Synthetic Minority Over-Sampling Technique for Regression

RLOC: Terrain-Aware Legged Locomotion Using Reinforcement Learning and Optimal Control

Mimicking the halo–galaxy connection using machine learning

Monthly notices of the Royal Astronomical Society

Solar Flare Index Prediction Using SDO/HMI Vector Magnetic Data Products with Statistical and Machine-learning Methods

High-fidelity reproduction of central galaxy joint distributions with neural networks

Machine learning for yield prediction for chemical reactions using in situ sensors

Journal of molecular graphics & modelling


DeepLab2 is a TensorFlow library for deep labeling, aiming to provide a unified and state-of-the-art TensorFlow codebase for dense pixel labeling tasks.

Axial-DeepLab: Stand-Alone Axial-Attention for Panoptic Segmentation

Panoptic-DeepLab: A Simple, Strong, and Fast Baseline for Bottom-Up Panoptic Segmentation

MaX-DeepLab: End-to-End Panoptic Segmentation with Mask Transformers

kMaX-DeepLab: k-means Mask Transformer

STEP: Segmenting and Tracking Every Pixel

MOAT: Alternating Mobile Convolution and Attention Brings Strong Vision Models

Waymo Open Dataset: Panoramic Video Panoptic Segmentation

DeepLab2: A TensorFlow Library for Deep Labeling

ReMaX: Relaxing for Better Training on Efficient Panoptic Segmentation

PolyMaX: General Dense Prediction with Mask Transformer


Code for Neural Motifs: Scene Graph Parsing with Global Context (CVPR 2018)

Aligning Linguistic Words and Visual Semantic Units for Image Captioning

PROCEEDINGS OF THE 27TH ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA (MM'19)

Graph Density-Aware Losses for Novel Compositions in Scene Graph Generation

Learning Visual Relation Priors for Image-Text Matching and Image Captioning with Neural Scene Graph Generators

Disentangled Motif-aware Graph Learning for Phrase Grounding

One-shot Scene Graph Generation

Generative Compositional Augmentations for Scene Graph Prediction

Addressing Class Imbalance in Scene Graph Parsing by Learning to Contrast and Score

Scene Graph Generation for Better Image Captioning?

Zero-shot Scene Graph Generation via Triplet Calibration and Reduction

ACM Transactions on Multimedia Computing, Communications, and Applications


[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

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

Large Language Models in Plant Biology


BtleJuice Bluetooth Smart (LE) Man-in-the-Middle framework

Playing With Danger: A Taxonomy and Evaluation of Threats to Smart Toys

A Framework for Preserving Privacy and Cybersecurity in Brain-Computer Interfacing Applications

BLEKeeper: Response Time Behavior Based Man-In-The-Middle Attack Detection


IDR

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

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity

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

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

Absence of Tangentially Migrating Glutamatergic Neurons in the Developing Avian Brain

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

Islands of retroelements are the major components of Drosophila centromeres

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

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

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


Usable Implementation of "Bootstrap Your Own Latent" self-supervised learning, from Deepmind, in Pytorch

Bootstrap your own latent: A new approach to self-supervised Learning

Understanding self-supervised Learning Dynamics without Contrastive Pairs

BYOL works even without batch statistics

An Empirical Study on Disentanglement of Negative-free Contrastive Learning

Similarity of Neural Architectures using Adversarial Attack Transferability

Leveraging Multi-Annotator Label Uncertainties as Privileged Information for Acute Respiratory Distress Syndrome Detection in Chest X-ray Images


The Polygenic and Monogenic Basis of Blood Traits and Diseases

Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci

Loss-of-function genomic variants highlight potential therapeutic targets for cardiovascular disease

Large-scale meta-analysis highlights the hypothalamic–pituitary–gonadal axis in the genetic regulation of menstrual cycle length

Genome-wide meta-analysis of iron status biomarkers and the effect of iron on all-cause mortality in HUNT

Mapping of susceptible variants for cold medicine-related Stevens–Johnson syndrome by whole-genome resequencing


Deep Visual-Semantic Alignments for Generating Image Descriptions

CIDEr: Consensus-based Image Description Evaluation

Microsoft COCO Captions: Data Collection and Evaluation Server

Conceptual Captions: A Cleaned, Hypernymed, Image Alt-text Dataset For Automatic Image Captioning

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

SCA-CNN: Spatial and Channel-wise Attention in Convolutional Networks for Image Captioning

SPICE: Semantic Propositional Image Caption Evaluation

Image Captioning with Semantic Attention

Sequence to Sequence -- Video to Text

Attention on Attention for Image Captioning

Exploring Visual Relationship for Image Captioning


Elastic Malware Benchmark for Empowering Researchers

EMBER: An Open Dataset for Training Static PE Malware Machine Learning Models

Explaining Vulnerabilities of Deep Learning to Adversarial Malware Binaries

A Review of Computer Vision Methods in Network Security

Leveraging Uncertainty for Improved Static Malware Detection Under Extreme False Positive Constraints

Out of Distribution Data Detection Using Dropout Bayesian Neural Networks

Sisyfos: A Modular and Extendable Open Malware Analysis Platform

On the Limitations of Continual Learning for Malware Classification

A Wolf in Sheep’s Clothing: Query-Free Evasion Attacks Against Machine Learning-Based Malware Detectors with Generative Adversarial Networks

AutoWS-Bench-101: Benchmarking Automated Weak Supervision with 100 Labels

IoTGeM: Generalizable Models for Behaviour-Based IoT Attack Detection


Find, circularise and annotate mitogenome from PacBio assemblies

MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics

marcelauliano/MitoHiFi: mitohifi_v2.0

Semi-automated assembly of high-quality diploid human reference genomes

The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

bioRxiv : the preprint server for biology

A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii

The genome sequence of the Common Carder Bee, Bombus pascuorum (Scopoli, 1763)

The genome sequence of the German wasp, Vespula germanica (Fabricius, 1793)

A draft reference genome of the red abalone, Haliotis rufescens, for conservation genomics

The genome sequence of the blue-rayed limpet, Patella pellucida Linnaeus, 1758


Line-By-Line Radiative Transfer Model by Atmospheric and Environmental Research

Simulated multispectral temperature and atmospheric composition retrievals for the JPL GEO-IR Sounder

The Hidden Companion in J1527: A 0.69 Solar-mass White Dwarf?

