Image segmentation - general superpixel segmentation & center detection & region growing

Supervised and unsupervised segmentation using superpixels, model estimation, and graph cut

Learning Continuous Implicit Representation for Near-Periodic Patterns

Region growing using superpixels with learned shape prior

Detection and Localization of Drosophila Egg Chambers in Microscopy Images


State-of-the-art deep learning based audio codec supporting both mono 24 kHz audio and stereo 48 kHz audio.

High Fidelity Neural Audio Compression

Speak Foreign Languages with Your Own Voice: Cross-Lingual Neural Codec
  Language Modeling

VioLA: Unified Codec Language Models for Speech Recognition, Synthesis,
  and Translation

HiFi-Codec: Group-residual Vector quantization for High Fidelity Audio
  Codec

UniAudio: An Audio Foundation Model Toward Universal Audio Generation

UniCATS: A Unified Context-Aware Text-to-Speech Framework with
  Contextual VQ-Diffusion and Vocoding

Latent-Domain Predictive Neural Speech Coding

CQNV: A combination of coarsely quantized bitstream and neural vocoder
  for low rate speech coding

ELLA-V: Stable Neural Codec Language Modeling with Alignment-guided
  Sequence Reordering


Short Read Sequence Typing for Bacterial Pathogens

Whole genome sequencing in clinical and public health microbiology

Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages

Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor

Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1

Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance

Population Structure and Antimicrobial Resistance of Invasive Serotype IV Group B Streptococcus, Toronto, Ontario, Canada

Spontaneous Emergence of Azithromycin Resistance in Independent Lineages of Salmonella Typhi in Northern India


Summary of related papers on visual attention. Related code will be released based on Jittor gradually.

Attention mechanisms in computer vision: A survey

Beyond Self-Attention: External Attention Using Two Linear Layers for Visual Tasks

Visual Attention Network


Publication-ready volcano plots with enhanced colouring and labeling

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair

Aging-associated deficit in CCR7 is linked to worsened glymphatic function, cognition, neuroinflammation, and β-amyloid pathology

A Genome-wide CRISPR Screen Reveals a Role for the Non-canonical Nucleosome-Remodeling BAF Complex in Foxp3 Expression and Regulatory T Cell Function

Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein

bioRxiv : the preprint server for biology

Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection

STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer

DAMPs/PAMPs induce monocytic TLR activation and tolerance in COVID-19 patients; nucleic acid binding scavengers can counteract such TLR agonists

Vesicular trafficking permits evasion of cGAS/STING surveillance during initial human papillomavirus infection

Diagnostic blood RNA profiles for human acute spinal cord injury

The Journal of experimental medicine/The journal of experimental medicine

Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing


UT-Sarulab MOS prediction system using SSL models

UTMOS: UTokyo-SaruLab System for VoiceMOS Challenge 2022

The Voicemos Challenge 2023: Zero-Shot Subjective Speech Quality Prediction for Multiple Domains

Text-to-speech synthesis from dark data with evaluation-in-the-loop data
  selection

How Generative Spoken Language Modeling Encodes Noisy Speech: Investigation from Phonetics to Syntactics


fast phage annotation program

Pharokka: a fast scalable bacteriophage annotation tool

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Predicting stop codon reassignment improves functional annotation of bacteriophages


Repo for the R package coloc

Identification of new susceptibility loci for type 2 diabetes and shared etiological pathways with coronary heart disease

Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture

Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses

A more accurate method for colocalisation analysis allowing for multiple causal variants

GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium

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

基因组蛋白质组与生物信息学报

Shared genetic etiology and causality between body fat percentage and cardiovascular diseases: a large-scale genome-wide cross-trait analysis

Mapping genetic determinants of 184 circulating proteins in 26,494 individuals to connect proteins and diseases

Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into the complex genetic architecture


A quality control analysis tool for high throughput sequencing data

METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

The structure, function, and evolution of a complete human chromosome 8

Best practices for bioinformatic characterization of neoantigens for clinical utility

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females

A comparative analysis of drinking water employing metagenomics

VISTA Re-programs Macrophage Biology Through the Combined Regulation of Tolerance and Anti-inflammatory Pathways

A growth factor–expressing macrophage subpopulation orchestrates regenerative inflammation via GDF-15

Nonclonal Emergence of Colistin Resistance Associated with Mutations in the BasRS Two-Component System in Escherichia coli Bloodstream Isolates


chromatin Variability Across Regions (of the genome!)

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

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

Chromatin accessibility maps provide evidence of multilineage gene priming in hematopoietic stem cells

Protocol for single-cell ATAC sequencing using combinatorial indexing in mouse lung adenocarcinoma


A gap-closing software tool that uses long reads to enhance genome assembly.

TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina

Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation

Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium

Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in Lactobacillus salivarius

The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China

Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics


A BERT model for scientific text.

S2ORC: The Semantic Scholar Open Research Corpus

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

A Survey of Deep Learning for Scientific Discovery

A Span-Based Model for Joint Overlapped and Discontinuous Named Entity Recognition

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

A deep-learning system bridging molecule structure and biomedical text with comprehension comparable to human professionals

SciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search

Biomedical Event Extraction as Multi-turn Question Answering

International Workshop on Health Text Mining and Information Analysis

How can natural language processing help model informed drug development?: a review

Process-Level Representation of Scientific Protocols with Interactive Annotation


Generic decoding of seen and imagined objects using hierarchical visual features

Design Guidelines for Prompt Engineering Text-to-Image Generative Models

Convolutional Neural Networks for Facial Expression Recognition

The Hallucination Machine: A Deep-Dream VR platform for Studying the Phenomenology of Visual Hallucinations

Interpretation of Prediction Models Using the Input Gradient

Hierarchical Neural Representation of Dreamed Objects Revealed by Brain Decoding with Deep Neural Network Features

Biases in Generative Art -- A Causal Look from the Lens of Art History

Deep Convolutional Networks as Models of Generalization and Blending Within Visual Creativity

Localized convolutional neural networks for geospatial wind forecasting

Using Artificial Intelligence Techniques to Emulate the Creativity of a Portrait Painter


HuatuoGPT, Towards Taming Language Models To Be a Doctor. (An Open Medical GPT)

LLaMA: Open and Efficient Foundation Language Models

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

HuatuoGPT, towards Taming Language Model to Be a Doctor

MedChatZH: a Better Medical Adviser Learns from Better Instructions


Image registration using pytorch

NODEO: A Neural Ordinary Differential Equation Based Optimization Framework for Deformable Image Registration


This repo presents a reference architecture for running serverless MapReduce jobs. This has been implemented using AWS Lambda and Amazon S3.

Guarding Serverless Applications with SecLambda

The server is dead, long live the server: Rise of Serverless Computing,
  Overview of Current State and Future Trends in Research and Industry


Translation models for 22 scheduled languages of India

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

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


Caffe implementation of Google MobileNet SSD detection network, with pretrained weights on VOC0712 and mAP=0.727.

Optimizing the Trade-off between Single-Stage and Two-Stage Object Detectors using Image Difficulty Prediction

Tiny-DSOD: Lightweight Object Detection for Resource-Restricted Usages

UAV Framework for Autonomous Onboard Navigation and People/Object Detection in Cluttered Indoor Environments

Cluster Pruning: An Efficient Filter Pruning Method for Edge AI Vision Applications

IEEE journal of selected topics in signal processing

The art and practice of data science pipelines

Con-Pi: A Distributed Container-Based Edge and Fog Computing Framework

Drone-Based Autonomous Motion Planning System for Outdoor Environments under Object Detection Uncertainty

A Care Robot with Ethical Sensing System for Older Adults at Home

A Room Monitoring System Using Deep Learning and Perspective Correction Techniques

Reducing Object Detection Uncertainty from RGB and Thermal Data for UAV Outdoor Surveillance


Additional exercises and data for EE364a. No solutions; for public consumption.

Alternating Subgradient Methods for Convex-Concave Saddle-Point Problems


[MICCAI 2019] [MEDIA 2020] Models Genesis

Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis

Models Genesis

Transferable Visual Words: Exploiting the Semantics of Anatomical Patterns for Self-Supervised Learning

SAM: Self-supervised Learning of Pixel-wise Anatomical Embeddings in
  Radiological Images

Advancing 3D medical image analysis with variable dimension transform based supervised 3D pre-training

Transfer Learning for Segmentation Problems: Choose the Right Encoder
  and Skip the Decoder


Synchronized Batch Normalization implementation in PyTorch.

MegDet: A Large Mini-Batch Object Detector

StudioGAN: A Taxonomy and Benchmark of GANs for Image Synthesis

Segmenting Ships in Satellite Imagery With Squeeze and Excitation U-Net


A Bulletproof Way to Generate Structured JSON from Language Models

14 examples of how LLMs can transform materials science and chemistry: a reflection on a large language model hackathon.

