Single-cell RNA-seq denoising using a deep count autoencoder

A comparison of automatic cell identification methods for single-cell RNA-sequencing data

Molecular profiling of driver events in metastatic uveal melanoma

Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data

基因组蛋白质组与生物信息学报

SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data

基因组蛋白质组与生物信息学报

A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening

Unsupervised cell functional annotation for single-cell RNA-seq


A high-performance Atari A3C agent in 180 lines of PyTorch

Self-Net: Lifelong Learning via Continual Self-Modeling

Learning rewards from exploratory demonstrations using probabilistic temporal ranking

Learning to Identify Critical States for Reinforcement Learning from Videos

The Impact of Negative Sampling on Contrastive Structured World Models

Learning rewards for robotic ultrasound scanning using probabilistic temporal ranking


The TechQA dataset -- http://ibm.biz/Tech_QA

The TechQA Dataset

Cheap and Good? Simple and Effective Data Augmentation for Low Resource Machine Reading

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

Mitigating Data Scarcity for Large Language Models


Uncertainty Quantification in Scientific Machine Learning: Methods, Metrics, and Comparisons

NeuralUQ: A comprehensive library for uncertainty quantification in neural differential equations and operators

Physics-informed neural networks for operator equations with stochastic data


[NeurIPS 2019 FL workshop] Federated Learning with Local and Global Representations

Think Locally, Act Globally: Federated Learning with Local and Global Representations

Personalized Federated Learning with First Order Model Optimization

FedBABU: Towards Enhanced Representation for Federated Image Classification

Efficient Distribution Similarity Identification in Clustered Federated Learning via Principal Angles Between Client Data Subspaces

Rethinking Data Heterogeneity in Federated Learning: Introducing a New Notion and Standard Benchmarks

Supernet Training for Federated Image Classification under System Heterogeneity


ProphetNet: Predicting Future N-gram for Sequence-to-Sequence Pre-training

Adversarial Retriever-Ranker for dense text retrieval

Distill-VQ: Learning Retrieval Oriented Vector Quantization By Distilling Knowledge from Dense Embeddings

LED: Lexicon-Enlightened Dense Retriever for Large-Scale Retrieval

CodeRetriever: A Large Scale Contrastive Pre-Training Method for Code Search

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

Soft-Labeled Contrastive Pre-training for Function-level Code Representation

Generative Dense Retrieval: Memory Can Be a Burden

EmbedDistill: A Geometric Knowledge Distillation for Information Retrieval

CodeRetriever: Unimodal and Bimodal Contrastive Learning for Code Search


Set of datasets for the deep learning recommendation model (DLRM).

Understanding data storage and ingestion for large-scale deep recommendation model training

Proceedings of the 49th Annual International Symposium on Computer Architecture

AutoShard: Automated Embedding Table Sharding for Recommender Systems

DreamShard: Generalizable Embedding Table Placement for Recommender Systems

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

Ad-Rec: Advanced Feature Interactions to Address Covariate-Shifts in Recommendation Networks


ChatMed: 中文医疗大模型，善于在线回答患者/用户的日常医疗相关问题！

CMB: A Comprehensive Medical Benchmark in Chinese

PromptCBLUE: A Chinese Prompt Tuning Benchmark for the Medical Domain

Datasets for Large Language Models: A Comprehensive Survey

AI Hospital: Interactive Evaluation and Collaboration of LLMs as Intern
  Doctors for Clinical Diagnosis

MedBench: A Large-Scale Chinese Benchmark for Evaluating Medical Large Language Models

Overview of the PromptCBLUE Shared Task in CHIP2023

Text2MDT: Extracting Medical Decision Trees from Medical Texts

A Survey on Medical Large Language Models: Technology, Application, Trustworthiness, and Future Directions

Integrating Physician Diagnostic Logic into Large Language Models: Preference Learning from Process Feedback

A Survey on Large Language Models from General Purpose to Medical Applications: Datasets, Methodologies, and Evaluations


Generative Spoken Dialogue Language Modeling

Breathing in Conversation

Towards human-like spoken dialogue generation between AI agents from written dialogue

Laughter Synthesis using Pseudo Phonetic Tokens with a Large-scale In-the-wild Laughter Corpus

Making Flow-Matching-Based Zero-Shot Text-to-Speech Laugh as You Like

Laugh Now Cry Later: Controlling Time-Varying Emotional States of
  Flow-Matching-Based Zero-Shot Text-to-Speech


SciFive: a text-text transformer model for biomedical literature

SciFive: a text-to-text transformer model for biomedical literature

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

Leveraging Biomolecule and Natural Language through Multi-Modal
  Learning: A Survey


Dataset for NAACL 2021 paper: "QMSum: A New Benchmark for Query-based Multi-domain Meeting Summarization"

Exploring Neural Models for Query-Focused Summarization

AWESOME: GPU Memory-constrained Long Document Summarization using Memory Mechanism and Global Salient Content

Meeting Summarization with Pre-training and Clustering Methods

E2LLM: Encoder Elongated Large Language Models for Long-Context Understanding and Reasoning


Produce elegant shaded error bars in MATLAB

Lipid peroxidation regulates long-range wound detection through 5-lipoxygenase in zebrafish

Flagellar energetics from high-resolution imaging of beating patterns in tethered mouse sperm

A Recursive Markov Boundary-Based Approach to Causal Structure Learning

Post-explant profiling of subcellular-scale carbon fiber intracortical electrodes and surrounding neurons enables modeling of recorded electrophysiology

The Panopticon—Assessing the Effect of Starvation on Prolonged Fly Activity and Place Preference

Sub-picoliter Traceability of Microdroplet Gravimetry and Microscopy


code for Graph Neural Networks for Link Prediction with Subgraph Sketching https://arxiv.org/abs/2209.15486

Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking

Revisiting Link Prediction: A Data Perspective

Simplifying Subgraph Representation Learning for Scalable Link Prediction

Text-space Graph Foundation Models: Comprehensive Benchmarks and New Insights


High Availability Shared Pipeline Engine

The Breakthrough Listen Search for Intelligent Life: A Wideband Data Recorder System for the Robert C. Byrd Green Bank Telescope

Publications of the Astronomical Society of the Pacific

Bifrost: a Python/C++ Framework for High-Throughput Stream Processing in Astronomy

Spectrometers and Polyphase Filterbanks in Radio Astronomy

The Breakthrough Listen search for intelligent life: Wide-bandwidth digital instrumentation for the CSIRO Parkes 64-m telescope

Publications of the Astronomical Society of Australia

The design and implementation of a ROACH2+GPU based correlator on the Tianlai dish array

Wideband Array Signal Processing with Real-Time Adaptive Interference Mitigation


web-based protein structure viewer and analysis tool interactively or in batch mode

Database resources of the National Center for Biotechnology Information

Database Resources of the National Center for Biotechnology Information

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode

Rhinovirus-A True Respiratory Threat or a Common Inconvenience of Childhood?

Biological Assembly Comparison with VAST.

STRUCTURAL BIOINFORMATICS: METHODS AND PROTOCOLS

Twelve Elements of Visualization and Analysis for Tertiary and Quaternary Structure of Biological Molecules


cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

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

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self-Organizing Maps

Cis-topic modelling of single-cell epigenomes

Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets


MS MARCO(Microsoft Machine Reading Comprehension) is a large scale dataset focused on machine reading comprehension, question answering, and passage ranking. A variant of this task will be the part of TREC and AFIRM 2019. For Updates about TREC 2019 please follow This Repository  Passage Reranking task Task Given a query q and a the 1000 most relevant passages P = p1, p2, p3,... p1000, as retrieved by BM25 a succeful system is expected to rerank the most relevant passage as high as possible. For this task not all 1000 relevant items have a human labeled relevant passage. Evaluation will be done using MRR

MS MARCO: A Human Generated MAchine Reading COmprehension Dataset

SPLADE: Sparse Lexical and Expansion Model for First Stage Ranking

SPLADE v2: Sparse Lexical and Expansion Model for Information Retrieval

From Distillation to Hard Negative Sampling: Making Sparse Neural IR Models More Effective

Interpretable & Time-Budget-Constrained Contextualization for Re-Ranking

Fast Passage Re-ranking with Contextualized Exact Term Matching and Efficient Passage Expansion

Neural Passage Retrieval with Improved Negative Contrast

Universal Vision-Language Dense Retrieval: Learning A Unified Representation Space for Multi-Modal Retrieval

Retrieving Supporting Evidence for Generative Question Answering

Proceedings of the Annual International ACM SIGIR Conference on Research and Development in Information Retrieval in the Asia Pacific Region

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


An open-source computer program for the analysis of wave diffraction and radiation of three-dimensional floating or submerged structures


Repository for benchmarking graph neural networks

Do Transformers Really Perform Bad for Graph Representation?

Benchmarking Graph Neural Networks

Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting

Adversarial Graph Augmentation to Improve Graph Contrastive Learning

Debiasing Graph Neural Networks via Learning Disentangled Causal Substructure

Graph Neural Networks with Local Graph Parameters

Learning Graph Normalization for Graph Neural Networks

Walking Out of the Weisfeiler Leman Hierarchy: Graph Learning Beyond Message Passing

On Structural Expressive Power of Graph Transformers

BeGin: Extensive Benchmark Scenarios and An Easy-to-use Framework for Graph Continual Learning


A Python package to learn the Koopman operator.

Learning Dynamical Systems via Koopman Operator Regression in Reproducing Kernel Hilbert Spaces

Sharp Spectral Rates for Koopman Operator Learning

Koopman Kernel Regression

A randomized algorithm to solve reduced rank operator regression

Consistent Long-Term Forecasting of Ergodic Dynamical Systems


ECMAScript parsing infrastructure for multipurpose analysis

Visualizing JIT Compiler Graphs

Measurement of the Usage of Web Clips in Underground Economy

Visualizing The Intermediate Representation of Just-in-Time Compilers


Behavior trees for Unity3D projects. Written with a code driven approach on the builder pattern.