Radiative transfer and inversion codes for characterizing planetary atmospheres: an overview

Frontiers in Astronomy and Space Sciences


Python interface of cpptraj

Allosteric Modulation of the CB1 Cannabinoid Receptor by Cannabidiol—A Molecular Modeling Study of the N-Terminal Domain and the Allosteric-Orthosteric Coupling

5-Nitroisoxazoles in SNAr Reactions: A Novel Chemo- and Regioselective Approach to Isoxazole-Based Bivalent Ligands of AMPA Receptors

International journal of molecular sciences

Theoretical insights into the molecular mechanism of I117V mutation in neuraminidase mediated reduction of oseltamivir drug susceptibility in A/H5N1 influenza virus

Conformational Change of Tetratricopeptide Repeats Region Triggers Activation of Phytochrome-Associated Protein Phosphatase 5


Splitting Conic Solver

Conic Optimization via Operator Splitting and Homogeneous Self-Dual Embedding

Differentiable Convex Optimization Layers

Learning heat diffusion graphs

Globally Convergent Type-I Anderson Acceleration for Nonsmooth Fixed-Point Iterations

Large-Scale Convex Optimization for Dense Wireless Cooperative Networks

A Survey of Recent Scalability Improvements for Semidefinite Programming with Applications in Machine Learning, Control, and Robotics

Evaluating the Holevo Cramér-Rao bound for multi-parameter quantum
  metrology

Chordal decomposition in operator-splitting methods for sparse semidefinite programs

LMI Properties and Applications in Systems, Stability, and Control Theory

Global Planning for Contact-Rich Manipulation via Local Smoothing of Quasi-Dynamic Contact Models


a Medical Genetics Sequence Analysis Pipeline

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

MDM2, MDM4 and EGFR Amplifications and Hyperprogression in Metastatic Acral and Mucosal Melanoma

Distinct Mutation Patterns Reveal Melanoma Subtypes and Influence Immunotherapy Response in Advanced Melanoma Patients

First-line exome sequencing in Palestinian and Israeli Arabs with neurological disorders is efficient and facilitates disease gene discovery

European journal of human genetics : EJHG

Disruption of MeCP2–TCF20 complex underlies distinct neurodevelopmental disorders

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

Diagnostic genome sequencing improves diagnostic yield: a prospective single-centre study in 1000 patients with inherited eye diseases

Investigating the effects of additional truncating variants in DNA-repair genes on breast cancer risk in BRCA1-positive women

First submicroscopic inversion of the OPA1 gene identified in dominant optic atrophy - a case report

Transcriptional and Mutational Profiling of B-Other Acute Lymphoblastic Leukemia for Improved Diagnostics

Genome sequencing and transcriptome profiling in twins discordant for Mayer-Rokitansky-Küster-Hauser syndrome


SwissArmyTransformer is a flexible and powerful library to develop your own Transformer variants.

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

Prefix-Tuning: Optimizing Continuous Prompts for Generation

GLM: General Language Model Pretraining with Autoregressive Blank Infilling

GPT Understands, Too

LMTuner: An user-friendly and highly-integrable Training Framework for fine-tuning Large Language Models


Pre-built implicit layer architectures with O(1) backprop, GPUs, and stiff+non-stiff DE solvers, demonstrating scientific machine learning (SciML) and physics-informed machine learning methods

Universal Differential Equations for Scientific Machine Learning

DiffEqFlux.jl - A Julia Library for Neural Differential Equations

NeuralFMU: Towards Structural Integration of FMUs into Neural Networks

NeuralFMU: Presenting a workflow for integrating hybrid NeuralODEs into real world applications


O2 software project for the ALICE experiment at CERN

ALICE Run 3 Analysis Framework

The ALICE Analysis Framework for LHC Run 3


Tensorflow implementation of contextualized word representations from bi-directional language models

Deep contextualized word representations

Dissecting Contextual Word Embeddings: Architecture and Representation

Linguistically-Informed Self-Attention for Semantic Role Labeling

nocaps: novel object captioning at scale

International Conference on Computer Vision

A Monolingual Approach to Contextualized Word Embeddings for Mid-Resource Languages

Meeting of the Association for Computational Linguistics

Evaluation of sentence embeddings in downstream and linguistic probing tasks

Probing Biomedical Embeddings from Language Models

UER: An Open-Source Toolkit for Pre-training Models

Polyglot Contextual Representations Improve Crosslingual Transfer

Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings


Online and batch-based concept and data drift detection algorithms to monitor and maintain ML performance.

On the Reliable Detection of Concept Drift from Streaming Unlabeled Data

Hellinger distance based drift detection for nonstationary environments

IEEE Symposium on Computational Intelligence in Dynamic and Uncertain Environments

Concept Drift Detection for Streaming Data

A PCA-Based Change Detection Framework for Multidimensional Data Streams

Drift detection using uncertainty distribution divergence

Frouros: A Python library for drift detection in machine learning systems

Mitigating ML Model Decay in Continuous Integration with Data Drift Detection: An Empirical Study


[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

IA-FaceS: A Bidirectional Method for Semantic Face Editing


Pipeline for initial analysis of droplet-based single-cell RNA-seq data

dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments

Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools

Characterization of cell-fate decision landscapes by estimating transcription factor dynamics


Python wrapper to Philipp Krähenbühl's dense (fully connected) CRFs with gaussian edge potentials.

Understanding Convolution for Semantic Segmentation

Deeply Supervised Salient Object Detection with Short Connections

IEEE Transactions on Pattern Analysis and Machine Intelligence

Unsupervised Moving Object Detection via Contextual Information Separation

Region Mutual Information Loss for Semantic Segmentation

Bounding boxes for weakly supervised segmentation: Global constraints get close to full supervision

A Collaborative Region Detection and Grading Framework for Forest Fire Smoke Using Weakly Supervised Fine Segmentation and Lightweight Faster-RCNN

ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture

Object-aware Contrastive Learning for Debiased Scene Representation

Guided Anisotropic Diffusion and Iterative Learning for Weakly Supervised Change Detection

Correlation Maximized Structural Similarity Loss for Semantic Segmentation


SmartSim Infrastructure Library Clients.

