A scalable SCENIC workflow for single-cell gene regulatory network analysis

Single‐cell RNA‐seq reveals clonal diversity and prognostic genes of relapsed multiple myeloma

A TCF4/BRD4-dependent regulatory network confers cross-resistance to targeted and immune checkpoint therapy in melanoma

Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors

Single-cell transcriptome profiling reveals immune and stromal cell heterogeneity in primary Sjögren’s syndrome


Simu5G - 5G NR and LTE/LTE-A user-plane simulation model for OMNeT++ & INET

Deployment and configuration of MEC apps with Simu5G

Platooning-as-a-Service in a Multi-Operator ETSI MEC Environment


The entmax mapping and its loss, a family of sparse softmax alternatives.

From Softmax to Sparsemax: A Sparse Model of Attention and Multi-Label Classification

Adaptively Sparse Transformers

Sparse Sequence-to-Sequence Models

Inducing Target-Specific Latent Structures for Aspect Sentiment Classification

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

Learning with Fenchel-Young Losses

Sparse Text Generation

Smoothing and Shrinking the Sparse Seq2Seq Search Space

Beyond Characters: Subword-level Morpheme Segmentation

Special Interest Group on Computational Morphology and Phonology Workshop

Weakly Supervised Learning Significantly Reduces the Number of Labels Required for Intracranial Hemorrhage Detection on Head CT

DeepSPIN: Deep Structured Prediction for Natural Language Processing

European Association for Machine Translation Conferences/Workshops


Measuring Massive Multitask Language Understanding | ICLR 2021

Holistic Evaluation of Language Models

Atlas: Few-shot Learning with Retrieval Augmented Language Models

Gemini 1.5: Unlocking multimodal understanding across millions of tokens
  of context

Aligning AI With Shared Human Values

Large Language Models Are Not Robust Multiple Choice Selectors

Don't Make Your LLM an Evaluation Benchmark Cheater

Proving Test Set Contamination in Black Box Language Models

Benchmarking Retrieval-Augmented Generation for Medicine

QA-LoRA: Quantization-Aware Low-Rank Adaptation of Large Language Models


A Graph Traversal Language (no longer active - see Apache TinkerPop)

G-CORE: A Core for Future Graph Query Languages

Efficient Snapshot Retrieval over Historical Graph Data

Digital Twin and Internet of Things—Current Standards Landscape

NScale: neighborhood-centric large-scale graph analytics in the cloud

Storing and Analyzing Historical Graph Data at Scale

GRAPHiQL: A graph intuitive query language for relational databases

Kaskade: Graph Views for Efficient Graph Analytics

Partitioning Graph Databases - A Quantitative Evaluation

Empowering In-Memory Relational Database Engines with Native Graph Processing

Compact and efficient representation of general graph databases


A drag-and-drop quantum circuit simulator that runs in your browser. A toy for exploring and understanding small quantum circuits.

Open source software in quantum computing

Factoring with n+2 clean qubits and n-1 dirty qubits

Visualizing quantum mechanics in an interactive simulation – Virtual Lab by Quantum Flytrap

Optical Engineering: The Journal of SPIE

Secure quantum computing for healthcare sector: A short analysis

"Equation missing" : A Cross-Platform Programming Framework for Quantum-Accelerated Scientific Computing

VENUS: A Geometrical Representation for Quantum State Visualization

VACSEN: A Visualization Approach for Noise Awareness in Quantum Computing

High-performance computing and computational intelligence applications with a multi-chaos perspective

Multi-Chaos, Fractal and Multi-Fractional Artificial Intelligence of Different Complex Systems

Playing with a Quantum Computer


Platform for designing and evaluating Graph Neural Networks (GNN)

Design Space for Graph Neural Networks

Identity-aware Graph Neural Networks

ROLAND: Graph Learning Framework for Dynamic Graphs

Relational Multi-Task Learning: Modeling Relations between Data and Tasks

DFG-NAS: Deep and Flexible Graph Neural Architecture Search

Optimal Inference in Contextual Stochastic Block Models


Code of the Unsupervised Traffic Accident Detection paper in Pytorch.

Unsupervised Traffic Accident Detection in First-Person Videos

Egocentric Vision-based Future Vehicle Localization for Intelligent Driving Assistance Systems

When, Where, and What? A New Dataset for Anomaly Detection in Driving Videos

Vision-Based Traffic Accident Detection and Anticipation: A Survey


A neural named entity recognition and multi-type normalization tool for biomedical text mining

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

A Neural Named Entity Recognition and Multi-Type Normalization Tool for Biomedical Text Mining

Visual Analytics of Twitter and Social Media Dataflows: a Casestudy of COVID-19 Rumors


Leaderboard Comparing LLM Performance at Producing Hallucinations when Summarizing Short Documents

TRUE: Re-evaluating Factual Consistency Evaluation

AlignScore: Evaluating Factual Consistency with A Unified Alignment Function

TrueTeacher: Learning Factual Consistency Evaluation with Large Language Models

MiniCheck: Efficient Fact-Checking of LLMs on Grounding Documents


Line-granularity, thread-aware deterministic and statistic pure-python profiler

Toward Efficient Interactions between Python and Native Libraries

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

Triangulating Python Performance Issues with Scalene

Zenix: Efficient Execution of Bulky Serverless Applications


Instruction Tuning for Large Language Models: A Survey

Aya Dataset: An Open-Access Collection for Multilingual Instruction
  Tuning

Datasets for Large Language Models: A Comprehensive Survey

Response Length Perception and Sequence Scheduling: An LLM-Empowered LLM Inference Pipeline

Safer-Instruct: Aligning Language Models with Automated Preference Data

Under the Surface: Tracking the Artifactuality of LLM-Generated Data

Self Information Update for Large Language Models through Mitigating Exposure Bias

SelectLLM: Can LLMs Select Important Instructions to Annotate?


Repository for benchmarking graph neural networks

Do Transformers Really Perform Bad for Graph Representation?

Benchmarking Graph Neural Networks

Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting

Adversarial Graph Augmentation to Improve Graph Contrastive Learning

Debiasing Graph Neural Networks via Learning Disentangled Causal Substructure

Graph Neural Networks with Local Graph Parameters

Learning Graph Normalization for Graph Neural Networks

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

On Structural Expressive Power of Graph Transformers

On the Temperature of Bayesian Graph Neural Networks for Conformal Prediction


Visual Question Answering in Pytorch

Multimodal Compact Bilinear Pooling for Visual Question Answering and Visual Grounding

MUTAN: Multimodal Tucker Fusion for Visual Question Answering

Hadamard Product for Low-rank Bilinear Pooling

Cycle-Consistency for Robust Visual Question Answering

A Question-Centric Model for Visual Question Answering in Medical Imaging

Dual Recurrent Attention Units for Visual Question Answering

Deep Equilibrium Multimodal Fusion


Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs

Alignment- and reference-free phylogenomics with colored de-Bruijn graphs

Succinct k-mer Sets Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform *

RGFA: powerful and convenient handling of assembly graphs


GraphGen4Code: a toolkit for creating code knowledge graphs based on WALA code analysis and extraction of documentation and forum content.

A Toolkit for Generating Code Knowledge Graphs

Large Scale Generation of Labeled Type Data for Python

KGLiDS: A Platform for Semantic Abstraction, Linking, and Automation of Data Science


It is a forest of random projection trees

ANN-Benchmarks: A Benchmarking Tool for Approximate Nearest Neighbor Algorithms

Approximate kNN Classification for Biomedical Data

ParlayANN: Scalable and Deterministic Parallel Graph-Based Approximate Nearest Neighbor Search Algorithms

Medical Image Retrieval via Nearest Neighbor Search on Pre-trained Image Features

A Survey on Efficient Processing of Similarity Queries over Neural Embeddings

Exact and/or Fast Nearest Neighbors


Reference implementation of real-time autoregressive wavenet inference

Deep Voice: Real-time Neural Text-to-Speech

A Universal Music Translation Network

Blow: a single-scale hyperconditioned flow for non-parallel raw-audio voice conversion

Neural Music Synthesis for Flexible Timbre Control

Sequence to Sequence Neural Speech Synthesis with Prosody Modification Capabilities

Digital Voicing of Silent Speech

TTS Skins: Speaker Conversion via ASR

Speaker independence of neural vocoders and their effect on parametric resynthesis speech enhancement

Phonetic Posteriorgrams based Many-to-Many Singing Voice Conversion via Adversarial Training

Parallel Synthesis for Autoregressive Speech Generation


Python Implementations of Word Sense Disambiguation (WSD) Technologies.

LEXenstein: A Framework for Lexical Simplification

PROCEEDINGS OF THE 53RD ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS AND THE 7TH INTERNATIONAL JOINT CONFERENCE ON NATURAL LANGUAGE PROCESSING (ACL-IJCNLP 2015): SYSTEM DEMONSTRATIONS

UNAL-NLP: Combining Soft Cardinality Features for Semantic Textual Similarity, Relatedness and Entailment

International Workshop on Semantic Evaluation

A Neural Approach to Pun Generation

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

Calculating the similarity between words and sentences using a lexical database and corpus statistics

Syn-QG: Syntactic and Shallow Semantic Rules for Question Generation

How to Avoid Sentences Spelling Boring? Towards a Neural Approach to Unsupervised Metaphor Generation

North American Chapter of the Association for Computational Linguistics

Data Augmentation in a Hybrid Approach for Aspect-Based Sentiment Analysis

Weisfeiler-Leman in the BAMBOO: Novel AMR Graph Metrics and a Benchmark for AMR Graph Similarity

Pun-GAN: Generative Adversarial Network for Pun Generation

Exploring morality in argumentation


A neural network library built in JavaScript

Moving Deep Learning into Web Browser: How Far Can We Go?