A Survey of Behavior Trees in Robotics and AI

KT-BT: A Framework for Knowledge Transfer Through Behavior Trees in Multirobot Systems

IKT-BT: Indirect Knowledge Transfer Behavior Tree Framework for Multi-Robot Systems Through Communication Eavesdropping


Methods for Image-Based Cell Profiling

CellProfiler 3.0: Next-generation image processing for biology

A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay

RNA Interference (RNAi) Screening in Drosophila

FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity

bioRxiv : the preprint server for biology

BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations

In vitro neutrophil migration is associated with inhaled corticosteroid treatment and serum cytokines in pediatric asthma


SuperNovae in object-oriented Python (SNooPy)

Are Type Ia Supernovae in Rest-frame H Brighter in More Massive Galaxies?

SN 2013aa and SN 2017cbv: Two Sibling Type Ia Supernovae in the Spiral Galaxy NGC 5643

Carnegie Supernova Project. II. Near-infrared Spectral Diversity and Template of Type Ia Supernovae


An R package to import Water Survey of Canada hydrometric data and make it tidy

tidyhydat: Extract and Tidy Canadian Hydrometric Data


Open source software for product footprinting.


In silico prediction of E. coli serotype

ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data

Molecular Characterization of Extended-Spectrum β-Lactamase–Producing Escherichia coli and Klebsiella pneumoniae Among the Pediatric Population in Qatar

Evolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island

Diversity of blaCTX-M-1-carrying plasmids recovered from Escherichia coli isolated from Canadian domestic animals

Use of Genomics to Investigate Historical Importation of Shiga Toxin–Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand

Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella

Genome Informatics and Machine Learning-Based Identification of Antimicrobial Resistance-Encoding Features and Virulence Attributes in Escherichia coli Genomes Representing Globally Prevalent Lineages, Including High-Risk Clonal Complexes

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada

Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada

Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria


Keyphrase Generation

Convolutional Sequence to Sequence Learning

Deep Keyphrase Generation

Simple Recurrent Units for Highly Parallelizable Recurrence

One Size Does Not Fit All: Generating and Evaluating Variable Number of Keyphrases

TNT-KID: Transformer-based neural tagger for keyword identification

An Empirical Study on Neural Keyphrase Generation

Does Order Matter? An Empirical Study on Generating Multiple Keyphrases as a Sequence

UniKeyphrase: A Unified Extraction and Generation Framework for Keyphrase Prediction

Keyphrase Extraction with Incomplete Annotated Training Data

Proceedings of the Seventh Workshop on Noisy User-generated Text (W-NUT 2021)

General-to-Specific Transfer Labeling for Domain Adaptable Keyphrase Generation


FlauBERT: Unsupervised Language Model Pre-training for French

BARThez: a Skilled Pretrained French Sequence-to-Sequence Model

Pre-training Polish Transformer-based Language Models at Scale

ASR-Generated Text for Language Model Pre-training Applied to Speech Tasks

Using ASR-Generated Text for Spoken Language Modeling

Proceedings of BigScience Episode #5 -- Workshop on Challenges & Perspectives in Creating Large Language Models

UoR-NCL at SemEval-2022 Task 3: Fine-Tuning the BERT-Based Models for Validating Taxonomic Relations

Proceedings of the 16th International Workshop on Semantic Evaluation (SemEval-2022)

Word Sense Disambiguation for Automatic Translation of Medical Dialogues into Pictographs

Recent Advances in Natural Language Processing


MCFOST radiative transfer code

A likely flyby of binary protostar Z CMa caught in action

On the rise times in FU Orionis events

Monthly Notices of the Royal Astronomical Society: Letters

Kinematic Structures in Planet-Forming Disks

Sustained FU Orionis-type outbursts from colliding discs in stellar flybys

A kinematic excess in the annular gap and gas depleted cavity in the disc around HD 169142

Spectroscopic and interferometric signatures of magnetospheric accretion in young stars

Morphology of the gas-rich debris disk around HD 121617 with SPHERE observations in polarized light


Genetic neural architecture search with Keras

Scaling tree-based automated machine learning to biomedical big data with a feature set selector

Automated Machine Learning: State-of-The-Art and Open Challenges

Monarch Butterfly Optimization Based Convolutional Neural Network Design

Neural Architecture Search for 1D CNNs—Different Approaches Tests and Measurements

Evolutionary Design of Convolutional Neural Networks for Human Activity Recognition in Sensor-Rich Environments

Resource Usage and Performance Trade-offs for Machine Learning Models in Smart Environments

MONCAE: Multi-Objective Neuroevolution of Convolutional Autoencoders


High-order Remap Miniapp

High-Order Multi-Material ALE Hydrodynamics

High-order local maximum principle preserving (MPP) discontinuous Galerkin finite element method for the transport equation

Efficient exascale discretizations: High-order finite element methods

The international journal of high performance computing applications

Monotonicity in high‐order curvilinear finite element arbitrary Lagrangian–Eulerian remap

International Journal for Numerical Methods in Fluids

Matrix-free subcell residual distribution for Bernstein finite element discretizations of linear advection equations

Computer Methods in Applied Mechanics and Engineering

Matrix-free subcell residual distribution for Bernstein finite elements: Monolithic limiting

High-performance finite elements with MFEM


Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

Opportunities and challenges in long-read sequencing data analysis

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis

Fast nanopore sequencing data analysis with SLOW5

Computer Architecture-Aware Optimisation of DNA Analysis Systems


A Python Library for Graph Outlier Detection (Anomaly Detection)

Variational Graph Auto-Encoders

Deep Anomaly Detection on Attributed Networks

Society for Industrial and Applied Mathematics eBooks

AnomalyDAE: Dual autoencoder for anomaly detection on attributed networks

One-class graph neural networks for anomaly detection in attributed networks

Outlier Aware Network Embedding for Attributed Networks

BOND: Benchmarking Unsupervised Outlier Node Detection on Static Attributed Graphs

DAGAD: Data Augmentation for Graph Anomaly Detection

PyGOD: A Python Library for Graph Outlier Detection

GAD-NR: Graph Anomaly Detection via Neighborhood Reconstruction

Improving Generalizability of Graph Anomaly Detection Models via Data Augmentation


Benchmark environments for reward modelling and imitation learning algorithms.

imitation: Clean Imitation Learning Implementations

Learn what matters: cross-domain imitation learning with task-relevant embeddings

On The Fragility of Learned Reward Functions

A Primer on Maximum Causal Entropy Inverse Reinforcement Learning

DERAIL: Diagnostic Environments for Reward And Imitation Learning


Open source version of the original ISET, a complement to ISETBIO

Neural Network Generalization: The Impact of Camera Parameters

A system for generating complex physically accurate sensor images for automotive applications

A convolutional neural network reaches optimal sensitivity for detecting some, but not all, patterns

Software-Defined Imaging: A Survey

Simulations of fluorescence imaging in the oral cavity

Accurate smartphone camera simulation using 3D scenes

Using simulation to quantify the performance of automotive perception systems

Image-quality metric system for color filter array evaluation


FeAture Explorer

Prediction of Post-hepatectomy Liver Failure in Patients With Hepatocellular Carcinoma Based on Radiomics Using Gd-EOB-DTPA-Enhanced MRI: The Liver Failure Model

Evaluating Solid Lung Adenocarcinoma Anaplastic Lymphoma Kinase Gene Rearrangement Using Noninvasive Radiomics Biomarkers

Diagnostic Performance of 2D and 3D T2WI-Based Radiomics Features With Machine Learning Algorithms to Distinguish Solid Solitary Pulmonary Lesion

Development and evaluation of a venous computed tomography radiomics model to predict lymph node metastasis from non-small cell lung cancer

Combination Analysis of a Radiomics-Based Predictive Model With Clinical Indicators for the Preoperative Assessment of Histological Grade in Endometrial Carcinoma

Multi-Parameter MR Radiomics Based Model to Predict 5-Year Progression-Free Survival in Endometrial Cancer

Hippocampal subfield alterations in pediatric patients with post-traumatic stress disorder

Social cognitive and affective neuroscience

Texture Analysis of Fat-Suppressed T2-Weighted Magnetic Resonance Imaging and Use of Machine Learning to Discriminate Nasal and Paranasal Sinus Small Round Malignant Cell Tumors

A Radiomics Model Based on Gd-EOB-DTPA-Enhanced MRI for the Prediction of Microvascular Invasion in Solitary Hepatocellular Carcinoma ≤ 5 cm

Development and External Validation of a Radiomics Model Derived from Preoperative Gadoxetic Acid-Enhanced MRI for Predicting Histopathologic Grade of Hepatocellular Carcinoma


Python Lex-Yacc

Feature-Based Software Design Pattern Detection

GLITCH: Automated Polyglot Security Smell Detection in Infrastructure as Code

Symmetry reduction of tensor networks in many-body theory I. Automated symbolic evaluation of SU(2) algebra

Semantic Systems : In the Era of Knowledge Graphs : 16th International Conference on Semantic Systems, SEMANTiCS 2020, Amsterdam, The Netherlands, September 7-10, 2020 : proceedings

MINDS: A Translator to Embed Mathematical Expressions Inside SPARQL Queries

Deciding Differential Privacy of Online Algorithms with Multiple Variables

Polyglot Code Smell Detection for Infrastructure as Code with GLITCH


A collection of Java libraries for basic AI algorithms (JAICore) and automated software composition, in particular AutoML (softwareconfiguration)

ML-Plan: Automated machine learning via hierarchical planning

Automated Multi-Label Classification based on ML-Plan

Single and Parallel Machine Scheduling with Variable Release Dates


[ARCHIVED] Cooperative primitives for CUDA C++. See https://github.com/NVIDIA/cccl

Revisiting Huffman Coding: Toward Extreme Performance on Modern GPU Architectures

Numerical scattering amplitudes with pySecDec

Who Says Elephants Can't Run: Bringing Large Scale MoE Models into Cloud Scale Production

Optimizing Huffman Decoding for Error-Bounded Lossy Compression on GPUs

Ultrafast Focus Detection for Automated Microscopy

Certified SAT solving with GPU accelerated inprocessing

Efficiently Processing Large Relational Joins on GPUs


Implementation of spatio-temporal graph convolutional network with PyTorch

Traffic Flow Prediction with Vehicle Trajectories

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

Uncertainty Quantification of Sparse Travel Demand Prediction with Spatial-Temporal Graph Neural Networks