Using Machine Learning at Scale in HPC Simulations with SmartSim: An Application to Ocean Climate Modeling

In Situ Framework for Coupling Simulation and Machine Learning with Application to CFD

Combining machine learning with computational fluid dynamics using OpenFOAM and SmartSim


Python library for supernova cosmology

Sifting for Sapphires: Systematic Selection of Tidal Disruption Events in iPTF

The Astrophysical journal. Supplement series

SALT3-NIR: Taking the Open-source Type Ia Supernova Model to Longer Wavelengths for Next-generation Cosmological Measurements

Out of One, Many: Distinguishing Time Delays from Lensed Supernovae

Deep learning unresolved lensed light curves


Compressed numerical arrays that support high-speed random access

cuSZ: An Efficient GPU-Based Error-Bounded Lossy Compression Framework for Scientific Data

PACT '20: PROCEEDINGS OF THE ACM INTERNATIONAL CONFERENCE ON PARALLEL ARCHITECTURES AND COMPILATION TECHNIQUES

Understanding GPU-Based Lossy Compression for Extreme-Scale Cosmological Simulations

Adaptive Configuration of In Situ Lossy Compression for Cosmology Simulations via Fine-Grained Rate-Quality Modeling

IEEE International Symposium on High-Performance Parallel Distributed Computing

FZ-GPU: A Fast and High-Ratio Lossy Compressor for Scientific Computing Applications on GPUs

Proceedings of the 32nd International Symposium on High-Performance Parallel and Distributed Computing

SZx: an Ultra-fast Error-bounded Lossy Compressor for Scientific Datasets

AMRIC: A Novel In Situ Lossy Compression Framework for Efficient I/O in Adaptive Mesh Refinement Applications

Optimizing Huffman Decoding for Error-Bounded Lossy Compression on GPUs

CEAZ: Accelerating Parallel I/O Via Hardware-Algorithm Co-Designed Adaptive Lossy Compression

A Survey on Error-Bounded Lossy Compression for Scientific Datasets

Statistical Analysis of ZFP: Understanding Bias


Create Customized Software using Natural Language Idea (through LLM-powered Multi-Agent Collaboration)

ChatDev: Communicative Agents for Software Development

Experiential Co-Learning of Software-Developing Agents

Scaling Large-Language-Model-based Multi-Agent Collaboration

Iterative Experience Refinement of Software-Developing Agents

Multi-Agent Software Development through Cross-Team Collaboration

Experimenting a New Programming Practice with LLMs


DESI simulations

The DESI Experiment Part II: Instrument Design

The Spectroscopic Data Processing Pipeline for the Dark Energy Spectroscopic Instrument

Zenodo (CERN European Organization for Nuclear Research)

DESI 2024 IV: Baryon Acoustic Oscillations from the Lyman Alpha Forest

LYACOLORE: synthetic datasets for current and future Lyman-alpha forest BAO surveys

Journal of Cosmology and Astroparticle Physics

A tomographic map of the large-scale matter distribution using the eBOSS—Stripe 82 Lyα forest

Optimal 1D Lyα Forest Power Spectrum Estimation – III. DESI early data

The Dark Energy Spectroscopic Instrument: one-dimensional power spectrum from first Ly α forest samples with Fast Fourier Transform

Detecting neutral hydrogen at z greater than or similar to 3 in large spectroscopic surveys of quasars

Monthly Notices of the Royal Astronomical Society

The effect of quasar redshift errors on Lyman-α forest correlation functions

Synthetic spectra for Lyman-α forest analysis in the Dark Energy Spectroscopic Instrument


Multichannel Igor Electrophysiology Suite

Sparse recurrent excitatory connectivity in the microcircuit of the adult mouse and human cortex

The Neurodata Without Borders ecosystem for neurophysiological data science

Synaptic connectivity to L2/3 of primary visual cortex measured by two-photon optogenetic stimulation

Multimodal cell type correspondence by intersectional mFISH in intact tissues

Human voltage-gated Na+and K+channel properties underlie sustained fast AP signaling

Genes associated with cognitive ability and HAR show overlapping expression patterns in human cortical neuron types

Cell-class-specific electric field entrainment of neural activity

bioRxiv : the preprint server for biology


Code for https://arxiv.org/abs/1611.10080

Deep Residual Learning for Image Recognition

Wider or Deeper: Revisiting the ResNet Model for Visual Recognition

In-Place Activated BatchNorm for Memory-Optimized Training of DNNs

Benchmarking the Robustness of Semantic Segmentation Models

Multiple Pathways: The Influence Mechanism of Greenspace Exposure on Mental Health—A Case Study of Hangzhou, China

Diagnostics in Semantic Segmentation


VizNet is a repository providing real-world datasets that enable, among other things, (re)running empirical studies with higher ecological validity

VizNet: Towards A Large-Scale Visualization Learning and Benchmarking Repository

A Survey on Semantics in Automated Data Science

A Vision for Semantically Enriched Data Science


R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)

Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s

Genetic variation in the HLA region is associated with susceptibility to herpes zoster

Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

Detection of trait-associated structural variations using short-read sequencing


Neural networks for microbe-metabolite interaction analysis

An overview of gradient descent optimization algorithms

Вестник компьютерных и информационных технологий

Learning representations of microbe–metabolite interactions

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity

What We Know So Far about the Metabolite-Mediated Microbiota-Intestinal Immunity Dialogue and How to Hear the Sound of This Crosstalk

Three-Dimensional Molecular Cartography of the Caribbean Reef-Building Coral Orbicella faveolata

Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium

Co-occurrence network analysis reveals the alterations of the skin microbiome and metabolome in adults with mild to moderate atopic dermatitis


RAxML Next Generation: faster, easier-to-use and more flexible

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Sarbecovirus ORF6 proteins hamper induction of interferon signaling

Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague

Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain

An investigation of irreproducibility in maximum likelihood phylogenetic inference

Highly Pathogenic Avian Influenza A(H5N1) Virus Clade 2.3.4.4b Infections in Wild Terrestrial Mammals, United States, 2022

Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia

A comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages

Characterization of the Complete Chloroplast Genomes of Buddleja colvilei and B. sessilifolia: Implications for the Taxonomy of Buddleja L.

Molecular epidemiology in current times


A python library for optimization, geared towards modular robots and evolutionary computing.

Lamarck's Revenge: Inheritance of Learned Traits Can Make Robot Evolution Better


⚡⚡⚡Blazing fast correlation functions on the CPU.