Front-end deep learning web apps development and deployment: a review

Applied intelligence (Dordrecht, Netherlands)

Approach for Improving User Interface Based on Gesture Recognition


Graphs and Graph Algorithms in C++, including Minimum Cost (Lifted) Multicuts

Joint Graph Decomposition and Node Labeling: Problem, Algorithms, Applications

Analysis and Optimization of Graph Decompositions by Lifted Multicuts

Improving primary-vertex reconstruction with a minimum-cost lifted multicut graph partitioning algorithm


Python Vietnamese Core NLP Toolkit

UIT-ViIC: A Dataset for the First Evaluation on Vietnamese Image Captioning

Combining Advanced Methods in Japanese-Vietnamese Neural Machine Translation

PROCEEDINGS OF 2018 10TH INTERNATIONAL CONFERENCE ON KNOWLEDGE AND SYSTEMS ENGINEERING (KSE)

Using Convolution Neural Network with BERT for Stance Detection in Vietnamese

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION

Miko Team: Deep Learning Approach for Legal Question Answering in ALQAC 2022


Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Fast and accurate long-read assembly with wtdbg2

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

HASLR: Fast Hybrid Assembly of Long Reads

Genome sequence of Malania oleifera, a tree with great value for nervonic acid production

Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans

Chromosome-level reference genome of the jellyfish Rhopilema esculentum

Improved Methods for Acetocarmine and Haematoxylin Staining to Visualize Chromosomes in the Filamentous Green Alga Zygnema (Charophyta)

bioRxiv : the preprint server for biology

Long-read sequencing in human genetics


Relax! Flux is the ML library that doesn't make you tensor

PyTorch: An Imperative Style, High-Performance Deep Learning Library

Surgical Data Science -- from Concepts toward Clinical Translation

Fashionable Modelling with Flux

Deep learning in electron microscopy

Machine Learning: Science and Technology

Julia language in machine learning: Algorithms, applications, and open issues

Learning with Combinatorial Optimization Layers: a Probabilistic Approach

Automatic Full Compilation of Julia Programs and ML Models to Cloud TPUs

Using scientific machine learning for experimental bifurcation analysis of dynamic systems

AbstractDifferentiation.jl: Backend-Agnostic Differentiable Programming in Julia

Automatic Differentiation using Constraint Handling Rules in Prolog


Tools to work with android .dex and java .class files

A First Look at Deep Learning Apps on Smartphones

R2-D2: ColoR-inspired Convolutional NeuRal Network (CNN)-based AndroiD Malware Detections

A Performance-Sensitive Malware Detection System Using Deep Learning on Mobile Devices

IEEE Transactions on Information Forensics and Security

StoryDroid: Automated Generation of Storyboard for Android Apps

ATVHunter: Reliable Version Detection of Third-Party Libraries for Vulnerability Identification in Android Applications

Secure Containers in Android: the Samsung KNOX Case Study

Android inter-app communication threats and detection techniques

Layered obfuscation: a taxonomy of software obfuscation techniques for layered security

A Method for Automatic Android Malware Detection Based on Static Analysis and Deep Learning

Towards a fair comparison and realistic evaluation framework of android malware detectors based on static analysis and machine learning


[CVPR 2023] Official Implementation of X-Decoder for generalized decoding for pixel, image and language

Generalized Decoding for Pixel, Image, and Language

A Simple Framework for Open-Vocabulary Segmentation and Detection

Segment Any Point Cloud Sequences by Distilling Vision Foundation Models

Learning to Follow Object-Centric Image Editing Instructions Faithfully


Phylogenetic ANalyses of DiversificAtion (in Julia)

Fifth mass extinction event triggered the diversification of the largest family of freshwater gastropods (Caenogastropoda: Truncatelloidea: Hydrobiidae)

Cladistics : the international journal of the Willi Hennig Society

Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches

The causes of species richness patterns among clades


MEGARA (Multi-Espectrógrafo en GTC de Alta Resolución para Astronomía) is a facility instrument designed for the 10.4m GTC telescope in La Palma (Spain).

The 60 pc Environment of FRB 20180916B

NGC 7469 as seen by MEGARA: new results from high-resolution IFU spectroscopy

Monthly notices of the Royal Astronomical Society

TXS 2116-077: A Gamma-Ray Emitting Relativistic Jet Hosted in a Galaxy Merger

MEGARA-GTC stellar spectral library – II. MEGASTAR first release

Monthly Notices of the Royal Astronomical Society

Spatially-resolved properties of the ionized gas in the HII galaxy J084220+115000


Surface Urban Energy and Water Balance Scheme


TransDecoder source

Long-read sequence assembly: a technical evaluation in barley

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

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

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

Firefly genomes illuminate parallel origins of bioluminescence in beetles

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

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

Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

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

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


Conduct simulation-based inference on strong gravitational lensing systems.

lenstronomy II: A gravitational lensing software ecosystem

From Images to Dark Matter: End-to-end Inference of Substructure from Hundreds of Strong Gravitational Lenses

JWST lensed quasar dark matter survey I: Description and First Results

A Strong Gravitational Lens Is Worth a Thousand Dark Matter Halos:
  Inference on Small-Scale Structure Using Sequential Methods


Deep Learning for Time Series Classification

Deep learning for time series classification: a review

Unsupervised Scalable Representation Learning for Multivariate Time Series

Interpretable Time Series Classification using Linear Models and Multi-resolution Multi-domain Symbolic Representations

Time Series Extrinsic Regression

Can We Ditch Feature Engineering? End-to-End Deep Learning for Affect Recognition from Physiological Sensor Data

Automatic Classification of Plasma Regions in Near-Earth Space With Supervised Machine Learning: Application to Magnetospheric Multi Scale 2016–2019 Observations

Frontiers in Astronomy and Space Sciences

Monash University, UEA, UCR Time Series Regression Archive

Monash University, UEA, UCR Time Series Extrinsic Regression Archive

Detection of Unilateral Arm Paresis after Stroke by Wearable Accelerometers and Machine Learning


Metagenomics-focused BAM file manipulation

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

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

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

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

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

Zenodo (CERN European Organization for Nuclear Research)

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

Moisture Modulates Soil Reservoirs of Active DNA and RNA Viruses

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

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

Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming


Python interface to download S-PLUS data just like splus.cloud. Good for ML workflows for example, downloading big chunks of data.

Data Release 2 of S-PLUS: accurate template-fitting based photometry covering ∼1000 square degrees in 12 optical filters

Estimating stellar population and emission-line properties in S-PLUS galaxies

The S-PLUS Fornax Project (S+FP): SExtractor detection and measurement
  of nearby galaxies in large photometric surveys


Simulation of X-ray Telescopes

Full-sky photon simulation of clusters and active galactic nuclei in the soft X-rays for eROSITA

Deep learning-based super-resolution and de-noising for XMM-newton images

The velocity structure of the intracluster medium during a major merger: Simulated microcalorimeter observations


The Financial Document Causality Detection Shared Task (FinCausal 2020)

The Financial Causality Extraction Shared Task (FinCausal 2022)

Domino at FinCausal 2020, Task 1 and 2: Causal Extraction System

JDD @ FinCausal 2020, Task 2: Financial Document Causality Detection

Fraunhofer IAIS at FinCausal 2020, Tasks 1 & 2: Using Ensemble Methods and Sequence Tagging to Detect Causality in Financial Documents

ATL at FinCausal 2022: Transformer Based Architecture for Automatic Causal Sentence Detection and Cause-Effect Extraction


Rarefaction scripts

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

RTK: efficient rarefaction analysis of large datasets

Dispersal strategies shape persistence and evolution of human gut bacteria

Antibiotics-induced monodominance of a novel gut bacterial order


Modification-induced misincorporation tRNA sequencing

Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation

Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq

Benchmarking tRNA-Seq quantification approaches by realistic tRNA-Seq data simulation identifies two novel approaches with higher accuracy


Northern Arizona SNP Pipeline

Origin, evolution, and global transmission of community-acquired Staphylococcus aureus ST8

Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts

Genomic relatedness of Staphylococcus pettenkoferi isolates of different origins


Windfarm Operations & Maintenance cost-Benefit Analysis Tool


Public release of TauREx3

TauREx 3: A Fast, Dynamic, and Extendable Framework for Retrievals

The ExoMolOP database: Cross sections and k-tables for molecules of interest in high-temperature exoplanet atmospheres

A comparison of exoplanet spectroscopic retrieval tools

ARES. III. Unveiling the Two Faces of KELT-7 b with HST WFC3

ARES IV: Probing the Atmospheres of the Two Warm Small Planets HD 106315c and HD 3167c with the HST/WFC3 Camera

Near-infrared transmission spectrum of TRAPPIST-1 h using Hubble WFC3 G141 observations

Exploring the Ability of Hubble Space Telescope WFC3 G141 to Uncover Trends in Populations of Exoplanet Atmospheres through a Homogeneous Transmission Survey of 70 Gaseous Planets

The Astrophysical Journal Supplement Series

ESA-Ariel Data Challenge NeurIPS 2022: Introduction to exo-atmospheric studies and presentation of the Atmospheric Big Challenge (ABC) Database

Correcting the effect of stellar spots on ARIEL transmission spectra - II. The limb-darkening effect

Toward Atmospheric Retrievals of Panchromatic Light Curves: ExPLOR-ing Generalized Inversion Techniques for Transiting Exoplanets with JWST and Ariel


Functional localizer experiment used to define category-selective cortical regions

Differential sustained and transient temporal processing across visual streams

Words as Visual Objects: Neural and Behavioral Evidence for High-Level Visual Impairments in Dyslexia

Attention enhances category representations across the brain with strengthened residual correlations to ventral temporal cortex

