Automatically exported from code.google.com/p/berkeleyparser

Building a comprehensive syntactic and semantic corpus of Chinese clinical texts

A Top-Down Neural Architecture towards Text-Level Parsing of Discourse Rhetorical Structure

Chinese Zero Pronoun Resolution with Deep Memory Network

Empirical Methods in Natural Language Processing

SCTB: A Chinese Treebank in Scientific Domain

International Conference on Computational Linguistics

Language Independent Dependency to Constituent Tree Conversion

Automatic Topological Field Identification in (Historical) German Texts

From generic partition refinement to weighted tree automata minimization

Supervised Syntax-based Alignment between English Sentences and Abstract Meaning Representation Graphs

Cross-language Projection of Dependency Trees with Constrained Partial Parsing for Tree-to-Tree Machine Translation

Proceedings of the First Conference on Machine Translation: Volume 1,
          Research Papers

DynamicPower at SemEval-2016 Task 8: Processing syntactic parse trees with a Dynamic Semantics core


SQuAD: 100,000+ Questions for Machine Comprehension of Text

Addressing Semantic Drift in Question Generation for Semi-Supervised Question Answering

Answer-driven Deep Question Generation based on Reinforcement Learning


【CVPR'2023 Highlight & TPAMI】Cap4Video: What Can Auxiliary Captions Do for Text-Video Retrieval?

Revisiting Classifier: Transferring Vision-Language Models for Video Recognition

Bidirectional Cross-Modal Knowledge Exploration for Video Recognition with Pre-trained Vision-Language Models


BERTje is a Dutch pre-trained BERT model developed at the University of Groningen. (EMNLP Findings 2020) "What’s so special about BERT’s layers? A closer look at the NLP pipeline in monolingual and multilingual models"

BERTje: A Dutch BERT Model

Exploring Cross-sentence Contexts for Named Entity Recognition with BERT

What's so special about BERT's layers? A closer look at the NLP pipeline in monolingual and multilingual models.

Pre-training Polish Transformer-based Language Models at Scale

WikiBERT models: deep transfer learning for many languages

Constructing Taxonomies from Pretrained Language Models

Deception detection in text and its relation to the cultural dimension of individualism/collectivism

Accurate and Reliable Classification of Unstructured Reports on Their Diagnostic Goal Using BERT Models


Erasing Concepts from Diffusion Models

Erasing Concepts from Diffusion Models

MACE: Mass Concept Erasure in Diffusion Models

UnlearnCanvas: A Stylized Image Dataset to Benchmark Machine Unlearning
  for Diffusion Models

One-dimensional Adapter to Rule Them All: Concepts, Diffusion Models and Erasing Applications

Get What You Want, Not What You Don't: Image Content Suppression for
  Text-to-Image Diffusion Models

Separable Multi-Concept Erasure from Diffusion Models


Global phylogenies of SARS-CoV-2 sequences

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

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

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

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

bioRxiv : the preprint server for biology

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

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

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

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

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

Divergent trajectory of replication and intrinsic pathogenicity of SARS-CoV-2 Omicron post-BA.2/5 subvariants in the upper and lower respiratory tract


Unsupervised Neural Machine Translation

Unsupervised Neural Machine Translation

Rapid Adaptation of Neural Machine Translation to New Languages

Revisiting Iterative Back-Translation from the Perspective of Compositional Generalization

Unsupervised Neural Machine Translation for English and Manipuri

Unsupervised Mandarin-Cantonese Machine Translation


Benchmarking and Visualization Tool for Adversarial Machine Learning

Feature Squeezing: Detecting Adversarial Examples in Deep Neural Networks

Proceedings 2018 Network and Distributed System Security Symposium

Backdoor Attacks and Countermeasures on Deep Learning: A Comprehensive Review

MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-Based Protein Structure Prediction

Feature Squeezing Mitigates and Detects Carlini/Wagner Adversarial Examples

Saliency Attack: Towards Imperceptible Black-box Adversarial Attack

Effective Universal Unrestricted Adversarial Attacks using a MOE Approach

On the Security of Randomized Defenses Against Adversarial Samples

DeepiSign-G: Generic Watermark to Stamp Hidden DNN Parameters for
  Self-contained Tracking


Deep learning ECG models implemented using PyTorch

LUDB: a new open-access validation tool for electrocardiogram delineation algorithms

Investigating Deep Learning Benchmarks for Electrocardiography Signal Processing

A novel deep learning package for electrocardiography research


Contrastive Predictive Coding for Automatic Speaker Verification

Representation Learning with Contrastive Predictive Coding

CoST: Contrastive Learning of Disentangled Seasonal-Trend Representations for Time Series Forecasting

A Survey on Time-Series Pre-Trained Models

Contrastive Predictive Coding Based Feature for Automatic Speaker Verification


Functional genomics and genome-wide association studies

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

Strategies for fine-mapping complex traits

Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits

Trans-ethnic Fine Mapping Highlights Kidney-Function Genes Linked to Salt Sensitivity

Leveraging genome characteristics to improve gene discovery for putamen subcortical brain structure

Unveiling blood pressure‐associated genes in aortic cells through integrative analysis of GWAS and RNA modification‐associated variants

Chronic Diseases and Translational Medicine


Documentation and description of AWS iGenomes S3 resource.

Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation

Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation

Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation


SingleCellNet: classify single cells across species and platforms

Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids

Computational methods for the integrative analysis of single-cell data

Leveraging the Cell Ontology to classify unseen cell types

Single-Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis

scMAGIC: accurately annotating single cells using two rounds of reference-based classification

A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data


FS-Mol  is A Few-Shot Learning Dataset of Molecules, containing molecular compounds with measurements of activity against a variety of protein targets. The dataset is presented with a model evaluation benchmark which aims to drive few-shot learning research in the domain of molecules and graph-structured data.

Strategies for Pre-training Graph Neural Networks

Molecule Attention Transformer

First fully-automated AI/ML virtual screening cascade implemented at a drug discovery centre in Africa

Context-enriched molecule representations improve few-shot drug discovery

PACIA: Parameter-Efficient Adapter for Few-Shot Molecular Property Prediction


Mutual information estimators and benchmark

Beyond Normal: On the Evaluation of Mutual Information Estimators

MINDE: Mutual Information Neural Diffusion Estimation

The Mixtures and the Neural Critics: On the Pointwise Mutual Information Profiles of Fine Distributions


[CAAI AIR'24] Bilateral Reference for High-Resolution Dichotomous Image Segmentation

ViTMatte: Boosting Image Matting with Pretrained Plain Vision Transformers

GCoNet+: A Stronger Group Collaborative Co-Salient Object Detector

Memory-aided Contrastive Consensus Learning for Co-salient Object Detection


A toolbox for differentially private data generation

Benchmarking Differentially Private Synthetic Data Generation Algorithms

CTAB-GAN+: Enhancing Tabular Data Synthesis

Effective and Privacy preserving Tabular Data Synthesizing

Differential Privacy: What is all the noise about?

The Elusive Pursuit of Replicating PATE-GAN: Benchmarking, Auditing, Debugging


Project for paper "Learning 3D Human Dynamics from Video"

Learning 3D Human Dynamics from Video

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

SMPLer-X: Scaling Up Expressive Human Pose and Shape Estimation


This repository contains tools to perform modern cache attacks on ARM.

ARMageddon: Cache Attacks on Mobile Devices

AutoLock: Why Cache Attacks on ARM Are Harder Than You Think

Undermining User Privacy on Mobile Devices Using AI


Weak lensing measurement pipeline for wide area surveys

Dark Energy Survey Year 1 results: weak lensing mass calibration of redMaPPer galaxy clusters

Monthly Notices of the Royal Astronomical Society

Consistent lensing and clustering in a low-S_8 Universe with BOSS, DES Year 3, HSC Year 1 and KiDS-1000

Dark Energy Survey Year 1 results: validation of weak lensing cluster member contamination estimates from P(z) decomposition

Lensing Without Borders. I. A Blind Comparison of the Amplitude of
  Galaxy-Galaxy Lensing Between Independent Imaging Surveys


Recipe for a General, Powerful, Scalable Graph Transformer

Union Subgraph Neural Networks

Diffusing Graph Attention

Gradformer: Graph Transformer with Exponential Decay


Evolving Directed Acyclic Graph

EvoDAG: A semantic Genetic Programming Python library

IEEE International Autumn Meeting on Power, Electronics and Computing

Semantic Genetic Programming for Sentiment Analysis

EvoMSA: A Multilingual Evolutionary Approach for Sentiment Analysis

IEEE Computational Intelligence Magazine

INGEOTEC at SemEval 2017 Task 4: A B4MSA Ensemble based on Genetic Programming for Twitter Sentiment Analysis

Meeting of the Association for Computational Linguistics

NEO 2015

INGEOTEC at SemEval-2019 Task 5 and Task 6: A Genetic Programming Approach for Text Classification

North American Chapter of the Association for Computational Linguistics

Selection Heuristics on Semantic Genetic Programming for Classification Problems

INGEOTEC at SemEval-2018 Task 1: EvoMSA and μTC for Sentiment Analysis


Class activation maps for your PyTorch models (CAM, Grad-CAM, Grad-CAM++, Smooth Grad-CAM++, Score-CAM, SS-CAM, IS-CAM, XGrad-CAM, Layer-CAM)

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

International Journal of Computer Vision

Learning Deep Features for Discriminative Localization

Grad-CAM++: Improved Visual Explanations for Deep Convolutional Networks

Workshop on Applications of Computer Vision

Score-CAM: Score-Weighted Visual Explanations for Convolutional Neural Networks

LayerCAM: Exploring Hierarchical Class Activation Maps for Localization

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

Axiom-based Grad-CAM: Towards Accurate Visualization and Explanation of CNNs

Smooth Grad-CAM++: An Enhanced Inference Level Visualization Technique for Deep Convolutional Neural Network Models

Image-Based Wheat Fungi Diseases Identification by Deep Learning

SS-CAM: Smoothed Score-CAM for Sharper Visual Feature Localization

IS-CAM: Integrated Score-CAM for axiomatic-based explanations


UNMAINTAINED - use klusta instead

High-dimensional cluster analysis with the Masked EM Algorithm

Impaired path integration in mice with disrupted grid cell firing

Dynamic control of hippocampal spatial coding resolution by local visual cues

Processing and Analysis of Multichannel Extracellular Neuronal Signals: State-of-the-Art and Challenges