Dark Energy Survey Year 1 results: weak lensing mass calibration of redMaPPer galaxy clusters

CORRFUNC - a suite of blazing fast correlation functions on the CPU

Nearest neighbour distributions: New statistical measures for cosmological clustering

Spatial clustering of dark matter haloes: secondary bias, neighbour bias, and the influence of massive neighbours on halo properties

The Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: exploring the halo occupation distribution model for emission line galaxies

How Are Galaxies Assigned to Halos? Searching for Assembly Bias in the SDSS Galaxy Clustering

Cosmological cross-correlations and nearest neighbour distributions

Monthly notices of the Royal Astronomical Society

Semi-analytic forecasts for JWST – VI. Simulated light-cones and galaxy clustering predictions

Towards accurate modelling of galaxy clustering on small scales: testing the standard ΛCDM + halo model

Do model emission line galaxies live in filaments at z ∼ 1?


Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to  Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA

PROTAC-Design-Evaluator (PRODE): An Advanced Method for In-Silico PROTAC Design

Harnessing Protein-Ligand Interaction Fingerprints to Predict New Scaffolds of RIPK1 Inhibitors

Generalized Protein Pocket Generation with Prior-Informed Flow Matching


WashU Epigenome Browser

WashU Epigenome Browser update 2022

The qBED track: a novel genome browser visualization for point processes

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser


Perform data science on data that remains in someone else's server

A Survey on Federated Learning Systems: Vision, Hype and Reality for Data Privacy and Protection

Privacy-Preserving Traffic Flow Prediction: A Federated Learning Approach

Secure and Robust Machine Learning for Healthcare: A Survey

End-to-end privacy preserving deep learning on multi-institutional medical imaging

Federated Learning and Differential Privacy: Software tools analysis, the Sherpa.ai FL framework and methodological guidelines for preserving data privacy

FALCON: Honest-Majority Maliciously Secure Framework for Private Deep Learning

From distributed machine learning to federated learning: a survey

Scalable Deep Learning on Distributed Infrastructures: Challenges, Techniques and Tools

Blockchain for federated learning toward secure distributed machine learning systems: a systemic survey

Soft Computing - A Fusion of Foundations, Methodologies and Applications

Block Hunter: Federated Learning for Cyber Threat Hunting in Blockchain-Based IIoT Networks

IEEE Transactions on Industrial Informatics


ALIbaba's Collection of Encoder-decoders from MinD (Machine IntelligeNce of Damo) Lab

Multi-Granularity Hierarchical Attention Fusion Networks for Reading Comprehension and Question Answering

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

mPLUG: Effective and Efficient Vision-Language Learning by Cross-modal Skip-connections

Raise a Child in Large Language Model: Towards Effective and Generalizable Fine-tuning

mPLUG-2: A Modularized Multi-modal Foundation Model Across Text, Image and Video

StructuralLM: Structural Pre-training for Form Understanding

PALM: Pre-training an Autoencoding&Autoregressive Language Model for Context-conditioned Generation

VECO: Variable and Flexible Cross-lingual Pre-training for Language Understanding and Generation

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

Lattice-BERT: Leveraging Multi-Granularity Representations in Chinese Pre-trained Language Models

From Dense to Sparse: Contrastive Pruning for Better Pre-trained Language Model Compression


Python Package for the Analysis of Paleoclimate Data. Documentation at


Pyodide is a Python distribution for the browser and Node.js based on WebAssembly

scadnano: A browser-based, scriptable tool for designing DNA nanostructures

CoLadder: Supporting Programmers with Hierarchical Code Generation in Multi-Level Abstraction

CoPrompt: Supporting Prompt Sharing and Referring in Collaborative Natural Language Programming

Teaching Programming to Novices Using the codeBoot Online Environment

WebAssembly enables low latency interoperable augmented and virtual reality software

ComputeGPT: A computational chat model for numerical problems


Program for aligning DNA sequences, a pairwise aligner.

Computational methods for 16S metabarcoding studies using Nanopore sequencing data

Computational and structural biotechnology journal

Adaptive sequence divergence forged new neurodevelopmental enhancers in humans

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis

SyntDB: defining orthologues of human long noncoding RNAs across primates

The Jasmine (Jasminum sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates

基因组蛋白质组与生物信息学报

De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing

Chromosome-scale assembly and whole-genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets

The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance

Chromosome-Level Genome Assembly of the Speckled Blue Grouper (Epinephelus cyanopodus) Provides Insight into Its Adaptive Evolution

Integrative Taxonomy of the Gall Mite Nothopoda todeica n. sp. (Eriophyidae) from the Disjunct Afro-Australasian Fern Todea barbara: Morphology, Phylogeny, and Mitogenomics


Real time semantic slam in ROS with a hand held RGB-D camera

Exploration for Object Mapping Guided by Environmental Semantics using UAVs

From Perception to Navigation in Environments with Persons: An Indoor Evaluation of the State of the Art

Semantic Mapping with Low-Density Point-Clouds for Service Robots in Indoor Environments

Low-Bandwidth and Compute-Bound RGB-D Planar Semantic SLAM

O2V-Mapping: Online Open-Vocabulary Mapping with Neural Implicit
  Representation


:id: Scan contig files against PubMLST typing schemes

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

PLSDB: a resource of complete bacterial plasmids

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome

Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries

Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

Deciphering the Structural Diversity and Classification of the Mobile Tigecycline Resistance Gene tet(X)-Bearing Plasmidome among Bacteria

A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition


A Memento Aggregator CLI and Server in Go

MemGator - A Portable Concurrent Memento Aggregator

MementoMap Framework for Flexible and Adaptive Web Archive Profiling

Impact of URI Canonicalization on Memento Count

Profiling Web Archival Voids for Memento Routing


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

NIMA: Neural Image Assessment

Biometric Quality: Review and Application to Face Recognition with FaceQnet

CLIP knows image aesthetics

State of the Art of Quality Assessment of Facial Images

Semantic Satellite Communications Based on Generative Foundation Model

Cross-Modal Generative Semantic Communications for Mobile AIGC: Joint
  Semantic Encoding and Prompt Engineering


Implementation and experiments  of graph embedding algorithms.

node2vec: Scalable Feature Learning for Networks

DeepWalk: Online Learning of Social Representations

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

LINE: Large-scale Information Network Embedding

Structural Deep Network Embedding

struc2vec: Learning Node Representations from Structural Identity

Seven-Layer Model in Complex Networks Link Prediction: A Survey

Network representation learning systematic review: ancestors and current development state

GRAPE for fast and scalable graph processing and random-walk-based embedding

Accurate and interpretable drug-drug interaction prediction enabled by knowledge subgraph learning

Better with Less: A Data-Active Perspective on Pre-Training Graph Neural Networks


Copy number calling and variant classification using targeted short read sequencing

Genomic characterization of metastatic breast cancers

Genetic mechanisms of target antigen loss in CAR19 therapy of acute lymphoblastic leukemia

Efficacy of BGJ398, a Fibroblast Growth Factor Receptor 1-3 Inhibitor, in Patients with Previously Treated Advanced Urothelial Carcinoma with FGFR3 Alterations.