Dissociable contributions of the medial parietal cortex to recognition memory


Python module for the analysis of light curves from the ESA Cheops mission

The CHEOPS Mission

IEEE International Workshop on Metrology for AeroSpace

Six transiting planets and a chain of Laplace resonances in TOI-178

The hot dayside and asymmetric transit of WASP-189 b seen by CHEOPS

CHEOPS observations of the HD 108236 planetary system: a fifth planet, improved ephemerides, and planetary radii

Analysis of Early Science observations with the CHaracterising ExOPlanets Satellite (CHEOPS) using pycheops

A pair of sub-Neptunes transiting the bright K-dwarf TOI-1064 characterized with CHEOPS

WASP-186 and WASP-187: two hot Jupiters discovered by SuperWASP and SOPHIE with additional observations by TESS

Spi-OPS: Spitzer and CHEOPS confirm the near-polar orbit of MASCARA-1 b and reveal a hint of dayside reflection

A search for transiting planets around hot subdwarfs : I. Methods and performance tests on light curves from Kepler, K2, TESS, and CHEOPS

Keele Research Repository (Keele University)

Investigating the architecture and internal structure of the TOI-561 system planets with CHEOPS, HARPS-N, and TESS


A fresh approach to deep learning written in MATLAB

Stable Architectures for Deep Neural Networks

Reversible Architectures for Arbitrarily Deep Residual Neural Networks

Learning across scales - A multiscale method for Convolution Neural Networks

slimTrain -- A Stochastic Approximation Method for Training Separable Deep Neural Networks


A novel application of the RAMP main engine for generating bottom-up stochastic electric vehicles load profiles.


ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes

ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes

Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic

Development and application of computational tools for RNA-Seq based transcriptome annotations

Use of a combined antibacterial synergy approach and the ANNOgesic tool to identify novel targets within the gene networks of multidrug-resistant Klebsiella pneumoniae


Code and Python library to process Robotic Total Stations data

Uncertainty analysis for accurate ground truth trajectories with robotic total stations

Benchmarking ground truth trajectories with robotic total stations


Method for encoding brain connectomes in multidimensional arrays (tensors).

The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services

Sparse multiway decomposition for analysis and modeling of diffusion imaging and tractography

Optimizing the Linear Fascicle Evaluation Algorithm for Multi-Core and Many-Core Systems

Evaluation of tractogram filtering methods using human-like connectome phantoms


Holistically-Attracted Wireframe Parsing [TPAMI'23] & [CVPR' 20]

HEAT: Holistic Edge Attention Transformer for Structured Reconstruction

Holistically-Attracted Wireframe Parsing: From Supervised to Self-Supervised Learning

A Comprehensive Review of Image Line Segment Detection and Description: Taxonomies, Comparisons, and Challenges


The Scott-Knott Effect Size Difference (ESD) test

The Impact of Automated Parameter Optimization on Defect Prediction Models

SQAPlanner: Generating Data-Informed Software Quality Improvement Plans

Predicting unstable software benchmarks using static source code features

Is My Transaction Done Yet? An Empirical Study of Transaction Processing Times in the Ethereum Blockchain Platform

Predicting Code Review Completion Time in Modern Code Review


OpenAQ API


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

PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences

Do Deep Learning Models Really Outperform Traditional Approaches in Molecular Docking?

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

Deep Confident Steps to New Pockets: Strategies for Docking Generalization.

FABind: Fast and Accurate Protein-Ligand Binding

Modeling Molecular Structures with Intrinsic Diffusion Models

A gastrointestinal locally activating Janus kinase inhibitor to treat ulcerative colitis


The Aegean source finding program and associated tools

GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey - I. A low-frequency extragalactic catalogue

Extragalactic Peaked-spectrum Radio Sources at Low Frequencies

The 154 MHz radio sky observed by the Murchison Widefield Array: noise, confusion, and first source count analyses

The ASKAP/EMU Source Finding Data Challenge

Publications of the Astronomical Society of Australia

GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM)
  survey II: Galactic Plane 345^∘ < l < 67^∘, 180^∘ < l <
  240^∘

Low-Frequency Spectral Energy Distributions of Radio Pulsars Detected with the Murchison Widefield Array

Interplanetary scintillation studies with the Murchison Widefield Array - II. Properties of sub-arcsecond compact sources at low radio frequencies

GaLactic and Extragalactic All-sky Murchison Widefield Array survey eXtended (GLEAM-X) I: Survey description and initial data release

Remnant radio galaxies discovered in a multi-frequency survey

The ASKAP-EMU Early Science Project: 888 MHz radio continuum survey of the Large Magellanic Cloud


A software package for privacy-preserving generation of a synthetic twin to a given sensitive data set.

Privacy-preserving data sharing via probabilistic modeling

Noise-Aware Statistical Inference with Differentially Private Synthetic Data


FINN.no Slate Dataset for Recommender Systems. A dataset containing all interactions (viewed items + response (clicked item / no click) for users over a longer time horizon.

FINN.no Slates Dataset: A new Sequential Dataset Logging Interactions, all Viewed Items and Click Responses/No-Click for Recommender Systems Research

Dynamic Slate Recommendation with Gated Recurrent Units and Thompson Sampling

Impression-Aware Recommender Systems


Causal Mixture Model for GWAS summary statistics

Bivariate causal mixture model quantifies polygenic overlap between complex traits beyond genetic correlation

Polygenic overlap and shared genetic loci between loneliness, severe mental disorders, and cardiovascular disease risk factors suggest shared molecular mechanisms

Characterizing the Genetic Overlap Between Psychiatric Disorders and Sleep-Related Phenotypes

Quantifying the Polygenic Architecture of the Human Cerebral Cortex: Extensive Genetic Overlap between Cortical Thickness and Surface Area

Extensive bidirectional genetic overlap between bipolar disorder and cardiovascular disease phenotypes

Identification of novel genomic risk loci shared between common epilepsies and psychiatric disorders

Genome-wide association study of cerebellar volume provides insights into heritable mechanisms underlying brain development and mental health

Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR

Shared genetic loci between Alzheimer's disease and multiple sclerosis: Crossroads between neurodegeneration and immune system

Genetic overlap between Alzheimer's disease and immune-mediated diseases: an atlas of shared genetic determinants and biological convergence.


High throughput protein function annotation with Human Readable Description (HRDs) and Gene Ontology (GO) Terms.

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut

Durum wheat genome highlights past domestication signatures and future improvement targets

The genome sequence of segmental allotetraploid peanut Arachis hypogaea

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

The barley pan-genome reveals the hidden legacy of mutation breeding

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Towards a whole-genome sequence for rye (Secale cereale L.).

The Plant journal : for cell and molecular biology

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus.


ColabFold on your local PC

ColabFold - Making protein folding accessible to all

Discovery and structure of a widespread bacterial ABC transporter specific for ergothioneine

Stepwise emergence of the neuronal gene expression program in early animal evolution

Solubility-Aware Protein Binding Peptide Design Using AlphaFold

Seasonal effects decouple SARS-CoV-2 haplotypes worldwide

DNA-binding mechanism and evolution of Replication Protein A

Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold

Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops


Learning to See in the Dark. CVPR 2018

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

Seeing Motion in the Dark

International Conference on Computer Vision

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

Learning to See in the Dark


SCOPE is a simulation model for radiative transfer, photosynthesis and energy fluxes in vegetation and soil.

Sun-induced fluorescence and gross primary productivity during a heat wave

Optimal inverse estimation of ecosystem parameters from observations of carbon and energy fluxes


Analysis pipeline for the GUIDE-seq assay.

High-level correction of the sickle mutation is amplified in vivo during erythroid differentiation

In vivo genome editing in mouse restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers

Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability

CRISPR-Cas9 engineering of the RAG2 locus via complete coding sequence replacement for therapeutic applications


A grammar of graphics for comparative genomics

Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae

Phased grapevine genome sequence of an Rpv12 carrier for biotechnological exploration of resistance to Plasmopara viticola

Widespread yet persistent low abundance of TIM5-like cyanophages in the oceans.

Population dynamics and characteristics of Klebsiella pneumoniae from healthy poultry in Norway

Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil

Short- and Long-Read Sequencing Reveals the Presence and Evolution of an IncF Plasmid Harboring blaCTX-M-15 and blaCTX-M-27 Genes in Escherichia coli ST131.

ExplorePipolin: reconstruction and annotation of piPolB-encoding bacterial mobile elements from draft genomes


Benchmark your model on out-of-distribution datasets with carefully collected human comparison data (NeurIPS 2021 Oral)

Scaling Up Your Kernels to 31x31: Revisiting Large Kernel Design in CNNs

Last Layer Re-Training is Sufficient for Robustness to Spurious Correlations

Partial success in closing the gap between human and machine vision

UniRepLKNet: A Universal Perception Large-Kernel ConvNet for Audio, Video, Point Cloud, Time-Series and Image Recognition

FFT-based Dynamic Token Mixer for Vision

Clarifying Myths About the Relationship Between Shape Bias, Accuracy, and Robustness

Canadian Conference on Computer and Robot Vision


Multiple-target linear models - CPU/GPU

Evidence of a predictive coding hierarchy in the human brain listening to speech

Semantic Representations during Language Comprehension Are Affected by Context

Deep Neural Networks and Brain Alignment: Brain Encoding and Decoding (Survey)

Voxelwise encoding models of body stimuli reveal a representational gradient from low-level visual features to postural features in occipitotemporal cortex


Electricity monitoring library - install in Arduino IDE's libraries folder then restart the IDE


A Python wrapper for the NOAA CO-OPS Tides & Currents Data and Metadata APIs.