Separable gain control of ongoing and evoked activity in the visual cortex by serotonergic input

Highly structured, partner-sex- and subject-sex-dependent cortical responses during social facial touch

Resolution of Spike Overlapping by Biogeography-Based Optimization

Coding of self-motion-induced and self-independent visual motion in the rat dorsomedial striatum

All-viral tracing of monosynaptic inputs to single birthdate-defined neurons in the intact brain


Large-scale Pre-training Corpus for Chinese 100G 中文预训练语料

CLUECorpus2020: A Large-scale Chinese Corpus for Pre-training Language Model

Pre-training Polish Transformer-based Language Models at Scale

A Zipf's law-based text generation approach for addressing imbalance in entity extraction

Disco-Bench: A Discourse-Aware Evaluation Benchmark for Language Modelling

Character, Word, or Both? Revisiting the Segmentation Granularity for Chinese Pre-trained Language Models


Create adversarial attacks against machine learning Windows malware detectors

Adversarial EXEmples: A Survey and Experimental Evaluation of Practical Attacks on Machine Learning for Windows Malware Detection

The Threat of Offensive AI to Organizations

secml-malware: Pentesting Windows Malware Classifiers with Adversarial EXEmples in Python

Efficient Malware Analysis Using Metric Embeddings


This is a Torch implementation of ["Deep Residual Learning for Image Recognition",Kaiming He, Xiangyu Zhang, Shaoqing Ren, Jian Sun](http://arxiv.org/abs/1512.03385) the winners of the 2015 ILSVRC and COCO challenges.

Deep Learning for Medical Image Processing: Overview, Challenges and Future

Regularizing CNNs with Locally Constrained Decorrelations

Recent Development on Detection Methods for the Diagnosis of Diabetic Retinopathy

Enhancing SDO/HMI images using deep learning

RoadNet-RT: High Throughput CNN Architecture and SoC Design for Real-Time Road Segmentation

Training deep neural networks for wireless sensor networks using loosely and weakly labeled images


Reference implementation of the paper VERSE: Versatile Graph Embeddings from Similarity Measures

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

GraphVite: A High-Performance CPU-GPU Hybrid System for Node Embedding

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

A Comparative Study for Unsupervised Network Representation Learning

Scalable Graph Embeddings via Sparse Transpose Proximities

FREDE: Anytime Graph Embeddings

Evaluating Node Embeddings of Complex Networks

Understanding Coarsening for Embedding Large-Scale Graphs

QUINT: Node embedding using network hashing

IEEE Transactions on Knowledge and Data Engineering

Node Embedding with Adaptive Similarities for Scalable Learning over Graphs

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


A python package for making arbitrarily structured, arbitrary-dimension boxes

An Improved Statistical Point-source Foreground Model for the Epoch of Reionization

Intensity mapping cross-correlations II: HI halo models including shot noise

Closing the window on fuzzy dark matter with the 21-cm signal

powerbox: A Python package for creating structured fields with isotropic power spectra

The importance of galaxy formation histories in models of reionization

21cmFirstCLASS I. Cosmological tool for ΛCDM and beyond

New tool for 21-cm cosmology. II. Investigating the effect of early linear fluctuations

Topological data analysis reveals differences between simulated galaxies and dark matter haloes

Effects of feedback-free starburst galaxies on the 21-cm signal and reionization history


[CVPR'22] Semi-Supervised Semantic Segmentation Using Unreliable Pseudo-Labels

Augmentation Matters: A Simple-yet-Effective Approach to Semi-supervised Semantic Segmentation

Semi-supervised Semantic Segmentation with Prototype-based Consistency Regularization

Using Unreliable Pseudo-Labels for Label-Efficient Semantic Segmentation


Transition-based UCCA Parser

A Transition-Based Directed Acyclic Graph Parser for UCCA

PROCEEDINGS OF THE 55TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS (ACL 2017), VOL 1

Semantic Structural Evaluation for Text Simplification

Simple and Effective Text Simplification Using Semantic and Neural Methods

Multitask Parsing Across Semantic Representations

TUPA at MRP 2019: A Multi-Task Baseline System

Proceedings of the Shared Task on Cross-Framework Meaning Representation Parsing at the 2019 Conference on Natural Language Learning

HUJI-KU at MRP~2020: Two Transition-based Neural Parsers

Paths to Relation Extraction through Semantic Structure


Query-Efficient Hard-label Black-box Attack:An Optimization-based Approach

Sign-OPT: A Query-Efficient Hard-label Adversarial Attack

Robustness for Non-Parametric Classification: A Generic Attack and Defense

On the Effectiveness of Small Input Noise for Defending Against Query-based Black-Box Attacks

Sparsity Meets Robustness: Channel Pruning for the Feynman-Kac Formalism Principled Robust Deep Neural Nets

Rethinking Image-Scaling Attacks: The Interplay Between Vulnerabilities in Machine Learning Systems

Preprocessors Matter! Realistic Decision-Based Attacks on Machine Learning Systems

Evading Black-box Classifiers Without Breaking Eggs

Geometrically Adaptive Dictionary Attack on Face Recognition

Automated Decision-based Adversarial Attacks


snipit: summarise snps relative to your reference sequence

Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape

Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection

medRxiv : the preprint server for health sciences

Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America

Viral Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Infection in mRNA-Vaccinated Individuals Treated and Not Treated with Nirmatrelvir-Ritonavir

Global Distribution of mcr Gene Variants in 214K Metagenomic Samples

Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates

Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland


Precision Radio Interferometry Simulator (for radio astronomy applications)

Hydrogen Epoch of Reionization Array (HERA)

Publications of the Astronomical Society of the Pacific

A Simplified, Lossless Reanalysis of PAPER-64

EFFECTS OF ANTENNA BEAM CHROMATICITY ON REDSHIFTED 21 cm POWER SPECTRUM AND IMPLICATIONS FOR HYDROGEN EPOCH OF REIONIZATION ARRAY

THE HYDROGEN EPOCH OF REIONIZATION ARRAY DISH. I. BEAM PATTERN MEASUREMENTS AND SCIENCE IMPLICATIONS

THE HYDROGEN EPOCH OF REIONIZATION ARRAY DISH. II. CHARACTERIZATION OF SPECTRAL STRUCTURE WITH ELECTROMAGNETIC SIMULATIONS AND ITS SCIENCE IMPLICATIONS

A Unified Calibration Framework for 21 cm Cosmology

Monthly notices of the Royal Astronomical Society

Detecting Cosmic Reionization Using the Bispectrum Phase

Detection of cosmic structures using the bispectrum phase. II. First results from application to cosmic reionization using the Hydrogen Epoch of Reionization Array

Imaging and Modeling Data from the Hydrogen Epoch of Reionization Array

Detection of cosmic structures using the bispectrum phase. I. Mathematical foundations


Experiments for understanding disentanglement in VAE latent representations

Self-Supervised Learning Disentangled Group Representation as Feature

Tutorial on Amortized Optimization

Evaluating the Disentanglement of Deep Generative Models through Manifold Topology

Disentanglement of Correlated Factors via Hausdorff Factorized Support

Human-interpretable model explainability on high-dimensional data

NEO: Non Equilibrium Sampling on the Orbit of a Deterministic Transform

Beta-VAE Reproducibility: Challenges and Extensions

The Manifold Hypothesis for Gradient-Based Explanations

Learning Geometry-aware Representations by Sketching

Disentangling Content and Motion for Text-Based Neural Video Manipulation


Softcite software mention recognizer, finding mentions and citations to software from within the academic literature

Softcite dataset: A dataset of software mentions in biomedical and economic research publications

Journal of the Association for Information Science and Technology

Mining Software Entities in Scientific Literature: Document-level NER for an Extremely Imbalance and Large-scale Task

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


A platform for analysis of Java bytecode

Mining Android API Usage to Generate Unit Test Cases for Pinpointing Compatibility Issues

Kex: A Platform For Analysis Of JVM Programs

TestSpark: IntelliJ IDEA's Ultimate Test Generation Companion

SPIDER: Specification-based Integration Defect Revealer


Distributed Communication-Optimal Matrix-Matrix Multiplication Algorithm

DISTAL: the distributed tensor algebra compiler

Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation

TAMM: Tensor Algebra for Many-body Methods

Efficiently Parallelizable Strassen-Based Multiplication of a Matrix by its Transpose


BrainSpace is an open-access toolbox that allows for the identification and analysis of gradients from neuroimaging and connectomics datasets | available in both Python and Matlab |

BrainSpace: a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets

Differences in subcortico-cortical interactions identified from connectome and microcircuit models in autism

An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization

Gradients of Connectivity as Graph Fourier Bases of Brain Activity

Linking cerebellar functional gradients to transdiagnostic behavioral dimensions of psychopathology

Whole‐brain functional gradients reveal cortical and subcortical alterations in patients with episodic migraine

Atypical connectome topography and signal flow in temporal lobe epilepsy

bioRxiv : the preprint server for biology

Gradients of brain organization: Smooth sailing from methods development
  to user community

Functional gradients reveal cortical hierarchy changes in multiple sclerosis

Compressed primary‐to‐transmodal gradient is accompanied with subcortical alterations and linked to neurotransmitters and cellular signatures in major depressive disorder


Examples of Solidity security issues

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

Zenodo (CERN European Organization for Nuclear Research)

A Framework and DataSet for Bugs in Ethereum Smart Contracts

Testing Smart Contracts Gets Smarter

Of degens and defrauders: Using open-source investigative tools to investigate decentralized finance frauds and money laundering

How Does Naming Affect LLMs on Code Analysis Tasks?


1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

Hi-C analysis: from data generation to integration

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

Chromosome Structure I: Loop extrusion or boundary:boundary pairing?