Urban Regional Function Guided Traffic Flow Prediction

Uncertainty Quantification via Spatial-Temporal Tweedie Model for Zero-inflated and Long-tail Travel Demand Prediction

Residual Correction in Real-Time Traffic Forecasting

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

SAUC: Sparsity-Aware Uncertainty Calibration for Spatiotemporal Prediction with Graph Neural Networks

Uncertainty-Aware Crime Prediction With Spatial Temporal Multivariate Graph Neural Networks


Span Model for Open Information Extraction on Accurate Corpus

OIE@OIA: an Adaptable and Efficient Open Information Extraction Framework

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

Constrained Tuple Extraction with Interaction-Aware Network

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

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

Open Information Extraction via Chunks


:exclamation: This is a read-only mirror of the CRAN R package repository.  MendelianRandomization — Mendelian Randomization Package

Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity

Association of Fibroblast Growth Factor 23 With Ischemic Stroke and Its Subtypes: A Mendelian Randomization Study

Low Intelligence Predicts Higher Risks of Coronary Artery Disease and Myocardial Infarction: Evidence From Mendelian Randomization Study

Genetically predicted basal metabolic rate and venous thromboembolism risk: a Mendelian randomization study

A multivariable Mendelian randomization analysis disentangling the causal relations between abdominal obesity, non-alcoholic fatty liver disease and cardiometabolic diseases


Multi-Objective Molecule Generation using Interpretable Substructures (ICML 2020)

MARS: Markov Molecular Sampling for Multi-objective Drug Discovery

Graph-based Molecular Representation Learning

How Much Space Has Been Explored? Measuring the Chemical Space Covered by Databases and Machine-Generated Molecules

An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries

Drug Discovery with Dynamic Goal-aware Fragments


named entity linking with latent relations

Improving Entity Linking by Modeling Latent Relations between Mentions

REL: An Entity Linker Standing on the Shoulders of Giants

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

Neural Entity Linking: A Survey of Models Based on Deep Learning

Learning Dynamic Context Augmentation for Global Entity Linking

Improving Entity Linking by Introducing Knowledge Graph Structure Information


Genome free discovery and classification of miRNAs from small RNA-Seq with random forests

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests

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

International journal of molecular sciences

The Multiverse of Plant Small RNAs: How Can We Explore It?


the datasets of the paper POG

Self-supervised Graph Learning for Recommendation

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

POG: Personalized Outfit Generation for Fashion Recommendation at Alibaba iFashion

Efficient Bi-Level Optimization for Recommendation Denoising

Linear-Time Graph Neural Networks for Scalable Recommendations

Diffusion Models for Generative Outfit Recommendation

Towards Robust Recommendation via Decision Boundary-aware Graph Contrastive Learning


Description and pointers of laion datasets

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

DataComp: In search of the next generation of multimodal datasets


An reimplement version of inpainting model in  Free-Form Image Inpainting with Gated Convolution

Generative Image Inpainting with Contextual Attention

A Benchmark for Inpainting of Clothing Images with Irregular Holes


Recurrent & convolutional neural network modules

Rationalizing Neural Predictions

Molding CNNs for text: non-linear, non-consecutive convolutions

Semi-supervised Question Retrieval with Gated Convolutions

Can I Trust the Explainer? Verifying Post-hoc Explanatory Methods

Learning from the Best: Rationalizing Prediction by Adversarial Information Calibration

Explaining Deep Neural Networks

Rationalizing predictions by adversarial information calibration


Molecular representation learning with language models and domain-relevant auxiliary tasks

Multimodal model with text and drug embeddings for adverse drug reaction classification

Quantifying the Gain in Weak-to-Strong Generalization

Traditional Machine and Deep Learning for Predicting Toxicity Endpoints

Target-Free Compound Activity Prediction via Few-Shot Learning


Learning Graph Models for Retrosynthesis Prediction

RetroXpert: Decompose Retrosynthesis Prediction Like A Chemist

Towards understanding retrosynthesis by energy-based models

��^2���������� as a Two-Step Graph Generative Models for Retrosynthesis Prediction

Modern Hopfield Networks for Few- and Zero-Shot Reaction Template Prediction

RetroComposer: Composing Templates for Template-Based Retrosynthesis Prediction

MARS: A Motif-based Autoregressive Model for Retrosynthesis Prediction


Official code for "Object counting and instance segmentation with image-level supervision", in CVPR 2019 and TPAMI 2020

Object Counting and Instance Segmentation with Image-level Supervision

Towards Partial Supervision for Generic Object Counting in Natural Scenes

Supervised and Weakly Supervised Deep Learning for Segmentation and Counting of Cotton Bolls Using Proximal Imagery


Automatic mapping of compiled circuits to low-noise sub-graphs

Suppressing Quantum Circuit Errors Due to System Variability

Characterizing quantum processors using discrete time crystals

Quantum Variational Rewinding for Time Series Anomaly Detection

Distributed Scheduling of Quantum Circuits with Noise and Time Optimization

Quantum Simulation on Noisy Superconducting Quantum Computers

Teaching Qubits to Sing: Mission Impossible?


Molecular standardisation tool

Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks

Journal of chemical information and modeling

Predicting drug-induced liver injury: The importance of data curation

KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images

Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout

Prediction and mechanistic analysis of drug-induced liver injury (DILI) based on chemical structure

eTOXlab, an open source modeling framework for implementing predictive models in production environments

The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives

A multi-task FP-GNN framework enables accurate prediction of selective PARP inhibitors

Systematic analysis of protein targets associated with adverse events of drugs from clinical trials and post-marketing reports

Allosteric Binders of ACE2 Are Promising Anti-SARS-CoV-2 Agents

bioRxiv : the preprint server for biology


Rank-based Gene Ontology analysis of gene expression data

A Sustained Immune Response Supports Long-Term Antiviral Immune Priming in the Pacific Oyster, Crassostrea gigas

Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi

Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral

Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico

General DNA Methylation Patterns and Environmentally-Induced Differential Methylation in the Eastern Oyster (Crassostrea virginica)

Differential basal expression of immune genes confers Crassostrea gigas resistance to Pacific Oyster Mortality Syndrome

Changes in Genome-Wide Methylation and Gene Expression in Response to Future pCO2 Extremes in the Antarctic Pteropod Limacina helicina antarctica

Plasticity to ocean warming is influenced by transgenerational, reproductive, and developmental exposure in a coral reef fish

Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection

Resilience of Atlantic Slippersnail Crepidula fornicata Larvae in the Face of Severe Coastal Acidification


Open-source implementation of the BilBOWA (Bilingual Bag-of-Words without Alignments) word embedding model.

BilBOWA: Fast Bilingual Distributed Representations without Word Alignments

Bilingual Distributed Word Representations from Document-Aligned Comparable Data

On the Role of Seed Lexicons in Learning Bilingual Word Embeddings

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

Multi-Modal Representations for Improved Bilingual Lexicon Learning

Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers)

BUCC 2017 Shared Task: a First Attempt Toward a Deep Learning Framework for Identifying Parallel Sentences in Comparable Corpora

Linking Tweets with Monolingual and Cross-Lingual News using Transformed Word Embeddings


Plug-and-play hydra sweepers for the EA-based multifidelity method DEHB and several population-based training variations, all proven to efficiently tune RL hyperparameters.

Population Based Training of Neural Networks

Provably Efficient Online Hyperparameter Optimization with Population-Based Bandits

DEHB: Evolutionary Hyberband for Scalable, Robust and Efficient Hyperparameter Optimization

Hyperparameters in Reinforcement Learning and How To Tune Them

Bayesian Generational Population-Based Training


Vecalign: Improved Sentence Alignment in Linear Time and Space

Empirical Methods in Natural Language Processing

Exploiting Sentence Order in Document Alignment

Effective Bitext Extraction From Comparable Corpora Using a Combination of Three Different Approaches

Workshop on Building and Using Comparable Corpora

SpanAlign: Sentence Alignment Method based on Cross-Language Span Prediction and ILP

International Conference on Computational Linguistics

KC4MT: A High-Quality Corpus for Multilingual Machine Translation

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION

KC4Align: Improving Sentence Alignment method for Low-resource Language Pairs

Pacific Asia Conference on Language, Information and Computation

Bitext Mining for Low-Resource Languages via Contrastive Learning

Domain Adaptation of Machine Translation with Crowdworkers

Finding the Right Recipe for Low Resource Domain Adaptation in Neural Machine Translation

Speaker Diarization of Scripted Audiovisual Content


Single-cell Hierarchical Poisson Factorization

Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

De novoGene Signature Identification from Single-Cell RNA-Seq with Hierarchical Poisson Factorization

Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq

A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease

A cell state specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma


Simple maze environments using mujoco-py

Learning Goal-Conditioned Policies Offline with Self-Supervised Reward Shaping

Walk the Random Walk: Learning to Discover and Reach Goals Without Supervision

Domain Adaptive Imitation Learning with Visual Observation


Code release for "LogME: Practical Assessment of Pre-trained Models for Transfer Learning" (ICML 2021) and Ranking and Tuning Pre-trained Models: A New Paradigm for Exploiting Model Hubs (JMLR 2022)

Transferability Estimation using Bhattacharyya Class Separability

On-target Adaptation

Unleashing the power of Neural Collapse for Transferability Estimation


Speaker embedding (d-vector) trained with GE2E loss

Generalized End-to-End Loss for Speaker Verification

Investigating on Incorporating Pretrained and Learnable Speaker Representations for Multi-Speaker Multi-Style Text-to-Speech

JTubeSpeech: corpus of Japanese speech collected from YouTube for speech recognition and speaker verification

MediumVC: Any-to-any voice conversion using synthetic specific-speaker speeches as intermedium features

Back Translation for Speech-to-text Translation Without Transcripts

DASpeech: Directed Acyclic Transformer for Fast and High-quality Speech-to-Speech Translation

Probing Deep Speaker Embeddings for Speaker-related Tasks


A PyTorch library for two-sample tests

Generating Multivariate Load States Using a Conditional Variational Autoencoder

GANs with Conditional Independence Graphs: On Subadditivity of Probability Divergences


DRLinFluids: An open-source Python platform of coupling deep reinforcement learning and OpenFOAM

Dynamic Feature-based Deep Reinforcement Learning for Flow Control of Circular Cylinder with Sparse Surface Pressure Sensing

Robust and adaptive deep reinforcement learning for enhancing flow control around a square cylinder with varying Reynolds numbers

Deep reinforcement learning-based active flow control of an elliptical cylinder: Transitioning from an elliptical cylinder to a circular cylinder and a flat plate

Effect of synthetic jets actuator parameters on deep reinforcement learning-based flow control performance in a square cylinder


Signature verification package, for learning representations from signature data, training user-dependent classifiers.