PureCN: copy number calling and SNV classification using targeted short read sequencing

Tracking the Evolution of Resistance to ALK Tyrosine Kinase Inhibitors Through Longitudinal Analysis of Circulating Tumor DNA

Characterizing dedifferentiation of thyroid cancer by integrated analysis

Combined PD-1, BRAF and MEK inhibition in advanced BRAF-mutant melanoma: safety run-in and biomarker cohorts of COMBI-i

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

Cell-free DNA captures tumor heterogeneity and driver alterations in rapid autopsies with pre-treated metastatic cancer

Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data


Unified-Modal Speech-Text Pre-Training for Spoken Language Processing

SpeechT5: Unified-Modal Encoder-Decoder Pre-Training for Spoken Language Processing

SpeechUT: Bridging Speech and Text with Hidden-Unit for Encoder-Decoder Based Speech-Text Pre-training

SpeechLM: Enhanced Speech Pre-Training with Unpaired Textual Data

WavLLM: Towards Robust and Adaptive Speech Large Language Model

Pre-Training Transformer Decoder for End-to-End ASR Model with Unpaired Speech Data

The YiTrans Speech Translation System for IWSLT 2022 Offline Shared Task

Joint Pre-Training with Speech and Bilingual Text for Direct Speech to Speech Translation

Robust Automatic Speech Recognition via WavAugment Guided Phoneme Adversarial Training


A Simple and Versatile Framework for Object Detection and Instance Recognition

Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks

Feature Pyramid Networks for Object Detection

Scale-Aware Trident Networks for Object Detection

Detection in Crowded Scenes: One Proposal, Multiple Predictions

SimpleDet: A Simple and Versatile Distributed Framework for Object Detection and Instance Recognition


Black-box optimization for Julia

First Sagittarius A* Event Horizon Telescope Results. IV. Variability, Morphology, and Black Hole Mass

The tadpole problem

Algorithmically solving the Tadpole Problem

Universal Off-Policy Evaluation

Multi-field inflation in high-slope potentials

A new light on the darkest corner of the landscape

Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions

The multi-field, rapid-turn inflationary solution

Architectures of Exoplanetary Systems. II. An Increase in Inner Planetary System Occurrence toward Later Spectral Types for Kepler’s FGK Dwarfs

Composing Modeling and Simulation with Machine Learning in Julia


A new data structure for accurate on-line accumulation of rank-based statistics such as quantiles and trimmed means

Computing Extremely Accurate Quantiles Using t-Digests

Moment-Based Quantile Sketches for Efficient High Cardinality Aggregation Queries

On the Runtime-Efficacy Trade-off of Anomaly Detection Techniques for Real-Time Streaming Data

QDS-COVID: A visual analytics system for interactive exploration of millions of COVID-19 healthcare records in Brazil

Circllhist -- A Log-Linear Histogram Data Structure for IT Infrastructure Monitoring

Asymmetric scale functions for t-digests


Medical imaging toolkit for deep learning

TorchIO: A Python library for efficient loading, preprocessing, augmentation and patch-based sampling of medical images in deep learning

Computer methods and programs in biomedicine

SAM: Self-Supervised Learning of Pixel-Wise Anatomical Embeddings in Radiological Images

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

Cooperative Training and Latent Space Data Augmentation for Robust Medical Image Segmentation

Anatomy-Aware Lymph Node Detection in Chest CT using Implicit Station Stratification

DeepAD: A Robust Deep Learning Model of Alzheimer's Disease Progression for Real-World Clinical Applications

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


Raiden Network

Flash: Efficient Dynamic Routing for Offchain Networks

Congestion Attacks in Payment Channel Networks

Drawing the Boundaries Between Blockchain and Blockchain-Like Systems: A Comprehensive Survey on Distributed Ledger Technologies


Machine learning for NeuroImaging in Python

Assessing and tuning brain decoders: Cross-validation, caveats, and guidelines

Action and object words are differentially anchored in the sensory motor system - A perspective on cognitive embodiment

Task-dependent fractal patterns of information processing in working memory

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

A reproducible benchmark of resting-state fMRI denoising strategies using fMRIPrep and Nilearn


A Monte Carlo ray tracer for the optical simulation of solar concentrating systems


Transpile trained scikit-learn estimators to C, Java, JavaScript and others.

Machine Learning for Microcontroller-Class Hardware: A Review

Physical Workload Tracking Using Human Activity Recognition with Wearable Devices

Real-Time Drink Trigger Detection in Free-living Conditions Using Inertial Sensors

Are Microcontrollers Ready for Deep Learning-Based Human Activity Recognition?

An Open-Source Tool for Classification Models in Resource-Constrained Hardware

Learning Wi-Fi Connection Loss Predictions for Seamless Vertical Handovers Using Multipath TCP

PROCEEDINGS OF THE IEEE LCN: 2019 44TH ANNUAL IEEE CONFERENCE ON LOCAL COMPUTER NETWORKS (LCN 2019)

Classical and machine learning methods for event reconstruction in NeuLAND

Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment

Lightweight On-Device Detection of Android Malware Based on the Koodous Platform and Machine Learning

Dynamic Decision Tree Ensembles for Energy-Efficient Inference on IoT Edge Nodes

Leveraging Models to Reduce Test Cases in Software Repositories


Overlay Network for distributed protocols

POSEIDON: Privacy-Preserving Federated Neural Network Learning

Scalable Privacy-Preserving Distributed Learning

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

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

Scalable and Privacy-Preserving Federated Principal Component Analysis

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


LIBLINEAR -- A Library for Large Linear Classification

CoType: Joint Extraction of Typed Entities and Relations with Knowledge Bases

One-trial correction of legacy AI systems and stochastic separation theorems

Implicit Kernel Learning

Indirect Supervision for Relation Extraction using Question-Answer Pairs


FreeVC: Towards High-Quality Text-Free One-Shot Voice Conversion

WavLM: Large-Scale Self-Supervised Pre-Training for Full Stack Speech Processing

Voice Conversion With Just Nearest Neighbors

Phoneme Hallucinator: One-shot Voice Conversion via Set Expansion

Parrot-Trained Adversarial Examples: Pushing the Practicality of Black-Box Audio Attacks against Speaker Recognition Models

HybridVC: Efficient Voice Style Conversion with Text and Audio Prompts


MIT Cheetah I Implementation

GenLoco: Generalized Locomotion Controllers for Quadrupedal Robots

STEP: State Estimator for Legged Robots Using a Preintegrated Foot Velocity Factor

WoLF: the Whole-body Locomotion Framework for Quadruped Robots

WALK-VIO: Walking-motion-Adaptive Leg Kinematic Constraint Visual-Inertial Odometry for Quadruped Robots


A library for directly calling PyTorch ML models from Fortran.