Chromosome Structure II: Stem-loops and circle-loops

lncRNA read-through regulates the BX-C insulator Fub-1

Systematic characterization of regulatory variants of blood pressure genes

The insulating activity of theDrosophilaBX-C chromatin boundaryFub-1is parasegmentally regulated by lncRNA read-through

Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae


Python programs for electron microscopy

FACT caught in the act of manipulating the nucleosome

Structure and drug resistance of the Plasmodium falciparum transporter PfCRT

Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase

Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

Cryo-EM analysis of PIP2 regulation in mammalian GIRK channels

Structure and mechanism of B-family DNA polymerase zeta specialized for translesion DNA synthesis

Structure of the radial spoke head and insights into its role in mechanoregulation of ciliary beating

Cryo-EM structure of the potassium-chloride cotransporter KCC4 in lipid nanodiscs

Molecular structures of the eukaryotic retinal importer ABCA4

Structural basis of the ligand binding and signaling mechanism of melatonin receptors


Generation-based, context-free grammar fuzzer. Refer to https://github.com/posidron/dharma for a maintained version.

The Art, Science, and Engineering of Fuzzing: A Survey

UNIFUZZ: A Holistic and Pragmatic Metrics-Driven Platform for Evaluating Fuzzers

Augmenting Greybox Fuzzing with Generative AI

Building Fast Fuzzers

RAT: Reinforcement-Learning-Driven and Adaptive Testing for Vulnerability Discovery in Web Application Firewalls

IEEE Transactions on Dependable and Secure Computing

CorbFuzz: Checking Browser Security Policies with Fuzzing

Visual-Aware Testing and Debugging for Web Performance Optimization

Exploring the Limits of ChatGPT in Software Security Applications


R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework

Structural variant evolution after telomere crisis

Most large structural variants in cancer genomes can be detected without long reads

Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers

Enhancer hijacking determines intra- and extrachromosomal circular MYCN amplicon architecture in neuroblastoma

3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression


Transfer Learning Library for Domain Adaptation, Task Adaptation, and Domain Generalization

Domain-Adversarial Training of Neural Networks

Unsupervised Domain Adaptation by Backpropagation

Learning Transferable Features with Deep Adaptation Networks

Adversarial Discriminative Domain Adaptation

Deep CORAL: Correlation Alignment for Deep Domain Adaptation

CyCADA: Cycle-Consistent Adversarial Domain Adaptation

Deep Transfer Learning with Joint Adaptation Networks

Conditional Adversarial Domain Adaptation

Maximum Classifier Discrepancy for Unsupervised Domain Adaptation

Invariant Risk Minimization


Python and JavaScript bindings for calling the Earth Engine API.

AGGREGATING CLOUD-FREE SENTINEL-2 IMAGES WITH GOOGLE EARTH ENGINE

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

sUAS Remote Sensing of Vineyard Evapotranspiration Quantifies Spatiotemporal Uncertainty in Satellite-Borne ET Estimates

CLOUD-DESKTOP REMOTE SENSING DATA MANAGEMENT TO ENSURE TIME SERIES ANALYSIS, INTEGRATION OF QGIS AND GOOGLE EARTH ENGINE

The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciences

Improving the congruency of satellite-based fertilizer maps with field-operable units using pneumatic spreaders


Pytorch-based framework for solving parametric constrained optimization problems, physics-informed system identification, and parametric model predictive control.

Learning Constrained Adaptive Differentiable Predictive Control Policies With Guarantees

Neural Ordinary Differential Equations for Nonlinear System Identification

Learning Stochastic Parametric Differentiable Predictive Control Policies

Koopman-based Differentiable Predictive Control for the Dynamics-Aware Economic Dispatch Problem

Finite basis Kolmogorov-Arnold networks: domain decomposition for
  data-driven and physics-informed problems

Differentiable Predictive Control with Safety Guarantees: A Control Barrier Function Approach

Learning for CasADi: Data-driven Models in Numerical Optimization

Towards Practical Physics-Informed ML Design and Evaluation for Power Grid

Neuro-physical dynamic load modeling using differentiable parametric optimization

Metric Learning to Accelerate Convergence of Operator Splitting Methods
  for Differentiable Parametric Programming


Infer Community Assembly Mechanisms by Phylogenetic bin-based null model analysis (Version 1)

Future climate conditions accelerate wheat straw decomposition alongside altered microbial community composition, assembly patterns, and interaction networks

Salinity Gradient Controls Microbial Community Structure and Assembly in Coastal Solar Salterns

Forest succession improves the complexity of soil microbial interaction and ecological stochasticity of community assembly: Evidence from Phoebe bournei-dominated forests in subtropical regions

Seasonal variations of microbial community structure, assembly processes, and influencing factors in karst river

Biochar Addition Altered Bacterial Community and Improved Photosynthetic Rate of Seagrass: A Mesocosm Study of Seagrass Thalassia hemprichii

Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments

Tree mycorrhizal type regulates leaf and needle microbial communities, affects microbial assembly and co-occurrence network patterns, and influences litter decomposition rates in temperate forest


Diagnosing and Enhancing VAE Models

Balancing reconstruction error and Kullback-Leibler divergence in Variational Autoencoders

Manifold-based Test Generation for Image Classifiers

Solving Inverse Problems by Joint Posterior Maximization with a VAE Prior


Codebase for ECCV18 "The Sound of Pixels"

The Sound of Pixels

Co-Separating Sounds of Visual Objects

TriBERT: Full-body Human-centric Audio-visual Representation Learning for Visual Sound Separation

Visually Guided Sound Source Separation With Audio-Visual Predictive Coding

IEEE transactions on neural networks and learning systems


A PyTorch implementation of  "Graph Convolutional Networks for Text Classification." (AAAI 2019)

Detecting East Asian Prejudice on Social Media

RubCSG at SemEval-2022 Task 5: Ensemble learning for identifying misogynous MEMEs


Learned Primal-Dual Reconstruction

Learned Primal-Dual Reconstruction

Learned convex regularizers for inverse problems

Learning to solve inverse problems using Wasserstein loss

End-to-end reconstruction meets data-driven regularization for inverse problems


The source code of NIPS17 'Universal Style Transfer via Feature Transforms'.

Arbitrary Style Transfer in Real-time with Adaptive Instance Normalization

Fast Patch-based Style Transfer of Arbitrary Style

Optimal Whitening and Decorrelation

Neural Comic Style Transfer: Case Study

Two-stream FCNs to balance content and style for style transfer


A Corpus for Multilingual Document Classification in Eight Languages.

Don't Use English Dev: On the Zero-Shot Cross-Lingual Evaluation of Contextual Embeddings

Robust Cross-lingual Embeddings from Parallel Sentences

RigoBERTa: A State-of-the-Art Language Model For Spanish

EMS: Efficient and Effective Massively Multilingual Sentence Embedding Learning


Sign Language Transformers (CVPR'20)

Sign Language Transformers: Joint End-to-end Sign Language Recognition and Translation

SLTUNET: A Simple Unified Model for Sign Language Translation

Frozen Pretrained Transformers for Neural Sign Language Translation

A Token-level Contrastive Framework for Sign Language Translation


Dynamic Memory Networks (https://arxiv.org/abs/1603.01417) in Tensorflow

Dynamic Memory Networks for Visual and Textual Question Answering

Query-Reduction Networks for Question Answering

Query-Regression Networks for Machine Comprehension.


INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes

Molecular therapy. Methods & clinical development

INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions

CAR density influences antitumoral efficacy of BCMA CAR T cells and correlates with clinical outcome

Assessment of HIV-1 integration in tissues and subsets across infection stages

Development of an in vitro genotoxicity assay to detect retroviral vector-induced lymphoid insertional mutants


Spectral Temporal Graph Neural Network for Multivariate Time-series Forecasting

Temporal Relational Ranking for Stock Prediction

Temporal-Relational Hypergraph Tri-Attention Networks for Stock Trend Prediction

Deep Coupling Network For Multivariate Time Series Forecasting


Visual Similarity research at Fynd. Contains code to reproduce 2 of our research papers.

Learning Fine-grained Image Similarity with Deep Ranking

Retrieving Similar E-Commerce Images Using Deep Learning

MILDNet: A Lightweight Single Scaled Deep Ranking Architecture


Hyperspectral-Classification   Pytorch

HybridSN: Exploring 3-D–2-D CNN Feature Hierarchy for Hyperspectral Image Classification

IEEE Geoscience and Remote Sensing Letters

Going Deeper With Contextual CNN for Hyperspectral Image Classification

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

HSI-CNN: A Novel Convolution Neural Network for Hyperspectral Image

Learning Deep Hierarchical Spatial–Spectral Features for Hyperspectral Image Classification Based on Residual 3D-2D CNN

SpectralNET: Exploring Spatial-Spectral WaveletCNN for Hyperspectral Image Classification

Multiscale Information Fusion for Hyperspectral Image Classification Based on Hybrid 2D-3D CNN

Embedded Hyperspectral Band Selection with Adaptive Optimization for Image Semantic Segmentation


This dataset contains 108,463 human-labeled and 656k noisily labeled pairs that feature the importance of modeling structure, context, and word order information for the problem of paraphrase identification.

Bilateral Multi-Perspective Matching for Natural Language Sentences

PAWS: Paraphrase Adversaries from Word Scrambling

PAWS-X: A Cross-lingual Adversarial Dataset for Paraphrase Identification

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

Is Supervised Syntactic Parsing Beneficial for Language Understanding? An Empirical Investigation

DABS: A Domain-Agnostic Benchmark for Self-Supervised Learning


Assembly statistic visualisation

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

Genome sequences identify three families of Coleoptera as morphologically derived click beetles (Elateridae)

Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly

International journal of molecular sciences

Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

First Genome Sequence of the Gunnison’s Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague

The Chromosome-Scale Reference Genome of Macadamia tetraphylla Provides Insights Into Fatty Acid Biosynthesis

De Novo Genome Assembly of the Electric Fish Brachyhypopomus occidentalis (Hypopomidae, Gymnotiformes)

The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution

The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species

Comparative Analysis of Annotation Pipelines Using the First Japanese White-Eye (Zosterops japonicus) Genome


A research library for pytorch-based neural network pruning, compression, and more.

