FSA (Fisheries Stock Assessment) package provides R functions to conduct typical introductory fisheries analyses.

Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis

Gut microbiota density influences host physiology and is shaped by host and microbial factors

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

Organic Amendments Alleviate Salinity Effects on Soil Microorganisms and Mineralisation Processes in Aerobic and Anaerobic Paddy Rice Soils

Size-Tunable Nanoneedle Arrays for Influencing Stem Cell Morphology, Gene Expression, and Nuclear Membrane Curvature

Dispersal–niche continuum index: a new quantitative metric for assessing the relative importance of dispersal versus niche processes in community assembly

Recycling pathways in cold-water coral reefs: Use of dissolved organic matter and bacteria by key suspension feeding taxa

Productive wetlands restored for carbon sequestration quickly become net CO2 sinks with site-level factors driving uptake variability

Differences in Biofilm Mass, Expression of Biofilm-Associated Genes, and Resistance to Desiccation between Epidemic and Sporadic Clones of Carbapenem-Resistant Acinetobacter baumannii Sequence Type 191

Changes in the Vaginal Microbiome during the Pregnancy to Postpartum Transition

Reproductive sciences (Thousand Oaks, Calif.)


Python/numpy bootstrap confidence interval estimation.

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

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

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

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

Monthly Notices of the Royal Astronomical Society

Elastic moduli fluctuations predict wave attenuation rates in glasses

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

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

Abstractive Compression of Captions with Attentive Recurrent Neural Networks

International Conference on Natural Language Generation


A fast parallel implementation of RNN Transducer.

Speech Recognition with Deep Recurrent Neural Networks

Sequence Transduction with Recurrent Neural Networks

A New Training Pipeline for an Improved Neural Transducer

Librispeech Transducer Model with Internal Language Model Prior Correction

Neural Transducer Training: Reduced Memory Consumption with Sample-wise Computation


CheXpert NLP tool to extract observations from radiology reports.

CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison

Deep learning in generating radiology reports: A survey

Deep Mining External Imperfect Data for Chest X-Ray Disease Screening

Structured dataset documentation: a datasheet for CheXpert

Cross-modal Contrastive Attention Model for Medical Report Generation

International Conference on Computational Linguistics

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

Leveraging Professional Radiologists' Expertise to Enhance LLMs'
  Evaluation for Radiology Reports

Enhancing chest X-ray datasets with privacy-preserving large language
  models and multi-type annotations: a data-driven approach for improved
  classification


STAR-Fusion codebase

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

The driver landscape of sporadic chordoma

A first-generation pediatric cancer dependency map

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

Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations

Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers

Familial thrombocytopenia due to a complex structural variant resulting in a WAC-ANKRD26 fusion transcript

Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma

Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival

Identification and Characterization of Non-Coding RNAs in Thymoma

Medical science monitor : international medical journal of experimental and clinical research


U-Net Biomedical Image Segmentation

Decentralized Federated Learning for Healthcare Networks: A Case Study on Tumor Segmentation

Systematic Evaluation of Image Tiling Adverse Effects on Deep Learning Semantic Segmentation

Implementation of a Modified U-Net for Medical Image Segmentation on Edge Devices

IEEE Transactions on Circuits and Systems II: Express Briefs

Addressing the Memory Bottleneck in AI Model Training


DPU on PYNQ

Efficient Edge-AI Application Deployment for FPGAs

Embedded Object Detection with Custom LittleNet, FINN and Vitis AI DCNN Accelerators

Journal of Low Power Electronics and Applications


A C++/Python simulator package for reinforcement learning

Interactive Grounded Language Acquisition and Generalization in a 2D World

Guided Feature Transformation (GFT): A Neural Language Grounding Module for Embodied Agents

Listen, Interact and Talk: Learning to Speak via Interaction

Interactive Language Acquisition with One-shot Visual Concept Learning through a Conversational Game


:rocket: State-of-the-art parsers for natural language.

Deep Biaffine Attention for Neural Dependency Parsing

Masked Language Modeling and the Distributional Hypothesis: Order Word Matters Pre-training for Little

Simpler but More Accurate Semantic Dependency Parsing

Investigating Typed Syntactic Dependencies for Targeted Sentiment Classification Using Graph Attention Neural Network

Efficient Second-Order TreeCRF for Neural Dependency Parsing

Fast and Accurate Neural CRF Constituency Parsing

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

Second-Order Semantic Dependency Parsing with End-to-End Neural Networks

Pushing on Text Readability Assessment: A Transformer Meets Handcrafted Linguistic Features

BiSyn-GAT+: Bi-Syntax Aware Graph Attention Network for Aspect-based Sentiment Analysis

Findings of the Association for Computational Linguistics: ACL 2022

Substructure Substitution: Structured Data Augmentation for NLP


Open-source C++ implementation of the recently proposed online active set strategy

Nonlinear Model Predictive Velocity Control of a VTOL Tiltwing UAV

International Conference on Robotics and Automation

Model predictive force control in milling based on an ensemble Kalman filter

Modelling, Analysis, and Control of OmniMorph: an Omnidirectional Morphing Multi-rotor UAV

Fast Iterative Region Inflation for Computing Large 2-D/3-D Convex
  Regions of Obstacle-Free Space

A Flexible MATLAB/Simulink Simulator for Robotic Floating-base Systems in Contact with the Ground


TorchCFM: a Conditional Flow Matching library

Improving and generalizing flow-based generative models with minibatch optimal transport

Diffusion Schrödinger Bridge Matching

Simulation-free Schrödinger bridges via score and flow matching

On the Stability of Iterative Retraining of Generative Models on their own Data

Generating and Imputing Tabular Data via Diffusion and Flow-based Gradient-Boosted Trees

Light and Optimal Schrödinger Bridge Matching

Neural Sinkhorn Gradient Flow

Optimal Flow Matching: Learning Straight Trajectories in Just One Step


A curated list of software and resources for exploring and visualizing (browsing) expression data

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

Mapping the Mouse Cell Atlas by Microwell-Seq

Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry

A human liver cell atlas reveals heterogeneity and epithelial progenitors

Human haematopoietic stem cell lineage commitment is a continuous process

A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

The bone marrow microenvironment at single-cell resolution

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation.

Giotto: a toolbox for integrative analysis and visualization of spatial expression data


Command language for IRAF based on Python.

Type IIn supernova light-curve properties measured from an untargeted survey sample

A refined dynamical mass for the black hole in the X-ray transient XTE J1859+226


Python API for Tesla Powerwall


Hagelslag supports segmentation and tracking of weather fields and scalable verification, including performance diagrams and reliability diagrams.


Wiktionary dump file parser and multilingual data extractor

Continuous Learning in Neural Machine Translation using Bilingual Dictionaries

Wiktextract: Wiktionary as Machine-Readable Structured Data

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION

KaLM at SemEval-2020 Task 4: Knowledge-aware Language Models for Comprehension And Generation

Mitigating Data Imbalance and Representation Degeneration in Multilingual Machine Translation

Taboo and Collaborative Knowledge Production: Evidence from Wikipedia

Proceedings of the ACM on Human-Computer Interaction


A fast radio interferometric calibration suite.

CUBICAL - fast radio interferometric calibration suite exploiting complex optimization

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

A new look at old friends – I. Imaging classical radio galaxies with uGMRT and MeerKAT

Nature of the unusual transient AT 2018cow from HI observations of its host galaxy

HAL (Le Centre pour la Communication Scientifique Directe)

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

MeerKATHI -- an end-to-end data reduction pipeline for MeerKAT and other radio telescopes

Mining mini-halos with MeerKAT I. Calibration and imaging

The Interstellar Medium in the Environment of the Supernova-less Long-duration GRB 111005A

The Astrophysical Journal Supplement Series

Solution intervals considered harmful: on the optimality of radio interferometric gain solutions

HI in and behind the Hubble Frontier Field Clusters: A Deep MeerKAT Pilot Search out to z∼ 0.5


Creative Commons Attribution Share Alike 4.0 International

SimulEval: A General Evaluation Toolkit for Simultaneous Translation

Information-Transport-based Policy for Simultaneous Translation

Streaming Simultaneous Speech Translation with Augmented Memory Transformer

An Empirical Study of End-to-end Simultaneous Speech Translation Decoding Strategies

End-to-End Simultaneous Speech Translation with Differentiable Segmentation

TransLLaMa: LLM-based Simultaneous Translation System

Unified Segment-to-Segment Framework for Simultaneous Sequence Generation

A Non-autoregressive Generation Framework for End-to-End Simultaneous Speech-to-Any Translation

The Xiaomi AI Lab’s Speech Translation Systems for IWSLT 2023 Offline Task, Simultaneous Task and Speech-to-Speech Task

Proceedings of the 20th International Conference on Spoken Language Translation (IWSLT 2023)

Implicit Memory Transformer for Computationally Efficient Simultaneous Speech Translation

Training Simultaneous Speech Translation with Robust and Random Wait-k-Tokens Strategy

Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing


Lisflood OS - LISFLOOD

Independence of Future Changes of River Runoff in Europe from the Pathway to Global Warming


GenieNLP: A versatile codebase for any NLP task

The Natural Language Decathlon: Multitask Learning as Question Answering

AutoQA: From Databases To QA Semantic Parsers With Only Synthetic Training Data

Schema2QA: High-Quality and Low-Cost Q&A Agents for the Structured Web

Contextual Semantic Parsing for Multilingual Task-Oriented Dialogues

X-RiSAWOZ: High-Quality End-to-End Multilingual Dialogue Datasets and Few-shot Agents


An R package for stock-assessment simulation with Stock Synthesis


AutoAWQ implements the AWQ algorithm for 4-bit quantization with a 2x speedup during inference. Documentation:

AWQ: Activation-aware Weight Quantization for LLM Compression and Acceleration

Demystifying the Compression of Mixture-of-Experts Through a Unified
  Framework

SmoothQuant+: Accurate and Efficient 4-bit Post-Training WeightQuantization for LLM

LimGen: Probing the LLMs for Generating Suggestive Limitations of Research Papers


Jupyter-friendly Python interface for C++ MINUIT2

The Completed SDSS-IV Extended Baryon Oscillation Spectroscopic Survey: Baryon Acoustic Oscillations with Lyα Forests

Spectral properties of 441 radio pulsars

The Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: measurement of the BAO and growth rate of structure of the emission line galaxy sample from the anisotropic power spectrum between redshift 0.6 and 1.1

The completed SDSS-IV extended baryon oscillation spectroscopic survey: growth rate of structure measurement from anisotropic clustering analysis in configuration space between redshift 0.6 and 1.1 for the emission-line galaxy sample

A New View on Auger Data and Cosmogenic Neutrinos in Light of Different Nuclear Disintegration and Air-shower Models

Is cosmic acceleration proven by local cosmological probes?