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

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

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

基因组蛋白质组与生物信息学报

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

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


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

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

One Embedder, Any Task: Instruction-Finetuned Text Embeddings

SongComposer: A Large Language Model for Lyric and Melody Composition in
  Song Generation

Evaluating the Generation Capabilities of Large Chinese Language Models

Compress to Impress: Unleashing the Potential of Compressive Memory in
  Real-World Long-Term Conversations

Efficient Knowledge Infusion via KG-LLM Alignment

Exploiting Duality in Open Information Extraction with Predicate Prompt

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

Sentiment analysis and prediction model based on Chinese government affairs microblogs

Zero-shot domain paraphrase with unaligned pre-trained language models


SCR1 is a high-quality open-source RISC-V MCU core in Verilog

Don't CWEAT It

Proceedings of the 41st IEEE/ACM International Conference on Computer-Aided Design

RVCoreP-32IC: A high-performance RISC-V soft processor with an efficient fetch unit supporting the compressed instructions


SV caller for nanopore data

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

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

A pipeline for complete characterization of complex germline rearrangements from long DNA reads

Is an SV caller compatible with sequencing data? An online recommendation tool to automatically recommend the optimal caller based on data features


baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677

medRxiv : the preprint server for health sciences

Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay

The episodic resurgence of highly pathogenic avian influenza H5 virus

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease


Statistical Analysis of RNA-Seq Tools

Quality control of transcription start site selection by nonsense-mediated-mRNA decay

A simple guide to de novo transcriptome assembly and annotation

Comparative Transcriptomics Suggests Early Modifications by Vintec® in Grapevine Trunk of Hormonal Signaling and Secondary Metabolism Biosynthesis in Response to Phaeomoniella chlamydospora and Phaeoacremonium minimum

Epitype-inducing temperatures drive DNA methylation changes during somatic embryogenesis in the long-lived gymnosperm Norway spruce


AdapterRemoval v2 - rapid adapter trimming, identification, and read merging

AdapterRemoval v2: rapid adapter trimming, identification, and read merging

Reconstructing the Deep Population History of Central and South America

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

Direct Antiviral Treatments for Hepatitis C Virus Have Off-Target Effects of Oncologic Relevance in Hepatocellular Carcinoma

Insights into the Host-Pathogen Interaction Pathways through RNA-Seq Analysis of Lens culinaris Medik. in Response to Rhizoctonia bataticola Infection

Mapache: a flexible pipeline to map ancient DNA

Genome-wide identification, characterization, and functional analysis of lncRNAs in Hevea brasiliensis

Identification of an Actionable Mutation of KIT in a Case of Extraskeletal Myxoid Chondrosarcoma

International journal of molecular sciences

Molecular Signature of Biological Aggressiveness in Clear Cell Sarcoma of the Kidney (CCSK)

Mechanisms of resistance to a PI3K inhibitor in gastrointestinal stromal tumors: an omic approach to identify novel druggable targets

DOAJ (DOAJ: Directory of Open Access Journals)


For releasing code related to compression methods for transformers, accompanying our publications

SliceGPT: Compress Large Language Models by Deleting Rows and Columns

SLEB: Streamlining LLMs through Redundancy Verification and Elimination
  of Transformer Blocks

LLaMA-NAS: Efficient Neural Architecture Search for Large Language
  Models


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

Recent advances and applications of deep learning methods in materials science

Opportunities and Challenges for Machine Learning in Materials Science

Distributed representations of atoms and materials for machine learning

Interdisciplinary Discovery of Nanomaterials Based on Convolutional Neural Networks


Security and Privacy Risk Simulator for Machine Learning (arXiv:2312.17667)

Deep Learning with Differential Privacy

Conference on Computer and Communications Security

Federated Optimization in Heterogeneous Networks

Membership Inference Attacks against Machine Learning Models

Model Inversion Attacks that Exploit Confidence Information and Basic Countermeasures

Evasion Attacks against Machine Learning at Test Time

Poisoning Attacks against Support Vector Machines

Inverting Gradients -- How easy is it to break privacy in federated learning?

Model-Contrastive Federated Learning

FedMD: Heterogenous Federated Learning via Model Distillation

SecureBoost: A Lossless Federated Learning Framework


A general-purpose, deep learning-first library for constrained optimization in PyTorch

Controlled Sparsity via Constrained Optimization or: How I Learned to Stop Tuning Penalties and Love Constraints

Nonparametric Partial Disentanglement via Mechanism Sparsity: Sparse Actions, Interventions and Sparse Temporal Dependencies

L_0onie: Compressing COINs with L_0-constraints

Balancing Act: Constraining Disparate Impact in Sparse Models

Active Reinforcement Learning for Robust Building Control


[NeurIPS 2023] ImageReward: Learning and Evaluating Human Preferences for Text-to-image Generation

ImageReward: Learning and Evaluating Human Preferences for Text-to-Image Generation

DPOK: Reinforcement Learning for Fine-tuning Text-to-Image Diffusion Models

Using Human Feedback to Fine-tune Diffusion Models without Any Reward Model

Confidence-aware Reward Optimization for Fine-tuning Text-to-Image
  Models


Accurately generate all possible forms of an English word e.g "election" --> "elect", "electoral", "electorate" etc.

A Lightweight Constrained Generation Alternative for Query-focused Summarization

An Extended Sequence Tagging Vocabulary for Grammatical Error Correction

Data Augmentation of Incorporating Real Error Patterns and Linguistic Knowledge for Grammatical Error Correction

Proceedings of the 25th Conference on Computational Natural Language Learning


A library for distributed ML training with PyTorch

CORA: Benchmarks, Baselines, and Metrics as a Platform for Continual Reinforcement Learning Agents

Improving Policy Learning via Language Dynamics Distillation

NetHack is Hard to Hack

Open RL Benchmark: Comprehensive Tracked Experiments for Reinforcement
  Learning

Katakomba: Tools and Benchmarks for Data-Driven NetHack

Cleanba: A Reproducible and Efficient Distributed Reinforcement Learning Platform


Pytorch 3D U-Net Convolution Neural Network (CNN) designed for medical image segmentation

Deeply-Supervised Nets

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

Models Genesis

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

Learning Semantics-enriched Representation via Self-discovery, Self-classification, and Self-restoration

Exploring the U-Net++ Model for Automatic Brain Tumor Segmentation

Deep Learning Using Augmentation via Registration: 1st Place Solution to the AutoImplant 2020 Challenge

Towards the Automatization of Cranial Implant Design in Cranioplasty

Fast and Accurate 3D Medical Image Segmentation with Data-swapping Method

Brain Tumor Segmentation Using Partial Depthwise Separable Convolutions

Cardiac MRI Image Segmentation for Left Ventricle and Right Ventricle using Deep Learning


Anti-Adblock Killer helps you keep your Ad-Blocker active, when you visit a website and it asks you to disable.

AdGraph: A Graph-Based Approach to Ad and Tracker Blocking

A First Look at Ad-block Detection: A New Arms Race on the Web

Block the blocker: Studying the effects of Anti Ad-blocking


TextGAN is a PyTorch framework for Generative Adversarial Networks (GANs) based text generation models.

MALCOM: Generating Malicious Comments to Attack Neural Fake News Detection Models

Improving GAN Training with Probability Ratio Clipping and Sample Reweighting

DGSAN: Discrete Generative Self-Adversarial Network

Feature-aware conditional GAN for category text generation

Stochastic Parrots Looking for Stochastic Parrots: LLMs are Easy to Fine-Tune and Hard to Detect with other LLMs


Official implementation of VQ-Diffusion

Vector Quantized Diffusion Model for Text-to-Image Synthesis

DIRE for Diffusion-Generated Image Detection

Improved Vector Quantized Diffusion Models

LayoutDiffusion: Improving Graphic Layout Generation by Discrete Diffusion Probabilistic Models

Diffusion Reward: Learning Rewards via Conditional Video Diffusion


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

Jukebox: A Generative Model for Music

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

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

DadaGP: A Dataset of Tokenized GuitarPro Songs for Sequence Models

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

Proceedings of the 16th ACM Conference on Recommender Systems

A Survey of AI Music Generation Tools and Models


Short Read Sequence Typing for Bacterial Pathogens

Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications

Whole genome sequencing in clinical and public health microbiology

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

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

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

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

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

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

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

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


Bayesian genotyper for structural variants

Parliament2: Accurate structural variant calling at scale

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle

In utero origin of myelofibrosis presenting in adult monozygotic twins

A New Next-Generation Sequencing Strategy for the Simultaneous Analysis of Mutations and Chromosomal Rearrangements at DNA Level in Acute Myeloid Leukemia Patients

The Journal of molecular diagnostics : JMD


Improving Dictionary Learning with Gated Sparse Autoencoders

Scaling and evaluating sparse autoencoders

Transcoders Find Interpretable LLM Feature Circuits

Missed Causes and Ambiguous Effects: Counterfactuals Pose Challenges for
  Interpreting Neural Networks


Training neural networks in TensorFlow 2.0 with 5x less memory

Checkmate: Breaking the Memory Wall with Optimal Tensor Rematerialization

Winner-Take-All Column Row Sampling for Memory Efficient Adaptation of Language Model

Survey on Large Scale Neural Network Training

Tempo: Accelerating Transformer-Based Model Training through Memory Footprint Reduction


Natural language detection library for Go

Understanding Longitudinal Behaviors of Toxic Accounts on Reddit

Twits, Toxic Tweets, and Tribal Tendencies: Trends in Politically Polarized Posts on Twitter

Sub-Standards and Mal-Practices: Misinformation's Role in Insular, Polarized, and Toxic Interactions


Deep learning software for colorizing black and white images with a few clicks.