Provable Filter Pruning for Efficient Neural Networks

Lost in Pruning: The Effects of Pruning Neural Networks beyond Test Accuracy

Compressing Neural Networks: Towards Determining the Optimal Layer-wise Decomposition

SiPPing Neural Networks: Sensitivity-informed Provable Pruning of Neural Networks

Sparse Flows: Pruning Continuous-depth Models

Characterizing and Improving the Robustness of Self-Supervised Learning through Background Augmentations

SVD-NAS: Coupling Low-Rank Approximation and Neural Architecture Search

Low-Regret Active learning


word2vec Google News model

Word2Vec

Detection and Resolution of Rumours in Social Media: A Survey

Hate Speech Detection: A Solved Problem? The Challenging Case of Long Tail on Twitter

All You Need is "Love": Evading Hate-speech Detection

Discourse-aware rumour stance classification in social media using sequential classifiers

Improving Fake News Detection by Using an Entity-enhanced Framework to Fuse Diverse Multimodal Clues

PROCEEDINGS OF THE 29TH ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA, MM 2021

Hash Embeddings for Efficient Word Representations

DepressionNet: A Novel Summarization Boosted Deep Framework for Depression Detection on Social Media

SIGIR '21 - PROCEEDINGS OF THE 44TH INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL

Token-Level Ensemble Distillation for Grapheme-to-Phoneme Conversion

Word Sense Disambiguation Based on Word Similarity Calculation Using Word Vector Representation from a Knowledge-based Graph

International Conference on Computational Linguistics


An easy to use reduction package for one-dimensional longslit spectroscopy.

SN 2023ixf in Messier 101: Photo-ionization of Dense, Close-in Circumstellar Material in a Nearby Type II Supernova

Flight of the Bumblebee: the Early Excess Flux of Type Ia Supernova 2023bee Revealed by TESS, Swift, and Young Supernova Experiment Observations

Very late-time spectroscopy of SN 2009ip: Constraints on the ongoing Hα emission


Validate FastQ Files

Isolation and Characterization of Human Intestinal Bacteria Cytobacillus oceanisediminis NB2 for Probiotic Potential

Comparative genomic analysis of monosporidial and monoteliosporic cultures for unraveling the complexity of molecular pathogenesis of Tilletia indica pathogen of wheat

Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples

Biofertilizer and biocontrol properties of Stenotrophomonas maltophilia BCM emphasize its potential application for sustainable agriculture

Computational host range prediction-The good, the bad, and the ugly


Swift Accel-Amplicon primer trimming tool for fast alignment-based primer trimming

The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies

SARS-CoV-2 ORF6 Disrupts Bidirectional Nucleocytoplasmic Transport through Interactions with Rae1 and Nup98

A direct capture method for purification and detection of viral nucleic acid enables epidemiological surveillance of SARS-CoV-2


VQ-VAE for Acoustic Unit Discovery and Voice Conversion

Neural Discrete Representation Learning

Unsupervised speech representation learning using WaveNet autoencoders

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

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

SQ-VAE: Variational Bayes on Discrete Representation with Self-annealed Stochastic Quantization

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

Robust universal neural vocoding

Discrete representations in neural models of spoken language


Code for "Actor-Attention-Critic for Multi-Agent Reinforcement Learning" ICML 2019

Scaling Up Multiagent Reinforcement Learning for Robotic Systems: Learn an Adaptive Sparse Communication Graph

Modeling the Interaction between Agents in Cooperative Multi-Agent Reinforcement Learning

Scalable Multi-Agent Inverse Reinforcement Learning via Actor-Attention-Critic

Correcting Experience Replay for Multi-Agent Communication

Dealing with Non-Stationarity in MARL via Trust-Region Decomposition


A package to annotate protein sequences

Fast and sensitive protein alignment using DIAMOND

Database resources of the National Center for Biotechnology Information

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

CDD/SPARCLE: the conserved domain database in 2020

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold

The Transporter Classification Database (TCDB): 2021 update

Mantis: flexible and consensus-driven genome annotation

Unification of functional annotation descriptions using text mining


A deep learning approach for predicting high-confidence neoantigens by considering both the presentation possibilities of mutant peptides and the potential immunogenicity of pMHC

DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity

Computational cancer neoantigen prediction: current status and recent advances

Unraveling tumor specific neoantigen immunogenicity prediction: a comprehensive analysis


Creative Commons Attribution Share Alike 4.0 International

The FLORES+ Machine Translation Benchmark

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

Machine Translation for Nko: Tools, Corpora and Baseline Results

Curated Datasets and Neural Models for Machine Translation of Informal Registers between Mayan and Spanish Vernaculars

Pushing the Limits of Zero-shot End-to-End Speech Translation


A simple library to deploy Keras neural networks in pure C for realtime applications

QNNVerifier: A Tool for Verifying Neural Networks using SMT-Based Model Checking

DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models

NeuroCodeBench: a plain C neural network benchmark for software verification


End-to-end model training and deployment reference for handwritten Chinese text recognition, and can also be extended to other languages.

Improving handwritten Chinese text recognition using neural network language models and convolutional neural network shape models

Writer-Aware CNN for Parsimonious HMM-Based Offline Handwritten Chinese Text Recognition

Recognition of Handwritten Chinese Text by Segmentation: A Segment-Annotation-Free Approach

High Performance Offline Handwritten Chinese Text Recognition with a New Data Preprocessing and Augmentation Pipeline

Offline Handwritten Chinese Text Recognition with Convolutional Neural Networks

Searching from the Prediction of Visual and Language Model for Handwritten Chinese Text Recognition


Implementation of Hang et al. 2020 "Hyperspectral Image Classification with Attention Aided CNNs" for tree species prediction

Capturing long‐tailed individual tree diversity using an airborne imaging and a multi‐temporal hierarchical model

Remote Sensing in Ecology and Conservation


Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

Sociobiology

Reconstruction of ancient microbial genomes from the human gut

Maternal fecal microbiome predicts gestational age, birth weight and neonatal growth in rural Zimbabwe.

Wekemo Bioincloud: A user‐friendly platform for meta‐omics data analyses

One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density

Effect of Fecal Microbiota Transplantation Combined With Mediterranean Diet on Insulin Sensitivity in Subjects With Metabolic Syndrome

Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching

Signature of Alzheimer’s Disease in Intestinal Microbiome: Results From the AlzBiom Study

Assessing saliva microbiome collection and processing methods

Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration


LLM that combines the principles of wizardLM and vicunaLM

What Do Llamas Really Think? Revealing Preference Biases in Language Model Representations

Combating Adversarial Attacks with Multi-Agent Debate


Tools and Utilities for msmc and msmc2

Yam genomics supports West Africa as a major cradle of crop domestication

Tracking human population structure through time from whole genome sequences

The evolutionary history and genomics of European blackcap migration

High-quality genome and methylomes illustrate features underlying evolutionary success of oaks

Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies

Large-scale genomic analysis reveals the genetic cost of chicken domestication

Demes: a standard format for demographic models

Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features

Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss

Rapid radiation in a highly diverse marine environment

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


This is the FER+ new label annotations for the Emotion FER dataset.

Training Deep Networks for Facial Expression Recognition with Crowd-Sourced Label Distribution

Improving Facial Emotion Recognition Systems Using Gradient and Laplacian Images

A pre-trained model vs dedicated convolution neural networks for emotion recognition

International Journal of Power Electronics and Drive Systems/International Journal of Electrical and Computer Engineering


sGDML - Reference implementation of the Symmetric Gradient Domain Machine Learning model

Machine learning of accurate energy-conserving molecular force fields

Towards exact molecular dynamics simulations with machine-learned force fields

sGDML: Constructing accurate and data efficient molecular force fields using machine learning

Towards Linearly Scaling and Chemically Accurate Global Machine Learning Force Fields for Large Molecules


Attentive Group Recommendation

ConsRec: Learning Consensus Behind Interactions for Group Recommendation

Deep Reinforcement Learning based Group Recommender System

DeepGroup: Representation Learning for Group Recommendation with Implicit Feedback


An R toolkit for estimation of cell composition from bulk expression data

A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response

Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis

Expression quantitative trait locus studies in the era of single-cell omics


calculate radial velocities from stellar spectra

Spectrum radial velocity analyser (SERVAL) - High-precision radial velocities and two alternative spectral indicators

e-Archivo (Universidad Carlos III de Madrid)

A candidate super-Earth planet orbiting near the snow line of Barnard's star

The CARMENES search for exoplanets around M dwarfs. Stellar atmospheric parameters of target stars with SteParSyn

The CARMENES search for exoplanets around M dwarfs: Two planets on opposite sides of the radius gap transiting the nearby M dwarf LTT 3780

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

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

TOI-1201 b: A mini-Neptune transiting a bright and moderately young M dwarf

On-sky commissioning of MAROON-X: a new precision radial velocity spectrograph for Gemini North

Ground-based and Airborne Instrumentation for Astronomy VIII

The CARMENES search for exoplanets around M dwarfs The enigmatic planetary system GJ 4276: one eccentric planet or two planets in a 2:1 resonance?

The TROY project - II. Multi-technique constraints on exotrojans in nine planetary systems


Given a global mean temperature pathway, generate random global climate fields consistent with it and with spatial and temporal correlation derived from an ESM

Fldgen v1.0: an emulator with internal variability and space–time correlation for Earth system models

Joint emulation of Earth System Model temperature-precipitation realizations with internal variability and space-time and cross-variable correlation: fldgen v2.0 software description


Language Is Not All You Need: Aligning Perception with Language Models

Grounding Language Models to Images for Multimodal Inputs and Outputs

Generative Pretraining in Multimodality

The VQA-Machine: Learning How to Use Existing Vision Algorithms to Answer New Questions

MAGMA -- Multimodal Augmentation of Generative Models through Adapter-based Finetuning

Linearly Mapping from Image to Text Space

Language Models are General-Purpose Interfaces

LaKo: Knowledge-driven Visual Question Answering via Late Knowledge-to-Text Injection

Vision Skills Needed to Answer Visual Questions

Proceedings of the ACM on Human-Computer Interaction

VQA-MHUG: A Gaze Dataset to Study Multimodal Neural Attention in Visual Question Answering


Filter and prioritize fusion calls

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs

TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism

Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1

Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR

New Molecular Considerations for Glioma: IDH, ATRX, BRAF, TERT, H3 K27M

Current neurology and neuroscience reports

Activation of human telomerase reverse transcriptase through gene fusion in clear cell sarcoma of the kidney

Recurrent pre‐existing and acquired DNA copy number alterations, including focal TERT gains, in neuroblastoma central nervous system metastases


An efficient PyTorch library for deep generative modeling.