The on-orbit calibration of DArk Matter Particle Explorer

Strange molecular partners of the
Zc(3900)
 and
Zc(4020)

Interacting radiation after Planck and its implications for the Hubble tension

Journal of Cosmology and Astroparticle Physics

Integral constraints in spectroscopic surveys


LOFAR solutions tool

Systematic effects in LOFAR data: A unified calibration strategy

LOFAR/H-ATLAS: A deep low-frequency survey of the Herschel-ATLAS North
  Galactic Pole field

The effect of the ionosphere on ultra-low-frequency radio-interferometric observations

LOFAR VLBI Studies at 55 MHz of 4C 43.15, a z=2.4 Radio Galaxy

LOFAR detection of a low-power radio halo in the galaxy cluster Abell 990

Monthly notices of the Royal Astronomical Society

Pushing sub-arcsecond resolution imaging down to 30 MHz with the trans-European International LOFAR Telescope


Deep Learning Library for Single Cell Analysis

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning

Spatial predictors of immunotherapy response in triple-negative breast cancer

Deep Learning in Single-Cell Analysis

SiCTeC: an inexpensive, easily assembled Peltier device for rapid temperature shifting during single-cell imaging

Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning

bioRxiv : the preprint server for biology


Building Optimization Performance Tests


A scikit-learn-compatible module to estimate prediction intervals and control risks based on conformal predictions.

Distribution-Free, Risk-Controlling Prediction Sets

Conformal prediction interval for dynamic time-series

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

Monitoring Model Deterioration with Explainable Uncertainty Estimation via Non-parametric Bootstrap

Beyond mirkwood: Enhancing SED Modeling with Conformal Predictions

Uncertainty Quantification of the Virial Black Hole Mass with Conformal Prediction

Conformal Prediction in Multi-User Settings: An Evaluation


XML Canonical resources for Greek Literature

An automatic model and Gold Standard for translation alignment of Ancient Greek

The GLAUx corpus: methodological issues in designing a long-term, diverse, multi-layered corpus of Ancient Greek

Workshop on Computational Approaches to Historical Language Change

BERT in Plutarch's Shadows

Hippocrates transformed: crafting a Hippocratic discourse of medical semiotics in English, 1850–1930

Humanities and Social Sciences Communications


An optimized graphs package for the Julia programming language

Learning with Combinatorial Optimization Layers: a Probabilistic Approach

Incremental Dead State Detection in Logarithmic Time

Wireless Network Scheduling With Discrete Propagation Delays: Theorems and Algorithms

Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data


Combinatorial Optimization with Graph Convolutional Networks and Guided Tree Search

Deep Learning on Graphs: A Survey

Learning What to Defer for Maximum Independent Sets

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

Adaptive solution prediction for combinatorial optimization


[ICCV 2023] Official PyTorch implementation for the paper "FreeDoM: Training-Free Energy-Guided Conditional Diffusion Model"

ArcFace: Additive Angular Margin Loss for Deep Face Recognition

IEEE Transactions on Pattern Analysis and Machine Intelligence

Manifold Preserving Guided Diffusion

Text-guided Explorable Image Super-resolution


VulDeePecker: A Deep Learning-Based System for Vulnerability Detection

Proceedings 2018 Network and Distributed System Security Symposium

SySeVR: A Framework for Using Deep Learning to Detect Software Vulnerabilities

IEEE Transactions on Dependable and Secure Computing

Deep Learning based Vulnerability Detection: Are We There Yet?

Transformer-Based Language Models for Software Vulnerability Detection

Efficient Feature Selection for Static Analysis Vulnerability Prediction

Deep Cost-Sensitive Kernel Machine for Binary Software Vulnerability Detection

Pacific-Asia Conference on Knowledge Discovery and Data Mining


Tutorial for surrogate gradient learning in spiking neural networks

Training Spiking Neural Networks Using Lessons From Deep Learning

The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks

The Heidelberg Spiking Data Sets for the Systematic Evaluation of Spiking Neural Networks

IEEE transactions on neural networks and learning systems

Surrogate Gradient Learning in Spiking Neural Networks

Brain Inspired Computing: A Systematic Survey and Future Trends

Toward robust and scalable deep spiking reinforcement learning

Explicitly Trained Spiking Sparsity in Spiking Neural Networks with Backpropagation


Particle swarm optimization (PSO) that supports constraints

Benchmarking Five Global Optimization Approaches for Nano-optical Shape Optimization and Parameter Reconstruction

A PSF-based approach to Kepler/K2 data – II. Exoplanet candidates in Praesepe (M 44)

Monthly Notices of the Royal Astronomical Society

A PSF-based approach to Kepler/K2 data - III. Search for exoplanets and variable stars within the open cluster M 67 (NGC 2682)

An artificial neural network to discover hypervelocity stars: candidates in Gaia DR1/TGAS

Planning a sports training program using Adaptive Particle Swarm Optimization with emphasis on physiological constraints

In Silico Modeling of Biofilm Formation by Nontypeable Haemophilus influenzae In Vivo

Advancing Standards-Free Methods for the Identification of Small Molecules in Complex Samples

Comparing Single-Objective Optimization Protocols for Calibrating the Birds Nest Aquifer Model—A Problem Having Multiple Local Optima

International journal of environmental research and public health

Searching for long faint astronomical high energy transients: a data driven approach

DARK SAGE: Next-generation semi-analytic galaxy evolution with multidimensional structure and minimal free parameters


Fast & Simple repository for pre-training and fine-tuning T5-style models

The MiniPile Challenge for Data-Efficient Language Models

nanoT5: A PyTorch Framework for Pre-training and Fine-tuning T5-style Models with Limited Resources

FLawN-T5: An Empirical Examination of Effective Instruction-Tuning Data
  Mixtures for Legal Reasoning


SKESA assembler

The Pfam protein families database in 2019

SKESA: strategic k-mer extension for scrupulous assemblies

Genomic Characteristics of Stx2e-Producing Escherichia coli Strains Derived from Humans, Animals, and Meats

High Prevalence and Persistence of Escherichia coli Strains Producing Shiga Toxin Subtype 2k in Goat Herds

Molecular characterisation of Acinetobacter baumannii isolates from bloodstream infections in a tertiary-level hospital in South Africa

In Vitro Activity of Ceftolozane-Tazobactam against Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa Obtained from Blood Cultures from Sentinel Public Hospitals in South Africa

Impact of wet-lab protocols on quality of whole-genome short-read sequences from foodborne microbial pathogens

The Emergence and Impact of the M1UK Lineage on Invasive Group A Streptococcus Disease in Aotearoa New Zealand

Bacterial and Genetic Features of Raw Retail Pork Meat: Integrative Analysis of Antibiotic Susceptibility, Whole-Genome Sequencing, and Metagenomics


Variant calling and somatic mutation/CNV detection for next-generation sequencing data

Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia

Vaccination decreases the risk of influenza A virus reassortment but not genetic variation in pigs

Lineage Divergence of Dendrolimus punctatus in Southern China Based on Mitochondrial Genome

Virologic Outcomes with Molnupiravir in Non-hospitalized Adult Patients with COVID-19 from the Randomized, Placebo-Controlled MOVe-OUT Trial

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

Protocol for the development of joint attention-based subclassification of autism spectrum disorder and validation using multi-modal data


Repository for Med2Vec project

Multi-layer Representation Learning for Medical Concepts

Intelligent Health Care: Applications of Deep Learning in Computational Medicine

TRACE: Early Detection of Chronic Kidney Disease Onset with Transformer-Enhanced Feature Embedding


Pytorch NLP library based on FastAI

A Neural Conversational Model

Massive Exploration of Neural Machine Translation Architectures

Depthwise Separable Convolutions for Neural Machine Translation

Texar: A Modularized, Versatile, and Extensible Toolkit for Text Generation


The official code for “DocTr: Document Image Transformer for Geometric Unwarping and Illumination Correction”, ACM MM, Oral Paper, 2021.

DocScanner: Robust Document Image Rectification with Progressive Learning

Marior: Margin Removal and Iterative Content Rectification for Document Dewarping in the Wild


[ICLR 2020] Contrastive Representation Distillation (CRD), and benchmark of recent knowledge distillation methods

Contrastive Representation Distillation

Knowledge Distillation via the Target-aware Transformer

Learning Student-Friendly Teacher Networks for Knowledge Distillation

CompRess: Self-Supervised Learning by Compressing Representations

Curriculum Temperature for Knowledge Distillation

Improved Feature Distillation via Projector Ensemble

What Makes a "Good" Data Augmentation in Knowledge Distillation -- A Statistical Perspective

Meta Knowledge Distillation

Distilling Knowledge by Mimicking Features

IEEE transactions on pattern analysis and machine intelligence

Distilling and Transferring Knowledge via cGAN-generated Samples for Image Classification and Regression


Short tutorial supplementing the Neural Networks and Deep Learning chapter from Artificial Intelligence in Surgery: An AI Primer for Surgical Practice designed to offer hands-on experience with artificial neural networks to surgeons with little to no coding experience.

EndoNet: A Deep Architecture for Recognition Tasks on Laparoscopic Videos

Weakly-Supervised Learning for Tool Localization in Laparoscopic Videos

Artificial Intelligence in Surgery: Neural Networks and Deep Learning


A suite of MiniZinc benchmarks.