Interpretable multiscale Machine Learning-Based Parameterizations of Convection for ICON


G2P with Tensorflow

The Zero Resource Speech Benchmark 2021: Metrics and baselines for unsupervised spoken language modeling

An investigation of phone-based subword units for end-to-end speech recognition

Grapheme-to-Phoneme Conversion with Convolutional Neural Networks

Creating DALI, a Large Dataset of Synchronized Audio, Lyrics, and Notes

Transactions of the International Society for Music Information Retrieval

End-to-end style-conditioned poetry generation: What does it take to learn from examples alone?

Proceedings of the 5th Joint SIGHUM Workshop on Computational Linguistics for Cultural Heritage, Social Sciences, Humanities and Literature

ASR for Non-standardised Languages with Dialectal Variation: the case of Swiss German

Workshop on NLP for Similar Languages, Varieties and Dialects

Towards Real-time Mispronunciation Detection in Kids' Speech

PronouncUR: An Urdu Pronunciation Lexicon Generator

Are word boundaries useful for unsupervised language learning?

Algorithms for Automatic Accentuation and Transcription of Russian Texts in Speech Recognition Systems


Acceleration package for neural networks on multi-core CPUs

EmBench: Quantifying Performance Variations of Deep Neural Networks across Modern Commodity Devices

The 3rd International Workshop on Deep Learning for Mobile Systems and Applications

High performance ultra-low-precision convolutions on mobile devices

High Performance and Portable Convolution Operators for Multicore Processors

Bonseyes AI Pipeline—Bringing AI to You

Learning to infer: RL-based search for DNN primitive selection on Heterogeneous Embedded Systems

Automating Generation of Low Precision Deep Learning Operators

Computation-efficient Deep Learning for Computer Vision: A Survey

Array Languages Make Neural Networks Fast

Proceedings of the 7th ACM SIGPLAN International Workshop on Libraries, Languages and Compilers for Array Programming

Accelerating CNN inference on long vector architectures via co-design

Multi-Component Optimization and Efficient Deployment of Neural-Networks on Resource-Constrained IoT Hardware


The HOL Light theorem prover

Formalization of Transform Methods using HOL Light

Formalization of Lerch's Theorem using HOL Light

Formal Analysis of Robotic Cell Injection Systems using Theorem Proving

Formalising Mathematics In Simple Type Theory

Safe, fast, concurrent proof checking for the lambda-pi calculus modulo rewriting

Proceedings of the 11th ACM SIGPLAN International Conference on Certified Programs and Proofs

A formal proof of modal completeness for provability logic

HOL Light QE

Distant decimals of π

The Space of Mathematical Software Systems - A Survey of Paradigmatic Systems.

Formal Modeling of Robotic Cell Injection Systems in Higher-order Logic


A framework for data augmentation for 2D and 3D image classification and segmentation

nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation

nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation

The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge

Automated brain extraction of multisequence MRI using artificial neural networks

TractSeg - Fast and accurate white matter tract segmentation

No New-Net

nnU-Net for Brain Tumor Segmentation

nnU-Net: Breaking the Spell on Successful Medical Image Segmentation.

MIScnn: a framework for medical image segmentation with convolutional neural networks and deep learning

Combined tract segmentation and orientation mapping for bundle-specific tractography


TransmogrifAI (pronounced trăns-mŏgˈrə-fī) is an AutoML library for building modular, reusable, strongly typed machine learning workflows on Apache Spark with minimal hand-tuning

Towards Automated Machine Learning: Evaluation and Comparison of AutoML Approaches and Tools

International Conference on Tools with Artificial Intelligence

AutoML to Date and Beyond: Challenges and Opportunities

Whither AutoML? Understanding the Role of Automation in Machine Learning Workflows


nanoflann: a C++11 header-only library for Nearest Neighbor (NN) search with KD-trees

FAST-LIO2: Fast Direct LiDAR-Inertial Odometry

ConvPoint: Continuous Convolutions for Point Cloud Processing

Learning Semantic Segmentation of Large-Scale Point Clouds with Random Sampling

IEEE transactions on pattern analysis and machine intelligence

Direct LiDAR Odometry: Fast Localization With Dense Point Clouds

SPlit: An Optimal Method for Data Splitting

CLASSIFICATION OF AERIAL PHOTOGRAMMETRIC 3D POINT CLOUDS

On generation of node distributions for meshless PDE discretizations

Classification of Aerial Photogrammetric 3D Point Clouds

Bridging the computational gap between mesoscopic and continuum modeling of red blood cells for fully resolved blood flow

Autonomous Cave Surveying With an Aerial Robot


A massively spiffy yet delicately unobtrusive compression library.

MuSCLE: Multi Sweep Compression of LiDAR using Deep Entropy Models

Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment

FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies

Binary Diffing as a Network Alignment Problem via Belief Propagation

International Conference on Automated Software Engineering

EFloat: Entropy-coded Floating Point Format for Deep Learning.

Prompt Fuzzing for Fuzz Driver Generation

The Tiny Time-series Transformer: Low-latency High-throughput Classification of Astronomical Transients using Deep Model Compression

EFloat: Entropy-coded Floating Point Format for Compressing Vector Embedding Models

Hierarchical Lowrank Arithmetic with Binary Compression

Probing Language Models for Pre-training Data Detection


Scalable embedding, reasoning, ranking for images and sentences with CLIP

User Preference-aware Fake News Detection

SemEval-2020 Task 1: Unsupervised Lexical Semantic Change Detection

Hate speech detection and racial bias mitigation in social media based on BERT model

OpenChat: Advancing Open-source Language Models with Mixed-Quality Data

SBERT-WK: A Sentence Embedding Method by Dissecting BERT-Based Word Models

Comparison of Diverse Decoding Methods from Conditional Language Models

Multi-label Categorization of Accounts of Sexism using a Neural Framework

Building and Using Personal Knowledge Graph to Improve Suicidal Ideation Detection on Social Media

Universal Text Representation from BERT: An Empirical Study

Transfer Learning from Transformers to Fake News Challenge Stance Detection (FNC-1) Task


Direct voxel grid optimization for fast radiance field reconstruction.