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

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

Linear Semantics in Generative Adversarial Networks

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

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

BEAGLE: Forensics of Deep Learning Backdoor Attack for Better Defense


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

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

ProtTrans: Towards Cracking the Language of Life’s Code Through Self-Supervised Learning

Controllable protein design with language models

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

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

Pretraining model for biological sequence data

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

Fine-tuning protein language models boosts predictions across diverse tasks

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

Multi-level Protein Representation Learning for Blind Mutational Effect Prediction


Diffusion map based embedding and alignment

A Systematic Relationship Between Functional Connectivity and Intracortical Myelin in the Human Cerebral Cortex

Anatomical and microstructural determinants of hippocampal subfield functional connectome embedding

Topographic gradients of intrinsic dynamics across neocortex

Multiscale communication in cortico-cortical networks

Multimodal phenotypic axes of Parkinson’s disease

LittleBrain: A gradient-based tool for the topographical interpretation of cerebellar neuroimaging findings

Mind blanking is a distinct mental state linked to a recurrent brain profile of globally positive connectivity during ongoing mentation

Exploring the embodied mind: functional connectome fingerprinting of meditation expertise

Domain adapted brain network fusion captures variance related to pubertal brain development and mental health

Asymmetric Functional Gradients in the Human Subcortex


Visualise Clusterings at Different Resolutions

Clustering trees: a visualization for evaluating clusterings at multiple resolutions

Brainstem ADCYAP1+ neurons control multiple aspects of sickness behaviour

Commensal microbiota divergently affect myeloid subsets in the mammalian central nervous system during homeostasis and disease

Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists

Functional Pdgfra fibroblast heterogeneity in normal and fibrotic mouse lung


Official Edison Lab toolboxes and scripts for analyzing metabolomics data.

Global Metabolomics of the Placenta Reveals Distinct Metabolic Profiles between Maternal and Fetal Placental Tissues Following Delivery in Non-Labored Women

Diabetes Leads to Alterations in Normal Metabolic Transitions of Pregnancy as Revealed by Time-Course Metabolomics

Integrated Metabolomics and Transcriptomics Suggest the Global Metabolic Response to 2-Aminoacrylate Stress in Salmonella enterica

Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a ridA Mutant of Salmonella enterica

RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking

Uncovering in vivo biochemical patterns from time-series metabolic dynamics


Fetch NCDC ISD, TMY3, or CZ2010 weather data that corresponds to ZIP Code Tabulation Areas or Latitude/Longitude.


RL starter files in order to immediately train, visualize and evaluate an agent without writing any line of code

State Entropy Maximization with Random Encoders for Efficient Exploration

Value Function Spaces: Skill-Centric State Abstractions for Long-Horizon Reasoning

Poisoning Deep Reinforcement Learning Agents with In-Distribution Triggers

Simplifying Deep Reinforcement Learning via Self-Supervision

Decentralized Reinforcement Learning: Global Decision-Making via Local Economic Transactions

Exploring through Random Curiosity with General Value Functions

Flexible Attention-Based Multi-Policy Fusion for Efficient Deep Reinforcement Learning

Heterogeneous Knowledge for Augmented Modular Reinforcement Learning

Maximum Entropy On-Policy Actor-Critic via Entropy Advantage Estimation


A set of Python tools for statistically analyzing data. This includes aspects of lattice QCD applications related to QCD phenomenology.

Equation of state and speed of sound of (2+1)-flavor QCD in strangeness-neutral matter at non-vanishing net baryon-number density

Streamlined data analysis in Python

The isentropic equation of state of (2+1)-flavor QCD: An update based on high precision Taylor expansion and Pade-resummed expansion at finite chemical potentials

Isothermal and isentropic speed of sound in (2+1)-flavor QCD at non-zero baryon chemical potential


automated photometry pipeline for small to medium-sized observatories

PHOTOMETRYPIPELINE: An automated pipeline for calibrated photometry

VaST: a variability search toolkit

High Confidence Optical Confirmations Among the High Signal-to-Noise Planck Cluster Candidates

Modulation of the Blazhko Cycle in LS Her


Sequential Monte Carlo in python

Waste-free Sequential Monte Carlo

On backward smoothing algorithms

The Normal-Generalised Gamma-Pareto Process: A Novel Pure-Jump Lévy Process with Flexible Tail and Jump-Activity Properties

Iterated INLA for State and Parameter Estimation in Nonlinear Dynamical
  Systems

Bayesian Windkessel calibration using optimized 0D surrogate models


Community Emissions Data System (CEDS)

Historical (1750–2014) anthropogenic emissions of reactive gases and aerosols from the Community Emissions Data System (CEDS)

The generation of gridded emissions data for CMIP6

Deep mitigation of CO2 and non-CO2 greenhouse gases toward 1.5 °C and 2 °C futures

A new global anthropogenic SO2 emission inventory for the last decade: a mosaic of satellite-derived and bottom-up emissions

Air pollution deaths attributable to fossil fuels: observational and modelling study

CEDS v_2021_04_21 Release Emission Data

Zenodo (CERN European Organization for Nuclear Research)

Impacts of emission changes in China from 2010 to 2017 on domestic and intercontinental air quality and health effect

Chinese industrial air pollution emissions based on the continuous emission monitoring systems network

CERESMIP: a climate modeling protocol to investigate recent trends in the Earth's Energy Imbalance


Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)

A smile is all you need: Predicting limiting activity coefficients from SMILES with natural language processing

Clapeyron.jl: An Extensible, Open-Source Fluid Thermodynamics Toolkit

Tidal pull of the Earth strips the proto-Moon of its volatiles

Potentials and challenges of polymer informatics: exploiting machine learning for polymer design

Materials Discovery using Max K-Armed Bandit

PUFFIN: A Path-Unifying Feed-Forward Interfaced Network for Vapor Pressure Prediction

Molecule Generation and Optimization for Efficient Fragrance Creation

Yamdb: easily accessible thermophysical properties of liquid metals and
  molten salts


CRSLab is an open-source toolkit for building Conversational Recommender System (CRS).

Advances and Challenges in Conversational Recommender Systems: A Survey

Towards Unified Conversational Recommender Systems via Knowledge-Enhanced Prompt Learning

CRSLab: An Open-Source Toolkit for Building Conversational Recommender System

C2-CRS: Coarse-to-Fine Contrastive Learning for Conversational Recommender System

A Unified Multi-task Learning Framework for Multi-goal Conversational Recommender Systems

User-Centric Conversational Recommendation with Multi-Aspect User Modeling

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

A Large Language Model Enhanced Conversational Recommender System

Improving Conversational Recommendation Systems via Counterfactual Data Simulation

INSPIRED2: An Improved Dataset for Sociable Conversational Recommendation


Error-bounded Lossy Data Compressor (for floating-point/integer datasets)

Improving Prediction-Based Lossy Compression Dramatically via Ratio-Quality Modeling

Accelerating Parallel Write via Deeply Integrating Predictive Lossy Compression with HDF5


A high-level Python library for Quantum Natural Language Processing

lambeq: An Efficient High-Level Python Library for Quantum NLP

Near-Term Advances in Quantum Natural Language Processing

NISQ Computers: A Path to Quantum Supremacy

Something Old, Something New: Grammar-based CCG Parsing with Transformer Models

A gentle introduction to Quantum Natural Language Processing


Beyond Accuracy: Behavioral Testing of NLP models with CheckList

Quantifying Social Biases in NLP: A Generalization and Empirical Comparison of Extrinsic Fairness Metrics

Fairness Testing: A Comprehensive Survey and Analysis of Trends

Seeing Like a Toolkit: How Toolkits Envision the Work of AI Ethics

Perturbation CheckLists for Evaluating NLG Evaluation Metrics

On the Blind Spots of Model-Based Evaluation Metrics for Text Generation

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

Probing Speech Emotion Recognition Transformers for Linguistic Knowledge

On Robustness and Bias Analysis of BERT-based Relation Extraction

Trusting RoBERTa over BERT: Insights from CheckListing the Natural Language Inference Task


Just Another JAva Package for Sequence Analysis

Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing

Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

Causalcall: Nanopore Basecalling Using a Temporal Convolutional Network

Pseudo-Chromosomal Genome Assembly in Combination with Comprehensive Transcriptome Analysis in Agaricus bisporus Strain KMCC00540 Reveals Mechanical Stimulus Responsive Genes Associated with Browning Effect

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing


A collection of Poisson lognormal models for multivariate count data analysis

Variational inference for probabilistic Poisson PCA

Variational inference for sparse network reconstruction from count data

The Poisson-lognormal model as a versatile framework for the joint analysis of species abundances

Zero-inflation in the Multivariate Poisson Lognormal Family


Data compression in TensorFlow

End-to-end Optimized Image Compression

Variational image compression with a scale hyperprior

High-Fidelity Generative Image Compression

Channel-wise Autoregressive Entropy Models for Learned Image Compression

CompressAI: a PyTorch library and evaluation platform for end-to-end compression research

Improving Inference for Neural Image Compression

An Introduction to Neural Data Compression

Variable-Rate Deep Image Compression through Spatially-Adaptive Feature Transform

Efficient Nonlinear Transforms for Lossy Image Compression

ProxIQA: A Proxy Approach to Perceptual Optimization of Learned Image Compression


Python library for real space quantum Monte Carlo

Recent developments in the PySCF program package

Excited states in variational Monte Carlo using a penalty method

A light weight regularization for wave function parameter gradients in quantum Monte Carlo

ipie: A Python-based Auxiliary-Field Quantum Monte Carlo Program with Flexibility and Efficiency on CPUs and GPUs

Bootstrap Embedding on a Quantum Computer

Quantification of electron correlation for approximate quantum calculations


CLIP+MLP Aesthetic Score Predictor

Optimizing Prompts for Text-to-Image Generation

LayoutLLM-T2I: Eliciting Layout Guidance from LLM for Text-to-Image Generation

Restart Sampling for Improving Generative Processes

HyperHuman: Hyper-Realistic Human Generation with Latent Structural Diffusion

X-IQE: eXplainable Image Quality Evaluation for Text-to-Image Generation with Visual Large Language Models

DEADiff: An Efficient Stylization Diffusion Model with Disentangled Representations

Not All Noises Are Created Equally:Diffusion Noise Selection and Optimization

Alignment of Diffusion Models: Fundamentals, Challenges, and Future

Quality and Quantity: Unveiling a Million High-Quality Images for Text-to-Image Synthesis in Fashion Design

Sampler Scheduler for Diffusion Models


GRU4Rec is the original Theano implementation of the algorithm in "Session-based Recommendations with Recurrent Neural Networks" paper, published at ICLR 2016 and its follow-up "Recurrent Neural Networks with Top-k Gains for Session-based Recommendations". The code is optimized for execution on the GPU.