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

Modelling and Solving Online Optimisation Problems

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

Learning Objective Boundaries for Constraint Optimization Problems


R interface to D3 chord diagrams

The LOTUS initiative for open knowledge management in natural products research

Using a Chord Diagram to Visualize Dynamics in Contraceptive Use: Bringing Data Into Practice

An Empirical Analysis of Synergies and Tradeoffs between Sustainable Development Goals

Optimizing COVID-19 vaccine distribution across the United States using deterministic and stochastic recurrent neural networks

Analyzing author collaborations by developing a follower-leader clustering algorithm and identifying top co-authoring countries: Cluster analysis

Analysis of RASFF notifications on contaminated dairy products from the last two decades: 2000-2020

Molecular evidence for extensive discontinuity between peracarid (Crustacea) fauna of Macaronesian islands and nearby continental coasts: over fifty candidate endemic species


Distribution package for the Prgressive Cactus multiple genome aligner.  Dependencies are linked as submodules

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

Comparative assembly hubs: Web-accessible browsers for comparative genomics

Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding

Evolutionarily conserved non-protein-coding regions in the chicken genome harbor functionally important variation


[AAAI-23 Oral] Official implementation of the paper "Are Transformers Effective for Time Series Forecasting?"

TSMixer: Lightweight MLP-Mixer Model for Multivariate Time Series Forecasting

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

The Capacity and Robustness Trade-off: Revisiting the Channel Independent Strategy for Multivariate Time Series Forecasting

Frequency-domain MLPs are More Effective Learners in Time Series Forecasting

Pathformer: Multi-scale Transformers with Adaptive Pathways for Time Series Forecasting

PETformer: Long-term Time Series Forecasting via Placeholder-enhanced Transformer

Attractor Memory for Long-Term Time Series Forecasting: A Chaos
  Perspective

Time-SSM: Simplifying and Unifying State Space Models for Time Series Forecasting

From Similarity to Superiority: Channel Clustering for Time Series
  Forecasting

Deep Coupling Network For Multivariate Time Series Forecasting


QGIS toolkit  for pre- and post-processing , visualizing , and running simulations  in the Weather Research and Forecasting (WRF) model

Open source QGIS toolkit for the Advanced Research WRF modelling system


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

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

Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function

Axon guidance pathways modulate neurotoxicity of ALS-associated UBQLN2

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

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

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


Prevent oil and gas companies from co-opting your work and extracting more fossil fuels with this software license.


ATOM3D: tasks on molecules in three dimensions

ATOM3D: Tasks On Molecules in Three Dimensions

AI in drug discovery and its clinical relevance

Pre‐Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding

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


Survival package for R

hsCRP Level and the Risk of Death or Recurrent Cardiovascular Events in Patients With Myocardial Infarction: a Healthcare‐Based Study

Journal of the American Heart Association : Cardiovascular and Cerebrovascular Disease

Automated image analysis of NSCLC biopsies to predict response to anti-PD-L1 therapy

Survival analysis: part II – applied clinical data analysis

Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response

Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes

Determinants of frailty development and progression using a multidimensional frailty index: Evidence from the English Longitudinal Study of Ageing

Integrative Tumor and Immune Cell Multi-omic Analyses Predict Response to Immune Checkpoint Blockade in Melanoma

When and where mortality occurs throughout the annual cycle changes with age in a migratory bird: individual vs population implications

Expressed fusion gene landscape and its impact in multiple myeloma

Unraveling the Host Plant Alternation of Cacopsylla pruni – Adults but Not Nymphs Can Survive on Conifers Due to Phloem/Xylem Composition


Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

Attention-Based Deep Neural Networks for Detection of Cancerous and Precancerous Esophagus Tissue on Histopathological Slides

Development and evaluation of a deep neural network for histologic classification of renal cell carcinoma on biopsy and surgical resection slides

Computational Pathology: A Survey Review and The Way Forward

Deep neural networks for automated classification of colorectal polyps on histopathology slides: A multi-institutional evaluation


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

The longitudinal dynamics and natural history of clonal haematopoiesis

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

The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

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

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

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

Genomic consequences of domestication of the Siamese fighting fish

Targeting MEK in vemurafenib-resistant hairy cell leukemia

Clonal haematopoiesis is not prevalent in survivors of childhood cancer

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


Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

Prediction of acute myeloid leukaemia risk in healthy individuals

Tobacco Exposure and Somatic Mutations in Normal Human Bronchial Epithelium

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

Mechanisms of APOBEC3 mutagenesis in human cancer cells

Recurrent intragenic rearrangements of EGFR and BRAF in soft tissue tumors of infants

A recurrent novel MGA-NUTM1 fusion identifies a new subtype of high-grade spindle cell sarcoma.

Single cell derived mRNA signals across human kidney tumors

Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma

Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers


A deep learning toolkit specialized for handwritten document analysis

A survey of historical document image datasets

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

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

Large-scale genealogical information extraction from handwritten Quebec parish records

Key-value information extraction from full handwritten pages

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

Handwritten Text Recognition from Crowdsourced Annotations

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


Python framework for Virtual Heart Rate

VIPL-HR: A Multi-modal Database for Pulse Estimation from Less-constrained Face Video

An Open Framework for Remote-PPG Methods and Their Assessment

pyVHR: a Python framework for remote photoplethysmography

Hiding Your Signals: A Security Analysis of PPG-based Biometric Authentication

Person Re-identification Attack on Wearable Sensing


An ecosystem of data, models and code pipelines to tackle flooding with ML


Small language toolkit for creation, interpolation and pruning of ARPA language models

TED-LIUM 3: Twice as Much Data and Corpus Repartition for Experiments on Speaker Adaptation

Arabic Speech Recognition by End-to-End, Modular Systems and Human

Multistream CNN for Robust Acoustic Modeling

ASAPP-ASR: Multistream CNN and Self-Attentive SRU for SOTA Speech Recognition

An enhanced automatic speech recognition system for Arabic

Proceedings of the Third Arabic Natural Language Processing Workshop

Word Error Rate Estimation Without ASR Output: e-WER2

Scribosermo: Fast Speech-to-Text models for German and other Languages

"This is Houston. Say again, please". The Behavox system for the Apollo-11 Fearless Steps Challenge (phase II)


Hamilton-Jacobi Reachability: A Brief Overview and Recent Advances

Safe Nonlinear Control Using Robust Neural Lyapunov-Barrier Functions

BaRC: Backward Reachability Curriculum for Robotic Reinforcement Learning

Reachability-Based Safety Guarantees using Efficient Initializations

Formal Certification Methods for Automated Vehicle Safety Assessment

Reach-Avoid Problems via Sum-of-Squares Optimization and Dynamic Programming

Hamilton-Jacobi Equations for Two Classes of State-Constrained Zero-Sum Games

TTR-Based Reward for Reinforcement Learning with Implicit Model Priors

Safety Verification of Model Based Reinforcement Learning Controllers

On Safety and Liveness Filtering Using Hamilton-Jacobi Reachability Analysis


Upper atmosphere climatological models in Python

Snakes on a Spaceship—An Overview of Python in Heliophysics

Journal of Geophysical Research: Space Physics

New results on equatorial thermospheric winds and temperatures from Ethiopia, Africa

Climatology of thermospheric neutral winds over Oukaïmeden Observatory in Morocco

Evaluation of Ionospheric Scintillation in GNSS Radio Occultation Measurements and Simulations

On a simple, data-aided analytic description of the morphology of equatorial F-region zonal plasma drifts

On Definition of BigData


Just another Hearthstone Simulator in C# .Net Core, with some A.I. approaches!

Mapping Hearthstone Deck Spaces through MAP-Elites with Sliding Boundaries

Improving Hearthstone AI by Combining MCTS and Supervised Learning Algorithms

Evolving the Hearthstone Meta

The Many AI Challenges of Hearthstone


OpenFOAM-preCICE adapter

preCICE v2: A sustainable and user-friendly coupling library

FEniCS-preCICE: Coupling FEniCS to other Simulation Software

Steady-state aeroelasticity of a ram-air wing for airborne wind energy applications

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

Gym-preCICE: Reinforcement Learning Environments for Active Flow Control


UQpy (Uncertainty Quantification with python) is a general purpose Python toolbox for modeling uncertainty in physical and mathematical systems.

Modern Monte Carlo methods for efficient uncertainty quantification and propagation: A survey

UQpy: A general purpose Python package and development environment for uncertainty quantification

Korali: Efficient and scalable software framework for Bayesian uncertainty quantification and stochastic optimization

UQpy v4.1: Uncertainty Quantification with Python

Korali: a High-Performance Computing Framework for Stochastic Optimization and Bayesian Uncertainty Quantification.

Reliable Visual Analytics, a Prerequisite for Outcome Assessment of Engineering Systems

Imprecise subset simulation


Turku Event Extraction System

The Genia Event Extraction Shared Task, 2013 Edition - Overview

Meeting of the Association for Computational Linguistics

Biomedical Event Extraction Using Convolutional Neural Networks and Dependency Parsing

Workshop on Biomedical Natural Language Processing

WBI-DDI: Drug-Drug Interaction Extraction using Majority Voting

Joint Conference on Lexical and Computational Semantics

EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction

Biomedical Event Extraction as Multi-turn Question Answering

International Workshop on Health Text Mining and Information Analysis

From POS tagging to dependency parsing for biomedical event extraction

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

Database : the journal of biological databases and curation


A library for performing coverage guided fuzzing of neural networks

TensorFuzz: Debugging Neural Networks with Coverage-Guided Fuzzing

Black-box Adversarial Sample Generation Based on Differential Evolution

Reducing DNN Properties to Enable Falsification with Adversarial Attacks

International Conference on Software Engineering


Unsupervised Statistical Machine Translation

An Effective Approach to Unsupervised Machine Translation

When Does Unsupervised Machine Translation Work?