Learning features for offline handwritten signature verification using deep convolutional neural networks

Characterizing and Evaluating Adversarial Examples for Offline Handwritten Signature Verification

IEEE Transactions on Information Forensics and Security

Meta-learning for fast classifier adaptation to new users of Signature Verification systems


REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability

Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease

The role of the NMD factor UPF3B in olfactory sensory neurons

SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis

Alterations in oligodendrocyte transcriptional networks reveal region-specific vulnerabilities to neurological disease


Version 5 of the CAFE phylogenetics software

CAFE 5 models variation in evolutionary rates among gene families

Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation

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

Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes

Genome-wide gene birth-death dynamics are associated with diet breadth variation in Lepidoptera


An experimental Solidity parser for Python built on top of a robust ANTLR4 grammar

Toward the Ontological Modeling of Smart Contracts: A Solidity Use Case

An Empirical Study on Real Bug Fixes in Smart Contracts Projects

A study of inline assembly in solidity smart contracts

Proceedings of the ACM on Programming Languages

Vulnerable Smart Contract Function Locating Based on Multi-Relational Nested Graph Convolutional Network

Understanding Solidity Event Logging Practices in the Wild


Implementation of Proximal Meta-Policy Search (ProMP) as well as related Meta-RL algorithm. Includes a useful experiment framework for Meta-RL.

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

RL^2: Fast Reinforcement Learning via Slow Reinforcement Learning

ProMP: Proximal Meta-Policy Search

Some Considerations on Learning to Explore via Meta-Reinforcement Learning

MAME : Model-Agnostic Meta-Exploration

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

Meta-Reinforcement Learning in Broad and Non-Parametric Environments

OCEAN: Online Task Inference for Compositional Tasks with Context Adaptation


A GPU based FX correlator for radio astronomy

Digital Signal Processing using Stream High Performance Computing: A 512-input Broadband Correlator for Radio Astronomy

Optimizing performance-per-watt on GPUs in high performance computing

Introduction to the Special Issue on Digital Signal Processing in Radio Astronomy

Commissioning the H i Observing Mode of the Beam Former for the Cryogenically Cooled Focal L-band Array for the GBT (FLAG)

COSMIC: An Ethernet-based Commensal, Multimode Digital Backend on the Karl G. Jansky Very Large Array for the Search for Extraterrestrial Intelligence

A study of two FRBs with low polarization fractions localized with the MeerTRAP transient buffer system

Monthly notices of the Royal Astronomical Society

Instrumentation for Radio Interferometers with Antennas on a Regular Grid


harmonization, liftover, and imputation of summary statistics from GWAS

Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

Population-Matched Transcriptome Prediction Increases TWAS Discovery and Replication Rate

Genetically regulated gene expression underlies lipid traits in Hispanic cohorts

Fine-mapping and QTL tissue-sharing information improve causal gene identification and transcriptome prediction performance


This repository is an archive. Refer to https://github.com/gvirtus/GVirtuS

A GPGPU Transparent Virtualization Component for High Performance Computing Clouds

On the Virtualization of CUDA Based GPU Remoting on ARM and X86 Machines in the GVirtuS Framework

International journal of parallel programming

Accelerating Linux and Android applications on low‐power devices through remote GPGPU offloading

Concurrency and Computation: Practice and Experience

A General-Purpose Virtualization Service for HPC on Cloud Computing: An Application to GPUs

Parallel Processing and Applied Mathematics

The High Performance Internet of Things: Using GVirtuS to Share High-End GPUs with ARM Based Cluster Computing Nodes

CUDA Virtualization and Remoting for GPGPU Based Acceleration Offloading at the Edge


This is the qualR package, it will help you bring São Paulo and Rio de Janeiro air quality data to your R session :brazil:.


An R package for Bayes Factor Design Analysis

Bayes factor design analysis: Planning for compelling evidence

The effectiveness of schema therapy for patients with anxiety disorders, OCD, or PTSD: A systematic review and research agenda

The British journal of clinical psychology

Associations between aerobic fitness, negative symptoms, cognitive deficits and brain structure in schizophrenia - a cross-sectional study

Additive Effects of Item-Specific and Congruency Sequence Effects in the Vocal Stroop Task

Registered report: The effects of incentivized lies on memory

Additional evidence that valence does not affect serial recall

Quarterly journal of experimental psychology (2006)


Download FASTQ files from SRA or ENA repositories.

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Plassembler: an automated bacterial plasmid assembly tool

Drug resistance prediction for Mycobacterium tuberculosis with reference graphs


Microbial community analysis tools in R

The Effects of Captivity on the Mammalian Gut Microbiome

Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment

Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome

Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia

The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline

In vitro Fermentation Reveals Changes in Butyrate Production Dependent on Resistant Starch Source and Microbiome Composition

Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite

Effect of Biofertilizers Application on Soil Biodiversity and Litter Degradation in a Commercial Apricot Orchard

Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils

The role of the gut microbiota in the dietary niche expansion of fishing bats


MeerKAT calibration and imaging scripts

Analysis of physical processes in eruptive YSOs with near-infrared spectra and multiwavelength light curves

Discovery of a radio-emitting neutron star with an ultra-long spin period of 76 s

The MeerKAT Galaxy Cluster Legacy Survey I. Survey Overview and Highlights.

The 1.28 GHz MeerKAT Galactic Center Mosaic

Radio and X-Ray Observations of the Luminous Fast Blue Optical Transient AT 2020xnd

Observations of a radio-bright, X-ray obscured GRS 1915+105

Monthly Notices of the Royal Astronomical Society

MIGHTEE: are giant radio galaxies more common than we thought?

Discovery of ASKAP J173608.2–321635 as a Highly Polarized Transient Point Source with the Australian SKA Pathfinder

Radio and optical observations of the possible AE Aqr twin, LAMOST J024048.51+195226.9

MERGHERS pilot: MeerKAT discovery of diffuse emission in nine massive Sunyaev-Zel'dovich-selected galaxy clusters from ACT


package for interacting with fisheries databases at openfisheries.org


Sarcasm detection on tweets using neural network

Magnets for Sarcasm: Making Sarcasm Detection Timely, Contextual and Very Personal

Multi-Modal Sarcasm Detection and Humor Classification in Code-Mixed Conversations

IEEE Transactions on Affective Computing

Irony Detection in Persian Language: A Transfer Learning Approach Using Emoji Prediction

PROCEEDINGS OF THE 12TH INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION (LREC 2020)


High-performance implementation of SLIM-based approaches for Top-N recommendation

Boosting Item-based Collaborative Filtering via Nearly Uncoupled Random Walks

ACM Transactions on Knowledge Discovery from Data

Local Collaborative Autoencoders

Differentiable Ranking Metric Using Relaxed Sorting for Top-K Recommendation

A Differentiable Ranking Metric Using Relaxed Sorting Operation for Top-K Recommender Systems


Fast exoplanet transmission spectrum calculator

petitRADTRANS: a Python radiative transfer package for exoplanet characterization and retrieval.

Forward Modeling and Retrievals with PLATON, a Fast Open-source Tool

Publications of the Astronomical Society of the Pacific

PLATON II: New Capabilities and a Comprehensive Retrieval on HD 189733b Transit and Eclipse Data

A broadband thermal emission spectrum of the ultra-hot Jupiter WASP-18b

A Hubble PanCET Study of HAT-P-11b: A Cloudy Neptune with a Low Atmospheric Metallicity

The Hubble Space Telescope PanCET Program: An Optical to Infrared Transmission Spectrum of HAT-P-32Ab

High atmospheric metal enrichment for a Saturn-mass planet

The Hubble PanCET Program: A Metal-rich Atmosphere for the Inflated Hot Jupiter HAT-P-41b

ACCESS: Confirmation of No Potassium in the Atmosphere of WASP-31b

An enhanced slope in the transmission spectrum of the hot Jupiter WASP-104b


TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

TSA-Seq reveals a largely “hardwired” genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function

Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2

Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice

Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs

Characterizing nascent transcription patterns of PROMPTs, eRNAs, and readthrough transcripts in the ENCODE4 deeply profiled cell lines

bioRxiv : the preprint server for biology

CRISPR/Cas9 generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural induction


A python toolkit for parsing captions (in natural language) into scene graphs (as symbolic representations).