Real-Time User-Guided Image Colorization with Learned Deep Priors

Image Colorization: A Survey and Dataset

GIMP-ML: Python Plugins for using Computer Vision Models in GIMP


WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

Comparative cellular analysis of motor cortex in human, marmoset and mouse

A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development

Active DNA demethylation regulates tracheary element differentiation in Arabidopsis


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

High Fidelity Neural Audio Compression

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

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

UniAudio: An Audio Foundation Model Toward Universal Audio Generation

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

NaturalSpeech 3: Zero-Shot Speech Synthesis with Factorized Codec and
  Diffusion Models

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

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

Latent-Domain Predictive Neural Speech Coding

The VoicePrivacy 2024 Challenge Evaluation Plan


An Efficient implementation of TransE and its extended models for Knowledge Representation Learning

A Survey on Knowledge Graphs: Representation, Acquisition, and Applications

IEEE transactions on neural networks and learning systems

DeepPath: A Reinforcement Learning Method for Knowledge Graph Reasoning

OpenKE: An Open Toolkit for Knowledge Embedding

Empirical Methods in Natural Language Processing

Word-Entity Duet Representations for Document Ranking

SIGIR'17: PROCEEDINGS OF THE 40TH INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL

Keyword Search on RDF Graphs - A Query Graph Assembly Approach

Learning Representation Mapping for Relation Detection in Knowledge Base Question Answering

Relation path embedding in knowledge graphs

Knowledge Embedding with Geospatial Distance Restriction for Geographic Knowledge Graph Completion

ISPRS International Journal of Geo-Information

Knowledge-aware attention network for protein-protein interaction extraction

Leveraging prior knowledge for protein–protein interaction extraction with memory network

Database : the journal of biological databases and curation


Temporal Graph Convolutional Network for Urban Traffic Flow Prediction Method

T-GCN: A Temporal Graph Convolutional Network for Traffic Prediction

IEEE Transactions on Intelligent Transportation Systems

Graph Neural Network for Traffic Forecasting: A Survey

Deep Learning on Traffic Prediction: Methods, Analysis and Future Directions

A3T-GCN: Attention Temporal Graph Convolutional Network for Traffic Forecasting

How to Build a Graph-Based Deep Learning Architecture in Traffic Domain: A Survey

AST-GCN: Attribute-Augmented Spatiotemporal Graph Convolutional Network for Traffic Forecasting

KST-GCN: A Knowledge-Driven Spatial-Temporal Graph Convolutional Network for Traffic Forecasting

Traffic prediction using artificial intelligence: Review of recent advances and emerging opportunities

Transportation Research Part C: Emerging Technologies

A Comprehensive Survey on Traffic Prediction.

Graph Neural Networks for Intelligent Transportation Systems: A Survey


A MATLAB software for the analysis of digital elevation models -

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

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

Drainage divide networks – Part 2: Response to perturbations

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

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

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


Creative Commons Attribution 4.0 International

Controlled Vocabularies (CVs) for use in CMIP6

Presentation and Evaluation of the IPSL‐CM6A‐LR Climate Model

Journal of Advances in Modeling Earth Systems

Requirements for a global data infrastructure in support of CMIP6

The CMIP6 Data Request (DREQ, version 01.00.31)

Sensitivity of deep ocean biases to horizontal resolution in prototype CMIP6 simulations with AWI-CM1.0

The CMIP6 Data Request (version 01.00.31)

Historical global ocean wave data simulated with CMIP6 anthropogenic and natural forcings

A Barotropic Solver for High-Resolution Ocean General Circulation Models

Journal of Marine Science and Engineering

Impact of Hydroclimate Change on the Management for the Multipurpose Reservoir: A Case Study in Meishan (China)


A Keras implementation of CapsNet in NIPS2017 paper "Dynamic Routing Between Capsules". Now test error ＝ 0.34%.

Dynamic Routing Between Capsules

CapsuleGAN: Generative Adversarial Capsule Network

Attention routing between capsules

HitNet: a neural network with capsules embedded in a Hit-or-Miss layer, extended with hybrid data augmentation and ghost capsules

MalCaps: A Capsule Network Based Model for the Malware Classification

Deep Medical Image Analysis with Representation Learning and Neuromorphic Computing

Towards an effective model for lung disease classification

CLAHE-CapsNet: Efficient retina optical coherence tomography classification using capsule networks with contrast limited adaptive histogram equalization

Multi-lane LBP-Gabor Capsule Network with K-means Routing for Medical Image Analysis

International Journal of Advanced Computer Science and Applications


A Fairness-aware Incentive Scheme for Federated Learning

PROCEEDINGS OF THE 3RD AAAI/ACM CONFERENCE ON AI, ETHICS, AND SOCIETY AIES 2020

Rethinking Privacy Preserving Deep Learning: How to Evaluate and Thwart Privacy Attacks

FedCG: Leverage Conditional GAN for Protecting Privacy and Maintaining Competitive Performance in Federated Learning

StarFL: Hybrid Federated Learning Architecture for Smart Urban Computing

ACM Transactions on Intelligent Systems and Technology

Toward Responsible AI: An Overview of Federated Learning for User-centered Privacy-preserving Computing

ACM Transactions on Interactive Intelligent Systems


DrWhy is the collection of tools for eXplainable AI (XAI). It's based on shared principles and simple grammar for exploration, explanation and visualisation of predictive models.

Opportunities and Challenges in Explainable Artificial Intelligence (XAI): A Survey

auditor: an R Package for Model-Agnostic Visual Validation and Diagnostics

The Merging Path Plot: adaptive fusing of k-groups with likelihood-based model selection

EPP: interpretable score of model predictive power


See how much of your cloud bill is spent on fossil fuels ,so you can do the right thing and switch. We're in a climate crisis, remember?


Deep End-to-end Causal Inference

Simultaneous Missing Value Imputation and Structure Learning with Groups

Towards Causal Foundation Model: on Duality between Causal Inference and Attention

Causal Reasoning in the Presence of Latent Confounders via Neural ADMG Learning

VISPUR: Visual Aids for Identifying and Interpreting Spurious Associations in Data-Driven Decisions

NeurIPS Competition Instructions and Guide: Causal Insights for Learning Paths in Education

Neural Structure Learning with Stochastic Differential Equations

Castor: Causal Temporal Regime Structure Learning

Human-in-the-Loop Causal Discovery under Latent Confounding using Ancestral GFlowNets

FiP: a Fixed-Point Approach for Causal Generative Modeling


Trained model files for dlib example programs.

MaskedFace-Net – A dataset of correctly/incorrectly masked face images in the context of COVID-19

Characterizing the Variability in Face Recognition Accuracy Relative to Race

Neonatal pain detection in videos using the iCOPEvid dataset and an ensemble of descriptors extracted from Gaussian of Local Descriptors

Fully Automatic Landmarking of Syndromic 3D Facial Surface Scans Using 2D Images

Improving Memory Utilization in Convolutional Neural Network Accelerators

DIF : Dataset of Perceived Intoxicated Faces for Drunk Person Identification

Eigenfaces-Based Steganography

Distillation of an End-to-End Oracle for Face Verification and Recognition Sensors

Regulating Facial Processing Technologies: Tensions Between Legal and Technical Considerations in the Application of Illinois BIPA

Estimating Structural Disparities for Face Models


Revisiting the Arcade Learning Environment: Evaluation Protocols and Open Problems for General Agents

Deep Reinforcement Learning at the Edge of the Statistical Precipice

Open RL Benchmark: Comprehensive Tracked Experiments for Reinforcement
  Learning

Stimulate the Potential of Robots via Competition

An Open-Loop Baseline for Reinforcement Learning Locomotion Tasks


Water Detect Algorithm


Fast, lightweight graphset operation library

Semantic Probabilistic Layers for Neuro-Symbolic Learning

DenseZDD: A Compact and Fast Index for Families of Sets

International Competition on Graph Counting Algorithms 2023

Dynamic traffic resources allocation under elastic demand of users with space-time prism constraints


CUDA-accelerated Fully Homomorphic Encryption Library

HEAX: An Architecture for Computing on Encrypted Data

SoK: Fully Homomorphic Encryption Compilers

ARK: Fully Homomorphic Encryption Accelerator with Runtime Data Generation and Inter-Operation Key Reuse

Non-Interactive Private Decision Tree Evaluation

Virtual Secure Platform: A Five-Stage Pipeline Processor over TFHE

Accelerating Encrypted Computing on Intel GPUs

HAAC: A Hardware-Software Co-Design to Accelerate Garbled Circuits

SoK: Fully Homomorphic Encryption Accelerators

Practical solutions in fully homomorphic encryption: a survey analyzing existing acceleration methods


[ICLR 2020; IPDPS 2019] Fast and accurate minibatch training for deep GNNs and large graphs (GraphSAINT: Graph Sampling Based Inductive Learning Method).

Graph Attention Networks

DropEdge: Towards Deep Graph Convolutional Networks on Node Classification

SIGN: Scalable Inception Graph Neural Networks

Scalable Graph Neural Networks via Bidirectional Propagation

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

Accurate, Efficient and Scalable Graph Embedding

International Parallel and Distributed Processing Symposium

Node Dependent Local Smoothing for Scalable Graph Learning

PaSca: A Graph Neural Architecture Search System under the Scalable Paradigm

C-SAW: A Framework for Graph Sampling and Random Walk on GPUs

PROCEEDINGS OF SC20: THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC20)


[CVPR 2020] Interpreting the Latent Space of GANs for Semantic Face Editing

Progressive Growing of GANs for Improved Quality, Stability, and Variation

InterFaceGAN: Interpreting the Disentangled Face Representation Learned by GANs

FakeSpotter: A Simple yet Robust Baseline for Spotting AI-Synthesized Fake Faces

EditGAN: High-Precision Semantic Image Editing

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

Smoothing the Disentangled Latent Style Space for Unsupervised Image-to-Image Translation

MaskFaceGAN: High-Resolution Face Editing With Masked GAN Latent Code Optimization

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

Surrogate Gradient Field for Latent Space Manipulation

High Resolution Face Editing with Masked GAN Latent Code Optimization


GUI for a Vocal Remover that uses Deep Neural Networks.