BERT4Rec: Sequential Recommendation with Bidirectional Encoder Representations from Transformer

International Conference on Information and Knowledge Management

Global Context Enhanced Graph Neural Networks for Session-based Recommendation

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

Evaluation of session-based recommendation algorithms

User modeling and user-adapted interaction

Contextual Hybrid Session-Based News Recommendation With Recurrent Neural Networks

News Session-Based Recommendations using Deep Neural Networks

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

DiffuRec: A Diffusion Model for Sequential Recommendation

Time is of the Essence: a Joint Hierarchical RNN and Point Process Model for Time and Item Predictions

Position-Enhanced and Time-aware Graph Convolutional Network for Sequential Recommendations


A simple notebook demonstrating prompt-based music generation via Mubert API

MusicLDM: Enhancing Novelty in Text-to-Music Generation Using Beat-Synchronous Mixup Strategies

MuseCoco: Generating Symbolic Music from Text

Mustango: Toward Controllable Text-to-Music Generation

Sparks of Large Audio Models: A Survey and Outlook

Exploring the Efficacy of Pre-trained Checkpoints in Text-to-Music Generation Task

ERNIE-Music: Text-to-Waveform Music Generation with Diffusion Models


What Does BERT Look At? An Analysis of BERT's Attention

Emergent linguistic structure in artificial neural networks trained by self-supervision

Attention is Not Only a Weight: Analyzing Transformers with Vector Norms

Analyzing Feed-Forward Blocks in Transformers through the Lens of Attention Map


A Multi-modal Model Chinese Spell Checker Released on ACL2021.

Read, Listen, and See: Leveraging Multimodal Information Helps Chinese Spell Checking

Improving Chinese Spelling Check by Character Pronunciation Prediction: The Effects of Adaptivity and Granularity

SDCL: Self-Distillation Contrastive Learning for Chinese Spell Checking

Block the Label and Noise: An N-Gram Masked Speller for Chinese Spell Checking

A Comprehensive Evaluation and Analysis Study for Chinese Spelling Check


ManTra-Net: Manipulation Tracing Network For Detection And Localization of Image Forgeries With Anomalous Features

ManTra-Net: Manipulation Tracing Network for Detection and Localization of Image Forgeries With Anomalous Features

SPAN: Spatial Pyramid Attention Network forImage Manipulation Localization

Image Manipulation Detection by Multi-View Multi-Scale Supervision

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

IEEE transactions on pattern analysis and machine intelligence

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


Re-implementation the code used in Voice Conversion from Non-parallel Corpora Using Variational Auto-encoder

Voice Conversion from Unaligned Corpora using Variational Autoencoding Wasserstein Generative Adversarial Networks

Voice Conversion Based on Cross-Domain Features Using Variational Auto Encoders

International Symposium on Chinese Spoken Language Processing

Nonparallel Voice Conversion With Augmented Classifier Star Generative Adversarial Networks

CVC: Contrastive Learning for Non-parallel Voice Conversion

WaveNet 聲碼器及其於語音轉換之應用 (WaveNet Vocoder and its Applications in Voice Conversion) [In Chinese]

International Conference on Computational Linguistics


PyTorch implementation of "WILDCAT: Weakly Supervised Learning of Deep ConvNets for Image Classification, Pointwise Localization and Segmentation", CVPR 2017

SoDeep: a Sorting Deep net to learn ranking loss surrogates

Weakly Supervised Attention-based Models Using Activation Maps for Citrus Mite and Insect Pest Classification

Minimizing Supervision in Multi-label Categorization


Single-cell RNA-seq Gene Expression Recovery

SAVER: gene expression recovery for single-cell RNA sequencing

False signals induced by single-cell imputation

SAVER: Gene expression recovery for UMI-based single cell RNA sequencing

Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen

A universal deep neural network for in-depth cleaning of single-cell RNA-Seq data

Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type Identification

Mouse Single Islet β Cell Transcriptomics Reveal Sexually Dimorphic Transcriptomes and Type 2 Diabetes Genes

scRNA‐seq data analysis method to improve analysis performance

Imputation Methods for scRNA Sequencing Data

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


Graph-based Attention Model

Neural Machine Translation by Jointly Learning to Align and Translate

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

GRAM: Graph-based Attention Model for Healthcare Representation Learning

Supervised multi-specialist topic model with applications on large-scale electronic health record data


Mapping and monitoring deep subglacial water activity in Antarctica using remote sensing and machine learning, with ICESat-2!


synthesiseable ieee 754 floating point library in verilog

Iodine: Verifying Constant-Time Execution of Hardware

CREST: Hardware Formal Verification with ANSI-C Reference Specifications

Solver-Aided Constant-Time Circuit Verification


Estimating effective elastic thickness of the lithosphere

Toward mapping the effective elastic thickness of planetary lithospheres from a spherical wavelet analysis of gravity and topography

Physics of the Earth and Planetary Interiors

Estimation of the effective elastic thickness of the lithosphere using inverse spectral methods: The state of the art

Effective elastic thickness over the Chinese mainland and surroundings estimated from a joint inversion of Bouguer admittance and coherence

What Controls Effective Elastic Thickness of the Lithosphere in the Pacific Ocean?

Journal of Geophysical Research: Solid Earth

Telewavesim: Python software for teleseismic body wave modeling


Attacking MQTT systems with Mosquittos (scalability and load testing utilities for MQTT environments)

Multiclass Classification Procedure for Detecting Attacks on MQTT-IoT Protocol

On MQTT Scalability in the Internet of Things: Issues, Solutions, and Future Directions

Journal of Electronics and Electrical Engineering


Aligning pretrained language models with instruction data generated by themselves.

Self-Instruct: Aligning Language Models with Self-Generated Instructions

Instruction Tuning with GPT-4

Instruction Tuning for Large Language Models: A Survey

Principle-Driven Self-Alignment of Language Models from Scratch with Minimal Human Supervision

AlpaGasus: Training A Better Alpaca with Fewer Data

Understanding LLMs: A Comprehensive Overview from Training to Inference

Camoscio: an Italian Instruction-tuned LLaMA

MUFFIN: Curating Multi-Faceted Instructions for Improving Instruction-Following

Ensemble-Instruct: Generating Instruction-Tuning Data with a Heterogeneous Mixture of LMs


Two simple and effective designs of vision transformer, which is on par with the Swin transformer

Twins: Revisiting the Design of Spatial Attention in Vision Transformers

EdgeViTs: Competing Light-weight CNNs on Mobile Devices with Vision Transformers

SBCFormer: Lightweight Network Capable of Full-size ImageNet Classification at 1 FPS on Single Board Computers


Environmental data for Antarctic and Southern Ocean science


Synaptic Plasticity Dynamics for Deep Continuous Local Learning (DECOLLE)

On-Chip Error-triggered Learning of Multi-layer Memristive Spiking Neural Networks

Embodied Neuromorphic Vision with Continuous Random Backpropagation

International Conference on Biomedical Robotics and Biomechatronics


StyleGAN - Official TensorFlow Implementation

A Style-Based Generator Architecture for Generative Adversarial Networks

Analyzing and Improving the Image Quality of StyleGAN

CNN-generated images are surprisingly easy to spot... for now

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

Deep Learning for Deepfakes Creation and Detection: A Survey

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

What makes fake images detectable? Understanding properties that generalize

Semantic Hierarchy Emerges in Deep Generative Representations for Scene Synthesis

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

Improving Transferability of Adversarial Patches on Face Recognition with Generative Models


92.45% on CIFAR-10 in Torch

Learning Efficient Convolutional Networks through Network Slimming

Going Deeper in Spiking Neural Networks: VGG and Residual Architectures

Asynchronous Decentralized Parallel Stochastic Gradient Descent

Learn To Pay Attention

Contextual Explanation Networks

Filter Distillation for Network Compression

Disentangling Adaptive Gradient Methods from Learning Rates

Learning Convolutional Neural Networks using Hybrid Orthogonal Projection and Estimation

GaDei: On Scale-up Training As A Service For Deep Learning

Cotton disease identification method based on pruning


Single Cell Analysis of Five'Ends

Profiling of transcribed cis-regulatory elements in single cells

SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells


Conditional BERT Contextual Augmentation

Data Augmentation using Pre-trained Transformer Models

PromDA: Prompt-based Data Augmentation for Low-Resource NLU Tasks

Feature-aware conditional GAN for category text generation

Effective Data Augmentation for Sentence Classification Using One VAE per Class


A light RINA implementation. Documentation is available in REAME.md (see below).

Learning to Find Usages of Library Functions in Optimized Binaries

IEEE Transactions on Software Engineering

A P4-Enabled RINA Interior Router for Software-Defined Data Centers

Addressing Bandwidth-Driven Flow Allocationin RINA


Microbiota fingerprints lose individually identifying features over time

The Fungal Microbiome Is an Important Component of Vineyard Ecosystems and Correlates with Regional Distinctiveness of Wine

Global assembly of microbial communities

The Maternal Milk Microbiome in Mammals of Different Types and Its Potential Role in the Neonatal Gut Microbiota Composition

Animals : an open access journal from MDPI

Microbial fingerprints reveal interaction between museum objects, curators, and visitors

The association between oral and gut microbiota in male patients with alcohol dependence

Distribution characteristics and potential risks of bioaerosols during scattered farming


Generic IoT data simulator. Provides possibility to replay datasets or generates data on fly. Supports various IoT platforms out of the box.