RegionCLIP: Region-based Language-Image Pretraining

Unified Visual-Semantic Embeddings: Bridging Vision and Language with Structured Meaning Representations

Learning Cross-modal Context Graph for Visual Grounding

Free-form Description Guided 3D Visual Graph Network for Object Grounding in Point Cloud

Learning to Generate Scene Graph from Natural Language Supervision

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

Relation-aware Instance Refinement for Weakly Supervised Visual Grounding

Learning Object Detection from Captions via Textual Scene Attributes

Coarse-to-Fine Contrastive Learning in Image-Text-Graph Space for Improved Vision-Language Compositionality

Non-Parallel Text Style Transfer with Self-Parallel Supervision


IP-Adapter: Text Compatible Image Prompt Adapter for Text-to-Image Diffusion Models

DALL-EVAL: Probing the Reasoning Skills and Social Biases of Text-to-Image Generation Models

Scalable 3D Captioning with Pretrained Models

Visual Programming for Text-to-Image Generation and Evaluation

CompoDiff: Versatile Composed Image Retrieval With Latent Diffusion

A Survey of Diffusion Based Image Generation Models: Issues and Their Solutions

The Male CEO and the Female Assistant: Probing Gender Biases in
  Text-To-Image Models Through Paired Stereotype Test

Getting it Right: Improving Spatial Consistency in Text-to-Image Models


An accurate and efficient deep learning method for single-cell RNA-seq data imputation

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data

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

基因组蛋白质组与生物信息学报

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

Distribution‐Agnostic Deep Learning Enables Accurate Single‐Cell Data Recovery and Transcriptional Regulation Interpretation


Modelling primary beams of radio astronomy antennas

Primary beam effects of radio astronomy antennas - II. Modelling MeerKAT L-band beams

The flickering nuclear activity of Fornax A

H i intensity mapping with MeerKAT: primary beam effects on foreground cleaning

Radio footprints of a minor merger in the Shapley Supercluster: From supercluster down to galactic scales

Mining Mini-Halos with MeerKAT I. Calibration and Imaging


Effects of Response Option Order on Likert-Type Psychometric Properties and Reactions

Educational and psychological measurement

Psychometric Properties of the Chinese Version of the Organization Big Five Scale

Brief Sensations Seeking Scale (BSSS): Validity Evidence in Mexican Adolescents

International journal of environmental research and public health


Foreign Contamination Screening caller scripts and documentation

Rapid and sensitive detection of genome contamination at scale with FCS-GX

Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture

Hiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in Fusarium oxysporum f.sp. ciceris

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

De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery

Chromosome-Level Genome Assembly of the Cape Cliff Lizard (Hemicordylus capensis)

Genetic confirmation of Octopus insularis (Leite and Haimovici, 2008) in South Florida, United States using physical features and de novo genome assembly

Microbial Metabolites of 3-n-butylphthalide as Monoamine Oxidase A Inhibitors

International journal of molecular sciences

Draft assembly and annotation of the Cuban crocodile (Crocodylus rhombifer) genome


All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")

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

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth

Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland

Phylogenetically and metabolically diverse autotrophs in the world’s deepest blue hole

Undocumented potential for primary productivity in a globally-distributed bacterial photoautotroph

MetaSanity: An integrated, customizable microbial genome evaluation and annotation pipeline

Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides


Protein-compound affinity prediction through unified RNN-CNN

DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks

ATOM3D: Tasks On Molecules in Three Dimensions

A brief review of protein–ligand interaction prediction

Computational and structural biotechnology journal

Trends and Potential of Machine Learning and Deep Learning in Drug Study at Single-Cell Level

Pretraining model for biological sequence data


NiiStat is a set of Matlab scripts for analyzing neuroimaging data from clinical populations

Brain lesions disrupting addiction map to a common human brain circuit

Removal of artifacts from resting-state fMRI data in stroke

Disruptions of the Human Connectome Associated With Hemispatial Neglect

A lesion and connectivity-based hierarchical model of chronic aphasia recovery dissociates patients and healthy controls

Impairments in Emotion Recognition and Risk-Taking Behavior After Isolated, Cerebellar Stroke

Consequence of stroke for feature recall and binding in visual working memory

Dissociable contributions of frontal and temporal brain regions to basic semantic composition

Right- and Left-Lateralised Neglect are not Anatomically Homologous: A Voxel-Lesion Symptom Mapping Study

Recursive hierarchical embedding in vision is impaired by posterior middle temporal gyrus lesions

The impact of etiology in lesion-symptom mapping – A direct comparison between tumor and stroke


SPARQL to SQL translation engine for multiple backends, such as DB2, PostgreSQL and Apache Spark

Expressive Reasoning Graph Store: A Unified Framework for Managing RDF and Property Graph Databases

ROSIE: Runtime Optimization of SPARQL Queries Using Incremental Evaluation

Leveraging Neighborhood Summaries for Efficient RDF Queries on RDBMS


Library for computing persistent homology

Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks

Topological Descriptors Help Predict Guest Adsorption in Nanoporous Materials

Generalized Penalty for Circular Coordinate Representation

Topological data analysis enhanced prediction of hydrogen storage in metal–organic frameworks (MOFs)

Persistent homology advances interpretable machine learning for nanoporous materials.

Algebraic and Geometric Models for Space Networking

Machine learning assisted high-throughput screening of zeolites for the selective adsorption of xylene isomers

Topological Methods in Machine Learning: A Tutorial for Practitioners


KnowFlow Automatic Water Monitoring device is an open sourced tool enable everyone having access to first hand water quality data with low cost.


iDb-A*: Iterative Search and Optimization for Optimal Kinodynamic Motion Planning

db-CBS: Discontinuity-Bounded Conflict-Based Search for Multi-Robot Kinodynamic Motion Planning


Maximum independent sets and vertex covers of large sparse graphs.

Finding Near-Optimal Independent Sets at Scale

DIFUSCO: Graph-based Diffusion Solvers for Combinatorial Optimization

DIMES: A Differentiable Meta Solver for Combinatorial Optimization Problems

What's Wrong with Deep Learning in Tree Search for Combinatorial Optimization

UDC: A Unified Neural Divide-and-Conquer Framework for Large-Scale Combinatorial Optimization Problems


An easy-to-use Python framework to generate adversarial jailbreak prompts.

AutoDAN: Generating Stealthy Jailbreak Prompts on Aligned Large Language Models

EasyJailbreak: A Unified Framework for Jailbreaking Large Language
  Models

Protecting Your LLMs with Information Bottleneck


Python utility to estimate, compare, and reweight RNA energetics across many secondary structure algorithms.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses

Deep learning models for predicting RNA degradation via dual crowdsourcing

RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning

Ribonanza: deep learning of RNA structure through dual crowdsourcing

RNA structure landscape ofS. cerevisiaeintrons


Python Keyphrase Extraction module

Simple Unsupervised Keyphrase Extraction using Sentence Embeddings

Unsupervised Keyphrase Extraction with Multipartite Graphs

pke: an open source python-based keyphrase extraction toolkit

International Conference on Computational Linguistics

KPTimes: A Large-Scale Dataset for Keyphrase Generation on News Documents

MDERank: A Masked Document Embedding Rank Approach for Unsupervised Keyphrase Extraction

AttentionRank: Unsupervised Keyphrase Extraction using Self and Cross Attentions

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

TNT-KID: Transformer-based neural tagger for keyword identification

KeyGames: A Game Theoretic Approach to Automatic Keyphrase Extraction

ArchivalQA: A Large-scale Benchmark Dataset for Open Domain Question Answering over Historical News Collections

A Comparative Assessment of State-Of-The-Art Methods for Multilingual Unsupervised Keyphrase Extraction

IFIP advances in information and communication technology


Core of Py-ORBIT code

Resonance identification studies at the CERN PS

Modeling Transverse Space Charge effects in IOTA with pyORBIT

Space Charge Driven Resonances in the CERN PS

Density distributions of tune shifts from space charge or beam-beam interactions in Gaussian bunches


A statistics and context decoding toolbox for neuroimaging.

BrainStat: A toolbox for brain-wide statistics and multimodal feature associations

Heritability of hippocampal functional and microstructural organisation

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

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

Functional gradients reveal cortical hierarchy changes in multiple sclerosis

Contracted functional connectivity profiles in autism

Differences in structural connectome organization across sleep quality


High Performance Implementation of Boris Particle Pusher on DPC++. A First Look at oneAPI

Optimized Computation of Tight Focusing of Short Pulses Using Mapping to Periodic Space

Optimized routines for event generators in QED-PIC codes

ML-Based Analysis of Particle Distributions in High-Intensity Laser Experiments: Role of Binning Strategy

Optimized event generator for strong-field QED simulations within the hi-χ framework


Tioga is a library for overset grid assembly on parallel distributed systems

ExaWind: A multifidelity modeling and simulation environment for wind energy

A parallel direct cut algorithm for high-order overset methods with application to a spinning golf ball

Validation of blade-resolved computational fluid dynamics for a MW-scale turbine rotor in atmospheric flow

SCIENCE OF MAKING TORQUE FROM WIND (TORQUE 2020), PTS 1-5

High-order computational fluid dynamics simulations of a spinning golf ball


Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes

Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance

Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity

Antimicrobial Resistance Genes in Bacteria Isolated From Japanese Honey, and Their Potential for Conferring Macrolide and Lincosamide Resistance in the American Foulbrood Pathogen Paenibacillus larvae

Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica

Variation of Metagenome From Feedstock to Digestate in Full-Scale Biogas Plants

Whole-genome sequence analysis of high-level penicillin-resistant strains and antimicrobial susceptibility of Neisseria gonorrhoeae clinical isolates from Thailand

Whole-metagenome shotgun sequencing of pig faecal microbiome


Wind Plant Integrated System Design and Engineering Model

Land-based wind turbines with flexible rail transportable blades – Part I: Conceptual design and aeroservoelastic performance

Distributed Aerodynamic Control using Active Trailing-Edge Flaps for Large Wind Turbines

Land-based wind turbines with flexible rail transportable blades – Part II: 3D FEM design optimization of the rotor blades


Netflow processing tools

A Survey of Network-based Intrusion Detection Data Sets

Flow length and size distributions in campus Internet traffic

Cyber Attack Detection thanks to Machine Learning Algorithms

Study of Multi-Class Classification Algorithms' Performance on Highly Imbalanced Network Intrusion Datasets

Modeling and Prediction of Daily Traffic Patterns—WASK and SIX Case Study

Malicious Overtones: Hunting Data Theft in the Frequency Domain with One-class Learning

An Effective Feature Extraction Mechanism for Intrusion Detection System

IEICE Transactions on Information and Systems


Smart Contract Weakness Classification and Test Cases

xFuzz: Machine Learning Guided Cross-Contract Fuzzing

MPro: Combining Static and Symbolic Analysis for Scalable Testing of Smart Contract

International Symposium on Software Reliability Engineering

A Security Reference Architecture for Blockchains

Security Threat Mitigation for Smart Contracts: A Comprehensive Survey

Mutation testing of smart contracts at scale

An Empirical Study Into the Success of Listed Smart Contracts in Ethereum

Gas limit aware mutation testing of smart contracts at scale.

To Healthier Ethereum: A Comprehensive and Iterative Smart Contract Weakness Enumeration


RTE+RRTMGP is a set of codes for computing radiative fluxes in planetary atmospheres.