Bilingual Lexicon Induction through Unsupervised Machine Translation

(Almost) Unsupervised Grammatical Error Correction using Synthetic Comparable Corpus

Workshop on Innovative Use of NLP for Building Educational Applications

CUNI Systems for the Unsupervised News Translation Task in WMT 2019

Towards Unsupervised Grammatical Error Correction using Statistical Machine Translation with Synthetic Comparable Corpus


This repository contains the source codes for the paper "AtlasNet: A Papier-Mâché Approach to Learning 3D Surface Generation ". The network is able to synthesize a mesh (point cloud + connectivity) from a low-resolution point cloud, or from an image.

Occupancy Networks: Learning 3D Reconstruction in Function Space

Learning joint reconstruction of hands and manipulated objects

Learning Gradient Fields for Shape Generation

Shape As Points: A Differentiable Poisson Solver

Info3D: Representation Learning on 3D Objects using Mutual Information Maximization and Contrastive Learning

Sketch2PQ: Freeform Planar Quadrilateral Mesh Design via a Single Sketch

ChartPointFlow for Topology-Aware 3D Point Cloud Generation

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

Deep Learning Assisted Optimization for 3D Reconstruction from Single 2D Line Drawings


The official homepage of the COCO-Stuff dataset.

COCO-Stuff: Thing and Stuff Classes in Context

OCNet: Object Context Network for Scene Parsing

SeaFormer: Squeeze-enhanced Axial Transformer for Mobile Semantic Segmentation

Editing a classifier by rewriting its prediction rules

Mind Reader: Reconstructing complex images from brain activities

Logic-induced Diagnostic Reasoning for Semi-supervised Semantic Segmentation

Label-efficient Segmentation via Affinity Propagation

Identifying and Benchmarking Natural Out-of-Context Prediction Problems

[Re] Don't Judge an Object by Its Context: Learning to Overcome Contextual Bias

From fat droplets to floating forests: cross-domain transfer learning using a PatchGAN-based segmentation model


Model Compression—YOLOv3 with multi lightweight backbones(ShuffleNetV2 HuaWei GhostNet), attention, prune and quantization

Squeeze-and-Excitation Networks

CBAM: Convolutional Block Attention Module

ECA-Net: Efficient Channel Attention for Deep Convolutional Neural Networks


Model extraction attacks on Machine-Learning-as-a-Service platforms.

Stealing Machine Learning Models via Prediction APIs

PRADA: Protecting against DNN Model Stealing Attacks

Stateful Detection of Model Extraction Attacks

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


SRAToolkit has been REPLACED - see README

A global reference for human genetic variation

Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells

11:40-11:50 Comparison of histone H3K4me3 between IVF and ICSI technologies and between boy and girl offspring

Alterations of the gut microbiota associated with the occurrence and progression of viral hepatitis

Frontiers in cellular and infection microbiology

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways


R package for working with CyToF data

Mass cytometry reveals a conserved immune trajectory of recovery in hospitalized COVID-19 patients

High-dimensional immunotyping of tumors grown in obese and non-obese mice

Computational Methods for Single-Cell Proteomics

Annual review of biomedical data science

A conserved immune trajectory of recovery in hospitalized COVID-19 patients

bioRxiv : the preprint server for biology


Point-NeRF: Point-based Neural Radiance Fields

Tetra-NeRF: Representing Neural Radiance Fields Using Tetrahedra

Ponder: Point Cloud Pre-training via Neural Rendering


Safe RLHF: Constrained Value Alignment via Safe Reinforcement Learning from Human Feedback

OPT: Open Pre-trained Transformer Language Models

Safe RLHF: Safe Reinforcement Learning from Human Feedback

Is DPO Superior to PPO for LLM Alignment? A Comprehensive Study

Beyond One-Preference-Fits-All Alignment: Multi-Objective Direct Preference Optimization

Human-Instruction-Free LLM Self-Alignment with Limited Samples

Red Teaming Game: A Game-Theoretic Framework for Red Teaming Language Models

Panacea: Pareto Alignment via Preference Adaptation for LLMs

Unmasking and Improving Data Credibility: A Study with Datasets for Training Harmless Language Models

RLHFPoison: Reward Poisoning Attack for Reinforcement Learning with Human Feedback in Large Language Models

Negating Negatives: Alignment without Human Positive Samples via
  Distributional Dispreference Optimization


Implementation of "Learning Combinatorial Optimization Algorithms over Graphs"

Deep Reinforcement Learning

Learning What to Defer for Maximum Independent Sets

Reinforcement learning on graphs: A survey


Virtual-Taobao simulators with OpenAI Gym interface

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

CIRS: Bursting Filter Bubbles by Counterfactual Interactive Recommender System

User Behavior Simulation with Large Language Model based Agents

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

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

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

Interactive System-wise Anomaly Detection


Quickly comparing your image classification models with the state-of-the-art models (such as DenseNet, ResNet, ...)

Deep Residual Learning for Image Recognition

Improved Regularization of Convolutional Neural Networks with Cutout

Deep Networks with Stochastic Depth

Regularization in ResNet with Stochastic Depth


Robust Open Reading Frame prediction (ANGLE re-implementation)

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

Transcriptional fates of human-specific segmental duplications in brain

A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes

Genome Sequence and Analysis of Nicotiana benthamiana, the Model Plant for Interactions between Organisms

Combining next-generation sequencing and single-molecule sequencing to explore brown plant hopper responses to contrasting genotypes of japonica rice

Full-Length Transcriptome Analyses of Genes Involved in Triterpenoid Saponin Biosynthesis of Psammosilene tunicoides Hairy Root Cultures With Exogenous Salicylic Acid

Full-length mRNA sequencing uncovers a widespread coupling between transcription and mRNA processing

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

The mechanism underlying asymmetric bending of lateral petals in Delphinium (Ranunculaceae)

Full-Length Transcriptome Analysis of the Ichthyotoxic Harmful Alga Heterosigma akashiwo (Raphidophyceae) Using Single-Molecule Real-Time Sequencing


IDR

Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity

Influenza virus repurposes the antiviral protein IFIT2 to promote translation of viral mRNAs

Absence of Tangentially Migrating Glutamatergic Neurons in the Developing Avian Brain

A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

Islands of retroelements are the major components of Drosophila centromeres

Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells

Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters

Emergence of novel cephalopod gene regulation and expression through large-scale genome reorganization


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

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

An empirical study on real bug fixes from solidity smart contract projects

Vulnerable smart contract function locating based on Multi-Relational Nested Graph Convolutional Network

A study of inline assembly in solidity smart contracts

Proceedings of the ACM on Programming Languages

Understanding Solidity Event Logging Practices in the Wild


中文医疗信息处理基准CBLUE: A Chinese Biomedical Language Understanding Evaluation Benchmark

CLUE: A Chinese Language Understanding Evaluation Benchmark

HuatuoGPT, towards Taming Language Model to Be a Doctor

General and Domain-adaptive Chinese Spelling Check with Error-consistent Pretraining


PyTorch implementations of algorithms for density estimation

Density estimation using Real NVP

Glow: Generative Flow with Invertible 1x1 Convolutions

Masked Autoregressive Flow for Density Estimation

Anomaly Detection with Density Estimation

The LHC Olympics 2020 a community challenge for anomaly detection in high energy physics

Gravitational-wave population inference with deep flow-based generative network

Normalizing flows for novelty detection in industrial time series data

Modeling the Gaia Color-Magnitude Diagram with Bayesian Neural Flows to Constrain Distance Estimates

Amortized Monte Carlo Integration

f-MICL: Understanding and Generalizing InfoNCE-based Contrastive
  Learning


Implementation of Attention-based Deep Multiple Instance Learning in PyTorch

Cancer Diagnosis Using Deep Learning: A Bibliographic Review

FLamby: Datasets and Benchmarks for Cross-Silo Federated Learning in Realistic Healthcare Settings

Breast Cancer Dataset, Classification and Detection Using Deep Learning

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

Interpretable and Interactive Deep Multiple Instance Learning for Dental Caries Classification in Bitewing X-rays


Current version of the SuperLearner R package

Enteropathogen antibody dynamics and force of infection among children in low-resource settings

Comparison of Mortality and Major Cardiovascular Events Among Adults With Type 2 Diabetes Using Human vs Analogue Insulins

A Fundamental Measure of Treatment Effect Heterogeneity

An Easy Implementation of CV-TMLE

Association of Cardiovascular Outcomes and Mortality With Sustained Long-Acting Insulin Only vs Long-Acting Plus Short-Acting Insulin Treatment

Using machine learning to predict help-seeking among 2016–2018 Pregnancy Risk Assessment Monitoring System participants with postpartum depression symptoms

Doubly robust estimators for the average treatment effect under positivity violations: introducing the e-score.


scale ethereum with snarks

A Survey: Security, Transparency, and Scalability Issues of NFT’s and Its Marketplaces

Enabling Blockchain Services for IoE with Zk-Rollups

Accountable Safety for Rollups

Zecale: Reconciling Privacy and Scalability on Ethereum


Hardnet descriptor model - "Working hard to know your neighbor's margins:  Local descriptor learning loss"

Local Descriptors Optimized for Average Precision

From handcrafted to deep local features

Explicit Spatial Encoding for Deep Local Descriptors

Review of Wide-Baseline Stereo Image Matching Based on Deep Learning

Compression of descriptor models for mobile applications

Learning and Crafting for the Wide Multiple Baseline Stereo


Collection of audio-focused loss functions in PyTorch

PriorGrad: Improving Conditional Denoising Diffusion Models with Data-Dependent Adaptive Prior

BinauralGrad: A Two-Stage Conditional Diffusion Probabilistic Model for Binaural Audio Synthesis

Tunet: A Block-Online Bandwidth Extension Model Based On Transformers And Self-Supervised Pretraining

A review of differentiable digital signal processing for music and speech synthesis

BigVSAN: Enhancing GAN-based Neural Vocoders with Slicing Adversarial Network


:postbox: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study

rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study

基因组蛋白质组与生物信息学报

Genome-Wide Association Study Reveals Novel Genomic Regions for Grain Yield and Yield-Related Traits in Drought-Stressed Synthetic Hexaploid Wheat

International journal of molecular sciences

Trait associations in the pangenome of pigeon pea (Cajanus cajan)

Genome-Wide Association Study Reveals Novel Genomic Regions Associated with 10 Grain Minerals in Synthetic Hexaploid Wheat

Genome-Wide Association Studies for Pasmo Resistance in Flax (Linum usitatissimum L.)