IoT Device Integration and Payment via an Autonomic Blockchain-Based Service for IoT Device Sharing

Situation-Aware IoT Data Generation towards Performance Evaluation of IoT Middleware Platforms

Refresh Rate-Based Caching and Prefetching Strategies for Internet of Things Middleware


OBOE: Extensible Observation Ontology

How to Integrate Experimental Research Approaches in Ecological and Environmental Studies: AnaEE France as an Example

The I-ADOPT Interoperability Framework for FAIRer data descriptions of biodiversity

Towards an interoperability framework for observable property terminologies


A bilinear pairing library for petlib

Coconut: Threshold Issuance Selective Disclosure Credentials with Applications to Distributed Ledgers

AStERISK: Auction-based Shared Economy ResolutIon Markets for Blockchain Platforms

Aggregate Signatures with Versatile Randomization and Issuer-Hiding Multi-Authority Anonymous Credentials

Proceedings of the 2023 ACM SIGSAC Conference on Computer and Communications Security

zksk: A Library for Composable Zero-Knowledge Proofs

Workshop on Privacy in the Electronic Society


Corruption and Perturbation Robustness (ICLR 2019)

Benchmarking Neural Network Robustness to Common Corruptions and Perturbations

Bayesian Deep Learning and a Probabilistic Perspective of Generalization

Improving robustness against common corruptions by covariate shift adaptation

Masked Siamese Networks for Label-Efficient Learning

A simple way to make neural networks robust against diverse image corruptions

Simulating a Primary Visual Cortex at the Front of CNNs Improves Robustness to Image Perturbations

Benchmarking Neural Network Robustness to Common Corruptions and Surface Variations

Towards Stable Test-Time Adaptation in Dynamic Wild World

Multiobjective Evolutionary Design of Deep Convolutional Neural Networks for Image Classification

Boosting Adversarial Training with Hypersphere Embedding


Feature selection in neural networks

LassoNet: A Neural Network with Feature Sparsity

Where to Pay Attention in Sparse Training for Feature Selection?

Weight Predictor Network with Feature Selection for Small Sample Tabular Biomedical Data

Supervised Feature Selection with Neuron Evolution in Sparse Neural Networks

Neural interval-censored survival regression with feature selection

GCondNet: A Novel Method for Improving Neural Networks on Small High-Dimensional Tabular Data

Interpretability with full complexity by constraining feature information

Effective Neural Network L_0 Regularization With BinMask

FastCPH: Efficient Survival Analysis for Neural Networks

Feature Selection in the Contrastive Analysis Setting


Modular Multi-scale Integrated Genome Graph Browser

GENCODE: The reference human genome annotation for The ENCODE Project

Resolving the complexity of the human genome using single-molecule sequencing

Superbubbles, Ultrabubbles and Cacti

MoMI-G: modular multi-scale integrated genome graph browser

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data

Sequence variation aware genome references and read mapping with the variation graph toolkit


Source files for building the IDM EMOD disease transmission model.

Potential effects of disruption to HIV programmes in sub-Saharan Africa caused by COVID-19: results from multiple mathematical models

Development of an oral once-weekly drug delivery system for HIV antiretroviral therapy

Implementation and applications of EMOD, an individual-based multi-disease modeling platform

The influence of mobility among high-risk populations on HIV transmission in Western Kenya

Individual and community-level benefits of PrEP in western Kenya and South Africa: Implications for population prioritization of PrEP provision


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

Revisiting Deep Learning Models for Tabular Data

TabTransformer: Tabular Data Modeling Using Contextual Embeddings

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

TransTab: Learning Transferable Tabular Transformers Across Tables

Transfer Learning with Deep Tabular Models

MambaTab: A Plug-and-Play Model for Learning Tabular Data

UniTabE: Pretraining a Unified Tabular Encoder for Heterogeneous Tabular Data

Tabular Few-Shot Generalization Across Heterogeneous Feature Spaces


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

Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images

Differentiable Zooming for Multiple Instance Learning on Whole-Slide Images

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

A General-Purpose Self-Supervised Model for Computational Pathology

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

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

International journal of molecular sciences

Feature Re-Embedding: Towards Foundation Model-Level Performance in
  Computational Pathology

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

Predicting Ki67, ER, PR, and HER2 Statuses from H&E-stained Breast Cancer Images

A Multimodal Knowledge-enhanced Whole-slide Pathology Foundation Model


Metagenomics-focused BAM file manipulation

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

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

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution

Zenodo (CERN European Organization for Nuclear Research)

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Moisture Modulates Soil Reservoirs of Active DNA and RNA Viruses

Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming


Patterns and behaviors for GPU computing

A Memory Bandwidth-Efficient Hybrid Radix Sort on GPUs

SIGMOD'17: PROCEEDINGS OF THE 2017 ACM INTERNATIONAL CONFERENCE ON MANAGEMENT OF DATA

GPU acceleration of ADMM for large-scale quadratic programming

Journal of Parallel and Distributed Computing

GPU LSM: A Dynamic Dictionary Data Structure for the GPU

MetaCache-GPU: Ultra-Fast Metagenomic Classification

Euler Meets GPU: Practical Graph Algorithms with Theoretical Guarantees


Julia library for homological persistence

Ripserer.jl: flexible and efficient persistent homology computation in Julia

Discrete Morse Sandwich: Fast Computation of Persistence Diagrams for Scalar Data -- An Algorithm and A Benchmark

Efficient two-parameter persistence computation via cohomology

Approximate Triangulations of Grassmann Manifolds

0-Dimensional Persistent Homology Analysis Implementation in Resource-Scarce Embedded Systems


R package to estimate public transport emissions based on GTFS data


Pythonic photometric redshift tools based on EAZY

First Batch of Candidate Galaxies at Redshifts 11 to 20 Revealed by the James Webb Space Telescope Early Release Observations

An Atlas of Color-selected Quiescent Galaxies at z > 3 in Public JWST Fields

CLEAR. II. Evidence for Early Formation of the Most Compact Quiescent Galaxies at High Redshift

Templates for Fitting Photometry of Ultra-high-redshift Galaxies

CLEAR: The Gas-phase Metallicity Gradients of Star-forming Galaxies at 0.6 < z < 2.6

ALMA Lensing Cluster Survey: Bright [CII] 158 μm Lines from a
  Multiply Imaged Sub-L^⋆ Galaxy at z=6.0719

The prevalence of galaxy overdensities around UV-luminous Lyman �� emitters in the Epoch of Reionization

CLEAR: The Ionization and Chemical-Enrichment Properties of Galaxies at
  1.1 < z < 2.3

On the (Lack of) Evolution of the Stellar Mass Function of Massive
  Galaxies from z=1.5 to 0.4

COSMOS2020: Exploring the Dawn of Quenching for Massive Galaxies at 3 < z < 5 with a New Color-selection Method


PyTorch-based library for Riemannian Manifold Hamiltonian Monte Carlo (RMHMC) and inference in Bayesian neural networks

Scaling Hamiltonian Monte Carlo Inference for Bayesian Neural Networks with Symmetric Splitting

Introducing an Explicit Symplectic Integration Scheme for Riemannian Manifold Hamiltonian Monte Carlo

The Peril of Popular Deep Learning Uncertainty Estimation Methods

Function-space Parameterization of Neural Networks for Sequential
  Learning

MCMC to address model misspecification in Deep Learning classification of Radio Galaxies

Evaluating Bayesian deep learning for radio galaxy classification


NCRF++, a Neural Sequence Labeling Toolkit. Easy use to any sequence labeling tasks (e.g. NER, POS, Segmentation). It includes character LSTM/CNN, word LSTM/CNN and softmax/CRF components.

Transfer Learning for Sequence Tagging with Hierarchical Recurrent Networks

Optimal Hyperparameters for Deep LSTM-Networks for Sequence Labeling Tasks

NCRF++: An Open-source Neural Sequence Labeling Toolkit

Design Challenges and Misconceptions in Neural Sequence Labeling

We Need to Talk About Random Splits

Fast and Accurate Neural CRF Constituency Parsing

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

Constituent Parsing as Sequence Labeling

A Pragmatic Guide to Geoparsing Evaluation

Adaptive Self-training for Few-shot Neural Sequence Labeling

NUBES: A Corpus of Negation and Uncertainty in Spanish Clinical Texts


Python API for LVIS Dataset

LVIS: A Dataset for Large Vocabulary Instance Segmentation

Overcoming Classifier Imbalance for Long-tail Object Detection with Balanced Group Softmax

Adaptive Class Suppression Loss for Long-Tail Object Detection


A deep learning toolkit specialized for handwritten document analysis

A Survey of Historical Document Image Datasets

General Models for Handwritten Text Recognition: Feasibility and State-of-the Art. German Kurrent as an Example

End-to-End Page-Level Assessment of Handwritten Text Recognition

Large-scale genealogical information extraction from handwritten Quebec parish records

Key-value information extraction from full handwritten pages

Open Source Handwritten Text Recognition on Medieval Manuscripts using Mixed Models and Document-Specific Finetuning

Handwritten Text Recognition from Crowdsourced Annotations

Improving Automatic Text Recognition with Language Models in the PyLaia Open-Source Library

Revisiting N-Gram Models: Their Impact in Modern Neural Networks for Handwritten Text Recognition


Essential Routines for Fundamental Astronomy. Maintainers: @eteq @mhvk @sergiopasra

Gammapy - A prototype for the CTA science tools

Towards new solutions for scientific computing: the case of Julia

The BlueMUSE data reduction pipeline: lessons learned from MUSE and first design choices

Software and Cyberinfrastructure for Astronomy VII


Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

SchNet - A deep learning architecture for molecules and materials.