Multi-scale Multi-band DenseNets for Audio Source Separation

FSD: An Initial Chinese Dataset for Fake Song Detection

Smooth Talking and Fast Music: Understanding the Importance of Voice and Music in Travel and Tourism Ads via Acoustic Analytics

Emilia: An Extensive, Multilingual, and Diverse Speech Dataset for
  Large-Scale Speech Generation

Benchmarks and leaderboards for sound demixing tasks

Leveraging Content-based Features from Multiple Acoustic Models for Singing Voice Conversion


OpenAI CLIP text encoders for multiple languages!

Learning Transferable Visual Models From Natural Language Supervision

Language-agnostic BERT Sentence Embedding

Cross-lingual and Multilingual CLIP

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION

SpeechCLIP: Integrating Speech with Pre-Trained Vision and Language Model

Exploiting Cultural Biases via Homoglyphs in Text-to-Image Synthesis

MuMUR : Multilingual Multimodal Universal Retrieval

Translation-Enhanced Multilingual Text-to-Image Generation

PR-MCS: Perturbation Robust Metric for MultiLingual Image Captioning

Towards Zero-shot Cross-lingual Image Retrieval and Tagging

Babel-ImageNet: Massively Multilingual Evaluation of Vision-and-Language Representations


Converts an xyz file to an RDKit mol object

GEOM: Energy-annotated molecular conformations for property prediction and molecular generation

A Generative Model for Molecular Distance Geometry

Machine learning based energy-free structure predictions of molecules, transition states, and solids

Symmetry-Aware Actor-Critic for 3D Molecular Design

Scalable Fragment-Based 3D Molecular Design with Reinforcement Learning

Navigating chemical reaction space with a steering wheel

Fast and Automated Identification of Reactions with Low Barriers: The Decomposition of 3-Hydroperoxypropanal

Fast and automated identification of reactions with low barriers using meta-MD simulations

CONFPASS: fast DFT re-optimizations of structures from conformation searches

Journal of chemical information and modeling

Machine Learning for Screening Large Organic Molecules


HSIM: HARMONI simulation pipeline

hsim: a simulation pipeline for the HARMONI integral field spectrograph on the European ELT

Monthly Notices of the Royal Astronomical Society

Direct imaging and spectroscopy of exoplanets with the ELT/HARMONI high-contrast module

Emission from the circumgalactic medium: from cosmological zoom-in simulations to multiwavelength observables

Monthly notices of the Royal Astronomical Society

HARMONI: the ELT's First-Light Near-infrared and Visible Integral Field Spectrograph

Spectral unmixing for exoplanet direct detection in hyperspectral data

Simulating supermassive black hole mass measurements for a sample of ultramassive galaxies using ELT/HARMONI high-spatial-resolution integral-field stellar kinematics

Simulating the detection and classification of high-redshift supernovae with HARMONI on the ELT

Behind the Mask: can HARMONI@ELT detect biosignatures in the reflected light of Proxima b?

HARMONI view of the host galaxies of active galactic nuclei around cosmic noon


A collection of tools to load, visualize, model-fit and image optical interferometry data coming from CHARA, NPOI and VLTI

VLTI-PIONIER imaging of the red supergiant V602 Carinae

Dynamical Surface Imaging of λ Andromedae

Long Term Evolution of Surface Features on the Red Supergiant AZ Cyg

Imaging the Inner Astronomical Unit of the Herbig Be Star HD 190073

The Great Dimming of the Hypergiant Star RW Cephei: CHARA Array Images and Spectral Analysis

Reconstructing the near- to mid-infrared environment in the stellar merger remnant V838 Monocerotis


Official Edison Lab toolboxes and scripts for analyzing metabolomics data.

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

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

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

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

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

Uncovering in vivo biochemical patterns from time-series metabolic dynamics


The message passing GAN https://arxiv.org/abs/2106.11535 and generative adversarial particle transformer https://arxiv.org/abs/2211.10295 architectures for generating particle clouds

Particle Cloud Generation with Message Passing Generative Adversarial Networks

Evaluating generative models in high energy physics

Graph Generative Adversarial Networks for Sparse Data Generation in High Energy Physics

DeepTreeGAN: Fast Generation of High Dimensional Point Clouds


Lowered Isothermal Model Explorer in Python

A family of lowered isothermal models

A stellar-mass black hole population in the globular cluster NGC 6101?

Globular cluster number density profiles using Gaia DR2

The effect of stellar-mass black holes on the central kinematics of ω Cen: a cautionary tale for IMBH interpretations

Radial anisotropy in ω Cen limiting the room for an intermediate-mass black hole

Testing lowered isothermal models with direct N-body simulations of globular clusters

The properties of energetically unbound stars in stellar clusters

Mass models of NGC 6624 without an intermediate-mass black hole

A supra-massive population of stellar-mass black holes in the globular cluster Palomar 5

The Hubble Space Telescope UV Legacy Survey of Galactic Globular Clusters. XXIII. Proper-motion Catalogs and Internal Kinematics


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

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

Rigorous Neural Network Simulations: A Model Substantiation Methodology for Increasing the Correctness of Simulation Results in the Absence of Experimental Validation Data

Dynamical Characteristics of Recurrent Neuronal Networks Are Robust Against Low Synaptic Weight Resolution

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

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


In defence of metric learning for speaker recognition

Pushing the limits of raw waveform speaker recognition

Graph Attention Networks for Speaker Verification

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

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

HierSpeech++: Bridging the Gap between Semantic and Acoustic Representation of Speech by Hierarchical Variational Inference for Zero-shot Speech Synthesis

ASVtorch toolkit: Speaker verification with deep neural networks

Magnitude-aware Probabilistic Speaker Embeddings

LMD: A Learnable Mask Network to Detect Adversarial Examples for Speaker Verification

Baselines and Protocols for Household Speaker Recognition


Open biodiversity data publication by the INBO

GPS tracking data of Lesser Black-backed Gulls and Herring Gulls breeding at the southern North Sea coast

A checklist recipe: making species data open and FAIR

Watervogels – Wintering waterbirds in Flanders, Belgium


HPXML to Home Energy Score Translator


BACTpipe: An assembly and annotation pipeline for bacterial genomics

Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation

Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli

Atlantic Salmon Mucins Inhibit LuxS-Dependent A. Salmonicida AI-2 Quorum Sensing in an N-Acetylneuraminic Acid-Dependent Manner

International journal of molecular sciences

Escherichia coli ST2797 Is Abundant in Wastewater and Might Be a Novel Emerging Extended-Spectrum Beta-Lactamase E. coli


Python-based Fermi-Löwdin orbital self-interaction-correction

Stretched or noded orbital densities and self-interaction correction in density functional theory.

Interpretation and Automatic Generation of Fermi‐Orbital Descriptors

PyFLOSIC: Python-based Fermi-Löwdin orbital self-interaction correction.


A tc command wrapper. Make it easy to set up traffic control of network bandwidth/latency/packet-loss/packet-corruption/etc. to a network-interface/Docker-container(veth).

MockFog 2.0: Automated Execution of Fog Application Experiments in the Cloud

Fedstellar: A Platform for Decentralized Federated Learning

Distributed Training for Deep Learning Models On An Edge Computing Network Using Shielded Reinforcement Learning


An annotated implementation of the Transformer paper.

Attention Is All You Need

The Annotated Transformer

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

Recursive Graphical Neural Networks for Text Classification


Java based tools for bulk downloading read/analysis files from ENA via FTP or Aspera.

The COMPARE Data Hubs

The European Nucleotide Archive in 2023

Accelerating surveillance and research of antimicrobial resistance – an online repository for sharing of antimicrobial susceptibility data associated with whole genome sequences


Official code for "DaisyRec 2.0: Benchmarking Recommendation for Rigorous Evaluation" (TPAMI2022) and "Are We Evaluating Rigorously? Benchmarking Recommendation for Reproducible Evaluation and Fair Comparison" (RecSys2020)

Embarrassingly Shallow Autoencoders for Sparse Data

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

RECSYS 2020: 14TH ACM CONFERENCE ON RECOMMENDER SYSTEMS

A Comprehensive Survey on Trustworthy Recommender Systems

Infinite Recommendation Networks: A Data-Centric Approach

Recommend for a Reason: Unlocking the Power of Unsupervised Aspect-Sentiment Co-Extraction

Improving Accountability in Recommender Systems Research Through Reproducibility


OTOv1-v3, NeurIPS, ICLR, TMLR, DNN Training, Compression, Structured Pruning, Erasing Operators, CNN, Diffusion, LLM

Only Train Once: A One-Shot Neural Network Training And Pruning Framework

OTOV2: Automatic, Generic, User-Friendly

LoRAShear: Efficient Large Language Model Structured Pruning and Knowledge Recovery

Automated Search-Space Generation Neural Architecture Search

DistiLLM: Towards Streamlined Distillation for Large Language Models

OTOv3: Automatic Architecture-Agnostic Neural Network Training and Compression from Structured Pruning to Erasing Operators


Unofficial implemention of lanenet model for real time lane detection

Towards End-to-End Lane Detection: an Instance Segmentation Approach

Verifying Controllers With Vision-Based Perception Using Safe Approximate Abstractions

Perception Contracts for Safety of ML-Enabled Systems

Proceedings of the ACM on Programming Languages

GAS: Generating Fast and Accurate Surrogate Models for Autonomous Vehicle Systems


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

Universal Phone Recognition with a Multilingual Allophone System

Intent Classification Using Pre-Trained Embeddings For Low Resource Languages

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

Analyzing discourse functions with acoustic features and phone embeddings: non-lexical items in Taiwan Mandarin

Taiwan Conference on Computational Linguistics and Speech Processing


This repository is a tool for visualizing an agent RL process from a grid2op format. It was made though a partnership between RTE and Artelys for the different challengers of the L2RPN RL Challenge.