Direct Voxel Grid Optimization: Super-fast Convergence for Radiance Fields Reconstruction

Voxurf: Voxel-based Efficient and Accurate Neural Surface Reconstruction

SpikingNeRF: Making Bio-inspired Neural Networks See through the Real World

SPC-NeRF: Spatial Predictive Compression for Voxel Based Radiance Field


Fast and accurate de novo assembler for long reads

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

基因组蛋白质组与生物信息学报

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims)

A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing

The genome of Cymbidium sinense revealed the evolution of orchid traits

Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.).

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

Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis

Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes

Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax


Simple image captioning model

Prefix-Tuning: Optimizing Continuous Prompts for Generation

Oscar: Object-Semantics Aligned Pre-training for Vision-Language Tasks

Unified Vision-Language Pre-Training for Image Captioning and VQA

ClipCap: CLIP Prefix for Image Captioning

A-OKVQA: A Benchmark for Visual Question Answering using World Knowledge

The Creativity of Text-to-Image Generation

Delving into Out-of-Distribution Detection with Vision-Language Representations

Discovering and Mitigating Visual Biases through Keyword Explanation

Semi-Supervised Domain Generalization for Object Detection via Language-Guided Feature Alignment


GANomaly: Semi-Supervised Anomaly Detection via Adversarial Training

Autoencoding Under Normalization Constraints

Proxy-bridged Image Reconstruction Network for Anomaly Detection in Medical Images

Generative Adversarial Networks for Anomaly Detection in Biomedical Imaging: A Study on Seven Medical Image Datasets

AMAD: Adversarial Multiscale Anomaly Detection on High-Dimensional and Time-Evolving Categorical Data


This repository contains the source code for the semantic image segmentation method described in the ICCV 2015 paper: Conditional Random Fields as Recurrent Neural Networks. http://crfasrnn.torr.vision/

International Conference on Computer Vision

On the Robustness of Semantic Segmentation Models to Adversarial Attacks

ModaNet: A Large-Scale Street Fashion Dataset with Polygon Annotations


Fast and flexible Gaussian Process regression in Python

Fast Direct Methods for Gaussian Processes

juliet: a versatile modelling tool for transiting and non-transiting exoplanetary systems

Monthly notices of the Royal Astronomical Society

A rocky planet transiting a nearby low-mass star

J C A P 1 0 ( 2 0 1 7 ) 0 0 9 ournal of C osmology and A stroparticle P hysics

Journal of Cosmology and Astroparticle Physics

Constraints on the interacting vacuum–geodesic CDM scenario

An Ultra-short Period Rocky Super-Earth with a Secondary Eclipse and a Neptune-like Companion around K2-141

Warm terrestrial planet with half the mass of Venus transiting a nearby star

A precise optical transmission spectrum of the inflated exoplanet WASP-52b

Monthly Notices of the Royal Astronomical Society

The spectral energy distribution of powerful starburst galaxies - I. Modelling the radio continuum

Non-detection of HC11N towards TMC-1: constraining the chemistry of large carbon-chain molecules


Miscellaneous collection of Python and R scripts for processing Iso-Seq data

De novo assembly of the cattle reference genome with single-molecule sequencing

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

Zenodo (CERN European Organization for Nuclear Research)

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease

The chromosome-scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis

Single-cell RNA-seq analysis of mouse preimplantation embryos by third-generation sequencing

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

Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe

Two novel venom proteins underlie divergent parasitic strategies between a generalist and a specialist parasite


Library for detecting anomalies in signals

Detecting Spacecraft Anomalies Using LSTMs and Nonparametric Dynamic Thresholding

TadGAN: Time Series Anomaly Detection Using Generative Adversarial Networks

Graph-Augmented Normalizing Flows for Anomaly Detection of Multiple Time Series

The Machine Learning Bazaar: Harnessing the ML Ecosystem for Effective System Development

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

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

Sintel: A Machine Learning Framework to Extract Insights from Signals

Proceedings of the 2022 International Conference on Management of Data

A Survey of Time Series Anomaly Detection Methods in the AIOps Domain

Making the End-User a Priority in Benchmarking: OrionBench for Unsupervised Time Series Anomaly Detection


Python language bindings for preCICE

FEniCS-preCICE: Coupling FEniCS to other Simulation Software

CFD/CSD Coupling for an Isolated Rotor Using preCICE

Gym-preCICE: Reinforcement Learning Environments for Active Flow Control


PDBFixer fixes problems in PDB files

An optimized chemical-genetic method for cell-specific metabolic labeling of RNA

The dynamic conformational landscape of the protein methyltransferase SETD8

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques

Molecular mechanism of LIP05 derived from Monascus purpureus YJX-8 for synthesizing fatty acid ethyl esters under aqueous phase

A Novel Machine Learning Approach Uncovers New and Distinctive Inhibitors for Cyclin-Dependent Kinase 9

An Open-Source Molecular Builder and Free Energy Preparation Workflow

The Dynamic Conformational Landscapes of the Protein Methyltransferase SETD8

Binding of a Pyrene-Based Fluorescent Amyloid Ligand to Transthyretin: A Combined Crystallographic and Molecular Dynamics Study

Comparative Evaluation of the Antibacterial and Antitumor Activities of 9-Phenylfascaplysin and Its Analogs

Prebound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin–BPTI Complex Using Random Acceleration Molecular Dynamics Simulations


A Large Quadcopter Swarm

CrazyChoir: Flying Swarms of Crazyflie Quadrotors in ROS 2

GCBF+: A Neural Graph Control Barrier Function Framework for Distributed
  Safe Multi-Agent Control

A Remote Sim2real Aerial Competition: Fostering Reproducibility and Solutions' Diversity in Robotics Challenges


ASTRA Tomography Toolbox

Generalized Sinkhorn Iterations for Regularizing Inverse Problems Using Optimal Mass Transport

Optical diffraction tomography with finite object support for the minimization of missing cone artifacts