ZMap is a fast single packet network scanner designed for Internet-wide network surveys.

One to Rule them All? A First Look at DNS over QUIC

Characterizing the VPN Ecosystem in the Wild

Zeroing in on Port 0 Traffic in the Wild

Passive and Active Network Measurement Conference

Identifying and characterizing ZMap scans: a cryptanalytic approach

An Evaluation on the Behaviors of Aftershock Sequence of November 26th, 2019 Earthquake, ML=6.3, North of Durrës, Albania

Muş Alparslan Üniversitesi Fen Bilimleri Dergisi


Pangeo website + discussion of general issues related to the project.


Unofficial implementation of the paper "Deferred Neural Rendering: Image Synthesis using Neural Textures" in Pytorch.

Deep Learning for Deepfakes Creation and Detection: A Survey

Countering Malicious DeepFakes: Survey, Battleground, and Horizon


An evolutionary context-integrated deep learning framework for protein engineering

SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering

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

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


Funnel-Transformer: Filtering out Sequential Redundancy for Efficient Language Processing

Survey: Exploiting Data Redundancy for Optimization of Deep Learning

NarrowBERT: Accelerating Masked Language Model Pretraining and Inference


A codebase that makes differentially private training of transformers easy.

Large Language Models Can Be Strong Differentially Private Learners

Automatic Clipping: Differentially Private Deep Learning Made Easier and Stronger

When Does Differentially Private Learning Not Suffer in High Dimensions?

Scalable and Efficient Training of Large Convolutional Neural Networks with Differential Privacy

Provably Confidential Language Modelling

A New Linear Scaling Rule for Private Adaptive Hyperparameter Optimization

Private Fine-tuning of Large Language Models with Zeroth-order Optimization

Auditing and Generating Synthetic Data with Controllable Trust Trade-offs

Coupling public and private gradient provably helps optimization


This code accompanies the the paper Trading with the Momentum Transformer: An Intelligent and Interpretable Architecture (https://arxiv.org/pdf/2112.08534.pdf).

Slow Momentum with Fast Reversion: A Trading Strategy Using Deep Learning and Changepoint Detection

Few-Shot Learning Patterns in Financial Time Series for Trend-Following Strategies


Code release for  Universal Domain Adaptation(CVPR 2019)

Universal Source-Free Domain Adaptation

On the Effectiveness of Image Rotation for Open Set Domain Adaptation

Benchmarking Domain Adaptation Methods on Aerial Datasets


Population genetic summary statistics

Genetic evidence for two founding populations of the Americas

The Demographic Development of the First Farmers in Anatolia

Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas

Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland

Assessing Genomic Admixture between Cryptic Plutella Moth Species following Secondary Contact

Genetic continuity and change among the Indigenous peoples of California


Code for "Superquadrics Revisited: Learning 3D Shape Parsing beyond Cuboids", CVPR 2019

Learning Shape Abstractions by Assembling Volumetric Primitives

3D-PRNN: Generating Shape Primitives with Recurrent Neural Networks

Reconstructing Superquadrics from Intensity and Color Images


Maximum entropy modelling of species geographic distributions.

The Genomic Footprints of the Fall and Recovery of the Crested Ibis

Simulating the effects of climate change across the geographical distribution of two medicinal plants in the genus Nardostachys

European badger habitat requirements in the Netherlands – combining ecological niche models with neighbourhood analysis

Spatial and environmental variation in phyllostomid bat (Chiroptera, Phyllostomidae) distribution in Mexico

Potential Suitable Habitats of Chili Pepper in China under Climate Change

Analysis of peste des petits ruminants virus spread and the risk of its introduction into the territory of the Russian Federation


Noise Conditional Score Networks (NeurIPS 2019, Oral)

Score-Based Generative Modeling through Stochastic Differential Equations

Generative Modeling by Estimating Gradients of the Data Distribution

Improved Techniques for Training Score-Based Generative Models

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

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

Estimating High Order Gradients of the Data Distribution by Denoising

Accelerating Score-based Generative Models for High-Resolution Image Synthesis

Imitation with Neural Density Models

Kernel Stein Generative Modeling


【CVPR2020, Interpretable Network】A Model-driven Deep Neural Network  for Single Image Rain Removal

Not Just Streaks: Towards Ground Truth for Single Image Deraining

Networks are Slacking Off: Understanding Generalization Problem in Image Deraining


[NeurIPS 2024] PointMamba: A Simple State Space Model for Point Cloud Analysis

Mamba: Linear-Time Sequence Modeling with Selective State Spaces

Point-BERT: Pre-training 3D Point Cloud Transformers with Masked Point Modeling

Masked Autoencoders for Point Cloud Self-supervised Learning


Reference code for the paper HistoGAN: Controlling Colors of GAN-Generated and Real Images via Color Histograms (CVPR 2021).

Training Generative Adversarial Networks with Limited Data

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

Image color correction, enhancement, and editing


Global alignment and alignment extension

Fast characterization of segmental duplications in genome assemblies

Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants

MONI: A Pangenomics Index for Finding MEMs

LJA: Assembling Long and Accurate Reads Using Multiplex de Bruijn Graphs


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

Hierarchical Attention Transfer Network for Cross-Domain Sentiment Classification

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

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

Diversity-Based Generalization for Unsupervised Text Classification under Domain Shift

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

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


AttacKG: Constructing Technique Knowledge Graph from Cyber Threat Intelligence Reports

EXTRACTOR: Extracting Attack Behavior from Threat Reports

AttacKG+:Boosting Attack Knowledge Graph Construction with Large Language Models


We evaluate many models used for biomedical and clinical nlp tasks, and train new models that perform much better.

Pretrained Language Models for Biomedical and Clinical Tasks: Understanding and Extending the State-of-the-Art

Empirical Methods in Natural Language Processing

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

BERN2: an advanced neural biomedical named entity recognition and normalization tool

BioM-Transformers: Building Large Biomedical Language Models with BERT, ALBERT and ELECTRA

Workshop on Biomedical Natural Language Processing

Web-Based Application Based on Human-in-the-Loop Deep Learning for Deidentifying Free-Text Data in Electronic Medical Records: Development and Usability Study


Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)

A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

Cenote-Taker 2 democratizes virus discovery and sequence annotation

Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA

Common Mechanisms of Virus-Mediated Oncogenesis in Bladder Cancers Arising In Solid Organ Transplant Recipients


Real-time High-Resolution Neural Network with Semantic Guidance for Crack Segmentation

Towards Interpretable Semantic Segmentation via Gradient-weighted Class Activation Mapping

CrackSeg9k: A Collection and Benchmark for Crack Segmentation Datasets and Frameworks

Real-time high-resolution neural network with semantic guidance for crack segmentation


Official code release for "GRAF: Generative Radiance Fields for 3D-Aware Image Synthesis"

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

GET3D: A Generative Model of High Quality 3D Textured Shapes Learned from Images

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

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

Sem2NeRF: Converting Single-View Semantic Masks to Neural Radiance Fields

Generating Part-Aware Editable 3D Shapes without 3D Supervision


This is the GitHub repository of the Building Efficiency Targeting Tool for Energy Retrofits (BETTER)


Text Simplification System and Dataset

Optimizing Statistical Machine Translation for Text Simplification

Transactions of the Association for Computational Linguistics

The (Un)Suitability of Automatic Evaluation Metrics for Text Simplification

International Conference on Computational Logic

Controllable Text Simplification with Lexical Constraint Loss

Meeting of the Association for Computational Linguistics

LENS: A Learnable Evaluation Metric for Text Simplification

On the Helpfulness of Document Context to Sentence Simplification

SimplifyUR: Unsupervised Lexical Text Simplification for Urdu

PROCEEDINGS OF THE 12TH INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION (LREC 2020)

Claim Optimization in Computational Argumentation

A Semi-Supervised Approach for Low-Resourced Text Generation

Divide-and-Conquer Text Simplification by Scalable Data Enhancement

Proceedings of the Workshop on Text Simplification, Accessibility, and Readability (TSAR-2022)

Neural Transduction of Letter Position Dyslexia using an Anagram Matrix Representation


EMNLP 2020: "Dialogue Response Ranking Training with Large-Scale Human Feedback Data"

ConveRT: Efficient and Accurate Conversational Representations from Transformers

A Systematic Evaluation of Response Selection for Open Domain Dialogue

NAISTeacher: A Prompt and Rerank Approach to Generating Teacher Utterances in Educational Dialogues

Workshop on Innovative Use of NLP for Building Educational Applications

A Transformer-based Response Evaluator for Open-Domain Spoken Conversation


a PyTorch implementation of the paper "Deep Gravity: enhancing mobility flows generation with deep neural networks and geographic information"

A Deep Gravity model for mobility flows generation

MobilityDL: A Review of Deep Learning From Trajectory Data


Code for the NAACL 2022 long paper "DiffCSE: Difference-based Contrastive Learning for Sentence Embeddings"

SimCSE: Simple Contrastive Learning of Sentence Embeddings

Equivariant Contrastive Learning

RankCSE: Unsupervised Sentence Representations Learning via Learning to Rank

ESCL: Equivariant Self-Contrastive Learning for Sentence Representations


Tool to plot synteny and structural rearrangements between genomes

plotsr: visualizing structural similarities and rearrangements between multiple genomes

Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes

plotsr: Visualising structural similarities and rearrangements between multiple genomes

The complete diploid reference genome of RPE-1 identifies human phased epigenetic landscapes

bioRxiv : the preprint server for biology


A method for training neural networks that are provably robust to adversarial attacks.