Spellburst: A Node-based Interface for Exploratory Creative Coding with Natural Language Prompts

Proceedings of the 36th Annual ACM Symposium on User Interface Software and Technology

Local Large Language Models for Complex Structured Medical Tasks

Sasha: creative goal-oriented reasoning in smart homes with large
  language models

RCAgent: Cloud Root Cause Analysis by Autonomous Agents with
  Tool-Augmented Large Language Models


text2vec, text to vector. 文本向量表征工具，把文本转化为向量矩阵，实现了Word2Vec、RankBM25、Sentence-BERT、CoSENT等文本表征、文本相似度计算模型，开箱即用。

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

One Embedder, Any Task: Instruction-Finetuned Text Embeddings

Evaluating the Generation Capabilities of Large Chinese Language Models

Geo-Encoder: A Chunk-Argument Bi-Encoder Framework for Chinese
  Geographic Re-Ranking


Gene cluster comparison figure generator

clinker & clustermap.js: automatic generation of gene cluster comparison figures

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome

Circulating androgen regulation by androgen-catabolizing gut bacteria in male mouse gut

The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos

A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin

Comparative Analysis of L-Fucose Utilization and Its Impact on Growth and Survival of Campylobacter Isolates

Thermophilin 13: In Silico Analysis Provides New Insight in Genes Involved in Bacteriocin Production


Panoramic stitching of single cell data

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations

Computational methods for the integrative analysis of single-cell data

Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research

CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation

IMGG: Integrating Multiple Single-Cell Datasets through Connected Graphs and Generative Adversarial Networks

International journal of molecular sciences


BSMN common data processing pipeline

Comprehensive identification of somatic nucleotide variants in human brain tissue


gvcf aggregation tool

University of Birmingham Identification of rare sequence variation underlying heritable pulmonary arterial hypertension

Next-generation sequencing for the diagnosis of MYH9-RD: Predicting pathogenic variants

Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error

Journal of computational biology : a journal of computational molecular cell biology

Identification of novel rare sequence variation underlying heritable pulmonary arterial hypertension


A Python package for benchmarking pathway database with functional enrichment and classification methods

The Cancer Genome Atlas Pan-Cancer analysis project

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data


Single-cell data analysis

A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation

A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data

Efficient and scalable integration of single-cell data using domain-adversarial and variational approximation


A SciUnit library for validation testing of spiking neural network models.

Reproducible Neural Network Simulations: Statistical Methods for Model Validation on the Level of Network Activity Data

DIGITAL AUDIO AND VIDEO FOR ONLINE ASSESSMENT

Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles

A System-on-Chip Based Hybrid Neuromorphic Compute Node Architecture for Reproducible Hyper-Real-Time Simulations of Spiking Neural Networks


variation discovery using long range information in linked-reads

Discovery of large genomic inversions using long range information

VALOR2: characterization of large-scale structural variants using linked-reads

Characterization of segmental duplications and large inversions using Linked-Reads

Discovery of large genomic inversions using pooled clone sequencing


rdefra: Interact with the UK AIR Pollution Database from DEFRA


A (very) simple script to QC Hi-C data.

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

A Reference Genome Assembly of American Bison, Bison bison bison

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

The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae

De Novo Assembly and Annotation of 11 Diverse Shrub Willow (Salix) Genomes Reveals Novel Gene Organization in Sex-Linked Regions


Simulation Sandbox for the Design and Evaluation of Stormwater Control Algorithms

pystorms: A simulation sandbox for the development and evaluation of stormwater control algorithms


R package to estimate public transport emissions based on GTFS data


Scoring tools for Media Forensics Evaluations

Beyond Pixels: Image Provenance Analysis Leveraging Metadata

Learning Transformation-Aware Embeddings for Image Forensics

On the Effectiveness of Image Manipulation Detection in the Age of
  Social Media


A survey of known lower bounds in arithmetic circuits.

On the complexity of partial derivatives

On Algebraic Branching Programs of Small Width

Succinct Hitting Sets and Barriers to Proving Algebraic Circuits Lower
  Bounds

An exponential lower bound for homogeneous depth-5 circuits over finite fields

Unbalancing Sets and An Almost Quadratic Lower Bound for Syntactically Multilinear Arithmetic Circuits

A Near-Optimal Depth-Hierarchy Theorem for Small-Depth Multilinear Circuits

Geometric complexity theory and matrix powering

The Chasm at Depth Four, and Tensor Rank : Old results, new insights

Hitting sets and reconstruction for dense orbits in VPe and ΣΠΣ circuits

On geometric complexity theory: Multiplicity obstructions are stronger than occurrence obstructions


Numerical Manufacturing And Design Tool (NuMAD) -- A design tool for wind and water turbine composite blades

Land-based wind turbines with flexible rail-transportable blades – Part 2: 3D finite element design  optimization of the rotor blades


Image Completion with Deep Learning in TensorFlow

Unsupervised Anomaly Detection with Generative Adversarial Networks to Guide Marker Discovery

Semantic Image Inpainting with Deep Generative Models

Digital Cardan Grille: A Modern Approach for Information Hiding


Python library for computing Finite-Amplitude Local Wave Activity from climate data.

Atmospheric blocking as a traffic jam in the jet stream

Local Finite-Amplitude Wave Activity as a Diagnostic of Anomalous Weather Events


ATOM3D: tasks on molecules in three dimensions

ATOM3D: Tasks On Molecules in Three Dimensions

AI in drug discovery and its clinical relevance

Pre-training of Equivariant Graph Matching Networks with Conformation
  Flexibility for Drug Binding

Pre-training Protein Models with Molecular Dynamics Simulations for Drug Binding


DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species
  Genome

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

Epigenomic language models powered by Cerebras

DNABERT-based explainable lncRNA identification in plant genome assemblies

Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings


Generate a dendrogram from a dataset

Investigating Fragmentation of Gas Structures in OB Cluster-forming Molecular Clump G33.92+0.11 with 1000 au Resolution Observations of ALMA

Structural and Dynamical Analysis of 0.1 pc Cores and Filaments in the 30 Doradus-10 Giant Molecular Cloud

Universal gravity-driven isothermal turbulence cascade in disk galaxies

A Parsec-scale Catalog of Molecular Clouds in the Solar Neighborhood Based on 3D Dust Mapping: Implications for the Mass–Size Relation


Open Energy Outlook for the United States


A high-performance Java Implementation of RDF2Vec

Semantic similarity and machine learning with ontologies

RDF2Vec Light -- A Lightweight Approach for Knowledge Graph Embeddings

Walk this Way! Entity Walks and Property Walks for RDF2vec

Putting RDF2vec in Order

Supervised Ontology and Instance Matching with MELT

The DLCC Node Classification Benchmark for Analyzing Knowledge Graph Embeddings

Refining Diagnosis Paths for Medical Diagnosis based on an Augmented
  Knowledge Graph

Ontology Matching Through Absolute Orientation of Embedding Spaces

Entity Type Prediction Leveraging Graph Walks and Entity Descriptions


Large Language Models Are Zero-Shot Time Series Forecasters

A decoder-only foundation model for time-series forecasting

Tiny Time Mixers (TTMs): Fast Pre-trained Models for Enhanced
  Zero/Few-Shot Forecasting of Multivariate Time Series

Unified Training of Universal Time Series Forecasting Transformers


Few-shot bioacoustic event detection at the DCASE 2022 challenge

Learning to detect an animal sound from five examples

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

Few-shot bioacoustic event detection at the DCASE 2023 challenge


An open-source toolbox for the evaluation of thermal response factors (g-functions) of geothermal borehole fields.


A framework for Big Data Optimization with multi-objective metaheuristics

jMetalSP: A framework for dynamic multi-objective big data optimization

Multi-objective Big Data Optimization with jMetal and Spark

InDM2: Interactive Dynamic Multi-Objective Decision Making Using Evolutionary Algorithms

Dynamic Multi-Objective Optimization with jMetal and Spark: A Case Study


Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

Building a PubMed knowledge graph

Probing Biomedical Embeddings from Language Models

Increase of stillbirth and decrease of late preterm infants during the COVID-19 pandemic lockdown

Archives of disease in childhood. Fetal and neonatal edition

Infusing Disease Knowledge into BERT for Health Question Answering, Medical Inference and Disease Name Recognition

FedED: Federated Learning via Ensemble Distillation for Medical Relation Extraction

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

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

Inexpensive Domain Adaptation of Pretrained Language Models: Case Studies on Biomedical NER and Covid-19 QA

Clinical Reading Comprehension: A Thorough Analysis of the emrQA Dataset

A pre-training and self-training approach for biomedical named entity recognition


Interactive GAN evolution of Mario and Zelda levels.

Interactive Evolution and Exploration Within Latent Level-Design Space of Generative Adversarial Networks

Tile pattern KL-divergence for analysing and evolving game levels

Proceedings of the Genetic and Evolutionary Computation Conference

Experience-Driven PCG via Reinforcement Learning: A Super Mario Bros Study

CPPN2GAN: Combining Compositional Pattern Producing Networks and GANs for Large-scale Pattern Generation

Hybrid Encoding for Generating Large Scale Game Level Patterns With Local Variations


SHallow shOtGUN profiler

Evaluating the Information Content of Shallow Shotgun Metagenomics

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

SHOGUN: a modular, accurate and scalable framework for microbiome quantification


Deep-learning based semantic and instance segmentation for 3D Electron Microscopy and other bioimage analysis problems based on pytorch.

Sparse Object-level Supervision for Instance Segmentation with Pixel Embeddings

Segment Anything for Microscopy

Structured Prediction Problem Archive


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


Official implementation of the TabPFN paper (https://arxiv.org/abs/2207.01848) and the tabpfn package.

TabPFN: A Transformer That Solves Small Tabular Classification Problems
  in a Second

Large Language Models for Automated Data Science: Introducing CAAFE for
  Context-Aware Automated Feature Engineering

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

Unlocking the Transferability of Tokens in Deep Models for Tabular Data

UniTabE: A Universal Pretraining Protocol for Tabular Foundation Model in Data Science


Minia is a short-read assembler based on a de Bruijn graph

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

HASLR: Fast Hybrid Assembly of Long Reads

Complete mitochondrial genome of the Antarctic copepod Tigriopus kingsejongenesis (Harpacticoida, Harpacticidae)

Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus) and their Blochmannia endosymbionts


A tensorflow library for building all kinds of models

Deep Residual Learning for Image Recognition

Very Deep Convolutional Networks for Large-Scale Image Recognition

U-Net: Convolutional Networks for Biomedical Image Segmentation

Densely Connected Convolutional Networks

Character-Based Text Classification using Top Down Semantic Model for Sentence Representation


Hybrid Asynchronous Decomposition Sampler prototype framework.

Accurate Computation of Relativistic Excitation Energies Using Quantum
  Annealing

Transit facility allocation: Hybrid quantum-classical optimization


folk music modelling with LSTM

Music transcription modelling and composition using deep learning

Artificial Intelligence and Music: Open Questions of Copyright Law and Engineering Praxis

Taking the Models back to Music Practice: Evaluating Generative Transcription Models built using Deep Learning

Explicitly Conditioned Melody Generation: A Case Study with Interdependent RNNs

On the encoding of natural music in computational models and human brains


中文自然语言处理工具包 Toolkit for Chinese natural language processing

Topic Memory Networks for Short Text Classification

Gated Recursive Neural Network for Chinese Word Segmentation

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

A Bilingual Attention Network for Code-switched Emotion Prediction

International Conference on Computational Linguistics

Applying deep matching networks to Chinese medical question answering: a study and a dataset

BMC medical informatics and decision making

Emotion Detection in Code-switching Texts via Bilingual and Sentimental Information

PROCEEDINGS OF THE 53RD ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS (ACL) AND THE 7TH INTERNATIONAL JOINT CONFERENCE ON NATURAL LANGUAGE PROCESSING (IJCNLP), VOL 2

Sentiment Classification towards Question-Answering with Hierarchical Matching Network

Empirical Methods in Natural Language Processing

Overview of the NLPCC 2015 Shared Task: Chinese Word Segmentation and POS Tagging for Micro-blog Texts


Optimal cutpoints in R: determining and validating optimal cutpoints in binary classification

Differential levels of plasma biomarkers of neurodegeneration in Lewy body dementia, Alzheimer’s disease, frontotemporal dementia and progressive supranuclear palsy

Journal of neurology, neurosurgery, and psychiatry

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

Prognostic and Therapeutic Potential of the OIP5 Network in Papillary Renal Cell Carcinoma

Prediction of Adrenocortical Carcinoma Relapse and Prognosis with a Set of Novel Multigene Panels

Oats Lower Age-Related Systemic Chronic Inflammation (iAge) in Adults at Risk for Cardiovascular Disease


A framework for Bayesian mixing models in R:

Spatial variability of sediment methane production and methanogen communities within a eutrophic reservoir: Importance of organic matter source and quantity

Limnology and oceanography/The l & o on cd-rom

A deconvolutional Bayesian mixing model approach for river basin sediment source apportionment

Coffee and shade trees show complementary use of soil water in a traditional agroforestry ecosystem

When the going gets tough, the tough get going: The enigma of survival strategies in harsh glacial stream environments

Phenological tracking associated with increased salmon consumption by brown bears

Food Web Structure and Trophic Dynamics of a Fish Community in an Ephemeral Floodplain Lake

Asymmetrical habitat coupling of an aquatic predator—The importance of individual specialization

Isotope hydrology and water sources in a heavily urbanized stream

Use of stable nitrogen isotopes to track plant uptake of nitrogen in a nature-based treatment system

Large contribution of pulsed subsidies to a predatory fish inhabiting large stream channels

Canadian journal of fisheries and aquatic sciences


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


Repository for TweetEval

BERTweet: A pre-trained language model for English Tweets

TweetEval: Unified Benchmark and Comparative Evaluation for Tweet Classification

TimeLMs: Diachronic Language Models from Twitter

A Holistic Approach to Undesired Content Detection in the Real World

Multilingual Detection of Personal Employment Status on Twitter

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

A curated dataset for hate speech detection on social media text

STTA: enhanced text classification via selective test-time augmentation

NUAA-QMUL-AIIT at Memotion 3: Multi-modal Fusion with
  Squeeze-and-Excitation for Internet Meme Emotion Analysis


[ICRA 2022] An opensource framework for cooperative detection. Official implementation for OPV2V.

PIXOR: Real-time 3D Object Detection from Point Clouds

Cooper: Cooperative Perception for Connected Autonomous Vehicles based on 3D Point Clouds

F-Cooper: Feature based Cooperative Perception for Autonomous Vehicle Edge Computing System Using 3D Point Clouds

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

OPV2V: An Open Benchmark Dataset and Fusion Pipeline for Perception with Vehicle-to-Vehicle Communication

The OpenCDA Open-Source Ecosystem for Cooperative Driving Automation Research

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


A versatile simulation and optimization platform for power-system planning and operations.


A circuit toolkit

Design Automation and Design Space Exploration for Quantum Computers

Logic Synthesis for Quantum Computing

Circuit optimization for IBM processors: A way to get higher fidelity and higher values of nonclassicality witnesses

Late Breaking Results: Reinforcement Learning for Scalable Logic Optimization with Graph Neural Networks


Ethereum contract for Bitcoin SPV: Live on https://etherscan.io/address/0x41f274c0023f83391de4e0733c609df5a124c3d4

A Survey on Blockchain Interoperability: Past, Present, and Future Trends

Enabling Cross-Chain Transactions: A Decentralized Cryptocurrency Exchange Protocol

Atomic Crosschain Transactions for Ethereum Private Sidechains

Towards Interoperable Blockchains: A Survey on the Role of Smart Contracts in Blockchain Interoperability

Survey of crosschain communications protocols

A Game-Theoretic Analysis of Cross-Chain Atomic Swaps with HTLCs

Anonymous State Pinning for Private Blockchains

Verifiable Computing Applications in Blockchain

An Electricity Cross-Chain Platform Based on Sidechain Relay

Verilay: A Verifiable Proof of Stake Chain Relay


R package for extracting and visualizing mutational patterns in base substitution catalogues

MutationalPatterns: comprehensive genome-wide analysis of mutational processes

Transient commensal clonal interactions can drive tumor metastasis

Stratification of HPV‐associated and HPV‐negative oropharyngeal squamous cell carcinomas based on DNA methylation epigenotypes

The cytidine deaminase APOBEC3G drives cancer mutagenesis and clonal evolution in bladder cancer

The chemotherapeutic drug CX-5461 is a potent mutagen in cultured human cells


SecMML (Queqiao): Secure MPC (multi-party computation) Machine Learning Framework.

Secure Quantized Training for Deep Learning

SoK: Training Machine Learning Models over Multiple Sources with Privacy Preservation

Private, Efficient, and Accurate: Protecting Models Trained by Multi-party Learning with Differential Privacy


The Open Images dataset

Efficient Processing of Deep Neural Networks: A Tutorial and Survey

ImageNet-trained CNNs are biased towards texture; increasing shape bias improves accuracy and robustness

The History Began from AlexNet: A Comprehensive Survey on Deep Learning
  Approaches

No Classification without Representation: Assessing Geodiversity Issues in Open Data Sets for the Developing World

Learning Intelligent Dialogs for Bounding Box Annotation

CT-SRCNN: Cascade Trained and Trimmed Deep Convolutional Neural Networks for Image Super Resolution

Learning Sparse Low-Precision Neural Networks With Learnable Regularization

Virtual-reality-based digital twin of office spaces with social distance measurement feature

Virtual reality & intelligent hardware/Xuni xianshi yu zhineng yingjian

The Deep Convolutional Neural Network Role in the Autonomous Navigation of Mobile Robots (SROBO)

VSE-ens: Visual-Semantic Embeddings with Efficient Negative Sampling


PyTorch implementation of the NIPS-17 paper "Poincaré Embeddings for Learning Hierarchical Representations"

Hyperbolic Neural Networks

Learning Continuous Hierarchies in the Lorentz Model of Hyperbolic Geometry

Unsupervised Hierarchy Matching with Optimal Transport over Hyperbolic Spaces

Robust Large-Margin Learning in Hyperbolic Space

Riemannian Adaptive Optimization Algorithm and Its Application to
  Natural Language Processing

Social centralization and semantic collapse: Hyperbolic embeddings of networks and text

Nested Subspace Arrangement for Representation of Relational Data

Unit Ball Model for Embedding Hierarchical Structures in the Complex Hyperbolic Space


An annotated implementation of the Transformer paper.

Attention Is All You Need

The Annotated Transformer

Proceedings of Workshop for NLP Open Source Software (NLP-OSS)

Recursive Graphical Neural Networks for Text Classification


Implements stochastic line search

Painless Stochastic Gradient: Interpolation, Line-Search, and Convergence Rates


Optical live-scan and ink fingerprint image quality assessment tool

Biometric Quality: Review and Application to Face Recognition with FaceQnet

Considerations on the Evaluation of Biometric Quality Assessment Algorithms


Design and Analysis of a Wake Steering Controller with Wind Direction Variability

A tutorial on the synthesis and validation of a closed-loop wind farm controller using a steady-state surrogate model

Model-based closed-loop wind farm control for power maximization using Bayesian Optimization: a large eddy simulation study

Zenodo (CERN European Organization for Nuclear Research)

Predicting the benefit of wake steering on the annual energy production of a wind farm using large eddy simulations and Gaussian process regression

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

Joint state-parameter estimation for a control-oriented LES wind farm model

Numerical Validation of Wind Plant Control Strategies

Actuator line model using simplified force calculation methods

The Importance of Wake Meandering on Wind Turbine Fatigue Loads in Wake

Distributed and Cooperative Control in Wind Farms

Optimal distribution width for ALM in LES for (NEW) MEXICO experiment

SCIENCE OF MAKING TORQUE FROM WIND (TORQUE 2018)


genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry

Rare compound heterozygous missense SPATA7 variations and risk of schizophrenia; whole-exome sequencing in a consanguineous family with affected siblings, follow-up sequencing and a case-control study

Impaired expression of metallothioneins contributes to allergen-induced inflammation in patients with atopic dermatitis


Package for local graph clustering

Flow-Based Local Graph Clustering with Better Seed Set Inclusion

p-Norm Flow Diffusion for Local Graph Clustering

Flow-based Algorithms for Improving Clusters: A Unifying Framework, Software, and Performance

Targeted pandemic containment through identifying local contact network bottlenecks

A Short Introduction to Local Graph Clustering Methods and Software


Creative Commons Attribution Share Alike 4.0 International

Open source remote sensing dataset with benchmarks


Static program analysis framework for Ethereum smart contract bytecode.

MadMax: surviving out-of-gas conditions in Ethereum smart contracts

Proceedings of the ACM on programming languages

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

International Conference on Software Engineering

Security Analysis Methods on Ethereum Smart Contract Vulnerabilities: A
  Survey

EtherSolve: Computing an Accurate Control-Flow Graph from Ethereum Bytecode

Smart Contract Vulnerability Detection Technique: A Survey

Standardising smart contracts: Automatically inferring ERC standards

Next-Paradigm Programming Languages: What Will They Look Like and What Changes Will They Bring?

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

Empirical Review of Smart Contract and DeFi Security: Vulnerability
  Detection and Automated Repair


ILSwiss is an Easy-to-run Imitation Learning (IL, or Learning from Demonstration, LfD) and also Reinforcement Learning (RL) framework (template) in PyTorch.

Plan Your Target and Learn Your Skills: Transferable State-Only
  Imitation Learning via Decoupled Policy Optimization

Curriculum Offline Imitation Learning


:microbe: A comprehensive R package for deep mining microbiome

MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Effects of Grass Silage Additive Type and Barley Grain Preservation Method on Rumen Fermentation, Microbial Community and Milk Production of Dairy Cows

Microbiota and Metabolite Modifications after Dietary Exclusion of Dairy Products and Reduced Consumption of Fermented Food in Young and Older Men

Taxonomic Diversity of the Microbial Biofilms Collected along the Thermal Streams on Kunashir Island

Gut Microbiota Alterations in Trace Amine-Associated Receptor 9 (TAAR9) Knockout Rats


TensorFlow implementation of "Image-to-Image Translation Using Conditional Adversarial Networks".

Image-to-Image Translation with Conditional Adversarial Networks

Conditional Generative Adversarial Networks for Speech Enhancement and Noise-Robust Speaker Verification

Fast Enhanced CT Metal Artifact Reduction Using Data Domain Deep Learning

Denoising Weak Lensing Mass Maps with Deep Learning

Nighttime Reflectance Generation in the Visible Band of Satellites

Deep Learning-Generated Nighttime Reflectance and Daytime Radiance of the Midwave Infrared Band of a Geostationary Satellite

This is not what I imagined: Error Detection for Semantic Segmentation through Visual Dissimilarity.

Deep learning for intensity mapping observations: component extraction

Monthly Notices of the Royal Astronomical Society: Letters


Long Range Arena for Benchmarking Efficient Transformers

FlashAttention: Fast and Memory-Efficient Exact Attention with
  IO-Awareness

Long Range Arena: A Benchmark for Efficient Transformers

Random Feature Attention

Flowformer: Linearizing Transformers with Conservation Flows

H-Transformer-1D: Fast One-Dimensional Hierarchical Attention for Sequences

Memory-efficient Transformers via Top-k Attention

Leveraging redundancy in attention with Reuse Transformers

On Learning the Transformer Kernel

PoNet: Pooling Network for Efficient Token Mixing in Long Sequences

Beyond Efficiency: A Systematic Survey of Resource-Efficient Large
  Language Models


Python/numpy bootstrap confidence interval estimation.

Stability of working memory in continuous attractor networks under the control of short-term plasticity

Numerical test of the Edwards conjecture shows that all packings are equally probable at jamming

The Drosophila microbiome has a limited influence on sleep, activity, and courtship behaviors

Elastic moduli fluctuations predict wave attenuation rates in glasses

CARPool: fast, accurate computation of large-scale structure statistics by pairing costly and cheap cosmological simulations

Monthly Notices of the Royal Astronomical Society

Crowdsourcing for translational research: analysis of biomarker expression using cancer microarrays

Fully automated leg tracking of Drosophila neurodegeneration models reveals distinct conserved movement signatures

Abstractive Compression of Captions with Attentive Recurrent Neural Networks

International Conference on Natural Language Generation


Circular visualization in R

Effect of high fat diet on phenotype, brain transcriptome and lipidome in Alzheimer’s model mice

Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics

Immune-mediated genetic pathways resulting in pulmonary function impairment increase lung cancer susceptibility

Identifying unknown Indian wolves by their distinctive howls: its potential as a non-invasive survey method

Genetic Architecture of Powdery Mildew Resistance Revealed by a Genome-Wide Association Study of a Worldwide Collection of Flax (Linum usitatissimum L.)

Climate change may induce connectivity loss and mountaintop extinction in Central American forests

Overview of Genomic Tools for Circular Visualization in next-Generation Genomic Sequencing Era

MetaMed: Linking Microbiota Functions with Medicine Therapeutics


Official implementations of PSENet, PAN and PAN++.

Efficient and Accurate Arbitrary-Shaped Text Detection with Pixel Aggregation Network

PAN++: Towards Efficient and Accurate End-to-End Spotting of Arbitrarily-Shaped Text

Turning a CLIP Model into a Scene Text Detector

FAST: Faster Arbitrarily-Shaped Text Detector with Minimalist Kernel
  Representation


Depends is a fast, comprehensive code dependency analysis tool

PyCG: Practical Call Graph Generation in Python

E-SC4R: Explaining Software Clustering for Remodularisation

Automated regression unit test generation for program merges

On the Opportunities of Green Computing: A Survey

Software Architecture Recovery with Information Fusion


Alex Dialogue Systems Framework

A Context-aware Natural Language Generator for Dialogue Systems

Annual Meeting of the Special Interest Group on Discourse and Dialogue

Off-line vs. On-line Evaluation of Recommender Systems in Small E-commerce

ACM Conference on Hypertext & Social Media

Free on-line speech recogniser based on Kaldi ASR toolkit producing word posterior lattices

Are the Multilingual Models Better? Improving Czech Sentiment with Transformers

Alex: Bootstrapping a Spoken Dialogue System for a New Domain by Real Users


Towards Multi-spatiotemporal-scale Generalized PDE Modeling

Clifford Neural Layers for PDE Modeling

PDE-Refiner: Achieving Accurate Long Rollouts with Neural PDE Solvers

Scalable Transformer for PDE Surrogate Modeling

Geometric Clifford Algebra Networks

Data efficiency and long term prediction capabilities for neural
  operator surrogate models of core and edge plasma codes


Open source Machine Learning library written in Java

Attentional multilabel learning over graphs: a message passing approach

Regularizing Model Complexity and Label Structure for Multi-Label Text Classification

Nearest Labelset Using Double Distances for Multi-label Classification


Winning Solution in NTIRE19 Challenges on Video Restoration and Enhancement (CVPR19 Workshops) - Video Restoration with Enhanced Deformable Convolutional Networks. EDVR has been merged into BasicSR and this repo is a mirror of BasicSR.

Deformable Convolutional Networks

EDVR: Video Restoration with Enhanced Deformable Convolutional Networks

Zooming Slow-Mo: Fast and Accurate One-Stage Space-Time Video Super-Resolution

MuCAN: Multi-Correspondence Aggregation Network for Video Super-Resolution

Understanding Deformable Alignment in Video Super-Resolution

Video Super Resolution Based on Deep Learning: A Comprehensive Survey

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


PyCIL: A Python Toolbox for Class-Incremental Learning

Overcoming catastrophic forgetting in neural networks

Learning without Forgetting

iCaRL: Incremental Classifier and Representation Learning

Gradient Episodic Memory for Continual Learning

Large Scale Incremental Learning

PODNet: Pooled Outputs Distillation for Small-Tasks Incremental Learning

Maintaining Discrimination and Fairness in Class Incremental Learning

DER: Dynamically Expandable Representation for Class Incremental Learning

Prototype Augmentation and Self-Supervision for Incremental Learning

FOSTER: Feature Boosting and Compression for Class-Incremental Learning


A fast multi-threaded k-mer counter

Predicting the impact of non-coding variants on DNA methylation

Chromosome-level assembly of the horseshoe crab genome provides insights into its genome evolution

High molecular weight glutenin gene diversity in Aegilops tauschii demonstrates unique origin of superior wheat quality

Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies

A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly

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

Fast Approximation of Frequent k-mers and Applications to Metagenomics

The chromosome-level genome of Gypsophila paniculata reveals the molecular mechanism of floral development and ethylene insensitivity

Natural Transformation of Riemerella columbina and Its Determinants

SPRISS: Approximating Frequent k-mers by Sampling Reads, and
  Applications


R package for modeling single cell UMI expression data using regularized negative binomial regression

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Spatial omics: Navigating to the golden era of cancer research

Single cell full-length transcriptome of human subcutaneous adipose tissue reveals unique and heterogeneous cell populations

Single cell qtSEQ: Cell-indexed quantitative and targeted RNA sequencing for sorted rare lymphocyte subpopulations

Cancer cell plasticity and MHC-II–mediated immune tolerance promote breast cancer metastasis to lymph nodes

The Journal of experimental medicine/The journal of experimental medicine

Dysregulated Cell–Cell Communication Characterizes Pulmonary Fibrosis

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq

Journal of translational genetics and genomics

Meta-analysis of single-cell and single-nucleus transcriptomics reveals kidney cell type consensus signatures

Single Cell Transcriptomic Analysis of the Identity and Function of Fibro/Adipogenic Progenitors in Healthy and Dystrophic Muscle


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

Empirical Methods in Natural Language Processing

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

PAC Prediction Sets for Meta-Learning

From Learning-to-Match to Learning-to-Discriminate:Global Prototype Learning for Few-shot Relation Classification

Ensemble Making Few-Shot Learning Stronger


Fast and accurate gene fusion detection from RNA-Seq data

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands

The landscape of chromothripsis across adult cancer types

Computational Oncology in the Multi-Omics Era: State of the Art

Modeling Clinical Responses to Targeted Therapies by Patient-Derived Organoids of Advanced Lung Adenocarcinoma

Clinical cancer research : an official journal of the American Association for Cancer Research

Next-Generation Sequencing Approaches for the Identification of Pathognomonic Fusion Transcripts in Sarcomas: The Experience of the Italian ACC Sarcoma Working Group

Unscrambling cancer genomes via integrated analysis of structural variation and copy number

The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi

NeoFuse: predicting fusion neoantigens from RNA sequencing data

Clinical application of whole transcriptome sequencing for the classification of patients with acute lymphoblastic leukemia


In defence of metric learning for speaker recognition

Pushing the limits of raw waveform speaker recognition

Graph Attention Networks for Speaker Verification

Three-class Overlapped Speech Detection using a Convolutional Recurrent Neural Network

ASVtorch toolkit: Speaker verification with deep neural networks

Magnitude-aware Probabilistic Speaker Embeddings

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

Baselines and Protocols for Household Speaker Recognition

On the potential of jointly-optimised solutions to spoofing attack detection and automatic speaker verification

A Multimodal Simultaneous Interpretation Prototype: Who Said What

Conference of the Association for Machine Translation in the Americas


Convolutional Neural Networks to predict the aesthetic and technical quality of images.

NIMA: Neural Image Assessment

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

Biometric Quality: Review and Application to Face Recognition with FaceQnet

CLIP knows image aesthetics


Single object tracking and segmentation.

Rethinking the competition between detection and ReID in Multi-Object
  Tracking

Learn to Match: Automatic Matching Network Design for Visual Tracking

One More Check: Making "Fake Background" Be Tracked Again

Towards Accurate Pixel-wise Object Tracking by Attention Retrieval

Divert More Attention to Vision-Language Tracking

WebUAV-3M: A Benchmark for Unveiling the Power of Million-Scale Deep UAV Tracking


Semi Supervised Learning for Medical Image Segmentation, a collection of literature reviews and code implementations.

Semi-supervised Learning for Network-Based Cardiac MR Image Segmentation

Medical Image Computing and Computer-Assisted Intervention

Deep Adversarial Networks for Biomedical Image Segmentation Utilizing Unannotated Images

Semi-Supervised Brain Lesion Segmentation with an Adapted Mean Teacher Model

Efficient Semi-supervised Gross Target Volume of Nasopharyngeal Carcinoma Segmentation via Uncertainty Rectified Pyramid Consistency

Semi-Supervised Medical Image Segmentation via Cross Teaching between
  CNN and Transformer

Mutual Consistency Learning for Semi-supervised Medical Image
  Segmentation

Uncertainty Guided Semi-supervised Segmentation of Retinal Layers in OCT Images

Local and Global Structure-Aware Entropy Regularized Mean Teacher Model for 3D Left Atrium Segmentation

Semi-supervised Segmentation of Liver Using Adversarial Learning with Deep Atlas Prior

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


List of gene lists for genomic analyses.

Transcript expression-aware annotation improves rare variant interpretation

Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes

CCR8-targeted specific depletion of clonally expanded Treg cells in tumor tissues evokes potent tumor immunity with long-lasting memory

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

Human and mouse essentiality screens as a resource for disease gene discovery

Transcript expression-aware annotation improves rare variant discovery and interpretation

The 3D mutational constraint on amino acid sites in the human proteome

Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing

Leveraging gene co-regulation to identify gene sets enriched for disease heritability

Human genetic analyses of organelles highlight the nucleus in age-related trait heritability


ANI-1 neural net potential with python interface (ASE)

Less is more: sampling chemical space with active learning

Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens

Journal of chemical theory and computation

Machine learning for protein folding and dynamics

Machine learning for molecular dynamics with strongly correlated electrons

Simple and efficient algorithms for training machine learning potentials
  to force data


Transformer-XL: Attentive Language Models Beyond a Fixed-Length Context

Stabilizing Transformers for Reinforcement Learning

Understanding and Improving Layer Normalization

Why are Adaptive Methods Good for Attention Models

A Constructive Prediction of the Generalization Error Across Scales

The Implicit and Explicit Regularization Effects of Dropout

Tensorized Embedding Layers for Efficient Model Compression

Recurrent Memory Transformer

Dynamic Evaluation of Transformer Language Models

Memory Transformer


Multiple-Instance Support Vector Machines

Attention-based Deep Multiple Instance Learning

Extracting microRNA-gene relations from biomedical literature using distant supervision

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data

Theory and Algorithms for Shapelet-Based Multiple-Instance Learning

Pain Intensity Estimation from Mobile Video Using 2D and 3D Facial Keypoints

pyLEMMINGS: Large Margin Multiple Instance Classification and Ranking for Bioinformatics Applications.


Variational Bayes HMM over x-vectors diarization

AISHELL-4: An Open Source Dataset for Speech Enhancement, Separation, Recognition and Speaker Diarization in Conference Scenario

Analysis of the BUT Diarization System for VoxConverse Challenge

BUT System Description for DIHARD Speech Diarization Challenge 2019

Magnitude-aware Probabilistic Speaker Embeddings

Multi-Stream Extension of Variational Bayesian HMM Clustering (MS-VBx) for Combined End-to-End and Vector Clustering-based Diarization

Separation Guided Speaker Diarization in Realistic Mismatched Conditions

Collar-aware Training for Streaming Speaker Change Detection in
  Broadcast Speech

The Newsbridge -Telecom SudParis VoxCeleb Speaker Recognition Challenge 2022 System Description


Allosaurus is a pretrained universal phone recognizer for more than 2000 languages

Universal Phone Recognition with a Multilingual Allophone System

Intent Classification Using Pre-Trained Embeddings For Low Resource Languages

Tusom2021: A Phonetically Transcribed Speech Dataset from an Endangered Language for Universal Phone Recognition Experiments


ROS 2 Navigation Framework and System

The Marathon 2: A Navigation System

Behavior Trees in Action: A Study of Robotics Applications

SROS2: Usable Cyber Security Tools for ROS 2

From the Desks of ROS Maintainers: A Survey of Modern & Capable Mobile
  Robotics Algorithms in the Robot Operating System 2

Regulated pure pursuit for robot path tracking

HuNavSim: A ROS 2 Human Navigation Simulator for Benchmarking Human-Aware Robot Navigation

Technical Development of the CeCi Social Robot

Portable Multi-Hypothesis Monte Carlo Localization for Mobile Robots

Autonomous Ground Navigation in Highly Constrained Spaces: Lessons
  learned from The 2nd BARN Challenge at ICRA 2023

Flexible Behavior Trees: In search of the mythical HFSMBTH for
  Collaborative Autonomy in Robotics


BNLP is a natural language processing toolkit for Bengali Language.

BNLP: Natural language processing toolkit for Bengali language

SAB at SemEval-2023 Task 2: Does Linguistic Information Aid in Named Entity Recognition?

Proceedings of the The 17th International Workshop on Semantic Evaluation (SemEval-2023)


Reformer, the efficient Transformer, in Pytorch

Reformer: The Efficient Transformer

GLU Variants Improve Transformer

ReZero is All You Need: Fast Convergence at Large Depth

Learning to Unknot

Long-Range Modeling of Source Code Files with eWASH: Extended Window Access by Syntax Hierarchy

ClusterFormer: Neural Clustering Attention for Efficient and Effective Transformer

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

A Comparative Analysis between Efficient Attention Mechanisms for Traffic Forecasting without Structural Priors


Real or Fake Text? Evaluation criteria for human-written and computer-generated text through the gamification of annotation. Published in EMNLP 2020.

Towards AI-Complete Question Answering: A Set of Prerequisite Toy Tasks

Automatic Detection of Generated Text is Easiest when Humans are Fooled

RoFT: A Tool for Evaluating Human Detection of Machine-Generated Text


Tools for the analysis of pulsar scintillation data

Precision Orbital Dynamics from Interstellar Scintillation Arcs for PSR J0437–4715

Modelling annual scintillation arc variations in PSR J1643-1224 using the Large European Array for Pulsars

Monthly notices of the Royal Astronomical Society

Probing the Local Interstellar Medium with Scintillometry of the Bright Pulsar B1133 + 16

The MSPSRπ catalogue: VLBA astrometry of 18 millisecond pulsars

Interstellar interferometry: precise curvature measurement from pulsar secondary spectra

A supernova remnant association for the fast-moving pulsar PSR J0908-4913

Monthly Notices of the Royal Astronomical Society: Letters

Analysis of the ionized interstellar medium and orbital dynamics of
  PSR~J1909-3744 using scintillation arcs

Orbital Dynamics and Extreme Scattering Event Properties from Long-term Scintillation Observations of PSR J1603−7202

Pulsar Double Lensing Sheds Light on the Origin of Extreme Scattering Events

High Resolution VLBI Astrometry of pulsar scintillation screens with the
  θ-θ Transform


Illumina analysis pipeline

An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity

Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis

In vivo cytidine base editing of hepatocytes without detectable off-target mutations in RNA and DNA

Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Antiviral treatment causes a unique mutational signature in cancers of transplantation recipients

Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

Molecular characterization of Barrett’s esophagus at single-cell resolution

A Single Complex Agpat2 Allele in a Patient With Partial Lipodystrophy

Somatic alterations compromised molecular diagnosis of DOCK8 hyper-IgE syndrome caused by a novel intronic splice site mutation

Preclinical Application of Conditional Reprogramming Culture System for Laryngeal and Hypopharyngeal Carcinoma


BSD 4-Clause "Original" or "Old" License

mechanoChemML library

Bayesian neural networks for weak solution of PDEs with uncertainty quantification

Label-free learning of elliptic partial differential equation solvers with generalizability across boundary value problems


A pure JavaScript medical research image viewer.

NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain

BrainBrowser: distributed, web-based neurological data visualization

Management and Quality Control of Large Neuroimaging Datasets: Developments From the Barcelonaβeta Brain Research Center

From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research

Mindcontrol: Organize, quality control, annotate, edit, and collaborate on neuroimaging processing results


Data-driven wavefront-based PSF modelling framework.

Rethinking data-driven point spread function modeling with a differentiable optical model

Rethinking the modeling of the instrumental response of telescopes with a differentiable optical model

Point spread function modelling for astronomical telescopes: a review focused on weak gravitational lensing studies

Frontiers in astronomy and space sciences


A python toolkit for rendering populations of dark matter halos for gravitational lensing simulations

Strong lensing signatures of self-interacting dark matter in low-mass haloes

The primordial matter power spectrum on sub-galactic scales

Quantum fluctuations masquerade as halos: Bounds on ultra-light dark
  matter from quadruply-imaged quasars

Constraining resonant dark matter self-interactions with strong gravitational lenses

Strong lensing constraints on primordial black holes as a dark matter candidate

Anisotropic strong lensing as a probe of dark matter self-interactions

An analytic surface density profile for ΛCDM halos and
  gravitational lensing studies


Deep learning model for predicting environmental variables on river systems


Python package for point cloud registration using probabilistic model (Coherent Point Drift, GMMReg, SVR, GMMTree, FilterReg, Bayesian CPD)

FilterReg: Robust and Efficient Probabilistic Point-Set Registration using Gaussian Filter and Twist Parameterization

An Adaptive Data Representation for Robust Point-Set Registration and Merging

International Conference on Computer Vision

Fast and Accurate Point Cloud Registration using Trees of Gaussian Mixtures

Comparison of 3D scan matching techniques for autonomous robot navigation in urban and agricultural environments

Best Buddies Registration for Point Clouds


An integrated high performance bioinformatics toolkit

Molecular identification of the wheat male fertility gene Ms1 and its prospects for hybrid breeding

Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy

Genetic Identification and Transcriptome Analysis of Lintless and Fuzzless Traits in Gossypium arboreum L.

International journal of molecular sciences

Reproductive Stage Drought Tolerance in Wheat: Importance of Stomatal Conductance and Plant Growth Regulators

Characterization and Genetic Mapping of Black Root Rot Resistance in Gossypium arboreum L.


Multi-scenario Extreme Weather Simulator (MEWS)


Line Modeling Engine

Water in star-forming regions (WISH): Physics and chemistry from clouds to disks as probed by Herschel spectroscopy

HAL (Le Centre pour la Communication Scientifique Directe)

Constraining Gas-phase Carbon, Oxygen, and Nitrogen in the IM Lup Protoplanetary Disk

The First Detection of 13C17O in a Protoplanetary Disk: A Robust Tracer of Disk Gas Mass

HOW DENSE IS YOUR GAS? ON THE RECOVERABILITY OF LVG MODEL PARAMETERS

Challenges and Techniques for Simulating Line Emission

Gravitational instabilities in a protosolar-like disc – II. Continuum emission and mass estimates

Monthly Notices of the Royal Astronomical Society

MAGRITTE, a modern software library for 3D radiative transfer: I. Non-LTE atomic and molecular line modelling

Arp 220: New Observational Insights into the Structure and Kinematics of the Nuclear Molecular Disks and Surrounding Gas

Synthetic line and continuum observations of simulated turbulent clouds: the apparent widths of filaments

A SUBLIME 3D Model for Cometary Coma Emission: The Hypervolatile-rich Comet C/2016 R2 (PanSTARRS)


Data Sets and Models for Evaluation of Lexical Semantic Change Detection

A Wind of Change: Detecting and Evaluating Lexical Semantic Change across Times and Domains

Simulating Lexical Semantic Change from Sense-Annotated Data

Discovery Team at SemEval-2020 Task 1: Context-sensitive Embeddings Not Always Better than Static for Semantic Change Detection

Zenodo (CERN European Organization for Nuclear Research)

BOS at SemEval-2020 Task 1: Word Sense Induction via Lexical Substitution for Lexical Semantic Change Detection

International Workshop on Semantic Evaluation

IMS at SemEval-2020 Task 1: How low can you go? Dimensionality in Lexical Semantic Change Detection

A collection of Swedish diachronic word embedding models trained on historical newspaper data

Effects of Pre- and Post-Processing on type-based Embeddings in Lexical Semantic Change Detection

JCT at SemEval-2020 Task 1: Combined Semantic Vector Spaces Models for Unsupervised Lexical Semantic Change Detection


Empirical Software Engineering journal (EMSE) open science and reproducible research initiative

Open Science in Software Engineering

Publish or perish, but do not forget your software artifacts

The open science initiative of the Empirical Software Engineering journal

Can we benchmark Code Review studies? A systematic mapping study of methodology, dataset, and metric

Quality Guidelines for Research Artifacts in Model-Driven Engineering

The Evolution of Code Review Research: A Systematic Mapping Study


KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

Diverse recruitment to a globally structured atmospheric microbiome

Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core

Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events

Leptospira enrichment culture followed by ONT metagenomic sequencing allows better detection of Leptospira presence and diversity in water and soil samples

LABRADOR—A Computational Workflow for Virus Detection in High-Throughput Sequencing Data

Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment

Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants

Frontiers in cellular and infection microbiology

Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks


High Quality Geophysical Analysis provides a general purpose Bayesian and deterministic inversion framework for various geophysical methods and spatially distributed / timeseries data

Bayesian inversion of marine CSEM data with a trans-dimensional self parametrizing algorithm

Trans-dimensional Bayesian inversion of airborne transient EM data from Taylor Glacier, Antarctica

Bayesian geophysical inversion with trans-dimensional Gaussian process machine learning

Bayesian inversion using nested trans-dimensional Gaussian processes


Creative Commons Attribution 4.0 International

Data, in citable form, produced by the Coudert research group

Heterometallic Metal–Organic Frameworks of MOF-5 and UiO-66 Families: Insight from Computational Chemistry

On the use of the IAST method for gas separation studies in porous materials with gate-opening behavior

Isolating the Role of the Node-Linker Bond in the Compression of UiO-66 Metal-Organic Frameworks

Emergence of Coupled Rotor Dynamics in Metal–Organic Frameworks via Tuned Steric Interactions

Journal of the American Chemical Society

Chiral Lanthanum Metal-Organic Framework with Gated CO2 Sorption and Concerted Framework Flexibility

van der Waals forces stabilize low-energy polymorphism in B2O3: Implications for the crystallization anomaly

Conformational chiral polymorphism in cis-bis-triphenylphosphine complexes of transition metals


Simple DAOPHOT-type photometry in Python translated from IDL AstroLib photometry algorithms.  Please email me with bugs, suggestions, omissions, etc.  The code is citable as part of the Astrophysics Source Code Library (http://ascl.net/1501.010).

DEJA VU ALL OVER AGAIN: THE REAPPEARANCE OF SUPERNOVA REFSDAL

ILLUMINATING A DARK LENS: A TYPE Ia SUPERNOVA MAGNIFIED BY THE FRONTIER FIELDS GALAXY CLUSTER ABELL 2744

SN REFSDAL: PHOTOMETRY AND TIME DELAY MEASUREMENTS OF THE FIRST EINSTEIN CROSS SUPERNOVA

Searching for Highly Magnified Stars at Cosmological Distances: Discovery of a Redshift 0.94 Blue Supergiant in Archival Images of the Galaxy Cluster MACS J0416.1-2403

Two Peculiar Fast Transients in a Strongly Lensed Host Galaxy

The Magnificent Five Images of Supernova Refsdal: Time Delay and Magnification Measurements

GRAWITA: VLT Survey Telescope observations of the gravitational wave sources GW150914 and GW151226

Target-of-Opportunity Observation Detectability of Kilonovae with WFST

Linear and Circular Polarimetry of the Optically Bright Relativistic Tidal Disruption Event AT 2022cmc


Recurrent Models of Visual Attention

Deep Attention Recurrent Q-Network

Learning from the memory of Atari 2600


Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)

The longitudinal dynamics and natural history of clonal haematopoiesis

The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Tumor to normal single cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer

Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning

Targeting MEK in vemurafenib-resistant hairy cell leukemia

Genomic consequences of domestication of the Siamese fighting fish

Clonal haematopoiesis is not prevalent in survivors of childhood cancer

Precise identification of cancer cells from allelic imbalances in single cell transcriptomes


The versatile ocean simulator, in pure Python, powered by JAX.

Veros v0.1 – a fast and versatile ocean simulator in pure Python

Fast, Cheap, and Turbulent—Global Ocean Modeling With GPU Acceleration in Python

Journal of advances in modeling earth systems

Ice core evidence for major volcanic eruptions at the onset of Dansgaard-Oeschger warming events

Differentiable Physics: A Position Piece


A Python Spectral Typing Suite

An Empirical Template Library of Stellar Spectra for a Wide Range of Spectral Classes, Luminosity Classes, and Metallicities Using SDSS BOSS Spectra

The Astrophysical journal. Supplement series/Astrophysical journal. Supplement series

Classifying Single Stars and Spectroscopic Binaries Using Optical Stellar Templates

TOI-2257 b: A highly eccentric long-period sub-Neptune transiting a nearby M dwarf

An Optical and X-Ray Study of the Contact Binary, BH Cassiopeiae

Publications of the Astronomical Society of the Pacific

Stars and brown dwarfs in the sigma Orionis cluster. IV. IDS/INT and OSIRIS/GTC spectroscopy and Gaia DR2 astrometry

Collisions of Terrestrial Worlds: The Occurrence of Extreme Mid-infrared Excesses around Low-mass Field Stars

Serendipitous discovery of radio flaring behaviour from a nearby M dwarf with MeerKAT

A Long-period Pre-ELM System Discovered from the LAMOST Medium-resolution Survey

A correction method for the telluric absorptions and application to Lijiang Observatory


Sokoban environment for OpenAI Gym

The Truth is in There: Improving Reasoning in Language Models with
  Layer-Selective Rank Reduction

There Is No Turning Back: A Self-Supervised Approach for Reversibility-Aware Reinforcement Learning

BabyAI 1.1

Scaling All-Goals Updates in Reinforcement Learning Using Convolutional Neural Networks

Transfer Learning and Curriculum Learning in Sokoban

Learning the Arrow of Time

Causal Reinforcement Learning: A Survey

Optimize Planning Heuristics to Rank, not to Estimate Cost-to-Goal

Potential-based Reward Shaping in Sokoban


An interactive web-tool for RNA-seq analysis

A chemical biology toolbox to study protein methyltransferases and epigenetic signaling

AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species

Dissecting the RecA-(In)dependent Response to Mitomycin C in Mycobacterium tuberculosis Using Transcriptional Profiling and Proteomics Analyses

The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus

Neuronally enriched microvesicle RNAs are differentially expressed in the serums of Parkinson’s patients

Heterogeneous Tfh cell populations that develop during enteric helminth infection predict the quality of type 2 protective response


Python halo mass function calculator

The Dearth of z~10 Galaxies in all HST Legacy Fields -- The Rapid
  Evolution of the Galaxy Population in the First 500 Myr

HMFcalc: An Online Tool for Calculating Dark Matter Halo Mass Functions

The halo model as a versatile tool to predict intrinsic alignments

The Rest-frame Optical (900 nm) Galaxy Luminosity Function atz∼ 4–7: Abundance Matching Points to Limited Evolution in theMSTAR/MHALORatio atz≥ 4

A model for multiproperty galaxy cluster statistics

How well do we know the halo mass function?

On the contribution of fluorescence to Lyα halos (LAHs) around
  star forming galaxies

The impact of scatter in the galaxy UV luminosity to halo mass relation on Ly α visibility during the epoch of reionization

The Massive and Distant Clusters of WISE Survey: MOO J1142+1527, A
  10^15 M_⊙ Galaxy Cluster at z=1.19

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


Collection of most color palettes in a single R package

Biotin pathway in novel Fodinibius salsisoli sp. nov., isolated from hypersaline soils and reclassification of the genus Aliifodinibius as Fodinibius

A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils

Genome assembly of three AmazonianMorphobutterfly species reveals Z-chromosome rearrangements between closely-related species living in sympatry


Various speech datasets made available to the public

Earnings-21: A Practical Benchmark for ASR in the Wild

Earnings-22: A Practical Benchmark for Accents in the Wild


Quality control, filtering, feature labeling, and other tools for working with data from photovoltaic energy systems.

Generation of Data-Driven Expected Energy Models for Photovoltaic Systems


An index of algorithms for offline reinforcement learning (offline-rl)

CORL: Research-oriented Deep Offline Reinforcement Learning Library

Reinforcement Learning and Bandits for Speech and Language Processing:
  Tutorial, Review and Outlook


Resources for the "SummEval: Re-evaluating Summarization Evaluation" paper

Factual Consistency Evaluation for Text Summarization via Counterfactual Estimation

Bidimensional Leaderboards: Generate and Evaluate Language Hand in Hand

Human Evaluation and Correlation with Automatic Metrics in Consultation Note Generation

Of Human Criteria and Automatic Metrics: A Benchmark of the Evaluation of Story Generation

How Ready are Pre-trained Abstractive Models and LLMs for Legal Case
  Judgement Summarization?

Investigating Entropy for Extractive Document Summarization

Multi-Dimensional Evaluation of Text Summarization with In-Context Learning

Is human scoring the best criteria for summary evaluation?

Reference-free Summarization Evaluation via Semantic Correlation and Compression Ratio

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


ERMIA: Memory-Optimized OLTP engine for Heterogeneous Workloads (SIGMOD 2016)

ERMIA: Fast Memory-Optimized Database System for Heterogeneous Workloads

SIGMOD'16: PROCEEDINGS OF THE 2016 INTERNATIONAL CONFERENCE ON MANAGEMENT OF DATA

Efficiently making (almost) any concurrency control mechanism serializable

An analysis of concurrency control protocols for in-memory databases with CCBench

CoroBase: Coroutine-Oriented Main-Memory Database Engine


Plug and Play Language Model implementation. Allows to steer topic and attributes of GPT-2 models.

Plug and Play Language Models: A Simple Approach to Controlled Text Generation

Authorship Attribution for Neural Text Generation

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

With Little Power Comes Great Responsibility

A Distributional Approach to Controlled Text Generation

TURINGBENCH: A Benchmark Environment for Turing Test in the Age of Neural Text Generation

Mix and Match: Learning-free Controllable Text Generationusing Energy Language Models

Detecting computer-generated disinformation

International journal of data science and analytics

Fine-Grained Controllable Text Generation Using Non-Residual Prompting

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

Ask what's missing and what's useful: Improving Clarification Question Generation using Global Knowledge

Tailor: A Prompt-Based Approach to Attribute-Based Controlled Text
  Generation


Reduce - tool for adding and correcting hydrogens in PDB files

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

EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction

Machine Learning to Identify Flexibility Signatures of Class A GPCR Inhibition

Modeling Molecular Structures with Intrinsic Diffusion Models

DSDP: A Blind Docking Strategy Accelerated by GPUs

Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and
  Binding Site Design


DTW (Dynamic Time Warping) python module

Data-driven unsupervised clustering of online learner behaviour

Mapping Paddy Rice Using Weakly Supervised Long Short-Term Memory Network with Time Series Sentinel Optical and SAR Images

ECG Adapted Fastest Route Algorithm to Localize the Ectopic Excitation Origin in CRT Patients

EyeTAP: Introducing a multimodal gaze-based technique using voice inputs with a comparative analysis of selection techniques

International journal of human-computer studies

Scalable Comparison of JavaScript V8 Bytecode Traces

PROCEEDINGS OF THE 11TH ACM SIGPLAN INTERNATIONAL WORKSHOP ON VIRTUAL MACHINES AND INTERMEDIATE LANGUAGES (VMIL '19)


PiML (Python Interpretable Machine Learning) toolbox for model development & diagnostics

GAMI-Net: An explainable neural network based on generalized additive models with structured interactions

Unwrapping The Black Box of Deep ReLU Networks: Interpretability,
  Diagnostics, and Simplification

Designing Inherently Interpretable Machine Learning Models

PiML Toolbox for Interpretable Machine Learning Model Development and
  Diagnostics


RoutingKit is a C++ library that provides advanced route planning functionality.

Scalable and Congestion-aware Routing for Autonomous Mobility-on-Demand via Frank-Wolfe Optimization

Faster and Better Nested Dissection Orders for Customizable Contraction Hierarchies

Efficient Route Planning with Temporary Driving Bans, Road Closures, and Rated Parking Areas

Fast, Exact and Scalable Dynamic Ridesharing

Simulating the Impact of Dynamic Rerouting on Metropolitan-scale Traffic Systems

Fast Many-to-Many Routing for Ridesharing with Multiple Pickup and
  Dropoff Locations

Nearest-Neighbor Queries in Customizable Contraction Hierarchies and Applications

A Fast and Tight Heuristic for A* in Road Networks

More Hierarchy in Route Planning Using Edge Hierarchies

Combining Predicted and Live Traffic with Time-Dependent A* Potentials


Fluid Earth is a WebGL-powered visualization of Earth's atmosphere and oceans


:no_entry: ARCHIVED :no_entry: Wraps UMAP Algorithm for Dimension Reduction

UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions

Ret deficiency decreases neural crest progenitor proliferation and restricts fate potential during enteric nervous system development

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


Evaluating Robustness of Neural Networks with Mixed Integer Programming

Provable defenses against adversarial examples via the convex outer adversarial polytope

Certified Defenses against Adversarial Examples

Algorithms for Verifying Deep Neural Networks

A Review of Formal Methods applied to Machine Learning

Global optimization of objective functions represented by ReLU networks

Training Provably Robust Models by Polyhedral Envelope Regularization

Rethinking Empirical Evaluation of Adversarial Robustness Using First-Order Attack Methods


Probabilistic Torch is library for deep generative models that extends PyTorch

Semi-Supervised Learning with Deep Generative Models

Learning Disentangled Representations with Semi-Supervised Deep Generative Models

Structured Disentangled Representations

Bayesian Layers: A Module for Neural Network Uncertainty


Global Biotic Interactions provides access to existing species interaction datasets


An efficient browser extension to block browser-based cryptocurrency miners all over the web.

SoK: Cryptojacking Malware

Cryptomining makes noise: Detecting cryptojacking via Machine Learning

Truth in Web Mining: Measuring the Profitability and Cost of Cryptominers as a Web Monetization Model

CoinPolice:Detecting Hidden Cryptojacking Attacks with Neural Networks


TLX - A Collection of Sophisticated C++ Data Structures, Algorithms, and Miscellaneous Helpers

A Critical Analysis of Recursive Model Indexes

Order-Preserving Key Compression for In-Memory Search Trees

There is No Such Thing as an "Index"! or: The next 500 Indexing Papers

Dynamic Interleaving of Content and Structure for Robust Indexing of Semi-Structured Hierarchical Data

Fine-Tuning Data Structures for Analytical Query Processing


Python tools for the Regional Ocean Modeling System (ROMS)


Flood Python Toolbox

FLOMPY: An Open-Source Toolbox for Floodwater Mapping Using Sentinel-1 Intensity Time Series


BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining

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

The Social Impact of Generative AI: An Analysis on ChatGPT

Proceedings of the 2023 ACM Conference on Information Technology for Social Good


A library for building an in-memory, Adaptive Learned indEX

ALEX: An Updatable Adaptive Learned Index

SIGMOD'20: PROCEEDINGS OF THE 2020 ACM SIGMOD INTERNATIONAL CONFERENCE ON MANAGEMENT OF DATA

DILI: A Distribution-Driven Learned Index

Micro-architectural Analysis of a Learned Index


Django-based clone of Amazon's Mechanical Turk service running in your local environment.

FinQA: A Dataset of Numerical Reasoning over Financial Data

ConvFinQA: Exploring the Chain of Numerical Reasoning in Conversational Finance Question Answering

Collecting Verified COVID-19 Question Answer Pairs

Empirical Methods in Natural Language Processing

Laughter Synthesis: Combining Seq2seq modeling with Transfer Learning

Analysis and Assessment of Controllability of an Expressive Deep Learning-based TTS system

Machine Translation Believability

OpenRT: An Open-source Framework for Reasoning Over Tabular Data

Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations)

Building OCR/NER Test Collections

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

VizAI : Selecting Accurate Visualizations of Numerical Data

ICE-Talk 2: Interface for Controllable Expressive TTS with perceptual assessment tool


DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort

Whole-genome CNV analysis: advances in computational approaches

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features

Parliament2: Accurate structural variant calling at scale

Structure-function analysis of oncogenic EGFR Kinase Domain Duplication reveals insights into activation and a potential approach for therapeutic targeting

Analysis pipelines for cancer genome sequencing in mice

Reference SVA insertion polymorphisms are associated with Parkinson’s Disease progression and differential gene expression

bric à brac controls sex pheromone choice by male European corn borer moths

PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes


The most accurate natural language detection library for Java and the JVM, suitable for long and short text alike

ActiveAnno: General-Purpose Document-Level Annotation Tool with Active Learning Integration

North American Chapter of the Association for Computational Linguistics

Cross-lingual citations in English papers: a large-scale analysis of prevalence, usage, and impact

QCRI's COVID-19 Disinformation Detector: A System to Fight the COVID-19 Infodemic in Social Media

DetectiveRedasers at ArAIEval Shared Task: Leveraging Transformer Ensembles for Arabic Deception Detection

You were saying? -- Spoken Language in the V3C Dataset

ReDASPersuasion at ArAIEval Shared Task: Multilingual and Monolingual Models For Arabic Persuasion Detection


Simple oligo analysis and primer design

Characterizing mobile element insertions in 5675 genomes

ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing

The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity


A (mostly) universal methylation extractor for BS-seq experiments.

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA

Retention of paternal DNA methylome in the developing zebrafish germline

Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha

Next-Generation Sequencing Technology: Current Trends and Advancements

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective

SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells

BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects

International journal of molecular sciences

WEE1 inhibition induces anti-tumor immunity by activating ERV and the dsRNA pathway

The Journal of experimental medicine/The journal of experimental medicine

The sperm epigenome does not display recurrent epimutations in patients with severely impaired spermatogenesis


ATAC-seq and DNase-seq processing pipeline

Unsupervised clustering and epigenetic classification of single cells

Accurate prediction of cell type-specific transcription factor binding

A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

TRPS1 shapes YAP/TEAD-dependent transcription in breast cancer cells

An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development

Modulating Androgen Receptor-Driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors

GimmeMotifs: an analysis framework for transcription factor motif analysis

Dynamic Erasure of Random X-Chromosome Inactivation during iPSC Reprogramming

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances cell-state reprogramming towards epithelial lineages

Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals


Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

High performance of targeted next generation sequencing on variance detection in clinical tumor specimens in comparison with current conventional methods

Journal of experimental & clinical cancer research : CR

SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling

The clonal evolution of metastatic colorectal cancer

Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells

The cytidine deaminase APOBEC3G drives cancer mutagenesis and clonal evolution in bladder cancer

Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures

Whole genome sequencing and its applications in medical genetics

FLT3-ITD Measurable Residual Disease Monitoring in Acute Myeloid Leukemia Using Next-Generation Sequencing


An efficient implementation of the popular sequence models for text generation, summarization, and translation tasks. https://arxiv.org/pdf/2106.04718.pdf

BART: Denoising Sequence-to-Sequence Pre-training for Natural Language
  Generation, Translation, and Comprehension

AMMUS : A Survey of Transformer-based Pretrained Models in Natural Language Processing

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

FastSeq: Make Sequence Generation Faster

EL-Attention: Memory Efficient Lossless Attention for Generation


Code release for ConvNeXt model

A ConvNet for the 2020s

More ConvNets in the 2020s: Scaling up Kernels Beyond 51x51 using
  Sparsity

A Simple and Effective Pruning Approach for Large Language Models

What Makes Convolutional Models Great on Long Sequence Modeling?

Revisiting Adversarial Training for ImageNet: Architectures, Training
  and Generalization across Threat Models

Alias-Free Convnets: Fractional Shift Invariance via Polynomial Activations

TOAST: Transfer Learning via Attention Steering

Robust Semantic Segmentation: Strong Adversarial Attacks and Fast
  Training of Robust Models

Receptive Field Refinement for Convolutional Neural Networks Reliably
  Improves Predictive Performance

VisDA 2022 Challenge: Domain Adaptation for Industrial Waste Sorting


A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Metformin Restores CNS Remyelination Capacity by Rejuvenating Aged Stem Cells

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

The Implication of Early Chromatin Changes in X Chromosome Inactivation

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

RNA m6 A modification enzymes shape innate responses to DNA by regulating interferon β.

Viable bacterial colonization is highly limited in the human intestine in utero

Transcriptome Assembly and Profiling of Candida auris Reveals Novel Insights into Biofilm-Mediated Resistance


Open-source framework for uncertainty and deep learning models in PyTorch :seedling:

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

mixup: Beyond Empirical Risk Minimization

Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles

Weight Uncertainty in Neural Networks

Evidential Deep Learning to Quantify Classification Uncertainty

BatchEnsemble: An Alternative Approach to Efficient Ensemble and Lifelong Learning

Deep Evidential Regression

Bayesian Uncertainty Estimation for Batch Normalized Deep Networks

Training independent subnetworks for robust prediction

Filter Response Normalization Layer: Eliminating Batch Dependence in the Training of Deep Neural Networks


Openai style api for open large language models, using LLMs just as chatgpt! Support for LLaMA, LLaMA-2, BLOOM, Falcon, Baichuan, Qwen, Xverse, SqlCoder, CodeLLaMA, ChatGLM, ChatGLM2, ChatGLM3 etc. 开源大模型的统一后端接口

LLaMA: Open and Efficient Foundation Language Models

BLOOM: A 176B-Parameter Open-Access Multilingual Language Model

A Survey of Large Language Models


SPINN (Stack-augmented Parser-Interpreter Neural Network): fast, batchable, context-aware TreeRNNs

Right for the Wrong Reasons: Diagnosing Syntactic Heuristics in Natural Language Inference

A Fast Unified Model for Parsing and Sentence Understanding

RNNs Implicitly Implement Tensor Product Representations


HAKE-Action in PyTorch

PaStaNet: Toward Human Activity Knowledge Engine

HOI Analysis: Integrating and Decomposing Human-Object Interaction

HAKE: Human Activity Knowledge Engine

HAKE: A Knowledge Engine Foundation for Human Activity Understanding


PyTorch code and models for the DINOv2 self-supervised learning method.

DINOv2: Learning Robust Visual Features without Supervision

Vision Transformers Need Registers

A General-Purpose Self-Supervised Model for Computational Pathology

Navigating Text-To-Image Customization:From LyCORIS Fine-Tuning to Model
  Evaluation

Very high resolution canopy height maps from RGB imagery using self-supervised vision transformer and convolutional decoder trained on aerial lidar

Does Progress On Object Recognition Benchmarks Improve Real-World
  Generalization?

Advancing Pose-Guided Image Synthesis with Progressive Conditional
  Diffusion Models

ENIGMA-51: Towards a Fine-Grained Understanding of Human-Object
  Interactions in Industrial Scenarios

Synchronization is All You Need: Exocentric-to-Egocentric Transfer for
  Temporal Action Segmentation with Unlabeled Synchronized Video Pairs

RAD-DINO: Exploring Scalable Medical Image Encoders Beyond Text
  Supervision


Representation learning on large graphs using stochastic graph convolutions.

Inductive Representation Learning on Large Graphs

DeepWalk: Online Learning of Social Representations

PROCEEDINGS OF THE 20TH ACM SIGKDD INTERNATIONAL CONFERENCE ON KNOWLEDGE DISCOVERY AND DATA MINING (KDD'14)

A Comprehensive Survey on Graph Neural Networks

IEEE transactions on neural networks and learning systems

Graph Neural Networks: A Review of Methods and Applications

FastGCN: Fast Learning with Graph Convolutional Networks via Importance Sampling

Deep Learning on Graphs: A Survey

Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks

GraphSAINT: Graph Sampling Based Inductive Learning Method

Inductive Representation Learning on Temporal Graphs

Representation Learning for Dynamic Graphs: A Survey