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

Detection of First Marker Trait Associations for Resistance Against Sclerotinia sclerotiorum in Brassica juncea–Erucastrum cardaminoides Introgression Lines

Molecular and genetic analysis of defensive responses of Brassica juncea – B. fruticulosa introgression lines to Sclerotinia infection

Genome-Wide Association Study for Multiple Biotic Stress Resistance in Synthetic Hexaploid Wheat

Genome-wide association study for yield and yield related traits under reproductive stage drought in a diverse indica-aus rice panel


This repository is a fork of Microsoft Research's homomorphic encryption implementation, the Simple Encrypted Arithmetic Library (SEAL).  This code wraps the SEAL build in a docker container and provides Python API's to the encryption library.

Practical Privacy-Preserving Data Science With Homomorphic Encryption: An Overview

Blind Faith: Privacy-Preserving Machine Learning using Function Approximation

PySEAL: A Python wrapper implementation of the SEAL homomorphic encryption library

A Tutorial Introduction to Lattice-based Cryptography and Homomorphic Encryption


Main package


Different implementations of "Weighted Prediction Error" for speech dereverberation

An Investigation into the Effectiveness of Enhancement in ASR Training and Test for CHiME-5 Dinner Party Transcription

End-to-End Far-Field Speech Recognition with Unified Dereverberation and Beamforming

STC Speaker Recognition Systems for the VOiCES From a Distance Challenge

Unsupervised training of neural mask-based beamforming

Acoustic modeling for Overlapping Speech Recognition: JHU Chime-5
  Challenge System

Speech Enhancement with Wide Residual Networks in Reverberant Environments


Generate fully parametric face images from the Basel Face Model 2017

Morphable Face Models - An Open Framework

Empirically Analyzing the Effect of Dataset Biases on Deep Face Recognition Systems

Training Deep Face Recognition Systems with Synthetic Data

Can Synthetic Faces Undo the Damage of Dataset Bias to Face Recognition and Facial Landmark Detection?


Clonal expansion and activation of tissue-resident memory-like TH17 cells expressing GM-CSF in the lungs of patients with severe COVID-19

Characterizing dedifferentiation of thyroid cancer by integrated analysis

Single-Cell Transcriptomics Reveals the Complexity of the Tumor Microenvironment of Treatment-Naive Osteosarcoma

CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes

Resolving the immune landscape of human prostate at a single-cell level in health and cancer

The developing mouse coronal suture at single-cell resolution

Human Bone Marrow Organoids for Disease Modeling, Discovery, and Validation of Therapeutic Targets in Hematologic Malignancies

Single-Cell Transcriptional Survey of Ileal-Anal Pouch Immune Cells From Ulcerative Colitis Patients

Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer

Macrophages orchestrate the expansion of a proangiogenic perivascular niche during cancer progression


A curated list of reproducible research case studies, projects, tutorials, and media

1,500 scientists lift the lid on reproducibility

Believe it or not: how much can we rely on published data on potential drug targets?

Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015

The Economics of Reproducibility in Preclinical Research

Variability in the analysis of a single neuroimaging dataset by many teams

Corrigendum: Many Analysts, One Data Set: Making Transparent How Variations in Analytic Choices Affect Results

Advances in Methods and Practices in Psychological Science

The generalizability crisis

Open science challenges, benefits and tips in early career and beyond

Reproducible Research Practices and Transparency across the Biomedical Literature

What is replication?


[Pedestron] Generalizable Pedestrian Detection: The Elephant In The Room. @ CVPR2021

Beyond Appearance: a Semantic Controllable Self-Supervised Learning Framework for Human-Centric Visual Tasks

Center and Scale Prediction: Anchor-free Approach for Pedestrian and Face Detection

Pedestrian Detection: Domain Generalization, CNNs, Transformers and Beyond

F2DNet: Fast Focal Detection Network for Pedestrian Detection

Confluence: A Robust Non-IoU Alternative to Non-Maxima Suppression in Object Detection

Bias Behind the Wheel: Fairness Analysis of Autonomous Driving Systems


Open Charge Map is the global public registry of electric vehicle charging locations. Established 2011. Help wanted.


Python implementation of Bayesian Knowledge Tracing and extensions

Modeling Individualization in a Bayesian Networks Implementation of Knowledge Tracing

User Modeling, Adaptation, and Personalization

KT-IDEM: Introducing Item Difficulty to the Knowledge Tracing Model

User Modeling, Adaption and Personalization

pyBKT: An Accessible Python Library of Bayesian Knowledge Tracing Models

Modeling Knowledge Acquisition from Multiple Learning Resource Types

Knowledge Tracing for Complex Problem Solving: Granular Rank-Based Tensor Factorization

Personalization in Human-AI Teams: Improving the Compatibility-Accuracy Tradeoff


Hera: Ewasm virtual machine conforming to the EVMC API

Characterizing and Detecting WebAssembly Runtime Bugs

VM Matters: A Comparison of WASM VMs and EVMs in the Performance of Blockchain Smart Contracts


A Python 3 Bitcoin blockchain parser

Knowledge Discovery in Cryptocurrency Transactions: A Survey

Steganographic Analysis of Blockchains

How to Not Get Caught When You Launder Money on Blockchain?

Illicit Activity Detection in Bitcoin Transactions using Timeseries Analysis

International Journal of Advanced Computer Science and Applications


A simulator of malaria epidemiology and control

Public health impact and cost-effectiveness of the RTS,S/AS01 malaria vaccine: a systematic comparison of predictions from four mathematical models

Malaria intervention scale-up in Africa: effectiveness predictions for health programme planning tools, based on dynamic transmission modelling

The influence of biological, epidemiological, and treatment factors on the establishment and spread of drug-resistant Plasmodium falciparum

Spectrum-Malaria: a user-friendly projection tool for health impact assessment and strategic planning by malaria control programmes in sub-Saharan Africa

Leveraging mathematical models of disease dynamics and machine learning to improve development of novel malaria interventions

Model-informed target product profiles of long acting-injectables for use as seasonal malaria prevention

Modelling the implications of stopping vector control for malaria control and elimination

Cost-Effectiveness of PBO versus Conventional Long-Lasting Insecticidal Bed Nets in Preventing Symptomatic Malaria in Nigeria: Results of a Pragmatic Randomized Trial

The American journal of tropical medicine and hygiene

An online analytical processing multi-dimensional data warehouse for malaria data

Simulation-Based Inference for Global Health Decisions


Accelerated finite element flow solvers

NekRS, a GPU-Accelerated Spectral Element Navier-Stokes Solver

Scalability of High-Performance PDE Solvers

GPU Algorithms for Efficient Exascale Discretizations

Tuning Spectral Element Preconditioners for Parallel Scalability on GPUs

Initial Guesses for Sequences of Linear Systems in a GPU-Accelerated Incompressible Flow Solver

Towards Exascale for Wind Energy Simulations

HipBone: A performance-portable GPU-accelerated C++ version of the NekBone benchmark

Stopping Criteria for the Conjugate Gradient Algorithm in High-Order Finite Element Methods


A flexible and extensible framework for gait recognition. You can focus on designing your own models and comparing with state-of-the-arts easily with the help of OpenGait.

GaitSet: Regarding Gait as a Set for Cross-View Gait Recognition

GaitPart: Temporal Part-Based Model for Gait Recognition

Gait Lateral Network: Learning Discriminative and Compact Representations for Gait Recognition

Gait Recognition in the Wild with Dense 3D Representations and A Benchmark

OpenGait: Revisiting Gait Recognition Toward Better Practicality

GaitEdge: Beyond Plain End-to-end Gait Recognition for Better Practicality

A Comprehensive Survey on Deep Gait Recognition: Algorithms, Datasets and Challenges

LidarGait: Benchmarking 3D Gait Recognition with Point Clouds

GaitGL: Learning Discriminative Global-Local Feature Representations for Gait Recognition

Learning Gait Representation From Massive Unlabelled Walking Videos: A Benchmark


Fast & scalable MCMC for all your exoplanet needs!

A planet within the debris disk around the pre-main-sequence star AU Microscopii

exoplanet: Gradient-based probabilistic inference for exoplanet data other astronomical time series

Analytic Planetary Transit Light Curves and Derivatives for Stars with Polynomial Limb Darkening

EXOFASTv2: A public, generalized, publication-quality exoplanet modeling code

Statistical analysis of Curiosity data shows no evidence for a strong seasonal cycle of martian methane

The Dark World: A Tale of WASP-43b in Reflected Light with HST WFC3/UVIS

A Fast, Two-dimensional Gaussian Process Method Based on Celerite: Applications to Transiting Exoplanet Discovery and Characterization

MCMCI: A code to fully characterise an exoplanetary system

Giant Outer Transiting Exoplanet Mass (GOT 'EM) Survey. I. Confirmation of an Eccentric, Cool Jupiter with an Interior Earth-sized Planet Orbiting Kepler-1514

SPInS, a pipeline for massive stellar parameter inference: A public Python tool to age-date, weigh, size up stars, and more


Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.

Structure and function of axo-axonic inhibition

Petascale neural circuit reconstruction: automated methods

Developmental Rewiring between Cerebellar Climbing Fibers and Purkinje Cells Begins with Positive Feedback Synapse Addition

Toward an Automated HPC Pipeline for Processing Large Scale Electron Microscopy Data

Igneous: Distributed dense 3D segmentation meshing, neuron skeletonization, and hierarchical downsampling


High-performance simulator of quantum circuits

Intel Quantum Simulator: a cloud-ready high-performance simulator of quantum circuits

Secure quantum computing for healthcare sector: A short analysis

Evaluation of Intel Memory Drive Technology Performance for Scientific Applications

PROCEEDINGS OF WORKSHOP ON MEMORY CENTRIC HIGH PERFORMANCE COMPUTING (MCHPC'18)

Evaluation of Quantum Approximate Optimization Algorithm based on the approximation ratio of single samples.