Analyzing Learned Molecular Representations for Property Prediction

Journal of chemical information and modeling

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

Pushing the Boundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism

Implementing graph neural networks with TensorFlow-Keras

MEGAN: Multi-Explanation Graph Attention Network


AGDISTIS - Agnostic Named Entity Disambiguation

Entity Linking Meets Deep Learning: Techniques and Solutions

MAG: A Multilingual, Knowledge-base Agnostic and Deterministic Entity Linking Approach

K-CAP 2017: PROCEEDINGS OF THE KNOWLEDGE CAPTURE CONFERENCE

CovidPubGraph: A FAIR Knowledge Graph of COVID-19 Publications

Knowledge Graphs for Multilingual Language Translation and Generation


A library for mining of path-based representations of code (and more)

code2vec: Learning Distributed Representations of Code

A General Path-Based Representation for Predicting Program Properties

Precise Learning of Source Code Contextual Semantics via Hierarchical Dependence Structure and Graph Attention Networks

Using Distributed Representation of Code for Bug Detection

Evaluation of Contrastive Learning with Various Code Representations for Code Clone Detection

Old but Gold: Reconsidering the value of feedforward learners for software analytics

Exploiting Token and Path-based Representations of Code for Identifying Security-Relevant Commits

A Comparison of Code Embeddings and Beyond


Tool Learning for Big Models, Open-Source Solutions of ChatGPT-Plugins

Tool Learning with Foundation Models

Data-Copilot: Bridging Billions of Data and Humans with Autonomous Workflow

Agent-Pro: Learning to Evolve via Policy-Level Reflection and Optimization

A Review of Large Language Models and Autonomous Agents in Chemistry

LLMs in the Imaginarium: Tool Learning through Simulated Trial and Error


Fine-grained TLS services classification with reject option

Network Traffic Classification based on Single Flow Time Series Analysis

NetTiSA: Extended IP Flow with Time-series Features for Universal Bandwidth-constrained High-speed Network Traffic Classification


Minimalist NMT for educational purposes

An Actor-Critic Algorithm for Sequence Prediction

Sequence-to-Sequence Learning as Beam-Search Optimization

Sockeye: A Toolkit for Neural Machine Translation

Participatory Research for Low-resourced Machine Translation: A Case Study in African Languages

Joey NMT: A Minimalist NMT Toolkit for Novices

Sparse and Continuous Attention Mechanisms

Learning Kernel-Smoothed Machine Translation with Retrieved Examples

Automatic Interlinear Glossing for Under-Resourced Languages Leveraging Translations

International Conference on Computational Linguistics

kNN-BOX: A Unified Framework for Nearest Neighbor Generation

Edit Distance Based Curriculum Learning for Paraphrase Generation

International Joint Conference on Natural Language Processing


Repository hosting code used to reproduce results in "Actions Speak Louder than Words: Trillion-Parameter Sequential Transducers for Generative Recommendations" (https://arxiv.org/abs/2402.17152).

Self-Attentive Sequential Recommendation

Turning Dross Into Gold Loss: is BERT4Rec really better than SASRec?

Proceedings of the 17th ACM Conference on Recommender Systems

Revisiting Neural Retrieval on Accelerators

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


A masked language modeling objective to train a model to predict any subset of the target words, conditioned on both the input text and a partially masked target translation.

Mask-Predict: Parallel Decoding of Conditional Masked Language Models

Non-Autoregressive Machine Translation with Latent Alignments

Deep Encoder, Shallow Decoder: Reevaluating Non-autoregressive Machine Translation

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

Exposing the Implicit Energy Networks behind Masked Language Models via Metropolis--Hastings

Hybrid-Regressive Neural Machine Translation

Hybrid-Regressive Paradigm for Accurate and Speed-Robust Neural Machine Translation

Findings of the Association for Computational Linguistics: ACL 2023

MR-P: A Parallel Decoding Algorithm for Iterative Refinement Non-Autoregressive Translation

Findings of the Association for Computational Linguistics: ACL 2022

Con-NAT: Contrastive Non-autoregressive Neural Machine Translation

Findings of the Association for Computational Linguistics: EMNLP 2022


Conditional Diffusion Probabilistic Model for Speech Enhancement

Denoising Diffusion Probabilistic Models

DiffWave: A Versatile Diffusion Model for Audio Synthesis

Noisy speech database for training speech enhancement algorithms and TTS models

A Study on Speech Enhancement Based on Diffusion Probabilistic Model

Noise-aware Speech Enhancement using Diffusion Probabilistic Model


PyTorch implementation of Deep Reinforcement Learning: Policy Gradient methods (TRPO, PPO, A2C) and Generative Adversarial Imitation Learning (GAIL). Fast Fisher vector product TRPO.

Proximal Policy Optimization Algorithms

Asynchronous Methods for Deep Reinforcement Learning

Trust Region Policy Optimization

First Order Constrained Optimization in Policy Space

Robust Learning from Observation with Model Misspecification

Imitation Learning in Discounted Linear MDPs without exploration assumptions


Multi Task RL Baselines

Multi-Task Reinforcement Learning with Context-based Representations

Learning Robust State Abstractions for Hidden-Parameter Block MDPs

Block Contextual MDPs for Continual Learning

PaCo: Parameter-Compositional Multi-Task Reinforcement Learning

Learning Action Translator for Meta Reinforcement Learning on Sparse-Reward Tasks

Contrastive Modules with Temporal Attention for Multi-Task Reinforcement Learning


Efficient Multi-Stage Video Denoising With Recurrent Spatio-Temporal Fusion. CVPR_2021.

Efficient Multi-Stage Video Denoising with Recurrent Spatio-Temporal Fusion

Real-time Streaming Video Denoising with Bidirectional Buffers

Proceedings of the 30th ACM International Conference on Multimedia

RViDeformer: Efficient Raw Video Denoising Transformer with a Larger Benchmark Dataset


A simplified PyTorch implementation of Siamese networks for tracking: SiamFC, SiamRPN, SiamRPN++, SiamVGG, SiamDW, SiamRPN-VGG.

Fully-Convolutional Siamese Networks for Object Tracking

SiamRPN++: Evolution of Siamese Visual Tracking with Very Deep Networks

Deeper and Wider Siamese Networks for Real-Time Visual Tracking

SiamVGG: Visual Tracking using Deeper Siamese Networks


Implementation of End-to-End Relation Extraction using LSTMs on Sequences and Tree Structures in ACL2016.

A Novel Cascade Binary Tagging Framework for Relational Triple Extraction

Joint entity recognition and relation extraction as a multi-head selection problem

Entity-Relation Extraction as Multi-Turn Question Answering

Neural End-to-End Learning for Computational Argumentation Mining

End-to-End Neural Relation Extraction with Global Optimization

Empirical Methods in Natural Language Processing

A Walk-based Model on Entity Graphs for Relation Extraction

Extracting Entities and Relations with Joint Minimum Risk Training

Pre-training Entity Relation Encoder with Intra-span and Inter-span Information

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

End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models


Faster R-CNN / R-FCN :bulb: C++ version based on Caffe

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

Cascade R-CNN: High Quality Object Detection and Instance Segmentation

Deformable Convolutional Networks

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

Light-Head R-CNN: In Defense of Two-Stage Object Detector


Implementation for paper: Causal Intervention for Weakly-Supervised Semantic Segmentation

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

Weakly Supervised Learning of Instance Segmentation with Inter-pixel Relations


Generalized Optimal Sparse Decision Trees

Generalized and Scalable Optimal Sparse Decision Trees

Fast Sparse Decision Tree Optimization via Reference Ensembles

Connecting Interpretability and Robustness in Decision Trees through Separation

Dive into Decision Trees and Forests: A Theoretical Demonstration


PyTorch Implementation of MADDPG (Lowe et. al. 2017)

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

Plan Better Amid Conservatism: Offline Multi-Agent Reinforcement Learning with Actor Rectification

Regularized Softmax Deep Multi-Agent Q-Learning

MADiff: Offline Multi-agent Learning with Diffusion Models

Correcting Experience Replay for Multi-Agent Communication


Exploring CNN and ViT for Semi-Supervised Medical Image Segmentation

When CNN Meet with ViT: Towards Semi-Supervised Learning for Multi-Class Medical Image Semantic Segmentation

Dual-Contrastive Dual-Consistency Dual-Transformer: A Semi-Supervised Approach to Medical Image Segmentation

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

Triple-View Feature Learning for Medical Image Segmentation

Exigent Examiner and Mean Teacher: An Advanced 3D CNN-Based Semi-Supervised Brain Tumor Segmentation Framework

Medical Image Learning with Limited and Noisy Data


OpenPCSeg: Open Source Point Cloud Segmentation Toolbox and Benchmark

Searching Efficient 3D Architectures with Sparse Point-Voxel Convolution

Scribble-Supervised LiDAR Semantic Segmentation

StreetSurf: Extending Multi-view Implicit Surface Reconstruction to Street Views

UniSeg: A Unified Multi-Modal LiDAR Segmentation Network and the OpenPCSeg Codebase

FRNet: Frustum-Range Networks for Scalable LiDAR Segmentation

Multi-Space Alignments Towards Universal LiDAR Segmentation

Annotator: A Generic Active Learning Baseline for LiDAR Semantic Segmentation

Calib3D: Calibrating Model Preferences for Reliable 3D Scene
  Understanding

An Empirical Study of Training State-of-the-Art LiDAR Segmentation
  Models

4D Contrastive Superflows are Dense 3D Representation Learners


PMC-VQA is a large-scale medical visual question-answering dataset, which contains 227k VQA pairs of 149k images that cover various modalities or diseases.

LLaMA: Open and Efficient Foundation Language Models

Instruction Tuning for Large Language Models: A Survey

PMC-VQA: Visual Instruction Tuning for Medical Visual Question Answering

Benchmarking and Boosting Radiology Report Generation for 3D
  High-Resolution Medical Images


REDItools are python scripts to investigate RNA editing at genomic scale.

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects

Exploring Additional Valuable Information From Single-Cell RNA-Seq Data

Frontiers in cell and developmental biology


LAION-5B: An open large-scale dataset for training next generation image-text models

Red-Teaming the Stable Diffusion Safety Filter

TWIGMA: A dataset of AI-Generated Images with Metadata From Twitter

LLMs for Cyber Security: New Opportunities

Generative AI and US Intellectual Property Law

UnsafeBench: Benchmarking Image Safety Classifiers on Real-World and AI-Generated Images


Mock spatially resolved spectral line observations of simulated galaxies.

Off the Baryonic Tully–Fisher Relation: A Population of Baryon-dominated Ultra-diffuse Galaxies

Robust H i kinematics of gas-rich ultra-diffuse galaxies: hints of a weak-feedback formation scenario

Monthly notices of the Royal Astronomical Society

The HI Velocity Function: a test of cosmology or baryon physics?

Monthly Notices of the Royal Astronomical Society

The diversity of rotation curves of simulated galaxies with cusps and cores

The redshift evolution of the baryonic Tully-Fisher relation in SIMBA

A comparison of the baryonic Tully–Fisher relation in MaNGA and IllustrisTNG

Using EAGLE simulations to study the effect of observational constraints on the determination of HI asymmetries in galaxies

ASymba: HI global profile asymmetries in the Simba simulation

A warm dark matter cosmogony may yield more low-mass galaxy detections in 21-cm surveys than a cold dark matter one

Determining the Dark Matter distribution in galaxies with Deep Learning