Learning to run a Power Network Challenge: a Retrospective Analysis

Towards an AI assistant for power grid operators

Towards an AI assistant for human grid operators


SED-fitting code for AGN and galaxies from a MCMC approach

AGNfitter: A BAYESIAN MCMC APPROACH TO FITTING SPECTRAL ENERGY DISTRIBUTIONS OF AGNs

Multi-wavelength Properties of Type 1 and Type 2 AGN Host Galaxies in the Chandra-COSMOS Legacy Survey

A Spectroscopic Follow-up Program of Very Massive Galaxies at 3 < z < 4: Confirmation of Spectroscopic Redshifts, and a High Fraction of Powerful AGNs

Evidence of underdeveloped torus and broad-line region of weak emission line quasars based on their spectral energy distribution


Creating multimodal multitask models

CodeXGLUE: A Machine Learning Benchmark Dataset for Code Understanding and Generation

Unsupervised Translation of Programming Languages

Pretrained Transformers as Universal Computation Engines

Many Heads but One Brain: Fusion Brain -- a Competition and a Single Multimodal Multitask Architecture


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

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

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


Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance


Machine learning assisted marginal likelihood (Bayesian evidence) estimation for Bayesian model selection

Machine learning assisted Bayesian model comparison: learnt harmonic mean estimator

Bayesian model comparison for simulation-based inference

Learned harmonic mean estimation of the marginal likelihood with normalizing flows

The future of cosmological likelihood-based inference: accelerated high-dimensional parameter estimation and model comparison

Learned harmonic mean estimation of the Bayesian evidence with
  normalizing flows


Tensor network simulations for finite temperature, open quantum system dynamics

Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue

Simulating Quantum Vibronic Dynamics at Finite Temperatures With Many Body Wave Functions at 0 K

MPSDynamics.jl: Tensor network simulations for finite-temperature
  (non-Markovian) open quantum system dynamics

Matrix Product State Simulations of Non-equilibirum Steady States and Transient Heat Flows in the Two-Bath Spin-Boson Model at Finite Temperatures

Managing temperature in open quantum systems strongly coupled with structured environments

Extending Non-Perturbative Simulation Techniques for Open-Quantum
  Systems to Excited-State Proton Transfer and Ultrafast Non-Adiabatic Dynamics

From Non-Markovian Dissipation to Spatiotemporal Control of Quantum Nanodevices


Package for processing and analyzing glycans and their role in biology.

Deep-Learning Resources for Studying Glycan-Mediated Host-Microbe Interactions.

Glycowork: A Python package for glycan data science and machine learning

The Role of Fucose-Containing Glycan Motifs Across Taxonomic Kingdoms

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy


The Honey Badger of BFT Protocols

FireLedger: A High Throughput Blockchain Consensus Protocol

Protocol for Asynchronous, Reliable, Secure and Efficient Consensus (PARSEC) Version 2.0

JUMBO: Fully Asynchronous BFT Consensus Made Truly Scalable


Resources about Design + AI (papers, datasets, events, companies, etc.)

May AI? Design Ideation with Cooperative Contextual Bandits

Beauty in artistic expressions through the eyes of networks and physics

Designing with AI for Digital Marketing

User Modeling, Adaptation, and Personalization

Category, process, and recommendation of design in an interactive evolutionary computation interior design experiment: a data-driven study

Artificial intelligence for engineering design, analysis and manufacturing

Learning to Select Elements for Graphic Design

International Conference on Multimedia Retrieval

Exemplar based experience transfer


A tensorflow library for building all kinds of models

Deep Residual Learning for Image Recognition

Very Deep Convolutional Networks for Large-Scale Image Recognition

U-Net: Convolutional Networks for Biomedical Image Segmentation

Densely Connected Convolutional Networks

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


A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

Compendium of secondary metabolite biosynthetic diversity encoded in bacterial genomes

BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

Diversity and taxonomic distribution of bacterial biosynthetic gene clusters predicted to produce compounds with therapeutically relevant bioactivities

Journal of industrial microbiology & biotechnology


The MaPLe compiler for efficient and scalable parallel functional programming

Provably space-efficient parallel functional programming

Symposium on Principles of Programming Languages

Entanglement detection with near-zero cost

Proceedings of the ACM on programming languages

DisLog: A Separation Logic for Disentanglement


Set of tools to assess and improve LLM security.

The Llama 3 Herd of Models

Llama Guard: LLM-based Input-Output Safeguard for Human-AI Conversations

JailbreakBench: An Open Robustness Benchmark for Jailbreaking Large
  Language Models

Purple Llama CyberSecEval: A Secure Coding Benchmark for Language Models

Refusal in Language Models Is Mediated by a Single Direction

CyberSecEval 2: A Wide-Ranging Cybersecurity Evaluation Suite for Large
  Language Models

Magpie: Alignment Data Synthesis from Scratch by Prompting Aligned LLMs
  with Nothing

Generative AI and Large Language Models for Cyber Security: All Insights
  You Need

SORRY-Bench: Systematically Evaluating Large Language Model Safety Refusal Behaviors

Lockpicking LLMs: A Logit-Based Jailbreak Using Token-level Manipulation


Compute SHAP values for your tree-based models using the TreeSHAP algorithm

Fast TreeSHAP: Accelerating SHAP Value Computation for Trees

Landscape of R packages for eXplainable Artificial Intelligence

Graph-guided random forest for gene set selection

Digital Biomarkers for Personalized Nutrition: Predicting Meal Moments and Interstitial Glucose with Non-Invasive, Wearable Technologies


The MPLAPACK: multiple precision version of BLAS and LAPACK

Automatic Fortran to C++ conversion with FABLE

MPLAPACK version 2.0.1 user manual

Multiple-Precision BLAS Library for Graphics Processing Units

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

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

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

Acceleration of Multiple Precision Matrix Multiplication using Ozaki scheme


Provides functions for hierarchical latent tree analysis on text data for hierarchical topic detection

Latent Tree Models for Hierarchical Topic Detection

Conformative Filtering for Implicit Feedback Data

A Novel Document Generation Process for Topic Detection based on Hierarchical Latent Tree Models

Topic Browsing for Research Papers with Hierarchical Latent Tree Analysis

PWA-PEM for Latent Tree Model and Hierarchical Topic Detection

International Conference on Intelligent Information Processing


Pytorch implementation of the Graph Attention Network model by Veličković et. al (2017, https://arxiv.org/abs/1710.10903)

Graph Attention Networks

AM-GCN: Adaptive Multi-channel Graph Convolutional Networks

Supervised Community Detection with Line Graph Neural Networks

Two Sides of the Same Coin: Heterophily and Oversmoothing in Graph Convolutional Neural Networks

Be Confident! Towards Trustworthy Graph Neural Networks via Confidence Calibration

Learning on Attribute-Missing Graphs

IEEE transactions on pattern analysis and machine intelligence

K-Core Based Temporal Graph Convolutional Network for Dynamic Graphs

IEEE Transactions on Knowledge and Data Engineering

You Shall Know a User by the Company It Keeps: Dynamic Representations for Social Media Users in NLP

AC-VRNN: Attentive Conditional-VRNN for multi-future trajectory prediction

IMF: Interactive Multimodal Fusion Model for Link Prediction


End-to-end ASR/LM implementation with PyTorch

Enhancing Monotonic Multihead Attention for Streaming ASR

CTC-synchronous Training for Monotonic Attention Model

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

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


Arduino library for communicating with XBee radios in API mode

Wireless Sensor Network Synchronization for Precision Agriculture Applications

A Comparative Study of LoRa and IEEE 802.15.4-Based IoT Deployments Inside School Buildings

A DIY Low-Cost Wireless Wind Data Acquisition System Used to Study an Arid Coastal Foredune

School buildings

Experiences from Using LoRa and IEEE 802.15.4 for IoT-Enabled Classrooms


All-in-one text de-duplication

Optimal Densification for Fast and Accurate Minwise Hashing

CulturaX: A Cleaned, Enormous, and Multilingual Dataset for Large Language Models in 167 Languages

IndicLLMSuite: A Blueprint for Creating Pre-training and Fine-Tuning Datasets for Indian Languages

Large Malaysian Language Model Based on Mistral for Enhanced Local Language Understanding

Sailor: Open Language Models for South-East Asia

Sequence-to-Sequence Spanish Pre-trained Language Models


Batch effects and the effective design of single-cell gene expression studies

Gene length and detection bias in single cell RNA sequencing protocols

Statistical methods for analysis of single-cell RNA-sequencing data

Identifying Differentially Expressed Genes of Zero Inflated Single Cell RNA Sequencing Data Using Mixed Model Score Tests


'ggplot2' Based Publication Ready Plots

High-Resolution Transcriptomic Profiling of the Heart During Chronic Stress Reveals Cellular Drivers of Cardiac Fibrosis and Hypertrophy

Complete Connectomic Reconstruction of Olfactory Projection Neurons in the Fly Brain

Single-cell transcriptomic atlas of primate cardiopulmonary aging

In vitro interaction network of a synthetic gut bacterial community

Osteocytes regulate senescence of bone and bone marrow

A Link Between Mitochondrial Dysfunction and the Immune Microenvironment of Salivary Glands in Primary Sjogren’s Syndrome

MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures

Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment: a randomized trial of preterm infants

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

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.


Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies

The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia

Geno-Spatial Distribution of Mycobacterium Tuberculosis and Drug Resistance Profiles in Myanmar–Thai Border Area

Tropical medicine and infectious disease

Natural Polymorphisms in Mycobacterium tuberculosis Conferring Resistance to Delamanid in Drug-Naive Patients

Use of Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Complex Drug Resistance from Early Positive Liquid Cultures

The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China

A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools

Analysis of Drug-Resistance Characteristics and Genetic Diversity of Multidrug-Resistant Tuberculosis Based on Whole-Genome Sequencing on the Hainan Island, China

Genomic analysis of Mycobacterium tuberculosis variant bovis strains isolated from bovine in the state of Mato Grosso, Brazil

Host-pathogen relationship in retreated tuberculosis with major rifampicin resistance–conferring mutations


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

SSD: Single Shot MultiBox Detector

Data-Free Quantization Through Weight Equalization and Bias Correction

Post-Training Piecewise Linear Quantization for Deep Neural Networks

GAN "Steerability" without optimization

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

Memory-Efficient CNN Accelerator Based on Interlayer Feature Map Compression

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

PSRR-MaxpoolNMS: Pyramid Shifted MaxpoolNMS with Relationship Recovery

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

Shift-and-Balance Attention


The GitHub repository for the paper: “Time Series is a Special Sequence: Forecasting with Sample Convolution and Interaction“. (NeurIPS 2022)

SCINet: Time Series Modeling and Forecasting with Sample Convolution and Interaction

Deep Learning Methods for Predicting Tap-Water Quality Time Series in South Korea

Neural Additive Models for Nowcasting

A Novel Hyperdimensional Computing Framework for Online Time Series
  Forecasting on the Edge


Towards A Standardized Tag Recommender Benchmarking Framework

Temporal Effects on Hashtag Reuse in Twitter: A Cognitive-Inspired Hashtag Recommendation Approach

The Influence of Frequency, Recency and Semantic Context on the Reuse of Tags in Social Tagging Systems

Attention Please! A Hybrid Resource Recommender Mimicking Attention-Interpretation Dynamics

The TagRec Framework as a Toolkit for the Development of Tag-Based Recommender Systems

Recommending Items in Social Tagging Systems Using Tag and Time Information

Modeling Popularity and Temporal Drift of Music Genre Preferences

Transactions of the International Society for Music Information Retrieval

Forgetting the Words but Remembering the Meaning: Modeling Forgetting in a Verbal and Semantic Tag Recommender

Modeling Cognitive Processes in Social Tagging to Improve Tag Recommendations


Research Framework for Single and Multi-Players  Multi-Arms Bandits (MAB) Algorithms, implementing all the state-of-the-art algorithms for single-player (UCB, KL-UCB, Thompson...) and multi-player (MusicalChair, MEGA, rhoRand, MCTop/RandTopM etc).. Available on PyPI: https://pypi.org/project/SMPyBandits/ and documentation on

What Doubling Tricks Can and Can't Do for Multi-Armed Bandits

Multi-Player Bandits Revisited

The Generalized Likelihood Ratio Test meets klUCB: an Improved Algorithm for Piece-Wise Non-Stationary Bandits.

KL-UCB-switch: optimal regret bounds for stochastic bandits from both a distribution-dependent and a distribution-free viewpoints

Decentralized spectrum learning for radio collision mitigation in ultra-dense IoT networks: LoRaWAN case study and experiments

contextual: Evaluating Contextual Multi-Armed Bandit Problems in R

Decentralized Spectrum Learning for IoT Wireless Networks Collision Mitigation

Efficient Training of Multi-task Combinarotial Neural Solver with Multi-armed Bandits

Multi-Armed Bandits in Brain-Computer Interfaces

Multi-armed Bandit Algorithm against Strategic Replication


PyTorch version of the paper 'Enhanced Deep Residual Networks for Single Image Super-Resolution' (CVPRW 2017)

Improved Training of Wasserstein GANs

Wasserstein GAN

Deep Back-Projection Networks For Super-Resolution

Unsupervised Image Super-Resolution using Cycle-in-Cycle Generative Adversarial Networks

Generative Adversarial Networks and Perceptual Losses for Video Super-Resolution

International Conference on Image Processing

Journey Towards Tiny Perceptual Super-Resolution

Multimodal Multi-Head Convolutional Attention with Various Kernel Sizes for Medical Image Super-Resolution

Revisiting RCAN: Improved Training for Image Super-Resolution

A Practical Contrastive Learning Framework for Single-Image Super-Resolution


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

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

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

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

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

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

The OpenCDA Open-Source Ecosystem for Cooperative Driving Automation Research

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


Open data sets related to the covid19 pandemic in Slovakia.

The impact of repeated mass antigen testing for COVID-19 on the prevalence of the disease

Analysis of Hazard Rate of Municipalities in Slovakia in Terms of COVID-19

International journal of environmental research and public health

Impact of the Euro 2020 championship on the spread of COVID-19

Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program

THE RELATION BETWEEN COVID INCIDENCE AND INTERNAL MOBILITY IN DISTRICTS IN SLOVAKIA

PROGNOSTICKÉ PRÁCE - PP (FORESIGHT, ANALYSIS AND RECOMMENDATIONS - FAR)


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

Automated Concatenation of Embeddings for Structured Prediction

Building a PubMed knowledge graph

Probing Biomedical Embeddings from Language Models

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

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

FedED: Federated Learning via Ensemble Distillation for Medical Relation Extraction

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

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

Clinical Reading Comprehension: A Thorough Analysis of the emrQA Dataset

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


Automated lung segmentation in CT

TotalSegmentator: robust segmentation of 104 anatomical structures in CT images

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

Integrative Analysis for COVID-19 Patient Outcome Prediction

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

Lung Cancer Segmentation With Transfer Learning: Usefulness of a Pretrained Model Constructed From an Artificial Dataset Generated Using a Generative Adversarial Network

Comparative study of deep learning methods for the automatic segmentation of lung, lesion and lesion type in CT scans of COVID-19 patients

Association of AI quantified COVID-19 chest CT and patient outcome

International journal of computer assisted radiology and surgery

Development and clinical implementation of tailored image analysis tools for COVID-19 in the midst of the pandemic: The synergetic effect of an open, clinically embedded software development platform and machine learning

Geometric Visual Similarity Learning in 3D Medical Image Self-supervised Pre-training

An Exploratory Characterization of Bugs in COVID-19 Software Projects


PyHessian is a Pytorch library for second-order based analysis and training of Neural Networks

PyHessian: Neural Networks Through the Lens of the Hessian

HAWQ-V2: Hessian Aware trace-Weighted Quantization of Neural Networks

Hessian-based Analysis of Large Batch Training and Robustness to Adversaries

Handcrafted Backdoors in Deep Neural Networks

Eigencurve: Optimal Learning Rate Schedule for SGD on Quadratic Objectives with Skewed Hessian Spectrums

BackdoorBench: A Comprehensive Benchmark and Analysis of Backdoor
  Learning

Fisher Information guided Purification against Backdoor Attacks


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

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

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

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

UniTabE: Pretraining a Unified Tabular Encoder for Heterogeneous Tabular Data

Curated LLM: Synergy of LLMs and Data Curation for tabular augmentation in ultra low-data regimes

Unlocking the Transferability of Tokens in Deep Models for Tabular Data

TabPFGen -- Tabular Data Generation with TabPFN

Tabular Data: Is Attention All You Need?

Large Language Models Can Automatically Engineer Features for Few-Shot
  Tabular Learning

Large Scale Transfer Learning for Tabular Data via Language Modeling


Official implementations of PSENet, PAN and PAN++.

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

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

Turning a CLIP Model into a Scene Text Detector

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


HOTA (and other) evaluation metrics for Multi-Object Tracking (MOT).

Performance Measures and a Data Set for Multi-Target, Multi-Camera Tracking

HOTA: A Higher Order Metric for Evaluating Multi-object Tracking

International journal of computer vision

Video Instance Segmentation

SoccerNet-Tracking: Multiple Object Tracking Dataset and Benchmark in Soccer Videos

BURST: A Benchmark for Unifying Object Recognition, Segmentation and Tracking in Video

TarViS: A Unified Approach for Target-based Video Segmentation

LettuceTrack: Detection and tracking of lettuce for robotic precision spray in agriculture

The 8th AI City Challenge

Benchmarking 2D Multi-Object Detection and Tracking Algorithms in Autonomous Vehicle Driving Scenarios

High-Temporal-Resolution Object Detection and Tracking Using Images and Events


:traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2

ggmsa: a visual exploration tool for multiple sequence alignment and associated data

A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.

Large-Scale Genome Scanning within Exonic Regions Revealed the Contributions of Selective Sweep Prone Genes to Host Divergence and Adaptation in Magnaporthe oryzae Species Complex

RT-PCR/MALDI-TOF Diagnostic Target Performance Reflects Circulating SARS-CoV-2 Variant Diversity in New York City

Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits

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


R-package for structural equation modeling based on GWAS summary data

Genomic structural equation modelling provides insights into the multivariate genetic architecture of complex traits

Social and non-social autism symptoms and trait domains are genetically dissociable

Zenodo (CERN European Organization for Nuclear Research)

Shared brain and genetic architectures between mental health and physical activity

Shared genetic influences on resting-state functional networks of the brain

Thirteen Independent Genetic Loci Associated with Preserved Processing Speed in a Study of Cognitive Resilience in 330,097 Individuals in the UK Biobank

A Common Genetic Factor Underlies Genetic Risk for Gynaecological and Reproductive Disorders and Is Correlated with Risk to Depression

Neurogenetic and multi-omic sources of overlap among sensation seeking, alcohol consumption, and alcohol use disorder

medRxiv : the preprint server for health sciences

Polygenic risk scores: effect estimation and model optimization

Chronic Overlapping Pain Conditions and Nociplastic Pain

Genetic Decomposition of the Heritable Component of Reported Childhood Maltreatment

Biological psychiatry global open science