Fast simulation of quantum algorithms using circuit optimization


Overlay Network for distributed protocols

POSEIDON: Privacy-Preserving Federated Neural Network Learning

Scalable Privacy-Preserving Distributed Learning

Secure and Efficient Multi-Signature Schemes for Fabric: An Enterprise Blockchain Platform

Privacy-preserving federated neural network learning for disease-associated cell classification

Scalable and Privacy-Preserving Federated Principal Component Analysis

chainBoost: A Secure Performance Booster for Blockchain-based Resource
  Markets


The main Embench repository

Comparative Analysis and Enhancement of CFG-based Hardware-Assisted CFI Schemes

Building Your Own Trusted Execution Environments Using FPGA

RVCoreP-32IM: An effective architecture to implement mul/div instructions for five stage RISC-V soft processors

RVfplib: A Fast and Compact Open-Source Floating-Point Emulation Library for Tiny RISC-V Processors

From MMU to MPU: Adaptation of the Pip Kernel to Constrained Devices

Artificial Intelligence, Soft Computing and Applications

One for All and All for One: GNN-based Control-Flow Attestation for Embedded Devices

MAFIA: Protecting the Microarchitecture of Embedded Systems Against Fault Injection Attacks

IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems


Python 3 version of FabSim

VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Sensitivity-driven simulation development: a case study in forced migration

Tutorial applications for Verification, Validation and Uncertainty Quantification using VECMA toolkit

Uncertainty quantification of dynamic earthquake rupture simulations


A Neural Framework for MT Evaluation

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

Unsupervised Cross-lingual Representation Learning at Scale

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

COMET: A Neural Framework for MT Evaluation

How Good Are GPT Models at Machine Translation? A Comprehensive Evaluation

Experts, Errors, and Context: A Large-Scale Study of Human Evaluation for Machine Translation

Learning Joint Multilingual Sentence Representations with Neural Machine Translation

Encouraging Divergent Thinking in Large Language Models through Multi-Agent Debate

To Ship or Not to Ship: An Extensive Evaluation of Automatic Metrics for Machine Translation

CometKiwi: IST-Unbabel 2022 Submission for the Quality Estimation Shared Task


ARMORY Adversarial Robustness Evaluation Test Bed

Deep Partition Aggregation: Provable Defense against General Poisoning Attacks

Study of Pre-processing Defenses against Adversarial Attacks on State-of-the-art Speaker Recognition Systems

Representation Learning to Classify and Detect Adversarial Attacks against Speaker and Speech Recognition Systems

Perceptual-based deep-learning denoiser as a defense against adversarial attacks on ASR systems

Mel Frequency Spectral Domain Defenses against Adversarial Attacks on Speech Recognition Systems

Constraining the Attack Space of Machine Learning Models with Distribution Clamping Preprocessing

SkeleVision: Towards Adversarial Resiliency of Person Tracking with Multi-Task Learning


PATO - the Phenotype And Trait Ontology

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Growing and cultivating the forest genomics database, TreeGenes

Database : the journal of biological databases and curation

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies

OHMI: the ontology of host-microbiome interactions

An Ontology-Based Expert System for Rice Disease Identification and Control Recommendation

TCDO: A Community-Based Ontology for Integrative Representation and Analysis of Traditional Chinese Drugs and Their Properties

Evidence-based complementary and alternative medicine : eCAM

“Opposite-of”-information improves similarity calculations in phenotype ontologies


A framework to monitor and improve the performance of PostgreSQL using Machine Learning methods.

Are We Ready For Learned Cardinality Estimation?

FLAT: Fast, Lightweight and Accurate Method for Cardinality Estimation

BayesCard: Revitilizing Bayesian Frameworks for Cardinality Estimation


Video classification tools using 3D ResNet

Can Spatiotemporal 3D CNNs Retrace the History of 2D CNNs and ImageNet?

Hierarchical Object-oriented Spatio-Temporal Reasoning for Video Question Answering


Deep Cascade of Convolutional Neural Networks for MR Image Reconstruction: Implementation & Demo

An overview of deep learning in medical imaging focusing on MRI

A Deep Cascade of Convolutional Neural Networks for MR Image Reconstruction

On instabilities of deep learning in image reconstruction and the potential costs of AI

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

Convolutional Recurrent Neural Networks for Dynamic MR Image Reconstruction

Adversarial and Perceptual Refinement for Compressed Sensing MRI Reconstruction

Pyramid Convolutional RNN for MRI Image Reconstruction

Motion Compensated Dynamic MRI Reconstruction With Local Affine Optical Flow Estimation

Generalizing Supervised Deep Learning MRI Reconstruction to Multiple and Unseen Contrasts using Meta-Learning Hypernetworks

The use of deep learning in medical imaging to improve spine care: A scoping review of current literature and clinical applications


Deep Ordinal Regression Network for Monocular Depth Estimation

Towards Real-Time Monocular Depth Estimation for Robotics: A Survey

Deep Multi-view Depth Estimation with Predicted Uncertainty


analyze text with empath

Analyzing Right-wing YouTube Channels: Hate, Violence and Discrimination

COM2SENSE: A Commonsense Reasoning Benchmark with Complementary Sentences

Fake news as we feel it: perception and conceptualization of the term "fake news" in the media

Beauty, the feeling

Understanding the Role of Affect Dimensions in Detecting Emotions from Tweets: A Multi-task Approach

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

Pretty Princess vs. Successful Leader: Gender Roles in Greeting Card Messages

Team Oulu at SemEval-2020 Task 12: Multilingual Identification of Offensive Language, Type and Target of Twitter Post Using Translated Datasets

International Workshop on Semantic Evaluation

Characterizing the public perception of WhatsApp through the lens of media

Characterising Authors on the Extent of their Paper Acceptance: A Case Study of the Journal of High Energy Physics

ACM/IEEE Joint Conference on Digital Libraries

Cross-platform analysis of user comments in YouTube videos linked on Reddit conspiracy theory forum


Learning to Cluster. A deep clustering strategy.

Learning to cluster in order to transfer across domains and tasks

Multi-class Classification without Multi-class Labels

Neural network-based clustering using pairwise constraints

Learning to Cluster for Proposal-Free Instance Segmentation

Mining Entity Synonyms with Efficient Neural Set Generation


Simple implementations of various popular Deep Reinforcement Learning algorithms using TensorFlow2

Proximal Policy Optimization Algorithms

Continuous control with deep reinforcement learning

Playing Atari with Deep Reinforcement Learning

Asynchronous Methods for Deep Reinforcement Learning

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

Trust Region Policy Optimization

Addressing Function Approximation Error in Actor-Critic Methods

Dueling Network Architectures for Deep Reinforcement Learning

Deep Recurrent Q-Learning for Partially Observable MDPs


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

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

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

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

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

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

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


Molecule Validation and Standardization

Molecular Generation with Recurrent Neural Networks (RNNs)

Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning

DeepFrag: a deep convolutional neural network for fragment-based lead optimization

NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules

A deep-learning view of chemical space designed to facilitate drug discovery

Skin Doctor: Machine Learning Models for Skin Sensitization Prediction that Provide Estimates and Indicators of Prediction Reliability

Identification and New Indication of Melanin-Concentrating Hormone Receptor 1 (MCHR1) Antagonist Derived from Machine Learning and Transcriptome-Based Drug Repositioning Approaches

PredPS: Attention-based graph neural network for predicting stability of compounds in human plasma

Computational and structural biotechnology journal

Molecular Similarity Perception Based on Machine-Learning Models

International journal of molecular sciences

Development and Experimental Validation of Regularized Machine Learning Models Detecting New, Structurally Distinct Activators of PXR


Codes for "Chameleon: Plug-and-Play Compositional Reasoning with Large Language Models".

Chain-of-Thought Prompting Elicits Reasoning in Large Language Models

Program of Thoughts Prompting: Disentangling Computation from Reasoning for Numerical Reasoning Tasks

Tool Documentation Enables Zero-Shot Tool-Usage with Large Language Models

What Are Tools Anyway? A Survey from the Language Model Perspective

ChunkAttention: Efficient Self-Attention with Prefix-Aware KV Cache and
  Two-Phase Partition


MDETR - Modulated Detection for End-to-End Multi-Modal Understanding

Position-Enhanced Visual Instruction Tuning for Multimodal Large Language Models

Transformer Module Networks for Systematic Generalization in Visual Question Answering

Extending Phrase Grounding with Pronouns in Visual Dialogues

Measuring CLEVRness: Blackbox testing of Visual Reasoning Models

A Joint Study of Phrase Grounding and Task Performance in Vision and Language Models

Team RUC_AIM3 Technical Report at ActivityNet 2021: Entities Object Localization

Which One Are You Referring To? Multimodal Object Identification in Situated Dialogue


Molecular De Novo design using Recurrent Neural Networks and Reinforcement Learning

Molecular De Novo Design through Deep Reinforcement Learning

Learning Multimodal Graph-to-Graph Translation for Molecular Optimization

MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization

Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation

Scaffold-constrained molecular generation

Journal of chemical information and modeling

Can AI reproduce observed chemical diversity?