Explaining and Harnessing Adversarial Examples

Towards Deep Learning Models Resistant to Adversarial Attacks

Certified Adversarial Robustness via Randomized Smoothing

Provable defenses against adversarial examples via the convex outer adversarial polytope

Evaluating Robustness of Neural Networks with Mixed Integer Programming

Scaling provable adversarial defenses

A Convex Relaxation Barrier to Tight Robustness Verification of Neural Networks

On the Geometry of Adversarial Examples

Tight Certification of Adversarially Trained Neural Networks via Nonconvex Low-Rank Semidefinite Relaxations


Pre-training Reusable Representations for Robotic Manipulation Using Diverse Human Video Data

R3M: A Universal Visual Representation for Robot Manipulation

VideoDex: Learning Dexterity from Internet Videos

SORNet: Spatial Object-Centric Representations for Sequential Manipulation

Pre-Trained Image Encoder for Generalizable Visual Reinforcement Learning

Structured World Models from Human Videos

Compositional Foundation Models for Hierarchical Planning

Learning and Retrieval from Prior Data for Skill-based Imitation Learning

Spatiotemporal Predictive Pre-training for Robotic Motor Control

H-InDex: Visual Reinforcement Learning with Hand-Informed Representations for Dexterous Manipulation


Library to implement graph neural networks in PyTorch

Graphs, Convolutions, and Neural Networks: From Graph Filters to Graph Neural Networks

Graphon Neural Networks and the Transferability of Graph Neural Networks

EdgeNets:Edge Varying Graph Neural Networks

Deep Representations for Time-varying Brain Datasets

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


This is the public repository for eigenvector-based SALSA features for polyphonic sound event localization and detection.

SALSA: Spatial Cue-Augmented Log-Spectrogram Features for Polyphonic Sound Event Localization and Detection

SALSA-Lite: A Fast and Effective Feature for Polyphonic Sound Event Localization and Detection with Microphone Arrays

DCASE 2021 Task 3: Spectrotemporally-aligned Features for Polyphonic Sound Event Localization and Detection

What Makes Sound Event Localization and Detection Difficult? Insights from Error Analysis


Extension of the original word2vec using different architectures

Two/Too Simple Adaptations of Word2Vec for Syntax Problems

North American Chapter of the Association for Computational Linguistics

Evaluation of Word Vector Representations by Subspace Alignment

State-of-the-art Chinese Word Segmentation with Bi-LSTMs

Learning the Curriculum with Bayesian Optimization for Task-Specific Word Representation Learning

Unsupervised POS Induction with Word Embeddings

Exploring Segment Representations for Neural Segmentation Models

Intrinsic Subspace Evaluation of Word Embedding Representations

Learning Word Representations from Scarce and Noisy Data with Embedding Subspaces

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

Putting RDF2vec in Order

Automated Detection of Non-Relevant Posts on the Russian Imageboard "2ch": Importance of the Choice of Word Representations


Yajta is a extensible library for bytecode probe insertion, built on top of javassist. Its transformations may be applied at load time with an agent or offline.

A journey among Java neutral program variants

Genetic Programming and Evolvable Machines

Java decompiler diversity and its application to meta-decompilation

Coverage-Based Debloating for Java Bytecode

The Strengths and Behavioral Quirks of Java Bytecode Decompilers


Visual Room Rearrangement

Simple but Effective: CLIP Embeddings for Embodied AI

Visual Room Rearrangement

TIDEE: Tidying Up Novel Rooms using Visuo-Semantic Commonsense Priors


Retrieve data from thousands of mesonet stations as Polars DataFrames from Synoptic's Weather API.


Configurable automation library for linux SBC boards including raspberry pi


An implementation of the tools described in the paper entitled "Graphical-model based estimation and inference for differential privacy"

Winning the NIST Contest: A scalable and general approach to differentially private synthetic data

PrivSyn: Differentially Private Data Synthesis

Benchmarking Differentially Private Synthetic Data Generation Algorithms

New Oracle-Efficient Algorithms for Private Synthetic Data Release

Iterative Methods for Private Synthetic Data: Unifying Framework and New Methods

Relaxed Marginal Consistency for Differentially Private Query Answering

Understanding how Differentially Private Generative Models Spend their Privacy Budget

DP-TBART: A Transformer-based Autoregressive Model for Differentially Private Tabular Data Generation

Privacy-preserving data release leveraging optimal transport and
  particle gradient descent


Code release for "Cut and Learn for Unsupervised Object Detection and Instance Segmentation" and "VideoCutLER: Surprisingly Simple Unsupervised Video Instance Segmentation"

Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour

The devil is in the object boundary: towards annotation-free instance
  segmentation using Foundation Models


A Large-Scale Few-Shot Relation Extraction Dataset

A Survey on Text Classification: From Shallow to Deep Learning

FewRel 2.0: Towards More Challenging Few-Shot Relation Classification

Learning from Context or Names? An Empirical Study on Neural Relation Extraction

Hierarchical Attention Prototypical Networks for Few-Shot Text Classification

Few-shot Relation Extraction via Bayesian Meta-learning on Relation Graphs

Incremental Few-shot Text Classification with Multi-round New Classes: Formulation, Dataset and System

Unified Semantic Typing with Meaningful Label Inference

Chain of Thought with Explicit Evidence Reasoning for Few-shot Relation Extraction

PAC Prediction Sets for Meta-Learning

Ensemble Making Few-Shot Learning Stronger


PCIC's Daily Climate Downscaling Library

Testing bias adjustment methods for regional climate change applications under observational uncertainty and resolution mismatch

A high-resolution daily global dataset of statistically downscaled CMIP6 models for climate impact analyses


Quantized Neural Network PACKage - mobile-optimized implementation of quantized neural network operators

DeepCABAC: A Universal Compression Algorithm for Deep Neural Networks

Wav2Vec2.0 on the Edge: Performance Evaluation

Demo Abstract: Real-Time Out-of-Distribution Detection on a Mobile Robot

Optimizing the Deployment of Tiny Transformers on Low-Power MCUs


DISTIL: Deep dIverSified inTeractIve Learning. An active/inter-active learning library built on py-torch for reducing labeling costs.

Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds

SIMILAR: Submodular Information Measures Based Active Learning In Realistic Scenarios

A Comparative Survey of Deep Active Learning

Effective Evaluation of Deep Active Learning on Image Classification Tasks

One-Round Active Learning

Zero-Round Active Learning

Pareto Optimization for Active Learning under Out-of-Distribution Data Scenarios

Learning to Rank for Active Learning via Multi-Task Bilevel Optimization

Data-Efficient Learning via Clustering-Based Sensitivity Sampling:
  Foundation Models and Beyond

A study of deep active learning methods to reduce labelling efforts in biomedical relation extraction


An opt-in digital jurisdiction for DAOs and sovereign individuals

When Ostrom Meets Blockchain: Exploring the Potentials of Blockchain for Commons Governance

A Survey on Blockchain-Based Self-Sovereign Patient Identity in Healthcare

A Blockchain-Supported Framework for Charging Management of Electric Vehicles

Emergent Outcomes of the veToken Model

An intrinsic integrity-driven rating model for a sustainable reputation system


A python tool that ingests WUDAPT information into WRF.

Local Climate Zones for Urban Temperature Studies

Bulletin of the American Meteorological Society

Evaluation of the ‘local climate zone’ scheme using temperature observations and model simulations

WUDAPT: An Urban Weather, Climate, and Environmental Modeling Infrastructure for the Anthropocene

WUDAPT, an efficient land use producing data tool for mesoscale models? Integration of urban LCZ in WRF over Madrid

Mapping Europe into local climate zones

LCZ Generator: A Web Application to Create Local Climate Zone Maps

Combining expert and crowd-sourced training data to map urban form and functions for the continental US

Evaluating the performance of a novel WUDAPT averaging technique to define urban morphology with mesoscale models


open-source neutrino interaction library

Equation of State Effects in Core-Collapse Supernovae

Formulating bulk viscosity for neutron star simulations

Long-term gravitational wave asteroseismology of supernovae: From core collapse to 20 seconds postbounce

Comparison of Electron Capture Rates in the N = 50 Region using 1D Simulations of Core-collapse Supernovae

Equation of state and neutrino transfer in supernovae and neutron stars

Gravitational Collapse of White Dwarfs to Neutron Stars. I. From Initial Conditions to Explosions with Neutrino-radiation Hydrodynamics Simulations

Gray two-moment neutrino transport: Comprehensive tests and improvements for supernova simulations


Solving LPs with convergent message passing

Deep Graph Matching via Blackbox Differentiation of Combinatorial Solvers

Making Higher Order MOT Scalable: An Efficient Approximate Solver for Lifted Disjoint Paths

Combinatorial Optimization for Panoptic Segmentation: A Fully Differentiable Approach

A Comparative Study of Graph Matching Algorithms in Computer Vision

MAP inference via Block-Coordinate Frank-Wolfe Algorithm

Fusion Moves for Graph Matching

Bottleneck potentials in Markov Random Fields


ATHENA: Advanced Techniques for High dimensional parameter spaces to Enhance Numerical Analysis

Hull Shape Design Optimization with Parameter Space and Model Reductions, and Self-Learning Mesh Morphing

Journal of Marine Science and Engineering

A Supervised Learning Approach Involving Active Subspaces for an Efficient Genetic Algorithm in High-Dimensional Optimization Problems

Enhancing CFD predictions in shape design problems by model and parameter space reduction

Advanced Modeling and Simulation in Engineering Sciences

Multi-fidelity data fusion through parameter space reduction with applications to automotive engineering

A multifidelity approach coupling parameter space reduction and nonintrusive POD with application to structural optimization of passenger ship hulls

A local approach to parameter space reduction for regression and classification tasks

Level set learning with pseudo-reversible neural networks for nonlinear dimension reduction in function approximation

Multi‐fidelity data fusion for the approximation of scalar functions with low intrinsic dimensionality through active subspaces


Interpretability in the Wild: a Circuit for Indirect Object Identification in GPT-2 small

A Primer on the Inner Workings of Transformer-based Language Models

Scaling and evaluating sparse autoencoders

pyvene: A Library for Understanding and Improving PyTorch Models via
  Interventions

LMExplainer: Grounding Knowledge and Explaining Language Models

Knowledge Mechanisms in Large Language Models: A Survey and Perspective

Knowledge Circuits in Pretrained Transformers


A basecaller for Oxford Nanopore Technologies' sequencers

Performance of neural network basecalling tools for Oxford Nanopore sequencing

Computational methods for 16S metabarcoding studies using Nanopore sequencing data

Computational and structural biotechnology journal

Helix: Algorithm/Architecture Co-design for Accelerating Nanopore Genome Base-calling


