Survey

Constrained Instance and Class Reweighting for Robust Learning under
  Label Noise


Towards Deep Radar Perception for Autonomous Driving: Datasets, Methods, and Challenges

Raw High-Definition Radar for Multi-Task Learning

ADCNet: Learning from Raw Radar Data via Distillation

Deep learning for radar data exploitation of autonomous vehicle


K-CAI NEURAL API - Keras based neural network API that will allow you to create parameter-efficient, memory-efficient, flops-efficient multipath models with new layer types. There are plenty of examples and documentation.

Learning Deep Features for Discriminative Localization

Grouped Pointwise Convolutions Reduce Parameters in Convolutional Neural Networks

Color-Aware Two-Branch DCNN for Efficient Plant Disease Classification

An Enhanced Scheme for Reducing the Complexity of Pointwise Convolutions in CNNs for Image Classification Based on Interleaved Grouped Filters without Divisibility Constraints


X-Transformer: Taming Pretrained Transformers for eXtreme Multi-label Text Classification

A Survey on Text Classification: From Shallow to Deep Learning

Taming Pretrained Transformers for Extreme Multi-label Text Classification

A Survey on Extreme Multi-label Learning


scripts and configuration files for Edinburgh neural MT submission to WMT 16 shared translation task

Six Challenges for Neural Machine Translation

Beyond English-Centric Multilingual Machine Translation

No Language Left Behind: Scaling Human-Centered Machine Translation

Edinburgh Neural Machine Translation Systems for WMT 16

A Convolutional Encoder Model for Neural Machine Translation

Linguistic Input Features Improve Neural Machine Translation

Neural Interactive Translation Prediction

Conference of the Association for Machine Translation in the Americas

A Multilingual View of Unsupervised Machine Translation

MSP: Multi-Stage Prompting for Making Pre-trained Language Models Better Translators

Neural Lattice Search for Domain Adaptation in Machine Translation

International Joint Conference on Natural Language Processing


A Kitti Road Segmentation model implemented in tensorflow.

MultiNet: Real-time Joint Semantic Reasoning for Autonomous Driving

The art and practice of data science pipelines

ANDA: A Novel Data Augmentation Technique Applied to Salient Object Detection

Masking Salient Object Detection, a Mask Region-based Convolutional Neural Network Analysis for Segmentation of Salient Objects

Towards a Change Taxonomy for Machine Learning Systems


Characterizing the Root Landscape of Certificate Transparency Logs

Identifying the Phishing Websites Using the Patterns of TLS Certificates

Aggregation-Based Gossip for Certificate Transparency

Postcertificates for Revocation Transparency


Software Development Vehicles to enable extended and early co-design: a
  RISC-V and HPC case of study


Discrete Global Grids for R: Spatial Analysis Done Right

People have shaped most of terrestrial nature for at least 12,000 years

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

Perceived global increase in algal blooms is attributable to intensified monitoring and emerging bloom impacts

Biodiversity Data Integration: The significance of data resolution and domain

Recent accelerated diversification in rosids occurred outside the tropics

Climatic drivers of latitudinal variation in Late Triassic tetrapod diversity

Source pools and disharmony of the world's island floras

Combining Conventional Statistics and Big Data to Map Global Tourism Destinations Before COVID-19

Yellow fever surveillance suggests zoonotic and anthroponotic emergent potential

Geovisualization of Hydrological Flow in Hexagonal Grid Systems

The Aleutians and Beyond: Distribution, Size Composition, and Catch Dynamics of the Aleutian Skate Bathyraja aleutica across the North Pacific

Animals : an open access journal from MDPI


Tutorials on how to implement a few key architectures for image classification using PyTorch and TorchVision.

Deep Residual Learning for Image Recognition

Very Deep Convolutional Networks for Large-Scale Image Recognition

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


XNect: Real-time Multi-person 3D Human Pose Estimation with a Single RGB Camera

Monocular 3D Multi-Person Pose Estimation by Integrating Top-Down and Bottom-Up Networks

Dual Networks Based 3D Multi-Person Pose Estimation From Monocular Video

IEEE transactions on pattern analysis and machine intelligence


Pytorch-Named-Entity-Recognition-with-BERT

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

Beyond I.I.D.: Three Levels of Generalization for Question Answering on Knowledge Bases

SeqMix: Augmenting Active Sequence Labeling via Sequence Mixup

ReTraCk: A Flexible and Efficient Framework for Knowledge Base Question Answering

TIARA: Multi-grained Retrieval for Robust Question Answering over Large
  Knowledge Bases

Embeddings of Label Components for Sequence Labeling: A Case Study of Fine-grained Named Entity Recognition

Breaking Writer's Block: Low-cost Fine-tuning of Natural Language Generation Models

FC-KBQA: A Fine-to-Coarse Composition Framework for Knowledge Base Question Answering

Creative Painting with Latent Diffusion Models

ScienceExamCER: A High-Density Fine-Grained Science-Domain Corpus for Common Entity Recognition


E2E system with LF-MMI; word N-gram for Mandarin

LAE: Language-Aware Encoder for Monolingual and Multilingual ASR

Consistent Training and Decoding For End-to-end Speech Recognition Using
  Lattice-free MMI

Improving Mandarin End-to-End Speech Recognition With Word N-Gram Language Model

Integrating Lattice-Free MMI Into End-to-End Speech Recognition

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

Automatic Prosody Annotation with Pre-Trained Text-Speech Model


Discrete Graph Structure Learning for Forecasting Multiple Time Series, ICLR 2021.

Pre-training Enhanced Spatial-temporal Graph Neural Network for Multivariate Time Series Forecasting

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

Online Metro Origin-Destination Prediction via Heterogeneous Information Aggregation

Sparse Graph Learning from Spatiotemporal Time Series

RadNet: Incident Prediction in Spatio-Temporal Road Graph Networks Using
  Traffic Forecasting

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


This is a C implementation of variational EM for latent Dirichlet allocation (LDA), a topic model for text or other discrete data.

Neural dynamics of semantic composition

Dense Distributions from Sparse Samples: Improved Gibbs Sampling Parameter Estimators for LDA

Recovery Guarantee of Non-negative Matrix Factorization via Alternating Updates

Gene expression based survival prediction for cancer patients—A topic modeling approach

Extracting Topics with Simultaneous Word Co-occurrence and Semantic Correlation Graphs: Neural Topic Modeling for Short Texts

Findings of the Association for Computational Linguistics: EMNLP 2021

Renormalization Analysis of Topic Models

Semantic Features Based N-Best Rescoring Methods for Automatic Speech Recognition

EvaLDA: Efficient Evasion Attacks Towards Latent Dirichlet Allocation

TopicModel4J: A Java Package for Topic Models


Graph Neural Network based Social Recommendation Model. SIGIR2019.

A Neural Influence Diffusion Model for Social Recommendation

DiffNet++: A Neural Influence and Interest Diffusion Network for Social Recommendation

Robust Preference-Guided Denoising for Graph based Social Recommendation


Toolkit for building machine learning models that generalize to unseen domains and are robust to privacy and other attacks.

Domain Generalization using Causal Matching

Alleviating Privacy Attacks via Causal Learning

The Connection between Out-of-Distribution Generalization and Privacy of ML Models

Hierarchical Variational Auto-Encoding for Unsupervised Domain Generalization


pytorch implementation of openpose including Hand and Body Pose Estimation.

Consistent 3D Hand Reconstruction in Video via self-supervised Learning

Towards Single Camera Human 3D-Kinematics


Implementation of VariBAD: A Very Good Method for Bayes-Adaptive Deep RL via Meta-Learning - Zintgraf et al. (ICLR 2020)

Meta reinforcement learning as task inference

Hypernetworks in Meta-Reinforcement Learning

HMRL: Hyper-Meta Learning for Sparse Reward Reinforcement Learning Problem

Improving Generalization in Meta-RL with Imaginary Tasks from Latent Dynamics Mixture

On the Practical Consistency of Meta-Reinforcement Learning Algorithms

Meta-Learning Parameterized Skills

Meta Reinforcement Learning with Finite Training Tasks -- a Density
  Estimation Approach

ODE-based Recurrent Model-free Reinforcement Learning for POMDPs