Exploring Chemical Space with Score-based Out-of-distribution Generation

Docking-based generative approaches in the search for new drug candidates

Automated patent extraction powers generative modeling in focused chemical spaces

FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction


g2p: English Grapheme To Phoneme Conversion

FastSpeech 2: Fast and High-Quality End-to-End Text to Speech

Generative Spoken Language Modeling from Raw Audio

Unsupervised Speech Recognition

Scaling Speech Technology to 1,000+ Languages

ProDiff: Progressive Fast Diffusion Model For High-Quality Text-to-Speech

Speak, Read and Prompt: High-Fidelity Text-to-Speech with Minimal Supervision

Meta-StyleSpeech : Multi-Speaker Adaptive Text-to-Speech Generation

Semantic-Preserved Communication System for Highly Efficient Speech Transmission

Probing the Information Encoded in X-vectors

Automatic Speech Recognition & Understanding

MUCS 2021: Multilingual and Code-Switching ASR Challenges for Low Resource Indian Languages


LEGACY - Graphical interface for spike sorting manual stage in Python

Hardware-accelerated interactive data visualization for neuroscience in Python

Multichannel Silicon Probes for Awake Hippocampal Recordings in Large Animals

State-dependent geometry of population activity in rat auditory cortex

Traumatic Brain Injury Preserves Firing Rates But Disrupts Laminar Oscillatory Coupling and Neuronal Entrainment in Hippocampal CA1

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

Hippocampal Interneuronal Dysfunction and Hyperexcitability in a Porcine Model of Concussion


The Munich Open-Source Large-Scale Multimedia Feature Extractor

The MuSe 2022 Multimodal Sentiment Analysis Challenge: Humor, Emotional Reactions, and Stress

The voice of COVID-19: Acoustic correlates of infection

The Journal of the Acoustical Society of America

The MuSe 2023 Multimodal Sentiment Analysis Challenge: Mimicked Emotions, Cross-Cultural Humour, and Personalisation

On the Impact of Word Error Rate on Acoustic-Linguistic Speech Emotion Recognition: An Update for the Deep Learning Era

M2H2: A Multimodal Multiparty Hindi Dataset For Humor Recognition in Conversations

A Comparison of Machine Learning Algorithms and Feature Sets for Automatic Vocal Emotion Recognition in Speech

Towards Multimodal Prediction of Spontaneous Humour: A Novel Dataset and First Results

A Voice-Based Biomarker for Monitoring Symptom Resolution in Adults with COVID-19: Findings from the Prospective Predi-COVID Cohort Study


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

The Pfam protein families database in 2019

Database Resources of the National Center for Biotechnology Information

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

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

Biological Assembly Comparison with VAST.

STRUCTURAL BIOINFORMATICS: METHODS AND PROTOCOLS

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


Java toolkit to create and convert W3C PROV data model representations, and build provenance-enabled applications in a variety of programming languages (java, python, typescript, javascript)

PAV ontology: provenance, authoring and versioning

Towards structured sharing of raw and derived neuroimaging data across existing resources

QProv: A provenance system for quantum computing

High-throughput Ingest of Provenance Records into Accumulo

Thoughtflow: Standards and Tools for Provenance Capture and Workflow Definition to Support Model‐Informed Drug Discovery and Development

CPT: pharmacometrics & systems pharmacology


A pytorch implementation of Paper "Improved Training of Wasserstein GANs"

Generative Models from the perspective of Continual Learning

Generative Adversarial Networks for Image Augmentation in Agriculture: A Systematic Review

Outlier-Robust Optimal Transport: Duality, Structure, and Statistical Analysis

MCL-GAN: Generative Adversarial Networks with Multiple Specialized Discriminators

Amortised Learning by Wake-Sleep

Robust Estimation under the Wasserstein Distance

IE-GAN: An Improved Evolutionary Generative Adversarial Network Using a New Fitness Function and a Generic Crossover Operator

Updating the generator in PPGN-h with gradients flowing through the encoder


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

A draft human pangenome reference

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing

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

Long Read based Human Genomic Structural Variation Detection with cuteSV


A circuit toolkit

Design Automation and Design Space Exploration for Quantum Computers

Logic Synthesis for Quantum Computing

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

Reinforcement Learning for Scalable Logic Optimization with Graph Neural Networks


Pretrained Transformers for Text Ranking: BERT and Beyond

Dense Text Retrieval Based on Pretrained Language Models: A Survey

Simplified Data Wrangling with ir_datasets

OpenMatch: An Open Source Library for Neu-IR Research

CMT in TREC-COVID Round 2: Mitigating the Generalization Gaps from Web to Special Domain Search

Utilizing BERT for Information Retrieval: Survey, Applications, Resources, and Challenges

Wikiformer: Pre-training with Structured Information of Wikipedia for Ad-hoc Retrieval

OpenMatch: An Open-Source Package for Information Retrieval.


Implementations of Reinforcement Learning and Planning algorithms

B-GAP: Behavior-Rich Simulation and Navigation for Autonomous Driving

Budgeted Reinforcement Learning in Continuous State Space

Building Safer Autonomous Agents by Leveraging Risky Driving Behavior Knowledge

International Conference on Communications, Computing, Cybersecurity, and Informatics

Explaining Reinforcement Learning Agents Through Counterfactual Action Outcomes

Decision Making for Autonomous Driving in Interactive Merge Scenarios via Learning-based Prediction


Easily share permanent links to ChatGPT conversations with your friends

A Survey of Large Language Models

MiniGPT-4: Enhancing Vision-Language Understanding with Advanced Large Language Models

MiniGPT-v2: large language model as a unified interface for vision-language multi-task learning

Deductive Verification of Chain-of-Thought Reasoning

LLaSM: Large Language and Speech Model

The Shifted and The Overlooked: A Task-oriented Investigation of User-GPT Interactions

GliDe with a CaPE: A Low-Hassle Method to Accelerate Speculative
  Decoding

RefGPT: Dialogue Generation of GPT, by GPT, and for GPT


Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests

Characterization of Bacterial and Fungal Community Dynamics by High-Throughput Sequencing (HTS) Metabarcoding during Flax Dew-Retting

Diversity and Structure of Bacterial Communities in the Gut of Spider: Thomisidae and Oxyopidae

Analysis of Phyllosphere Microorganisms and Potential Pathogens of Tobacco Leaves

Jia-Wei-Si-Miao-Yong-An decoction modulates intestinal flora and metabolites in acute coronary syndrome model

Apolipoprotein H induces sex-specific steatohepatitis and gut dysbiosis during chronic hepatitis B infection

Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP)

Animals : an open access journal from MDPI

Characterization of the Fecal Microbiota in Gastrointestinal Cancer Patients and Healthy Controls


Fast and customizable text tokenization library with BPE and SentencePiece support

Boosting Neural Machine Translation with Similar Translations

An Overview on Language Models: Recent Developments and Outlook

Integrating Domain Terminology into Neural Machine Translation

International Conference on Computational Linguistics

Incorporating External Annotation to improve Named Entity Translation in NMT

European Association for Machine Translation Conferences/Workshops

Priming Neural Machine Translation

HAL (Le Centre pour la Communication Scientifique Directe)

LIMSI @ WMT 2020

Empirical Methods in Natural Language Processing

The Ubiqus English-Inuktitut System for WMT20

Example-Based Machine Translation from Text to a Hierarchical Representation of Sign Language

Collecting domain specific data for MT: an evaluation of the ParaCrawlpipeline

SYSTRAN @ WMT 2021: Terminology Task

Zenodo (CERN European Organization for Nuclear Research)


SLAM performance evaluation framework

Introducing SLAMBench, a performance and accuracy benchmarking methodology for SLAM

International Conference on Robotics and Automation

SLAMBench2: Multi-Objective Head-to-Head Benchmarking for Visual SLAM

Robust SLAM Systems: Are We There Yet?

SLAMBooster: An Application-aware Controller for Approximation in SLAM


A Happy and lightweight Python Package that Provides an API to search for articles on Google News and returns a JSON response.

Integrating Pattern- and Fact-based Fake News Detection via Model Preference Learning

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

KoLA: Carefully Benchmarking World Knowledge of Large Language Models

Geographic and Geopolitical Biases of Language Models

Understanding Divergent Framing of the Supreme Court Controversies: Social Media vs. News Outlets

Making Changes in Webpages Discoverable: A Change-Text Search Interface for Web Archives


This is the implementation of Noise2Void training.

Noise2Void - Learning Denoising from Single Noisy Images

Noisier2Noise: Learning to Denoise from Unpaired Noisy Data

Noise2Context: Context-assisted Learning 3D Thin-layer Low Dose CT Without Clean Data

Fluorescence microscopy datasets for training deep neural networks

Deformation-Compensated Learning for Image Reconstruction Without Ground Truth

Live-cell imaging powered by computation

N2V2 -- Fixing Noise2Void Checkerboard Artifacts with Modified Sampling Strategies and a Tweaked Network Architecture

Repair of noise-induced damage to stereocilia F-actin cores is facilitated by XIRP2 and its novel mechanosensor domain

Improved Imaging by Invex Regularizers with Global Optima Guarantees

Diffusion-based deep learning method for augmenting ultrastructural imaging and volume electron microscopy


A tool to quickly and easily create inputs for power systems models

Power availability of PV plus thermal batteries in real-world electric power grids


An inductive logic programming system

Learning programs by learning from failures

Inductive logic programming at 30: a new introduction

Predicate Invention by Learning From Failures

Learning logic programs by combining programs

Learning MDL logic programs from noisy data

The KANDY Benchmark: Incremental Neuro-Symbolic Learning and Reasoning
  with Kandinsky Patterns


Generate Diverse Counterfactual Explanations for any machine learning model.

Counterfactual Explanations without Opening the Black Box: Automated Decisions and the GDPR

Explaining machine learning classifiers through diverse counterfactual explanations

Proceedings of the 2020 Conference on Fairness, Accountability, and Transparency

Multi-Objective Counterfactual Explanations

Preserving Causal Constraints in Counterfactual Explanations for Machine Learning Classifiers

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

Counterfactual Explanations Can Be Manipulated

Towards Unifying Feature Attribution and Counterfactual Explanations: Different Means to the Same End

National Conference on Artificial Intelligence

Explainable AI meets Healthcare: A Study on Heart Disease Dataset

Verifying Individual Fairness in Machine Learning Models

Towards a multi-stakeholder value-based assessment framework for algorithmic systems

Conference on Fairness, Accountability and Transparency


TT

Normalization for multimodal type theory

Logical Relations as Types: Proof-Relevant Parametricity for Program Modules

Formalizing π4(S3) ≅Z/2Z and Computing a Brunerie Number in Cubical Agda

An inductive-recursive universe generic for small families

Cubical methods in homotopy type theory and univalent foundations

Mathematical Structures in Computer Science

Domain Theory in Constructive and Predicative Univalent Foundations


Semantics of C in K

Exploring C semantics and pointer provenance

Proceedings of the ACM on Programming Languages

Understanding GCC Builtins to Develop Better Tools

Deductive Verification of Programs with Underspecified Semantics by Model Extraction.

The Right Kind of Non-Determinism: Using Concurrency to Verify C Programs with Underspecified Semantics


trends.earth - measure land change


A Wikidata Python module integrating the MediaWiki API and the Wikidata SPARQL endpoint

Wikidata as a knowledge graph for the life sciences

Using Shape Expressions (ShEx) to Share RDF Data Models and to Guide Curation with Rigorous Validation

WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

Joint Open Knowledge Base Canonicalization and Linking

A protocol for adding knowledge to Wikidata, a case report

Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience

Statistical Knowledge Assessment for Large Language Models

The Janus System: Multi-paradigm Programming in Prolog and Python

International Conference on Logic Programming

COMBO: A Complete Benchmark for Open KG Canonicalization


C++ logic network library

A Simulation-Guided Paradigm for Logic Synthesis and Verification

IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems

Irredundant Buffer and Splitter Insertion and Scheduling-Based Optimization for AQFP Circuits

Impact of Sequential Design on the Cost of Adiabatic Quantum-Flux Parametron Circuits

IEEE transactions on applied superconductivity

An Automated Testing and Debugging Toolkit for Gate-Level Logic Synthesis Applications


EUTelescope -- A Generic Pixel Telescope Data Analysis Framework

Feasibility of track-based multiple scattering tomography

EUTelescope: A modular reconstruction framework for beam telescope data

Resolution studies with the DATURA beam telescope

The Measurement of Position Resolution of RD53A Pixel Modules


Community curated plugins for core-lightning

Imbalance measure and proactive channel rebalancing algorithm for the Lightning Network

HIDE & SEEK: Privacy-Preserving Rebalancing on Payment Channel Networks

Wiser: Increasing Throughput in Payment Channel Networks with Transaction Aggregation

D-LNBot: A Scalable, Cost-Free and Covert Hybrid Botnet on Bitcoin's Lightning Network

Online Admission Control and Rebalancing in Payment Channel Networks


This is the development home of the workflow management system Snakemake. For general information, see

Sustainable data analysis with Snakemake

CRISPAltRations: a validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing

Mapache: a flexible pipeline to map ancient DNA

RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data

A Workflow Management System Guide


An open source library for face detection in images. The face detection speed can reach 1000FPS.

Feature refinement: An expression-specific feature learning and fusion method for micro-expression recognition

HEU Emotion: a large-scale database for multimodal emotion recognition in the wild

A Survey on Masked Facial Detection Methods and Datasets for Fighting Against COVID-19

IEEE Transactions on Artificial Intelligence

Detect Faces Efficiently: A Survey and Evaluations

IEEE Transactions on Biometrics, Behavior, and Identity Science

YuNet: A Tiny Millisecond-level Face Detector

PersonRank: Detecting Important People in Images

Objective Class-based Micro-Expression Recognition through Simultaneous Action Unit Detection and Feature Aggregation

MERBench: A Unified Evaluation Benchmark for Multimodal Emotion Recognition

MER 2024: Semi-Supervised Learning, Noise Robustness, and
  Open-Vocabulary Multimodal Emotion Recognition

Automated assessment of grating acuity in infants and toddlers using an eye-tracking system


The SentiWordNet sentiment lexicon

Semantic Features for Optimizing Supervised Approach of Sentiment Analysis on Product Reviews

CyberWallE at SemEval-2020 Task 11: An Analysis of Feature Engineering for Ensemble Models for Propaganda Detection

Enhancing Embedding-Based Chinese Word Similarity Evaluation with Concepts and Synonyms Knowledge

Computer Modeling in Engineering & Sciences

A Systematic Review of Aspect-based Sentiment Analysis (ABSA): Domains, Methods, and Trends

Computational Sarcasm Analysis on Social Media: A Systematic Review

An integrated fuzzy neural network with topic-aware auto-encoding for sentiment analysis

Soft Computing - A Fusion of Foundations, Methodologies and Applications

An Improved Method for Extractive Based Opinion Summarization Using Opinion Mining

Computer systems science and engineering

TopFuzz4SA: An Integrated Fuzzy Neural Network with Topic-aware Auto-encoding for Sentiment Analysis

Practical Approach on Implementation of WordNets for South African Languages

Sentiment-enhanced Graph-based Sarcasm Explanation in Dialogue


Implementation of Generating Diverse High-Fidelity Images with VQ-VAE-2 in PyTorch

A Survey of Deep Learning for Scientific Discovery

Conditional Sound Generation Using Neural Discrete Time-Frequency Representation Learning

f-DM: A Multi-stage Diffusion Model via Progressive Signal Transformation

High- and Low-level image component decomposition using VAEs for improved reconstruction and anomaly detection

PatchGame: Learning to Signal Mid-level Patches in Referential Games

Topological Neural Discrete Representation Learning à la Kohonen


AI agent using GPT-4V(ision) capable of using a mouse/keyboard to interact with web UI

WebVoyager: Building an End-to-End Web Agent with Large Multimodal Models

OSWorld: Benchmarking Multimodal Agents for Open-Ended Tasks in Real
  Computer Environments

Large Multimodal Agents: A Survey

Building the Future of Responsible AI: A Reference Architecture for Designing Large Language Model based Agents

Towards Responsible AI in the Era of Generative AI: A Reference Architecture for Designing Foundation Model based Systems


i-RevNet Pytorch Code

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

i-RevNet: Deep Invertible Networks

Mimic and Fool: A Task-Agnostic Adversarial Attack

IEEE transactions on neural networks and learning systems


Gammatone-based spectrograms, using gammatone filterbanks or Fourier transform weightings.

Neural speech restoration at the cocktail party: Auditory cortex recovers masked speech of both attended and ignored speakers

Heard or Understood? Neural Tracking of Language Features in a Comprehensible Story, an Incomprehensible Story and a Word List


Revisiting Self-Supervised Visual Representation Learning

Automatic Shortcut Removal for Self-Supervised Representation Learning


Realtime Multi-Person 2D Pose Estimation using Part Affinity Fields

Extremely Lightweight Quantization Robust Real-Time Single-Image Super Resolution for Mobile Devices

Anchor-based Plain Net for Mobile Image Super-Resolution

Collapsible Linear Blocks for Super-Efficient Super Resolution

Neural Network Quantization with AI Model Efficiency Toolkit (AIMET)

QuickSRNet: Plain Single-Image Super-Resolution Architecture for Faster Inference on Mobile Platforms


A self-supervised domain-general learning framework for human ventral stream representation

Mitigating dataset harms requires stewardship: Lessons from 1000 papers

Video Face Clustering with Unknown Number of Clusters

Understanding Unequal Gender Classification Accuracy from Face Images

Bias, awareness, and ignorance in deep-learning-based face recognition

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

On Hallucinating Context and Background Pixels from a Face Mask using Multi-scale GANs

Composite recurrent network with internal denoising for facial alignment in still and video images in the wild

FRMDB: Face Recognition Using Multiple Points of View

Recent Advances of Differential Privacy in Centralized Deep Learning: A Systematic Survey


Directory of Fortran codes on GitHub, arranged by topic

Simultaneous Discovery, Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model

The Millennial model: in search of measurable pools and transformations for modeling soil carbon in the new century

PRIDE PPP-AR: an open-source software for GPS PPP ambiguity resolution

A strategy for automated analysis of passive microseismic data to image seismic anisotropy and fracture characteristics

The spatial extent of rainfall events and its relation to precipitation scaling

Efficient Mesh Generation and Deformation for Aerodynamic Shape Optimization

Measuring the Level and Uncertainty of Trend Inflation

Paleo calendar-effect adjustments in time-slice and transient climate-model simulations (PaleoCalAdjust v1.0): impact and strategies for data analysis

Separating the Impact of Individual Land Surface Properties on the Terrestrial Surface Energy Budget in both the Coupled and Uncoupled Land–Atmosphere System

Adjoint‐State Traveltime Tomography: Eikonal Equation‐Based Methods and Application to the Anza Area in Southern California

Journal of Geophysical Research: Solid Earth


Code for the CVPR2021 paper "Patch-NetVLAD: Multi-Scale Fusion of Locally-Global Descriptors for Place Recognition"

StructVPR: Distill Structural Knowledge with Weighting Samples for Visual Place Recognition

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

CricaVPR: Cross-image Correlation-aware Representation Learning for
  Visual Place Recognition


Command line Java Decompiler

Auto-completing Bug Reports for Android Applications

FUSION: A Tool for Facilitating and Augmenting Android Bug Reporting

Hybroid: A Novel Hybrid Android Malware Detection Framework

Erzincan Üniversitesi Fen Bilimleri Enstitüsü Dergisi


Implementation of the Wave-U-Net for audio source separation

Wave-U-Net: A Multi-Scale Neural Network for End-to-End Audio Source Separation

End-to-end music source separation: is it possible in the waveform domain?

UNetGAN: A Robust Speech Enhancement Approach in Time Domain for Extremely Low Signal-to-noise Ratio Condition

End-to-End Sound Source Separation Conditioned On Instrument Labels

Sams-Net: A Sliced Attention-based Neural Network for Music Source Separation

Genre-Conditioned Acoustic Models for Automatic Lyrics Transcription of Polyphonic Music

Source Separation Using Dilated Time-Frequency DenseNet for Music Identification in Broadcast Contents

Integrating Dilated Convolution into DenseLSTM for Audio Source Separation


Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

A Reference Genome Sequence for Giant Sequoia

Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch)

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

bioRxiv : the preprint server for biology

Chromosome-level assembly of the Caenorhabditis remanei genome reveals conserved patterns of nematode genome organization

Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts

Computational and structural biotechnology journal

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