Ordinal regression algorithms

Ordinal Common-sense Inference

SeerNet at SemEval-2018 Task 1: Domain Adaptation for Affect in Tweets

Relevance Scoring of Triples Using Ordinal Logistic Classification - The Celosia Triple Scorer at WSDM Cup 2017


Machine learning with Mill.jl for JSON documents

Mapping the Internet: Modelling Entity Interactions in Complex Heterogeneous Networks

A Framework for End-to-End Learning on Semantic Tree-Structured Data

Mill.jl and JsonGrinder.jl: automated differentiable feature extraction for learning from raw JSON data


R package for the joint analysis of multiple single-cell RNA-seq datasets

Computational methods for the integrative analysis of single-cell data

A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma

Zenodo (CERN European Organization for Nuclear Research)

Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging

DISSECTING TUMOR TRANSCRIPTIONAL HETEROGENEITY FROM SINGLE-CELL RNA-SEQ DATA BY GENERALIZED BINARY COVARIANCE DECOMPOSITION


Industrial Benchmark

Deep Reinforcement Learning: An Overview

Learning and Policy Search in Stochastic Dynamical Systems with Bayesian Neural Networks

Interpretable Policies for Reinforcement Learning by Genetic Programming

NeoRL: A Near Real-World Benchmark for Offline Reinforcement Learning

A Benchmark Environment Motivated by Industrial Control Problems

IEEE Symposium Series on Computational Intelligence

Comparing Model-free and Model-based Algorithms for Offline Reinforcement Learning

Generating interpretable fuzzy controllers using particle swarm optimization and genetic programming

Proceedings of the Genetic and Evolutionary Computation Conference Companion

Batch reinforcement learning on the industrial benchmark: First experiences

International Joint Conference on Neural Network

User-Interactive Offline Reinforcement Learning

Introduction to the "Industrial Benchmark"


Using the Output Embedding to Improve Language Models

Pointing the Unknown Words

Edinburgh Neural Machine Translation Systems for WMT 16

Diverse Beam Search: Decoding Diverse Solutions from Neural Sequence Models

Nematus: a Toolkit for Neural Machine Translation

Linguistic Input Features Improve Neural Machine Translation

Noisy Activation Functions

Improving Neural Machine Translation with Conditional Sequence Generative Adversarial Nets

Improved Neural Machine Translation with a Syntax-Aware Encoder and Decoder

How Grammatical is Character-level Neural Machine Translation? Assessing MT Quality with Contrastive Translation Pairs


JKind - An infinite-state model checker for safety properties in Lustre

The JKind Model Checker

Towards Realizability Checking of Contracts using Theories

Requirements Analysis of a Quad-Redundant Flight Control System

Machine-Checked Proofs For Realizability Checking Algorithms


Keras Temporal Convolutional Network.

An Empirical Evaluation of Generic Convolutional and Recurrent Networks for Sequence Modeling

Time Series Change Point Detection with Self-Supervised Contrastive Predictive Coding

Fast and accurate annotation of acoustic signals with deep neural networks

Beyond Correlation: A Path-Invariant Measure for Seismogram Similarity

Nozzle Thermal Estimation for Fused Filament Fabricating 3D Printer Using Temporal Convolutional Neural Networks

Real-time detection of anomalies in large-scale transient surveys

Investigating the Effects of Training Set Synthesis for Audio Segmentation of Radio Broadcast

The LSST-DESC 3x2pt Tomography Optimization Challenge

A Temporal Type-2 Fuzzy System for Time-Dependent Explainable Artificial Intelligence

IEEE Transactions on Artificial Intelligence

El-CID: a filter for gravitational-wave electromagnetic counterpart identification


Quantized Neural Networks (QNNs) on PYNQ

FINN: A Framework for Fast, Scalable Binarized Neural Network Inference

Symposium on Field Programmable Gate Arrays

FINN-R: An End-to-End Deep-Learning Framework for Fast Exploration of Quantized Neural Networks

Toolflows for Mapping Convolutional Neural Networks on FPGAs: A Survey and Future Directions

DAC-SDC Low Power Object Detection Challenge for UAV Applications

FAT: Training Neural Networks for Reliable Inference Under Hardware Faults

Efficient Error-Tolerant Quantized Neural Network Accelerators

IEEE International Symposium on Defect and Fault Tolerance in VLSI and Nanotechnology Systems

Memory-Efficient Dataflow Inference for Deep CNNs on FPGA

A Threshold Neuron Pruning for a Binarized Deep Neural Network on an FPGA

IEICE Transactions on Information and Systems

A Deep Learning Accelerator Based on a Streaming Architecture for Binary Neural Networks

Evolutionary Bin Packing for Memory-Efficient Dataflow Inference Acceleration on FPGA

Genetic and Evolutionary Computation Conference


Awesome Deep Graph Clustering is a collection of SOTA, novel deep graph clustering methods (papers, codes, and datasets).

Deep Graph Clustering via Dual Correlation Reduction

Hard Sample Aware Network for Contrastive Deep Graph Clustering

A Survey of Deep Graph Clustering: Taxonomy, Challenge, Application, and Open Resource

Efficient Graph Convolution for Joint Node Representation Learning and Clustering

Dink-Net: Neural Clustering on Large Graphs

Fine-grained Attributed Graph Clustering

Society for Industrial and Applied Mathematics eBooks

Reinforcement Graph Clustering with Unknown Cluster Number

Uncertainty in GNN Learning Evaluations: The Importance of a Consistent Benchmark for Community Detection

Improved Dual Correlation Reduction Network With Affinity Recovery

IEEE Transactions on Neural Networks and Learning Systems

Graph Clustering with High-Order Contrastive Learning


massively-parallel cosmology simulator

Strong Bound on Canonical Ultralight Axion Dark Matter from the Lyman-Alpha Forest

Modeling biased tracers at the field level

The ASTRID simulation: the evolution of Supermassive Black Holes

An efficient and accurate hybrid method for simulating non-linear neutrino structure

Monthly notices of the Royal Astronomical Society

The ASTRID Simulation: Galaxy Formation and Reionization

Bayesian emulator optimisation for cosmology: application to the Lyman-alpha forest

Journal of Cosmology and Astroparticle Physics

An emulator for the Lyman-α forest

Limits on the Light Dark Matter-Proton Cross Section from Cosmic Large-Scale Structure.

An emulator for the Lyman-α forest in beyond-ΛCDM cosmologies

Inhomogeneous He ii reionization in hydrodynamic simulations

Monthly Notices of the Royal Astronomical Society


Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

From Piz Daint to the Stars: Simulation of Stellar Mergers using High-Level Abstractions

Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

octo-tiger: a new, 3D hydrodynamic code for stellar mergers that uses hpx parallelization

Accelerating Octo-Tiger: Stellar Mergers on Intel Knights Landing with HPX

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

From Merging Frameworks to Merging Stars: Experiences using HPX, Kokkos and SIMD Types

From Task-Based GPU Work Aggregation to Stellar Mergers: Turning Fine-Grained CPU Tasks into Portable GPU Kernels

Betelgeuse as a Merger of a Massive Star with a Companion

Evaluating HPX and Kokkos on RISC-V using an astrophysics application Octo-Tiger

Proceedings of the SC '23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis

Hydrodynamic simulations of WD-WD mergers and the origin of RCB stars


one-click face swap

InstantID: Zero-shot Identity-Preserving Generation in Seconds

Concept-centric Personalization with Large-scale Diffusion Priors

DF40: Toward Next-Generation Deepfake Detection


Mastering Atari with Discrete World Models

Mastering Visual Continuous Control: Improved Data-Augmented Reinforcement Learning

Reinforcement Learning with Action-Free Pre-Training from Videos

TransDreamer: Reinforcement Learning with Transformer World Models

Structured World Models from Human Videos

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

Curiosity-Driven Exploration via Latent Bayesian Surprise

Exploration and preference satisfaction trade-off in reward-free learning

DreamingV2: Reinforcement Learning with Discrete World Models without Reconstruction

Frustratingly Easy Regularization on Representation Can Boost Deep Reinforcement Learning


First version of the code - last update Dec 2015

MadDM v.3.0: A comprehensive tool for dark matter studies

SkyFACT: high-dimensional modeling of gamma-ray emission with adaptive templates and penalized likelihoods

Features in cosmic-ray lepton data unveil the properties of nearby cosmic accelerators

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

Bayesian analysis of the break in DAMPE lepton spectra

A simple and natural interpretations of the DAMPE cosmic-ray electron/positron spectrum within two sigma deviations

Late decaying 2-component dark matter scenario as an explanation of the AMS-02 positron excess

Constraining the halo size from possible density profiles of hydrogen gas of Milky Way Galaxy

Diffusive origin for the cosmic-ray spectral hardening reveals signatures of a nearby source in the leptons and protons data

Positron excess from cosmic ray interactions in galactic molecular clouds


Open Domain Question Answering Using Early Fusion of Knowledge Bases and Text

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

Meeting of the Association for Computational Linguistics

SQALER: Scaling Question Answering by Decoupling Multi-Hop and Logical Reasoning


Pytorch implementation of Graph U-Nets (ICML19)

Graph U-Nets

Deep Graph Mapper: Seeing Graphs Through the Neural Lens

Hierarchical message-passing graph neural networks

Adversarial Attacks on Graph Classification via Bayesian Optimisation

State of the Art and Potentialities of Graph-level Learning

Deep Graph Mapper: Seeing Graphs through the Neural Lens

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


Annotated dataset of 100 works of fiction to support tasks in natural language processing and the computational humanities.

An Annotated Dataset of Coreference in English Literature

Named Entity Recognition and Classification in Historical Documents: A Survey

Literary Event Detection

An annotated dataset of literary entities

North American Chapter of the Association for Computational Linguistics

Measuring Information Propagation in Literary Social Networks

The Project Dialogism Novel Corpus: A Dataset for Quotation Attribution in Literary Texts

Improving Automatic Quotation Attribution in Literary Novels

Challenges to Evaluating the Generalization of Coreference Resolution Models: A Measurement Modeling Perspective

Computational Storytelling and Emotions: A Survey

Comparing Annotated Datasets for Named Entity Recognition in English Literature

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION