Assignment of known mutational signatures to individual samples and individual somatic mutations

Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment


:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

HPV Sequencing Facilitates Ultrasensitive Detection of HPV Circulating Tumor DNA

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

MinION nanopore sequencing identifies the position and structure of bacterial antibiotic resistance determinants in a multidrug-resistant strain of enteroaggregative Escherichia coli

A Bidimensional Segregation Mode Maintains Symbiont Chromosome Orientation toward Its Host

Isolation and characterization of vB_XciM_LucasX, a new jumbo phage that infects Xanthomonas citri and Xanthomonas fuscans


MeteoInfo: GIS, scientific computation and visualization environment.


PrefRec: Recommender Systems with Human Preferences for Reinforcing Long-term User Engagement

ResAct: Reinforcing Long-term Engagement in Sequential Recommendation
  with Residual Actor


A flexible framework for rapid genome analysis and interpretation

One-step generation of complete gene knockout mice and monkeys by CRISPR/Cas9-mediated gene editing with multiple sgRNAs

Mapping and characterization of structural variation in 17,795 human genomes

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

CRISPR/Cas9-mediated targeted chromosome elimination

NGSeasy: a next generation sequencing pipeline in Docker containers

The Fusion of CLEC12A and MIR223HG Arises from a trans-Splicing Event in Normal and Transformed Human Cells

International journal of molecular sciences

DNAscan: a fast, computationally and memory efficient bioinformatics pipeline for the analysis of DNA next-generation-sequencing data


Automated machine learning (AutoML) with grammar-based genetic programming

Evolution of Scikit-Learn Pipelines with Dynamic Structured Grammatical Evolution

The Technological Emergence of AutoML: A Survey of Performant Software and Applications in the Context of Industry


Tools for using fonts in R graphics

Insects and associated arthropods analyzed during medicolegal death investigations in Harris County, Texas, USA: January 2013- April 2016

Identification of Quantitative Trait Loci Relating to Flowering Time, Flag Leaf and Awn Characteristics in a Novel Triticum dicoccum Mapping Population

Environmental Controls of Size Distribution of Modern Planktonic Foraminifera in the Tropical Indian Ocean


COVID-CT-Dataset: A CT Scan Dataset about COVID-19

U-Net and Its Variants for Medical Image Segmentation: A Review of Theory and Applications

Sample-Efficient Deep Learning for COVID-19 Diagnosis Based on CT Scans

A deep transfer learning model with classical data augmentation and CGAN to detect COVID-19 from chest CT radiography digital images

COVID-19 open source data sets: a comprehensive survey

Dynamic Fusion based Federated Learning for COVID-19 Detection

Automated Detection and Forecasting of COVID-19 using Deep Learning Techniques: A Review

Efficient deep learning approach for augmented detection of Coronavirus disease

Momentum contrastive learning for few-shot COVID-19 diagnosis from chest CT images

Identifying COVID19 from Chest CT Images: A Deep Convolutional Neural Networks Based Approach


MedTagger is a light weight clinical NLP system built upon Apache UIMA.

COVID-19 SignSym: a fast adaptation of a general clinical NLP tool to identify and normalize COVID-19 signs and symptoms to OMOP common data model

Journal of the American Medical Informatics Association : JAMIA

Extracting COVID-19 diagnoses and symptoms from clinical text: A new annotated corpus and neural event extraction framework

An aberration detection-based approach for sentinel syndromic surveillance of COVID-19 and other novel influenza-like illnesses

medRxiv : the preprint server for health sciences

An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C)

A fast, resource efficient, and reliable rule-based system for COVID-19 symptom identification

Extraction of Sleep Information from Clinical Notes of Alzheimer's Disease Patients Using Natural Language Processing


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

ShapeWorld - A new test methodology for multimodal language understanding

Multimodality in Meta-Learning: A Comprehensive Survey

Deep learning evaluation using deep linguistic processing

SLASH: Embracing Probabilistic Circuits into Neural Answer Set
  Programming

Scalable Neural-Probabilistic Answer Set Programming


Lightweight nudity detection

Erasing Concepts from Diffusion Models

Safe Latent Diffusion: Mitigating Inappropriate Degeneration in Diffusion Models

FLIRT: Feedback Loop In-context Red Teaming

Holistic Evaluation of Text-To-Image Models

Visual Writing Prompts: Character-Grounded Story Generation with Curated Image Sequences

Towards Safe Self-Distillation of Internet-Scale Text-to-Image Diffusion
  Models

Mind-proofing Your Phone: Navigating the Digital Minefield with GreaseTerminator

MemeCap: A Dataset for Captioning and Interpreting Memes

Mitigating Inappropriateness in Image Generation: Can there be Value in
  Reflecting the World's Ugliness?

MilaNLP at SemEval-2022 Task 5: Using Perceiver IO for Detecting Misogynous Memes with Text and Image Modalities

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


Netperf is a benchmark that can be used to measure the performance of many different types of networking. It provides tests for both unidirectional throughput, and end-to-end latency.

IoT-KEEPER: Securing IoT Communications in Edge Networks

Benchmarking tunnel and encryption methodologies in cloud environments


Py-SPHViewer is a framework for rendering cosmological simulations in Python using the Smoothed Particle Hydrodynamics scheme.

Universal structure of dark matter haloes over a mass range of 20 orders of magnitude

Einasto profiles and the dark matter power spectrum

Monthly notices of the Royal Astronomical Society. Letters

Pericentric passage-driven star formation in satellite galaxies and their hosts: CLUES from local group simulations

Monthly Notices of the Royal Astronomical Society


Flexible audio loudness meter in Python with implementation of ITU-R BS.1770-4 loudness algorithm

LibriMix: An Open-Source Dataset for Generalizable Speech Separation

Surfboard: Audio Feature Extraction for Modern Machine Learning

HUI-Audio-Corpus-German: A high quality TTS dataset

CLEAR: A Dataset for Compositional Language and Elementary Acoustic Reasoning.


Largest realworld open-source graph dataset - Worked done under IBM-Illinois Discovery Accelerator Institute and Amazon Research Awards and in collaboration with NVIDIA Research.

Semi-Supervised Classification with Graph Convolutional Networks

Graph Attention Networks

Inductive Representation Learning on Large Graphs

Demystifying Structural Disparity in Graph Neural Networks: Can One Size
  Fit All?

IGB: Addressing The Gaps In Labeling, Features, Heterogeneity, and Size of Public Graph Datasets for Deep Learning Research


A surrogate benchmark for neural architecture search

How Powerful are Performance Predictors in Neural Architecture Search?

Surrogate NAS Benchmarks: Going Beyond the Limited Search Spaces of
  Tabular NAS Benchmarks

Speedy Performance Estimation for Neural Architecture Search

NAS-Bench-x11 and the Power of Learning Curves

NAS-Bench-Suite-Zero: Accelerating Research on Zero Cost Proxies

On Redundancy and Diversity in Cell-based Neural Architecture Search

Approximate Neural Architecture Search via Operation Distribution Learning


Policy learning via doubly robust empirical welfare maximization over trees

Efficient Policy Learning

Offline Multi-Action Policy Learning: Generalization and Optimization

Learning Optimal Prescriptive Trees from Observational Data

Using causal forests to assess heterogeneity in cost-effectiveness analysis


The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

The water lily genome and the early evolution of flowering plants

A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

The genome of broomcorn millet

Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution

The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish

Genomic basis of homoploid hybrid speciation within chestnut trees

High-depth resequencing reveals hybrid population and insecticide resistance characteristics of fall armyworm (Spodoptera frugiperda) invading China

Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation

The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation


X Inertial-aided Visual Odometry

Unsupervised Depth Completion from Visual Inertial Odometry

Geo-Supervised Visual Depth Prediction

Monocular Visual-Inertial Depth Estimation

Learned Monocular Depth Priors in Visual-Inertial Initialization

Risk-Averse MPC via Visual-Inertial Input and Recurrent Networks for Online Collision Avoidance

Learned Uncertainty Calibration for Visual Inertial Localization


IFCtoRDF is a set of reusable Java components that allows to parse IFC-SPF files and convert them into RDF graphs.

An Approach of Automatic SPARQL Generation for BIM Data Extraction

Analyzing Contextual Linking of Heterogeneous Information Models from the Domains BIM and UIM

ISPRS international journal of geo-information

Including widespread geometry schemas into Linked Data-based BIM applied to built heritage

Proceedings of the Institution of Civil Engineers. Smart infrastructure and construction

PRACTICAL EXAMPLES ON BIM-GIS INTEGRATION BASED ON SEMANTIC WEB TRIPLESTORES

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

Applying Knowledge Graphs as Integrated Semantic Information Model for the Computerized Engineering of Building Automation Systems

Automated extraction of attributes of IFC objects based on graph theory and SPARQL query

IOP conference series. Materials science and engineering


Track and predict the energy consumption and carbon footprint of training deep learning models.

Carbontracker: Tracking and Predicting the Carbon Footprint of Training Deep Learning Models

Unraveling the Hidden Environmental Impacts of AI Solutions for
  Environment

eco2AI: Carbon Emissions Tracking of Machine Learning Models as the First Step Towards Sustainable AI

Towards Climate Awareness in NLP Research

Locally orderless tensor networks for classifying two- and three-dimensional medical images

The journal of machine learning for biomedical imaging

Energy Consumption of Deep Generative Audio Models

Segmenting two-dimensional structures with strided tensor networks

MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality
  Microscopy

Efficiency is Not Enough: A Critical Perspective of Environmentally
  Sustainable AI

Efficient Multi-Organ Segmentation Using SpatialConfiguration-Net with Low GPU Memory Requirements


Python package for automated analysis and management of gridded climate data


Recovering genes from targeted sequence capture data

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

A Phylogenomic Perspective on Evolution and Discordance in the Alpine-Arctic Plant Clade Micranthes (Saxifragaceae)

Phylogenetic relationships of Atractylodes lancea, A. chinensis and A. macrocephala, revealed by complete plastome and nuclear gene sequences

hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution


Supplementary Materials for Tshitoyan et al. "Unsupervised word embeddings capture latent knowledge from materials science literature", Nature (2019).

Recent advances and applications of deep learning methods in materials science

Opportunities and Challenges for Machine Learning in Materials Science

Distributed representations of atoms and materials for machine learning

Interdisciplinary Discovery of Nanomaterials Based on Convolutional
  Neural Networks


Python interface for accessing the near real-world offline reinforcement learning (NeoRL) benchmark datasets

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

FinRL: A Deep Reinforcement Learning Library for Automated Stock Trading in Quantitative Finance

A Benchmark Environment Motivated by Industrial Control Problems

IEEE Symposium Series on Computational Intelligence

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

Reward-Consistent Dynamics Models are Strongly Generalizable for Offline
  Reinforcement Learning


Interface to the public ECMWF API Web Services


Comprehensive suite for rule-based learning

RuleKit: A Comprehensive Suite for Rule-Based Learning

Survival Prediction of Children Undergoing Hematopoietic Stem Cell
  Transplantation Using Different Machine Learning Classifiers by Performing
  Chi-squared Test and Hyper-parameter Optimization: A Retrospective Analysis


Effsize - a package for efficient effect size computation

DDX3X and DDX3Y are redundant in protein synthesis

Student, instructor, and observer agreement regarding frequencies of scientific teaching practices using the Measurement Instrument for Scientific Teaching-Observable (MISTO)

The Impact of Acute Ingestion of a Ketone Monoester Drink on LPS-Stimulated NLRP3 Activation in Humans with Obesity

Trichuris muris whey acidic protein induces type 2 protective immunity against whipworm

Avaliação de Estudantes quanto a Práticas Docentes para Criatividade na Pós-graduação

Development and Validation of a Novel Robot-Based Assessment of Upper Limb Sensory Processing in Chronic Stroke

Problem solving in fawn‐footed mosaic‐tailed rats Melomys cervinipes is not significantly influenced by maternal care or genetic effects

Journal of experimental zoology. Part A, Ecological and integrative physiology

Mental health among unaccompanied refugee minors after settling in Norway: A matched cross-sectional study

A corticostriatal pathway mediating self-efficacy enhancement


Miscellaneous tools for BloodHound

Scalable Edge Blocking Algorithms for Defending Active Directory Style Attack Graphs


Molecular Property Prediction: A Multilevel Quantum Interactions Modeling Perspective

Alchemy: A Quantum Chemistry Dataset for Benchmarking AI Models

Deep Learning for Optoelectronic Properties of Organic Semiconductors


pbsv - PacBio structural variant (SV) calling and analysis tools

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing

A draft human pangenome reference

A robust benchmark for detection of germline large deletions and insertions

Long-read-based human genomic structural variation detection with cuteSV

Towards population-scale long-read sequencing

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

Benchmarking challenging small variants with linked and long reads

Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads

Current status of structural variation studies in plants

Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape


Learning Graph Normalization for Graph Neural Networks

Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift

Layer Normalization


[ICLR 2019] ProxylessNAS: Direct Neural Architecture Search on Target Task and Hardware

AMC: AutoML for Model Compression and Acceleration on Mobile Devices

Hardware-Centric AutoML for Mixed-Precision Quantization

Semi-Supervised Neural Architecture Search

AdvantageNAS: Efficient Neural Architecture Search with Credit Assignment


Creative Commons Attribution Share Alike 4.0 International

The official repository for the EuroCrops dataset.

EuroCrops: All you need to know about the Largest Harmonised Open Crop
  Dataset Across the European Union

Challenges and Opportunities of Large Transnational Datasets: A Case
  Study on European Administrative Crop Data


MOSS-RLHF

A Survey of Large Language Models

Secrets of RLHF in Large Language Models Part I: PPO

Secrets of RLHF in Large Language Models Part II: Reward Modeling


A MATLAB software for the analysis of digital elevation models -

Bumps in river profiles: uncertainty assessment and smoothing using quantile regression techniques

Drainage divide networks – Part 1: Identification and ordering in digital elevation models

Fault activity, tectonic segmentation, and deformation pattern of the western Himalaya on Ma timescales inferred from landscape morphology

Drainage divide networks – Part 2: Response to perturbations

Predicting discharge capacity of vegetated compound channels: uncertainty and identifiability of one-dimensional process-based models

Sensitivity of subglacial drainage to water supply distribution at the Kongsfjord basin, Svalbard


Code for the paper "Jukebox: A Generative Model for Music"

Jukebox: A Generative Model for Music

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

DadaGP: A Dataset of Tokenized GuitarPro Songs for Sequence Models

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

Exploiting Negative Preference in Content-based Music Recommendation with Contrastive Learning

Proceedings of the 16th ACM Conference on Recommender Systems

A Survey of AI Music Generation Tools and Models


Code repo for "A Simple Baseline for Bayesian Uncertainty in Deep Learning"

Averaging Weights Leads to Wider Optima and Better Generalization

Pitfalls of In-Domain Uncertainty Estimation and Ensembling in Deep Learning

Neural networks with late-phase weights

Do Bayesian Variational Autoencoders Know What They Don't Know?

A Physics inspired Functional Operator for Model Uncertainty
  Quantification in the RKHS


[EMNLP 2023 Outstanding Paper Award] Is ChatGPT Good at Search? LLMs as Re-Ranking Agent

Is ChatGPT Good at Search? Investigating Large Language Models as Re-Ranking Agents

Instruction Distillation Makes Large Language Models Efficient Zero-shot
  Rankers


To make it easy to benchmark AI accelerators

XSP: Across-Stack Profiling and Analysis of Machine Learning Models on GPUs

AI Matrix: A Deep Learning Benchmark for Alibaba Data Centers

Benanza: Automatic μBenchmark Generation to Compute "Lower-bound" Latency and Inform Optimizations of Deep Learning Models on GPUs

International Parallel and Distributed Processing Symposium


Code for Nature energy manuscript


An R package for accessing elevation data

A Generalizable and Accessible Approach to Machine Learning with Global Satellite Imagery

Auxiliary-task learning for geographic data with autoregressive embeddings

Integrative systematic revision of a new genus of Eumolpinae (Coleoptera: Chrysomelidae) endemic to New Caledonia: Dematotrichus gen. nov. and its numerous new hairy species

Landscape Genetic Connectivity and Evidence for Recombination in the North American Population of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans

Analysis of intrinsic evolutionary factors leading to microendemic distributions in New Caledonian leaf beetles


Integrating the TensorFlow 1.15 C-API into OpenFOAM 5.0 for data-driven CFD algorithm development

A turbulent eddy-viscosity surrogate modeling framework for
  Reynolds-Averaged Navier-Stokes simulations

Deploying deep learning in OpenFOAM with TensorFlow

Machine learning accelerated turbulence modeling of transient flashing jets


Python package and data files for manipulating phonological segments (phones, phonemes) in terms of universal phonological features.

PanPhon: A Resource for Mapping IPA Segments to Articulatory Feature Vectors

International Conference on Computational Linguistics

Polyglot Neural Language Models: A Case Study in Cross-Lingual Phonetic Representation Learning

Simple and Effective Zero-shot Cross-lingual Phoneme Recognition

Modeling Noisiness to Recognize Named Entities using Multitask Neural Networks on Social Media

North American Chapter of the Association for Computational Linguistics

Keyphrase Extraction from Disaster-related Tweets

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

Phonosemantic biases found in Leipzig-Jakarta lists of 66 languages

Language-Agnostic Meta-Learning for Low-Resource Text-to-Speech with Articulatory Features

FonBund: A Library for Combining Cross-lingual Phonological Segment Data

PROCEEDINGS OF THE ELEVENTH INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION (LREC 2018)

Colexifications for Bootstrapping Cross-lingual Datasets: The Case of Phonology, Concreteness, and Affectiveness

The Post-Stroke Speech Transcription (PSST) Challenge


Code repository for supporting the paper "Atlas Few-shot Learning with Retrieval Augmented Language Models",(https//arxiv.org/abs/2208.03299)

Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer

Atlas: Few-shot Learning with Retrieval Augmented Language Models

Self-RAG: Learning to Retrieve, Generate, and Critique through
  Self-Reflection

RA-DIT: Retrieval-Augmented Dual Instruction Tuning

WikiChat: Stopping the Hallucination of Large Language Model Chatbots by Few-Shot Grounding on Wikipedia

RAVEN: In-Context Learning with Retrieval Augmented Encoder-Decoder
  Language Models

The Effect of Scaling, Retrieval Augmentation and Form on the Factual Consistency of Language Models


[ICCV 2019] TSM: Temporal Shift Module for Efficient Video Understanding

Non-local Neural Networks

Temporal Segment Networks: Towards Good Practices for Deep Action Recognition

The EPIC-KITCHENS Dataset: Collection, Challenges and Baselines

Generic Event Boundary Detection: A Benchmark for Event Segmentation

Class-Incremental Learning for Action Recognition in Videos

Video Moment Localization using Object Evidence and Reverse Captioning


ENCODE ChIP-seq pipeline

Base-resolution models of transcription factor binding reveal soft motif syntax

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

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

SETD2 loss perturbs the kidney cancer epigenetic landscape to promote metastasis and engenders actionable dependencies on histone chaperone complexes

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

Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements

Genome-wide CRISPR-Cas9 screen identified KLF11 as a druggable suppressor for sarcoma cancer stem cells

The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression

The Journal of experimental medicine/The journal of experimental medicine

Reshaping of the androgen-driven chromatin landscape in normal prostate cells by early cancer drivers and effect on therapeutic sensitivity

Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers


中文自然语言处理数据集，平时做做实验的材料。欢迎补充提交合并。

A Pilot Study for Chinese SQL Semantic Parsing

The First Evaluation of Chinese Human-Computer Dialogue Technology

TableQA: a Large-Scale Chinese Text-to-SQL Dataset for Table-Aware SQL Generation.

FewJoint: A Few-shot Learning Benchmark for Joint Language Understanding

Location reference recognition from texts: A survey and comparison

Improving exchange rate forecasting via a new deep multimodal fusion model

Applied intelligence (Dordrecht, Netherlands)

Data Set and Evaluation of Automated Construction of Financial Knowledge Graph

Chinese Named Entity Recognition Based on BERT and Lightweight Feature Extraction Model


Making Protein Design accessible to all via Google Colab!

Protein Sequence and Structure Co-Design with Equivariant Translation

Solubility-Aware Protein Binding Peptide Design Using AlphaFold

PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design


pyltp: the python extension for LTP

Crafting Adversarial Examples for Neural Machine Translation

Meeting of the Association for Computational Linguistics

Neural Multitask Learning for Simile Recognition

Empirical Methods in Natural Language Processing

Generating Sports News from Live Commentary: A Chinese Dataset for Sports Game Summarization

International Joint Conference on Natural Language Processing

Combining Part-of-Speech Tags and Self-Attention Mechanism for Simile Recognition

Low-Resource Sequence Labeling via Unsupervised Multilingual Contextualized Representations

Hiring Now: A Skill-Aware Multi-Attention Model for Job Posting Generation

Constructing Uyghur Name Entity Recognition System using Neural Machine Translation Tag Projection

Multi-task Learning for Chinese Word Usage Errors Detection


Library to compute surface distance based performance metrics for segmentation tasks.

Deep learning to achieve clinically applicable segmentation of head and neck anatomy for radiotherapy

TotalSegmentator: Robust Segmentation of 104 Anatomic Structures in CT Images.

Comparative validation of multi-instance instrument segmentation in endoscopy: Results of the ROBUST-MIS 2019 challenge

Clinical implementation of MRI-based organs-at-risk auto-segmentation with convolutional networks for prostate radiotherapy

Automatic post-stroke lesion segmentation on MR images using 3D residual convolutional neural network

Automatic lung segmentation in routine imaging is a data diversity problem, not a methodology problem

Deep Learning Initialized and Gradient Enhanced Level-Set Based Segmentation for Liver Tumor From CT Images

Oropharyngeal primary tumor segmentation for radiotherapy planning on magnetic resonance imaging using deep learning

Physics and imaging in radiation oncology

Loss Weightings for Improving Imbalanced Brain Structure Segmentation Using Fully Convolutional Networks

Cutting-edge 3D Medical Image Segmentation Methods in 2020: Are Happy Families All Alike?


Systematic dataset of Covid-19 policy, from Oxford University

A global panel database of pandemic policies (Oxford COVID-19 Government Response Tracker)

Collectivism predicts mask use during COVID-19

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

COVID-19 open source data sets: a comprehensive survey

Effects of COVID-19 lockdown on global air quality and health

A global analysis of the impact of COVID-19 stay-at-home restrictions on crime

Explaining the homogeneous diffusion of COVID-19 nonpharmaceutical interventions across heterogeneous countries

Risk Attitudes and Human Mobility during the COVID-19 Pandemic

Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe

Mathematical Modeling of Epidemic Diseases; A Case Study of the COVID-19 Coronavirus

HIT-COVID, a global database tracking public health interventions to COVID-19


[CVPR'24 Highlight] GPT4Point: A Unified Framework for Point-Language Understanding and Generation.

3D-LLM: Injecting the 3D World into Large Language Models

Point-Bind & Point-LLM: Aligning Point Cloud with Multi-modality for 3D
  Understanding, Generation, and Instruction Following

PointLLM: Empowering Large Language Models to Understand Point Clouds


TransDecoder source

NRG1 functions downstream of EDS1 to regulate TIR-NLR-mediated plant immunity in Nicotiana benthamiana

Long-read sequence assembly: a technical evaluation in barley

Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil

Firefly genomes illuminate parallel origins of bioluminescence in beetles

The genome of Rhizophagus clarus HR1 reveals a common genetic basis for auxotrophy among arbuscular mycorrhizal fungi

Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)

The mosaic oat genome gives insights into a uniquely healthy cereal crop

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

SMRT sequencing of full-length transcriptome of flea beetle Agasicles hygrophila (Selman and Vogt)

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution


The Apache Kafka C/C++ library

Programmable Event Detection for In-Band Network Telemetry

Security and privacy preserving data aggregation in cloud computing

Architecture of the data aggregation and streaming system for the European Spallation Source neutron instrument suite

Software-based data acquisition and processing for neutron detectors at European Spallation Source—early experience from four detector designs

The Boon and Bane of Cross-Signing: Shedding Light on a Common Practice in Public Key Infrastructures

A Real-Time Streaming System for Customized Network Traffic Capture


Taming Transformers for High-Resolution Image Synthesis

Vector-quantized Image Modeling with Improved VQGAN

Visual Prompting via Image Inpainting

Geometry-Free View Synthesis: Transformers and no 3D Priors

Aligning Latent and Image Spaces to Connect the Unconnectable

SlotFormer: Unsupervised Visual Dynamics Simulation with Object-Centric
  Models

Look Outside the Room: Synthesizing A Consistent Long-Term 3D Scene Video from A Single Image

FlexIT: Towards Flexible Semantic Image Translation

Enhance the Visual Representation via Discrete Adversarial Training

MoVQ: Modulating Quantized Vectors for High-Fidelity Image Generation


A simple, open database of local government climate action plan documents and emissions data.


POET pipeline for reduction of Spitzer data

Absence of a thick atmosphere on the terrestrial exoplanet LHS 3844b

TESS Hunt for Young and Maturing Exoplanets (THYME). II. A 17 Myr Old Transiting Hot Jupiter in the Sco-Cen Association

TESS Hunt for Young and Maturing Exoplanets (THYME). V. A Sub-Neptune Transiting a Young Star in a Newly Discovered 250 Myr Association

The First Habitable-zone Earth-sized Planet from TESS. II. Spitzer Confirms TOI-700 d

Introducing a New Spitzer Master BLISS Map to Remove the Instrument Systematic Phase-curve-parameter Degeneracy, as Demonstrated by a Reanalysis of the 4.5 μm WASP-43b Phase Curve

K2 and Spitzer phase curves of the rocky ultra-short-period planet K2-141 b hint at a tenuous rock vapor atmosphere

Phase Curves of Hot Neptune LTT 9779b Suggest a High-metallicity Atmosphere

A Mirage or an Oasis? Water Vapor in the Atmosphere of the Warm Neptune TOI-674 b

Wolf 503 b: Characterization of a Sub-Neptune Orbiting a Metal-poor K Dwarf

Hazy with a chance of star spots: constraining the atmosphere of the
  young planet, K2-33b


Inforex is a web system for text corpora construction.

Multi-Level Sentiment Analysis of PolEmo 2.0: Extended Corpus of Multi-Domain Consumer Reviews

Conference on Computational Natural Language Learning

The Second Cross-Lingual Challenge on Recognition, Normalization, Classification, and Linking of Named Entities across Slavic Languages

Slav-NER: the 3rd Cross-lingual Challenge on Recognition, Normalization, Classification, and Linking of Named Entities across Slavic Languages

Workshop on Balto-Slavic Natural Language Processing

Inforex --- a Collaborative Systemfor Text Corpora Annotation and Analysis Goes Open

Recent Advances in Natural Language Processing


UNFINISHED: use this instead: https://github.com/JRCSTU/gearshift_calculation_tool


How to predict extreme events in climate using rare event algorithms and modern tools of machine learning

Probabilistic forecasts of extreme heatwaves using convolutional neural networks in a regime of lack of data

Robust intra-model teleconnection patterns for extreme heatwaves

Extreme heatwave sampling and prediction with analog Markov chain and
  comparisons with deep learning


Monitorización de alumnos en la plataforma Moodle

Monitoring of Student Learning in Learning Management Systems: An Application of Educational Data Mining Techniques

Usefulness of Digital Game-Based Learning in Nursing and Occupational Therapy Degrees: A Comparative Study at the University of Burgos

International journal of environmental research and public health

Teacher Training Effectiveness in Self-Regulation in Virtual Environments


This repository supports epidemiological and disease-dynamic analyses of data from the REal Time Assessment of Community Transmission (REACT) study. It includes both code and data. For code-related enquiries please contact Oliver Eales: oliver (dot) eales (at) unimelb (dot) edu (dot) au

Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Rapid increase in Omicron infections in England during December 2021: REACT-1 study

Predictive symptoms for COVID-19 in the community: REACT-1 study of over 1 million people

Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England

Omicron SARS-CoV-2 epidemic in England during February 2022: A series of cross-sectional community surveys

Breakthrough SARS-CoV-2 infections in double and triple vaccinated adults and single dose vaccine effectiveness among children in Autumn 2021 in England: REACT-1 study

Local prevalence of transmissible SARS-CoV-2 infection : an integrative causal model for debiasing fine-scale targeted testing data


Code to evaluate and tune SPARK VIO pipeline.

Kimera: an Open-Source Library for Real-Time Metric-Semantic Localization and Mapping

3D Dynamic Scene Graphs: Actionable Spatial Perception with Places, Objects, and Humans

Incremental Visual-Inertial 3D Mesh Generation with Structural Regularities


Implementation of Sequence Generative Adversarial Nets with Policy Gradient

SeqGAN: Sequence Generative Adversarial Nets with Policy Gradient

Adversarial Ranking for Language Generation

Toward Diverse Text Generation with Inverse Reinforcement Learning

Jointly Measuring Diversity and Quality in Text Generation Models

Generative adversarial networks in time series: A survey and taxonomy

Code-switched Language Models Using Dual RNNs and Same-Source
  Pretraining

CM-Gen: A Neural Framework for Chinese Metaphor Generation with Explicit Context Modelling

Nominal Metaphor Generation with Multitask Learning


The Termination Problem Database

Proving Non-Termination and Lower Runtime Bounds with LoAT (System
  Description)

Improving Automatic Complexity Analysis of Integer Programs

Automatic Complexity Analysis of Integer Programs via Triangular Weakly Non-Linear Loops

Targeting Completeness: Using Closed Forms for Size Bounds of Integer Programs

Improving Dependency Tuples for Almost-Sure Innermost Termination of
  Probabilistic Term Rewriting

Proving Termination of C Programs with Lists


Gradient Unwarping in Python

The impact of B1+ correction on MP2RAGE cortical T1 and apparent cortical thickness at 7T.

Mapping Short Association Fibers in the Early Cortical Visual Processing Stream Using In Vivo Diffusion Tractography

A massive 7T fMRI dataset to bridge cognitive and computational neuroscience

Same Brain, Different Look? – the Impact of Scanner, Sequence and Preprocessing on Diffusion Imaging Outcome Parameters

High-resolution quantitative and functional MRI indicate lower myelination of thin and thick stripes in human secondary visual cortex

CHIASM, the human brain albinism and achiasma MRI dataset

Assessing methods for geometric distortion compensation in 7T gradient echo fMRI data

Multi-scale structural alterations of the thalamus and basal ganglia in focal epilepsy using 7T MRI.


Code for the model presented in the paper: "code2seq: Generating Sequences from Structured Representations of Code"

Code Prediction by Feeding Trees to Transformers

Adversarial Examples for Models of Code

Self-Supervised Contrastive Learning for Code Retrieval and Summarization via Semantic-Preserving Transformations

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

Semantic Robustness of Models of Source Code

A Literature Study of Embeddings on Source Code

Embedding Java Classes with code2vec: Improvements from Variable Obfuscation

Research Commons (University of Waikato)

Understanding neural code intelligence through program simplification

PROCEEDINGS OF THE 29TH ACM JOINT MEETING ON EUROPEAN SOFTWARE ENGINEERING CONFERENCE AND SYMPOSIUM ON THE FOUNDATIONS OF SOFTWARE ENGINEERING (ESEC/FSE '21)

On the Evaluation of Commit Message Generation Models: An Experimental Study

A Search-Based Testing Framework for Deep Neural Networks of Source Code Embedding


CRyPTIC data processing pipelines

A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis

A data compendium of Mycobacterium tuberculosis antibiotic resistance

TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis


Real Time Speech Enhancement in the Waveform Domain (Interspeech 2020)We provide a PyTorch implementation of the paper Real Time Speech Enhancement in the Waveform Domain. In which, we present a causal speech enhancement model working on the raw waveform that runs in real-time on a laptop CPU. The proposed model is based on an encoder-decoder architecture with skip-connections. It is optimized on both time and frequency domains, using multiple loss functions. Empirical evidence shows that it is capable of removing various kinds of background noise including stationary and non-stationary noises, as well as room reverb. Additionally, we suggest a set of data augmentation techniques applied directly on the raw waveform which further improve model performance and its generalization abilities.

Parallel Wavegan: A Fast Waveform Generation Model Based on Generative Adversarial Networks with Multi-Resolution Spectrogram

Improving Speech Enhancement through Fine-Grained Speech Characteristics

Restoring speech intelligibility for hearing aid users with deep learning

Self-Supervised Learning for Speech Enhancement through Synthesis

TAPLoss: A Temporal Acoustic Parameter Loss for Speech Enhancement

Neural Comb Filtering Using Sliding Window Attention Network for Speech Enhancement

Circuits, systems, and signal processing


Chinese-Vicuna: A Chinese Instruction-following LLaMA-based Model —— 一个中文低资源的llama+lora方案，结构参考alpaca

LLaMA: Open and Efficient Foundation Language Models

LoRA: Low-Rank Adaptation of Large Language Models

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

GPT Can Solve Mathematical Problems Without a Calculator

LLaMA-Reviewer: Advancing Code Review Automation with Large Language Models through Parameter-Efficient Fine-Tuning

Examining User-Friendly and Open-Sourced Large GPT Models: A Survey on
  Language, Multimodal, and Scientific GPT Models


FMIFlux.jl is a free-to-use software library for the Julia programming language, which offers the ability to place FMUs (fmi-standard.org) everywhere inside of your ML topologies and still keep the resulting model trainable with a standard (or custom) FluxML training process.

NeuralFMU: Towards Structural Integration of FMUs into Neural Networks

NeuralFMU: Presenting a Workflow for Integrating Hybrid NeuralODEs into Real-World Applications

Hybrid modeling of the human cardiovascular system using NeuralFMUs


An Open Source Python package for the extraction of fine-grained and time-stamped co-editing networks from git repositories.

git2net - Mining Time-Stamped Co-Editing Networks from Large git Repositories

Analysing Time-Stamped Co-Editing Networks in Software Development Teams using git2net


A framework for Quantification written in Python

Optimizing Text Quantifiers for Multivariate Loss Functions

Tweet Sentiment Quantification: An Experimental Re-Evaluation

QuaPy: A Python-Based Framework for Quantification

LeQua@CLEF2022: Learning to Quantify


Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

A Compendium of Mutational Signatures of Environmental Agents

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

Tobacco smoking and somatic mutations in human bronchial epithelium

Somatic mutations and clonal dynamics in healthy and cirrhotic human liver

Mutational signatures of ionizing radiation in second malignancies

Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study

The genome as a record of environmental exposure

Clonal dynamics of haematopoiesis across the human lifespan

Genomic patterns of progression in smoldering multiple myeloma

The longitudinal dynamics and natural history of clonal haematopoiesis


Numenta published papers code and data

Evaluating Real-Time Anomaly Detection Algorithms -- The Numenta Anomaly Benchmark

International Conference on Machine Learning and Applications

Why Neurons Have Thousands of Synapses, a Theory of Sequence Memory in Neocortex

How Can We Be So Dense? The Benefits of Using Highly Sparse Representations.

DNA Replication Control in Microbial Cell Factories

Sequence learning, prediction, and replay in networks of spiking neurons

Going Beyond the Point Neuron: Active Dendrites and Sparse Representations for Continual Learning

Grid Cell Path Integration For Movement-Based Visual Object Recognition


A simple, fully convolutional model for real-time instance segmentation.

YOLACT: Real-time Instance Segmentation

Enhancing Geometric Factors in Model Learning and Inference for Object Detection and Instance Segmentation

Human segmentation in surveillance video with deep learning

Dynamic Object Tracking and Masking for Visual SLAM

Metamorphic Testing for Object Detection Systems

Real-Time Instance Segmentation for Detection of Underwater Litter as a Plastic Source

Journal of marine science and engineering

Developing a Free and Open-Source Semi-Automated Building Exterior Crack Inspection Software for Construction and Facility Managers


Trained caffe models

Protein-Ligand Scoring with Convolutional Neural Networks

Journal of chemical information and modeling

3D Convolutional Neural Networks and a CrossDocked Dataset for Structure-Based Drug Design

Visualizing Convolutional Neural Network Protein-Ligand Scoring

Journal of molecular graphics & modelling/Journal of molecular graphics and modelling

libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications

An Equivariant Generative Framework for Molecular Graph-Structure
  Co-Design


End-to-end ASR/LM implementation with PyTorch

Enhancing Monotonic Multihead Attention for Streaming ASR

CTC-synchronous Training for Monotonic Attention Model

StableEmit: Selection Probability Discount for Reducing Emission Latency of Streaming Monotonic Attention ASR

VAD-free Streaming Hybrid CTC/Attention ASR for Unsegmented Recording


A Wes Anderson color palette for R

Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

The sensitivity of modeled snow accumulation and melt to precipitation phase methods across a climatic gradient

High-resolution genome-wide functional dissection of transcriptional regulatory regions in human

Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assays

Evaluating the bio-economic performance of a Callo de hacha (Atrina maura, Atrina tuberculosa & Pinna rugosa) fishery restoration plan in La Paz, Mexico

Shedding light on large-scale solar impacts: An analysis of property values and proximity to photovoltaics across six U.S. states

Cuvier’s beaked whale foraging dives identified via machine learning using depth and triaxial acceleration

Gridlines approach for dynamic analysis in speech ultrasound data: A multimodal app

Techniques and Methods for Investigating Speech Articulation


The MPLAPACK: multiple precision version of BLAS and LAPACK

Automatic Fortran to C++ conversion with FABLE

Multiple-Precision BLAS Library for Graphics Processing Units

MPLAPACK version 2.0.1 user manual

Acceleration of multiple precision matrix multiplication based on multi-component floating-point arithmetic using AVX2

Transfer efficiency enhancement and eigenstate properties in locally symmetric disordered finite chains

Acceleration of Multiple Precision Matrix Multiplication using Ozaki
  scheme

Performance Evaluation of Strassen Matrix Multiplication Supporting Triple-Double Precision Floating-Point Arithmetic

Acceleration of complex matrix multiplication using arbitrary precision
  floating-point arithmetic


Calling and Phasing of Single-Nucleotide and Structural Variants of the LDLR Gene Using Oxford Nanopore MinION

International journal of molecular sciences

ONT long-read WGS for variant discovery and orthogonal confirmation of short read WGS derived genetic variants in clinical genetic testing


Helper package with multiple U-Net implementations in Keras as well as useful utility tools helpful when working with image semantic segmentation tasks. This library and underlying tools come from multiple projects I performed working on semantic segmentation tasks

U-Net: Convolutional Networks for Biomedical Image Segmentation

ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic

Automatic Segmentation of Retinal Fluid and Photoreceptor Layer from Optical Coherence Tomography Images of Diabetic Macular Edema Patients Using Deep Learning and Associations with Visual Acuity

Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint

SILVIA: An eXplainable Framework to Map Bark Beetle Infestation in Sentinel-2 Images

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


Pseudo-Relevance Feedback for Multiple Representation Dense Retrieval

International Conference on the Theory of Information Retrieval

Transfer Learning Approaches for Building Cross-Language Dense Retrieval Models

Query Embedding Pruning for Dense Retrieval

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

On Single and Multiple Representations in Dense Passage Retrieval

On Approximate Nearest Neighbour Selection for Multi-Stage Dense Retrieval

Improving zero-shot retrieval using dense external expansion

SpaceQA: Answering Questions about the Design of Space Missions and Space Craft Concepts


Neuroimaging in PyTorch

Model-based multi-parameter mapping

An MRF-UNet Product of Experts for Image Segmentation


Various public documents, whitepapers and articles about APT campaigns

HOLMES: Real-time APT Detection through Correlation of Suspicious
  Information Flows

SLEUTH: Real-time Attack Scenario Reconstruction from COTS Audit Data

Hiding in Plain Sight: A Longitudinal Study of Combosquatting Abuse

SecureBERT: A Domain-Specific Language Model for Cybersecurity

Abstract 18673: Human Enzyme Replacement Therapy in a Patient With Familial Lecithin Cholesterol Acyltransferase Deficiency: Rapid Appearance of Normal Appearing HDL

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

AULD: Large Scale Suspicious DNS Activities Detection via Unsupervised Learning in Advanced Persistent Threats


A Resistance Capacitance Model for an Energetic Simulation of a Building


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

Leveraging Neighborhood Summaries for Efficient RDF Queries on RDBMS

ROSIE: Runtime Optimization of SPARQL Queries Using Incremental
  Evaluation

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


STAR based ENCODE Long RNA-Seq processing pipeline

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients

Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16

Landscape of innate lymphoid cells in human head and neck cancer reveals divergent NK cell states in the tumor microenvironment

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

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

Cell type–specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells

The Journal of experimental medicine/The journal of experimental medicine

Global translation during early development depends on the essential transcription factor PRDM10

The microdissected gene expression landscape of nasopharyngeal cancer reveals vulnerabilities in FGF and noncanonical NF-κB signaling

Loss of Nup210 results in muscle repair delays and age-associated alterations in muscle integrity

PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments


RT-GENE: Real-Time Eye Gaze and Blink Estimation in Natural Environments

RT-GENE: Real-Time Eye Gaze Estimation in Natural Environments

RT-BENE: A Dataset and Baselines for Real-Time Blink Estimation in Natural Environments

International Conference on Computer Vision

Non-Intrusive Real Time Eye Tracking Using Facial Alignment for Assistive Technologies

IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society


Optical ray tracing for luminescent materials and spectral converter photovoltaic devices

Luminescent solar concentrators with fiber geometry

Development of an Off‐Grid Solar‐Powered Autonomous Chemical Mini‐Plant for Producing Fine Chemicals

An Open-Source Monte Carlo Ray-Tracing Simulation Tool for Luminescent Solar Concentrators with Validation Studies Employing Scattering Phosphor Films

Numerical Method for Calculation of Power Conversion Efficiency and Colorimetrics of Rectangular Luminescent Solar Concentrators

Ray trace modeling to characterize efficiency of unconventional luminescent solar concentrator geometries


Train Gradient Boosting models that are both high-performance *and* Fair!

Equality of Opportunity in Supervised Learning

Promoting Fairness through Hyperparameter Optimization

FairGBM: Gradient Boosting with Fairness Constraints


MobileNetV1, MobileNetV2, VGG based SSD/SSD-lite implementation in Pytorch 1.0 / Pytorch 0.4. Out-of-box support for retraining on Open Images dataset. ONNX and Caffe2 support. Experiment Ideas like CoordConv.

SSD: Single Shot MultiBox Detector

Data-Free Quantization Through Weight Equalization and Bias Correction

Post-Training Piecewise Linear Quantization for Deep Neural Networks

GAN "Steerability" without optimization

Visual Diagnosis of the Varroa Destructor Parasitic Mite in Honeybees Using Object Detector Techniques

Memory-Efficient CNN Accelerator Based on Interlayer Feature Map Compression

Finding the Task-Optimal Low-Bit Sub-Distribution in Deep Neural
  Networks

PSRR-MaxpoolNMS: Pyramid Shifted MaxpoolNMS with Relationship Recovery

Analysis and a Solution of Momentarily Missed Detection for Anchor-based Object Detectors

Shift-and-Balance Attention


Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Identification of acquired antimicrobial resistance genes

The journal of antimicrobial chemotherapy/Journal of antimicrobial chemotherapy

In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr

Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing

Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing

Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America

Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies


PCR-GLOBWB (PCRaster Global Water Balance) is a large-scale hydrological model intended for global to regional studies and developed at the Department of Physical Geography, Utrecht University (Netherlands). Contact: Edwin Sutanudjaja (E.H.Sutanudjaja@uu.nl).

PCR-GLOBWB 2: a 5 arcmin global hydrological and water resources model

Spring enhancement and summer reduction in carbon uptake during the 2018 drought in northwestern Europe

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

Current wastewater treatment targets are insufficient to protect surface water quality

FutureStreams, a global dataset of future streamflow and water temperature


MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

Method development for cross-study microbiome data mining: Challenges and opportunities

Computational and structural biotechnology journal

MAGScoT - a fast, lightweight, and accurate bin-refinement software

A Nitrate-Transforming Bacterial Community Dominates in the Miscanthus Rhizosphere on Nitrogen-Deficient Volcanic Deposits of Miyake-jima


A pure-python fully automated and unattended fuzzing framework.

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

Snipuzz: Black-box Fuzzing of IoT Firmware via Message Snippet Inference

Complex Structure and Dynamics of the Heart

PropFuzz — An IT-security fuzzing framework for proprietary ICS protocols

International Conference on Applied Electronics

Test Data Generation for Stateful Network Protocol Fuzzing Using a Rule-Based State Machine

清华大学学报：自然科学英文版

Berserker: ASN.1-based Fuzzing of Radio Resource Control Protocol for 4G and 5G

State Selection Algorithms and Their Impact on The Performance of Stateful Network Protocol Fuzzing

ESRFuzzer: an enhanced fuzzing framework for physical SOHO router devices to discover multi-Type vulnerabilities

BackREST: A Model-Based Feedback-Driven Greybox Fuzzer for Web Applications.

Lifting Network Protocol Implementation to Precise Format Specification with Security Applications


A suite of Arabic natural language processing tools developed by the CAMeL Lab at New York University Abu Dhabi.

CAMeL Tools: An Open Source Python Toolkit for Arabic Natural Language Processing

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

Sa‘7r: A Saudi Dialect Irony Dataset

Camelira: An Arabic Multi-Dialect Morphological Disambiguator

Data Augmentation Methods for Anaphoric Zero Pronouns


Astronomy related procedures in the commercial IDL language

TESS reveals that the nearby Pisces-Eridanus stellar stream is only 120
  Myr old

The GALAH survey: the data reduction pipeline

Monthly Notices of the Royal Astronomical Society

Evidence of Particle Acceleration in the Superbubble 30 Doradus C with NuSTAR

NuSTAR Observations of G11.2–0.3


Use the HYSPLIT model from inside R and do more with it

Marine and terrestrial influences on ice nucleating particles during continuous springtime measurements in an Arctic oilfield location

Summertime surface PM&lt;sub&gt;1&lt;/sub&gt; aerosol composition and size by source region at the Lampedusa island in the central Mediterranean Sea

Chemical composition and source apportionment of atmospheric aerosols on the Namibian coast

Combining Regulatory Instruments and Low-Cost Sensors to Quantify the Effects of 2020 California Wildfires on PM2.5 in San Joaquin Valley


Provides a function to measure the energy usage of another function.

Energy and Policy Considerations for Deep Learning in NLP

Energy Usage Reports: Environmental awareness as part of algorithmic accountability


This repository contains the code and implementation details of the CascadeTabNet paper "CascadeTabNet: An approach for end to end table detection and structure recognition from image-based documents"

Deep learning for table detection and structure recognition: A survey


A 3D vision library from 2D keypoints: monocular and stereo 3D detection for humans, social distancing, and body orientation.

Unsupervised Monocular Depth Estimation with Left-Right Consistency

MonoLoco: Monocular 3D Pedestrian Localization and Uncertainty Estimation

Perceiving Humans: From Monocular 3D Localization to Social Distancing

MonStereo: When Monocular and Stereo Meet at the Tail of 3D Human Localization


a Lightweight library for sequential learning agents, including reinforcement learning

Decision Transformer: Reinforcement Learning via Sequence Modeling

A Simple Way to Initialize Recurrent Networks of Rectified Linear Units

Direct then Diffuse: Incremental Unsupervised Skill Discovery for State Covering and Goal Reaching

Building a Subspace of Policies for Scalable Continual Learning

SaLinA: Sequential Learning of Agents

Learning a subspace of policies for online adaptation in Reinforcement
  Learning


GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

Research in Computational Molecular Biology

Technology dictates algorithms: Recent developments in read alignment

Nanopore sequencing in microgravity

Evaluation of tools for long read RNA-seq splice-aware alignment

Robust long-read native DNA sequencing using the ONT CsgG Nanopore system

Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art

A spectral algorithm for fast de novo layout of uncorrected long nanopore reads

From command-line bioinformatics to bioGUI

Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm
  Co-Design


[EMNLP 2021] SimCSE: Simple Contrastive Learning of Sentence Embeddings https://arxiv.org/abs/2104.08821

Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks

DiffCSE: Difference-based Contrastive Learning for Sentence Embeddings

TSDAE: Using Transformer-based Sequential Denoising Auto-Encoder for Unsupervised Sentence Embedding Learning

Learning Dense Representations of Phrases at Scale

Is Neural Topic Modelling Better than Clustering? An Empirical Study on Clustering with Contextual Embeddings for Topics

AlignScore: Evaluating Factual Consistency with A Unified Alignment Function

EASE: Entity-Aware Contrastive Learning of Sentence Embedding

Virtual Augmentation Supported Contrastive Learning of Sentence Representations

PCL: Peer-Contrastive Learning with Diverse Augmentations for Unsupervised Sentence Embeddings


A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum

Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients

Diversity of Mycobacterium tuberculosis across Evolutionary Scales

Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms

The journal of infectious diseases (Online. University of Chicago Press)/The Journal of infectious diseases

Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses

Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand

Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO

LoLoPicker: detecting low allelic-fraction variants from low-quality cancer samples

First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order


Image to prompt with BLIP and CLIP

Prompting AI Art: An Investigation into the Creative Skill of Prompt
  Engineering

Benchmarking Deepart Detection

Prompt Expansion for Adaptive Text-to-Image Generation

Prompting for Discovery: Flexible Sense-Making for AI Art-Making with
  Dreamsheets

Diffusing Colors: Image Colorization with Text Guided Diffusion

Probabilistic Copyright Protection Can Fail for Text-to-Image Generative
  Models


Multi-Turn Response Selection for Chatbots with Deep Attention Matching Network

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

One Time of Interaction May Not Be Enough: Go Deep with an Interaction-over-Interaction Network for Response Selection in Dialogues

Meeting of the Association for Computational Linguistics

Proactive Human-Machine Conversation with Explicit Conversation Goals

What does BERT know about books, movies and music? Probing BERT for Conversational Recommendation

RECSYS 2020: 14TH ACM CONFERENCE ON RECOMMENDER SYSTEMS

IART: Intent-aware Response Ranking with Transformers in Information-seeking Conversation Systems

Discovering Dialog Structure Graph for Open-Domain Dialog Generation

Learning to Expand: Reinforced Pseudo-relevance Feedback Selection for
  Information-seeking Conversations


Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute

Connecting MHC-I-binding motifs with HLA alleles via deep learning

TypeLoader2: Automated submission of novel HLA and killer‐cell immunoglobulin‐like receptor alleles in full length


GFF and GVF specification documents

ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database

The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

Frontiers in bioengineering and biotechnology

Hamster PIWI proteins bind to piRNAs with stage-specific size variations during oocyte maturation

Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings

The Journal of molecular diagnostics/The journal of molecular diagnostics

fagin: synteny-based phylostratigraphy and finer classification of young genes

Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation

SilkPathDB: a comprehensive resource for the study of silkworm pathogens

Database : the journal of biological databases and curation

List.MID: A MIDI-Based Benchmark for Evaluating RDF Lists

Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools

Approaches in Gene Coexpression Analysis in Eukaryotes


Tools for conformal inference in regression

Distribution-Free Predictive Inference for Regression

Conformal Prediction Under Covariate Shift

MAPIE: an open-source library for distribution-free uncertainty
  quantification

Efficient and minimal length parametric conformal prediction regions

conformalInference.multi and conformalInference.fd: Twin Packages for
  Conformal Prediction

Merging uncertainty sets via majority vote


tsl: a PyTorch library for processing spatiotemporal data.

Filling the G_ap_s: Multivariate Time Series Imputation by Graph Neural
  Networks

Learning to Reconstruct Missing Data from Spatiotemporal Graphs with
  Sparse Observations


Multivariate imputation and matrix completion algorithms implemented in Python

Matrix Completion and Low-Rank SVD via Fast Alternating Least Squares

BRITS: Bidirectional Recurrent Imputation for Time Series

Handling Missing Data with Graph Representation Learning

Modeling Personality vs. Modeling Personalidad: In-the-wild Mobile Data Analysis in Five Countries Suggests Cultural Impact on Personality Models.

Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices

Uncertainty-Gated Stochastic Sequential Model for EHR Mortality Prediction

RDIS: Random Drop Imputation With Self-Training for Incomplete Time Series Data

Missing Features Reconstruction Using a Wasserstein Generative Adversarial Imputation Network

Improving Load Forecasting of Electric Vehicle Charging Stations Through Missing Data Imputation


Python package for API access to news articles and events in the Event Registry

Political and Economic Patterns in COVID-19 News: From Lockdown to Vaccination


SuperGlue: Learning Feature Matching with Graph Neural Networks (CVPR 2020, Oral)

SuperPoint: Self-Supervised Interest Point Detection and Description

Navigating to Objects Specified by Images

Semi-Supervised Keypoint Detector and Descriptor for Retinal Image
  Matching

Self-Calibrating Anomaly and Change Detection for Autonomous Inspection Robots

Towards Seamless Adaptation of Pre-trained Models for Visual Place
  Recognition


tracking medical datasets, with a focus on medical imaging


DeepPrivacy: A Generative Adversarial Network for Face Anonymization

Image Inpainting with Learnable Feature Imputation

DisguisOR: Holistic Face Anonymization for the Operating Room

A False Sense of Privacy: Towards a Reliable Evaluation Methodology for the Anonymization of Biometric Data


d3 library to build circular graphs

eccDNAdb: a database of extrachromosomal circular DNA profiles in human cancers

PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes

zDB: bacterial comparative genomics made easy


State-of-the-art learned data structure that enables fast lookup, predecessor, range searches and updates in arrays of billions of items using orders of magnitude less space than traditional indexes

Are Updatable Learned Indexes Ready?

DILI: A Distribution-Driven Learned Index


fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

The evolution of lung cancer and impact of subclonal selection in TRACERx

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches

Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy

Genetic Epidemiology of Amyotrophic Lateral Sclerosis in Norway: A 2-Year Population-Based Study

The impact of genomic structural variation on the transcriptome, chromatin, and proteome in the human brain

Towards a gene-level map of resilience to genetic variants associated with autism


Federated Learning Benchmark - Federated Learning on Non-IID Data Silos: An Experimental Study (ICDE 2022)

FedDM: Iterative Distribution Matching for Communication-Efficient Federated Learning

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

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


A micro-benchmark suite to assess the stability of taint-analysis tools for Android

I know what leaked in your pocket: uncovering privacy leaks on Android Apps with Static Taint Analysis

Ghera: A Repository of Android App Vulnerability Benchmarks

Predictive Models in Software Engineering

Are free Android app security analysis tools effective in detecting known vulnerabilities?

Security code smells in Android ICC

Revisiting the impact of common libraries for android-related investigations

Journal of systems and software/The Journal of systems and software

Making DidFail Succeed: Enhancing the CERT Static Taint Analyzer for Android App Sets

TaintBench: Automatic real-world malware benchmarking of Android taint analyses

IIFA: Modular Inter-app Intent Information Flow Analysis of Android Applications

Feature importance in Android malware detection

Trust, Security And Privacy In Computing And Communications

DexLego: Reassembleable Bytecode Extraction for Aiding Static Analysis


Semi-Lagrangian Library

Variational Framework for Structure-Preserving Electromagnetic Particle-in-Cell Methods

A mass-conserving sparse grid combination technique with biorthogonal
  hierarchical basis functions for kinetic simulations


SAGECal is a fast, memory efficient and GPU accelerated radio interferometric calibration program. It supports all source models including points, Gaussians and Shapelets. Distributed calibration using MPI and consensus optimization is enabled. Both spectral and spatial priors can be used as constraints. Tools to build/restore sky models are included.

Improved upper limits on the 21 cm signal power spectrum of neutral hydrogen at z ≈ 9.1 from LOFAR

Monthly notices of the Royal Astronomical Society

Modelling and peeling extended sources with shapelets: A Fornax A case study

Publications of the Astronomical Society of Australia/Publications Astronomical Society of Australia

Data multiplexing in radio interferometric calibration

Adaptive ADMM in Distributed Radio Interferometric Calibration

GPU acceleration of the SAGECal calibration package for the SKA.


Simulation for survey (cadence, strategy) based on Python

Kilonova Luminosity Function Constraints Based on Zwicky Transient Facility Searches for 13 Neutron Star Merger Triggers during O3

Detectability of kilonovae in optical surveys: post-mortem examination of the LVC O3 run follow-up

A Data Science Platform to Enable Time-domain Astronomy

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

Inferring Kilonova Population Properties with a Hierarchical Bayesian Framework. I. Nondetection Methodology and Single-event Analyses

Lensed type Ia supernovae in light of SN Zwicky and iPTF16geu

Constraints Based on Non-detection of Kilonova Optical Searching


hybrid assembly pipeline for bacterial genomes

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

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

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

HASLR: Fast Hybrid Assembly of Long Reads

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1

WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil

Genome-Based Analysis of Klebsiella spp. Isolates from Animals and Food Products in Germany, 2013–2017

Detection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA


1D, super-resolution brightness profile reconstruction for interferometric sources

frankenstein: protoplanetary disc brightness profile reconstruction at sub-beam resolution with a rapid Gaussian process

A super-resolution analysis of the DSHARP survey: Substructure is common in the inner 30 au

Dust traps and the formation of cavities in transition discs: a millimetre to sub-millimetre comparison survey

Inner edges of planetesimal belts: collisionally eroded or truncated?

Deprojecting and constraining the vertical thickness of exoKuiper belts


Full-Stack OpenFlow Framework in Ruby

Software-Defined Networking: A Comprehensive Survey

SDN Controllers: Benchmarking & Performance Evaluation

QoS improvement with an optimum controller selection for software-defined networks

Software-Defined Networking: Categories, Analysis, and Future Directions

A Novel Scheme for Controller Selection in Software-Defined Internet-of-Things (SD-IoT)

Elastic and Adaptive Resource Orchestration Architecture on 3-Tier Network Virtualization Model

IEICE transactions on information and systems


A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.

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

From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Twelve years of SAMtools and BCFtools

Nextflow enables reproducible computational workflows

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

BCFtools/csq: haplotype-aware variant consequences

WhatsHap: fast and accurate read-based phasing

Single-nucleotide conservation state annotation of the SARS-CoV-2 genome

bioRxiv : the preprint server for biology


Personal diploid genome creation and coordinate conversion

Genomes of the Mouse Collaborative Cross

HELLS and PRDM9 form a pioneer complex to open chromatin at meiotic recombination hot spots

Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains

Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans


The ApolloScape Open Dataset for Autonomous Driving and its Application.

The ApolloScape Open Dataset for Autonomous Driving and Its Application

IEEE transactions on pattern analysis and machine intelligence

TrafficPredict: Trajectory Prediction for Heterogeneous Traffic-Agents

AADS: Augmented autonomous driving simulation using data-driven algorithms

DVI: Depth Guided Video Inpainting for Autonomous Driving

A Survey on Automated Driving System Testing: Landscapes and Trends

Unsupervised Learning of Depth from Monocular Videos Using 3D-2D Corresponding Constraints

CVPR 2019 WAD Challenge on Trajectory Prediction and 3D Perception


Synthesis Format Conversion Tool

A High-Level LTL Synthesis Format: TLSF v1.0

The 5th Reactive Synthesis Competition (SYNTCOMP 2018): Benchmarks,
  Participants & Results

The 4th Reactive Synthesis Competition (SYNTCOMP 2017): Benchmarks, Participants & Results

The Reactive Synthesis Competition: SYNTCOMP 2016 and Beyond

The Temporal Logic Synthesis Format TLSF v1.2

Synthesis of Compact Strategies for Coordination Programs

Tools and Algorithms for the Construction and Analysis of Systems


High-Performance Face Recognition Library on PaddlePaddle & PyTorch

LowKey: Leveraging Adversarial Attacks to Protect Social Media Users from Facial Recognition

Landmark Guidance Independent Spatio-channel Attention and Complementary Context Information based Facial Expression Recognition

Face.evoLVe: A High-Performance Face Recognition Library

ATFaceGAN: Single Face Image Restoration and Recognition from Atmospheric Turbulence

IEEE International Conference on Automatic Face & Gesture Recognition

M2FPA: A Multi-Yaw Multi-Pitch High-Quality Database and Benchmark for Facial Pose Analysis

Affect Expression Behaviour Analysis in the Wild using Spatio-Channel
  Attention and Complementary Context Information

Technical Challenges for Training Fair Neural Networks

Survey on the Analysis and Modeling of Visual Kinship: A Decade in the Making

Boosting Semi-Supervised Face Recognition with Noise Robustness

Fast and Reliable Probabilistic Face Embeddings in the Wild


CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

Single-cell roadmap of human gonadal development

Spatial multiomics map of trophoblast development in early pregnancy

Spatially resolved multiomics of human cardiac niches

Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment

Single-cell RNA sequencing depicts the local cell landscape in thyroid-associated ophthalmopathy

CellPhoneDB v5: inferring cell-cell communication from single-cell
  multiomics data

A spatiotemporal gene expression and cell atlases of the developing rat ovary


R package for deriving social mixing matrices from survey data.

The epidemiologic impact and cost-effectiveness of new tuberculosis vaccines on multidrug-resistant tuberculosis in India and China

Germany’s fourth COVID-19 wave was mainly driven by the unvaccinated

Germany's current COVID-19 crisis is mainly driven by the unvaccinated

Risk of COVID-19 hospitalisation rises exponentially with age, inversely proportional to T-cell production

Changing social contact patterns among US workers during the COVID-19 pandemic: April 2020 to December 2021.

medRxiv : the preprint server for health sciences


Source code for generating the QGreenland package hosted at https://qgreenland.org/


chimeraviz is an R package that automates the creation of chimeric RNA visualizations.

Molecular characterization of organoids derived from pancreatic intraductal papillary mucinous neoplasms

chimeraviz: a tool for visualizing chimeric RNA

Immuno-genomic classification of colorectal cancer organoids reveals cancer cells with intrinsic immunogenic properties associated with patient survival

Journal of experimental & clinical cancer research : CR

Clinker: visualizing fusion genes detected in RNA-seq data

RNA-sequencing of IDH-wild-type glioblastoma with chromothripsis identifies novel gene fusions with potential oncogenic properties

Detailed Molecular and Immune Marker Profiling of Archival Prostate Cancer Samples Reveals an Inverse Association between TMPRSS2:ERG Fusion Status and Immune Cell Infiltration

FuSpot: a web-based tool for visual evaluation of fusion candidates


Main package


OpenFlow 1.3 switch.

A Survey on Software Defined Networking: Architecture for Next Generation Network

Journal of network and systems management

Timed Consistent Network Updates in Software-Defined Networks

HoneyDOC: An Efficient Honeypot Architecture Enabling All-Round Design

IEEE journal on selected areas in communications

Time4: Time for SDN

IEEE transactions on network and service management/IEEE eTransactions on network and service management

The Road to BOFUSS: The Basic OpenFlow User-space Software Switch

The Case for Data Plane Timestamping in SDN

Conference on Computer Communications Workshops

EdgeML: Towards Network-Accelerated Federated Learning over Wireless
  Edge

Towards a Stateful Forwarding Abstraction to Implement Scalable Network Functions in Software and Hardware

A SDN-based Flexible System for On-the-Fly Monitoring and Treatment of Security Events


Tools for dealing with APOGEE data

ON GALACTIC DENSITY MODELING IN THE PRESENCE OF DUST EXTINCTION

The age–metallicity structure of the Milky Way disc using APOGEE

Monthly Notices of the Royal Astronomical Society

THE CHEMICAL HOMOGENEITY OF OPEN CLUSTERS

The 3D Kinematics of the Orion Nebula Cluster: NIRSPEC-AO Radial Velocities of the Core Population

The Milky Way tomography with APOGEE: intrinsic density distribution and structure of mono-abundance populations

The peculiar globular cluster Palomar 1 and persistence in the SDSS-APOGEE data base

Searching for the extra-tidal stars of globular clusters using high-dimensional analysis and a core particle spray code

Testing the chemical homogeneity of chemically tagged dissolved birth clusters

Carbon-enhanced metal-poor stars in the SDSS–APOGEE data base

Functional Data Analysis for Extracting the Intrinsic Dimensionality of Spectra: Application to Chemical Homogeneity in the Open Cluster M67


Repository for the HiRID ICU Benchmark (HiB) project

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

Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling

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

Generating synthetic mixed-type longitudinal electronic health records for artificial intelligent applications

HiRID-ICU-Benchmark -- A Comprehensive Machine Learning Benchmark on High-resolution ICU Data


A tool to retrieve malware directly from the source for security researchers.

A Survey of Deep Learning Techniques for Cybersecurity in Mobile Networks

IEEE Communications surveys and tutorials/IEEE communications surveys and tutorials

Malware Detection with Neural Network Using Combined Features

Communications in computer and information science

Application of Distance Metric Learning to Automated Malware Detection


Source code for the General Ocean Turbulence Model

Summer Oxygen Dynamics on a Southern Arabian Gulf Coral Reef

Drivers of phytoplankton responses to summer wind events in a stratified lake: A modeling study

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

Model-based data analysis of the effect of winter mixing on primary production in a lake under reoligotrophication


R package for bcbio RNA-seq analysis.

ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair

bcbioRNASeq: R package for bcbio RNA-seq analysis

TET2lesions enhance the aggressiveness ofCEBPA-mutant AML by rebalancingGATA2expression


Bioinformatics tool to find integrons in bacterial genomes

IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella

Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand

Zenodo (CERN European Organization for Nuclear Research)

Coexistence of blaNDM-1 and blaIMP-4 in One Novel Hybrid Plasmid Confers Transferable Carbapenem Resistance in an ST20-K28 Klebsiella pneumoniae

Prevalence and Population Diversity of Listeria monocytogenes Isolated from Dairy Cattle Farms in the Cantabria Region of Spain

Animals : an open access journal from MDPI

Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems


Registration of cells across sessions.

Tracking the Same Neurons across Multiple Days in Ca2+ Imaging Data

Dorsal periaqueductal gray ensembles represent approach and avoidance states

Neural signatures of auditory hypersensitivity following acoustic trauma

Optogenetic frequency scrambling of hippocampal theta oscillations dissociates working memory retrieval from hippocampal spatiotemporal codes

Accelerated social representational drift in the nucleus accumbens in a model of autism


Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

NGL viewer: web-based molecular graphics for large complexes

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

Binder 2.0 - Reproducible, interactive, sharable environments for science at scale

Proceedings of the Python in Science Conferences

3Dmol.js: molecular visualization with WebGL

Web-based molecular graphics for large complexes

Proceedings of the 21st International Conference on Web3D Technology

MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures

Towards an efficient compression of 3D coordinates of macromolecular structures


Lucid library adapted for PyTorch

Similarity and Matching of Neural Network Representations

Robust Feature-Level Adversaries are Interpretability Tools

Don't trust your eyes: on the (un)reliability of feature visualizations

A Unifying Principle for the Functional Organization of Visual Cortex

bioRxiv : the preprint server for biology

DORA: Exploring Outlier Representations in Deep Neural Networks

TorchEsegeta: Framework for Interpretability and Explainability of Image-based Deep Learning Models

Pruning for Feature-Preserving Circuits in CNNs

Visualizing the Diversity of Representations Learned by Bayesian Neural
  Networks

Improve Convolutional Neural Network Pruning by Maximizing Filter Variety


PyTorch model training and layer saturation monitor

SVCCA: Singular Vector Canonical Correlation Analysis for Deep Learning Dynamics and Interpretability

(Input) Size Matters for CNN Classifiers

Should You Go Deeper? Optimizing Convolutional Neural Network Architectures without Training

Spectral Analysis of Latent Representations

Feature Space Saturation during Training


Implementation of Graph Convolutional Networks in TensorFlow

Semi-Supervised Classification with Graph Convolutional Networks

A Comprehensive Survey on Graph Neural Networks

IEEE transactions on neural networks and learning systems

Graph Neural Networks: A Review of Methods and Applications

Revisiting Semi-Supervised Learning with Graph Embeddings

FastGCN: Fast Learning with Graph Convolutional Networks via Importance Sampling

Deep Learning on Graphs: A Survey

Beyond Homophily in Graph Neural Networks: Current Limitations and Effective Designs

On Asymptotic Behaviors of Graph CNNs from Dynamical Systems Perspective

Graph Representation Learning via Graphical Mutual Information Maximization

AM-GCN: Adaptive Multi-channel Graph Convolutional Networks


Utility for analyzing Transformer based representations of language.

minicons: Enabling Flexible Behavioral and Representational Analyses of
  Transformer Language Models

COMPS: Conceptual Minimal Pair Sentences for testing Robust Property Knowledge and its Inheritance in Pre-trained Language Models

Language model acceptability judgements are not always robust to context

A Better Way to Do Masked Language Model Scoring

Experimental Contexts Can Facilitate Robust Semantic Property Inference
  in Language Models, but Inconsistently


A Python toolkit of the BOP benchmark for 6D object pose estimation.

T-LESS: An RGB-D Dataset for 6D Pose Estimation of Texture-less Objects

BOP: Benchmark for 6D Object Pose Estimation

BOP Challenge 2020 on 6D Object Localization

Pose Estimation of Specific Rigid Objects


A K8s operator to reduce CO2 footprint of your clusters


Code for geophysical 3D/2D Finite Difference modelling, Marchenko algorithms, 2D/3D x-w migration and utilities.

Monitoring induced distributed double-couple sources using Marchenko-based virtual receivers

Virtual Sources and Receivers in the Real Earth: Considerations for Practical Applications

Journal of geophysical research. Solid earth

Virtual acoustics in inhomogeneous media with single-sided access

3D Marchenko applications: implementation and examples

3-D Virtual Seismology

IEEE transactions on geoscience and remote sensing

Virtual sources and receivers in the real Earth, a method for induced seismicity monitoring


I decide to sync up this repo and self-critical.pytorch. (The old master is in old master branch for archive)

Bottom-Up and Top-Down Attention for Image Captioning and Visual Question Answering

Self-critical Sequence Training for Image Captioning

Few-Shot Bot: Prompt-Based Learning for Dialogue Systems

Twin Networks: Matching the Future for Sequence Generation

Generating Diverse and Meaningful Captions

Rethinking Surgical Captioning: End-to-End Window-Based MLP Transformer Using Patches

Retrieval, Analogy, and Composition: A framework for Compositional Generalization in Image Captioning

Findings of the Association for Computational Linguistics: EMNLP 2021

Neural Image Captioning


CCL 2022 汉语学习者文本纠错评测

MuCGEC: a Multi-Reference Multi-Source Evaluation Dataset for Chinese Grammatical Error Correction

YACLC: A Chinese Learner Corpus with Multidimensional Annotation


ACOLITE: generic atmospheric correction module

Using Optical Water Types to Monitor Changes in Optically Complex Inland and Coastal Waters

Analysis and Classification of Stormwater and Wastewater Runoff From the Tijuana River Using Remote Sensing Imagery

Validation of Landsat 8 high resolution Sea Surface Temperature using surfers


SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Mechanisms of APOBEC3 mutagenesis in human cancer cells

The mutational signature profile of known and suspected human carcinogens in mice

The landscape of genetic aberrations in myxofibrosarcoma

Whole-genome analysis identifies novel drivers and high-risk double-hit events in relapsed/refractory myeloma

Identification of New Genes Involved in Germline Predisposition to Early-Onset Gastric Cancer

International journal of molecular sciences

Unravelling the instability of mutational signatures extraction via archetypal analysis

Somatic structural variation signatures in pediatric brain tumors

medRxiv : the preprint server for health sciences


Simple web service providing a word embedding model

A comparison of word embeddings for the biomedical natural language processing

A clinical text classification paradigm using weak supervision and deep representation

BMC medical informatics and decision making

Towards Deep Learning in Hindi NER: An approach to tackle the Labelled
  Data Scarcity

Synchronization in Interpersonal Speech

ASU: An Experimental Study on Applying Deep Learning in Twitter Named Entity Recognition.

International Conference on Computational Linguistics

Towards Lexical Chains for Knowledge-Graph-based Word Embeddings

Recent Advances in Natural Language Processing

Semantically Enhanced Models for Commonsense Knowledge Acquisition

A Deep Representation Empowered Distant Supervision Paradigm for
  Clinical Information Extraction


Laplace approximations for Deep Learning.

Laplace Redux -- Effortless Bayesian Deep Learning

Bayesian Deep Learning via Subnetwork Inference

Adapting the Linearised Laplace Model Evidence for Modern Deep Learning

Mixtures of Laplace Approximations for Improved Post-Hoc Uncertainty in
  Deep Learning

NeuralEF: Deconstructing Kernels by Deep Neural Networks


ProSPr: Protein Structure Prediction

ProSPr: Democratized Implementation of Alphafold Protein Distance Prediction Network

Evaluation of Deep Neural Network ProSPr for Accurate Protein Distance Predictions on CASP14 Targets

The whole is greater than its parts: ensembling improves protein contact prediction

Accelerating Antimicrobial Peptide Discovery with Latent Structure


Mummer alignment tool

Technology dictates algorithms: Recent developments in read alignment

A chromosome-level draft genome of the grain aphid Sitobion miscanthi

The genome of Nautilus pompilius illuminates eye evolution and biomineralization

Analysis of an improved Cyanophora paradoxa genome assembly

DNA research : an international journal for rapid publication of reports on genes and genomes

Construction of Pseudomolecules for the Chinese Chestnut (Castanea mollissima) Genome

Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Tracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16

Campylobacter bacteriophage DA10: an excised temperate bacteriophage targeted by CRISPR-cas

Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators

A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome


Tool to extract indicators of compromise from security reports in PDF format

Enabling Efficient Cyber Threat Hunting With Cyber Threat Intelligence

Automated Dataset Generation System for Collaborative Research of Cyber Threat Analysis

Malware triage for early identification of Advanced Persistent Threat
  activities

The Rise of GoodFATR: A Novel Accuracy Comparison Methodology for Indicator Extraction Tools

Identifying Authorship Style in Malicious Binaries: Techniques, Challenges & Datasets.


Spongy Castle - a repackage of Bouncy Castle for Android (which ships a crippled version of BC)

How Reliable is the Crowdsourced Knowledge of Security Implementation?

2FE: Two-Factor Encryption for Cloud Storage

Secure Audio-Visual Data Exchange for Android In-Vehicle Ecosystems


Topology Optimization using Python

TopologyGAN: Topology Optimization Using Generative Adversarial Networks Based on Physical Fields Over the Initial Domain

3D Topology Optimization using Convolutional Neural Networks

A Comparative Study of the Application of Different Commercial Software for Topology Optimization

Sensitivity Analysis of Key Formulations of Topology Optimization on an Example of Cantilever Bending Beam

From Concept to Manufacturing: Evaluating Vision-Language Models for
  Engineering Design

Topology optimization using PETSc: a Python wrapper and extended functionality

Structural and multidisciplinary optimization


A framework for using LSTMs to detect anomalies in multivariate time series data. Includes spacecraft anomaly data and experiments from the Mars Science Laboratory and SMAP missions.

Deep Learning for Anomaly Detection: A Survey

Detecting Spacecraft Anomalies Using LSTMs and Nonparametric Dynamic Thresholding

A review on outlier/anomaly detection in time series data

TranAD: Deep Transformer Networks for Anomaly Detection in Multivariate
  Time Series Data

An Evaluation of Anomaly Detection and Diagnosis in Multivariate Time Series

Deep Learning-Based Anomaly Detection in Cyber-Physical Systems: Progress and Opportunities

Unsupervised Time Series Outlier Detection with Diversity-Driven Convolutional Ensembles

Combining OC-SVMs With LSTM for Detecting Anomalies in Telemetry Data With Irregular Intervals

Sintel: A Machine Learning Framework to Extract Insights from Signals

Proceedings of the 2022 International Conference on Management of Data

AER: Auto-Encoder with Regression for Time Series Anomaly Detection


Tools for detecting wildlife in aerial images using active learning

AIDE: Accelerating image-based ecological surveys with interactive machine learning


High-Resolution 3D Human Digitization from A Single Image.

PIFuHD: Multi-Level Pixel-Aligned Implicit Function for High-Resolution 3D Human Digitization

GETAvatar: Generative Textured Meshes for Animatable Human Avatars

Occupancy Planes for Single-view RGB-D Human Reconstruction


A Python implementation of Deep Belief Networks built upon NumPy and TensorFlow with scikit-learn compatibility

A Hybrid Hidden Markov Model for Pipeline Leakage Detection

A Neural Network Aided Real-Time Hospital Recommendation System

Indonesian journal of science and technology


Code for "Heterogeneous Graph Transformer" (WWW'20), which is based on pytorch_geometric

Heterogeneous Graph Transformer

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

DiffMG: Differentiable Meta Graph Search for Heterogeneous Graph Neural Networks

xFraud: Explainable Fraud Transaction Detection

OAG-BERT: Towards a Unified Backbone Language Model for Academic Knowledge Services

Differentiable Meta Multigraph Search with Partial Message Propagation on Heterogeneous Information Networks


fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).

Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach

TargetDB: A target information aggregation tool and tractability predictor

SHREC 2022: Protein-ligand binding site recognition

Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery

Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations

Journal of chemical information and modeling

EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for
  Ligand Binding Site Prediction


Large scale K-means and K-nn implementation on NVIDIA GPU / CUDA

Cluster-Former: Clustering-based Sparse Transformer for Long-Range Dependency Encoding

Context Mover's Distance & Barycenters: Optimal transport of contexts for building representations

Deep Kernel Learning for Clustering

Zoom: SSD-based Vector Search for Optimizing Accuracy, Latency and Memory.

Correlating Twitter Language with Community-Level Health Outcomes

A Generic Distributed Clustering Framework for Massive Data

Modeling Dynamics of Facial Behavior for Mental Health Assessment