Deep Learning Driven Noise Reduction for Reduced Flux Computed Tomography

Parallel-beam X-ray CT datasets of apples with internal defects and label balancing for machine learning

Neutron imaging data processing using the Mantid framework

VI EUROPEAN CONFERENCE ON NEUTRON SCATTERING (ECNS2015)


QKeras: a quantization deep learning library for Tensorflow Keras

Automatic heterogeneous quantization of deep neural networks for low-latency inference on the edge for particle detectors

Fast convolutional neural networks on FPGAs with hls4ml

Machine Learning: Science and Technology

Compressing deep neural networks on FPGAs to binary and ternary precision with HLS4ML

CrossLight: A Cross-Layer Optimized Silicon Photonic Neural Network Accelerator

Distance-Weighted Graph Neural Networks on FPGAs for Real-Time Particle Reconstruction in High Energy Physics

Charged particle tracking via edge-classifying interaction networks

Ps and Qs: Quantization-Aware Pruning for Efficient Low Latency Neural Network Inference

Graph Neural Networks for Charged Particle Tracking on FPGAs

ROBIN: A Robust Optical Binary Neural Network Accelerator

Enabling Binary Neural Network Training on the Edge


COMPAS rapid binary population synthesis code

Cygnus X-1 contains a 21–solar mass black hole—Implications for massive star winds

Impact of massive binary star and cosmic evolution on gravitational wave observations I: black hole-neutron star mergers

The role of mass transfer and common envelope evolution in the formation of merging binary black holes

Simple recipes for compact remnant masses and natal kicks

Polluting the pair-instability mass gap for binary black holes through super-Eddington accretion in isolated binaries

Rapid Stellar and Binary Population Synthesis with COMPAS

The Redshift Evolution of the Binary Black Hole Merger Rate: A Weighty Matter

Impact of Massive Binary Star and Cosmic Evolution on Gravitational Wave
  Observations II: Double Compact Object Rates and Properties

Massive Stellar Triples Leading to Sequential Binary Black Hole Mergers in the Field

Binary population synthesis with probabilistic remnant mass and kick prescriptions


MISP (core software) - Open Source Threat Intelligence and Sharing Platform

Investigating Sharing of Cyber Threat Intelligence and Proposing A New Data Model for Enabling Automation in Knowledge Representation and Exchange

Open Dataset of Phishing and Tor Hidden Services Screen-captures

Collaborative Information Sharing for ML-Based Threat Detection

Carl-Hauser - Open Source Image Matching Algorithms Benchmarking Framework.


An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.

PyBioNetFit and the Biological Property Specification Language

Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States

medRxiv : the preprint server for health sciences

Bayesian inference using qualitative observations of underlying continuous variables

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Bayesian Uncertainty Quantification for Systems Biology Models Parameterized Using Qualitative Data


Code for the MADDPG algorithm from the paper "Multi-Agent Actor-Critic for Mixed Cooperative-Competitive Environments"

Learning Transferable Cooperative Behavior in Multi-Agent Teams

PIC: Permutation Invariant Critic for Multi-Agent Deep Reinforcement Learning

Collective eXplainable AI: Explaining Cooperative Strategies and Agent Contribution in Multiagent Reinforcement Learning With Shapley Values

A New Framework for Multi-Agent Reinforcement Learning -- Centralized Training and Exploration with Decentralized Execution via Policy Distillation

Robust Multi-Agent Reinforcement Learning with State Uncertainty

Multi-agent reinforcement learning with approximate model learning for competitive games

Deep Reinforcement Learning

Deep reinforcement learning of event-triggered communication and control for multi-agent cooperative transport

Modeling the Interaction between Agents in Cooperative Multi-Agent Reinforcement Learning


Geometric loss functions between point clouds, images and volumes

Deep Generalized Schrödinger Bridge

A Neural Tangent Kernel Perspective of GANs

Mirror Diffusion Models for Constrained and Watermarked Generation

On Leveraging the Visual Modality for Neural Machine Translation

Knowledge Distillation for 6D Pose Estimation by Aligning Distributions of Local Predictions

KNOT: Knowledge Distillation using Optimal Transport for Solving NLP Tasks

Estimating Regression Predictive Distributions with Sample Networks

Impact of data for forecasting on performance of model predictive control in buildings with smart energy storage

Federated Distillation of Natural Language Understanding with Confident Sinkhorns.


SortMeRNA: next-generation sequence filtering and alignment tool

A simple guide to de novo transcriptome assembly and annotation

A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer

Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames

Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists

Functional meta-omics provide critical insights into long- and short-read assemblies

Applications of Machine Learning Models to Predict and Prevent Obesity: A Mini-Review

Clostridium scindens secretome suppresses virulence gene expression of Clostridioides difficile in a bile acid-independent manner

Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study


Official repo for consistency models.

Consistency Models

One-step Diffusion with Distribution Matching Distillation

A Geometric Perspective on Diffusion Models

Unified Discrete Diffusion for Categorical Data

CoSIGN: Few-Step Guidance of ConSIstency Model to Solve General INverse Problems


Optimal Control for Switched Systems

Perceptive Locomotion Through Nonlinear Model-Predictive Control

Articulated Object Interaction in Unknown Scenes with Whole-Body Mobile Manipulation

Combining Learning-based Locomotion Policy with Model-based Manipulation for Legged Mobile Manipulators

A Collision-Free MPC for Whole-Body Dynamic Locomotion and Manipulation

Adaptive CLF-MPC With Application to Quadrupedal Robots

International Conference on Robotics and Automation

Offline motion libraries and online MPC for advanced mobility skills

The International Journal of Robotics Research

Versatile multicontact planning and control for legged loco-manipulation

N^2M^2: Learning Navigation for Arbitrary Mobile Manipulation Motions in Unseen and Dynamic Environments

Planar Bipedal Locomotion with Nonlinear Model Predictive Control: Online Gait Generation using Whole-Body Dynamics

Keep It Upright: Model Predictive Control for Nonprehensile Object Transportation With Obstacle Avoidance on a Mobile Manipulator


A Julia/JuMP Package for Gas Network Optimization

Operation of Natural Gas Pipeline Networks With Storage Under Transient Flow Conditions

IEEE Transactions on Control Systems Technology

Graph-Based Modeling and Decomposition of Energy Infrastructures

Robust Gas Pipeline Network Expansion Planning to Support Power System Reliability

Demand Response Analogues for Residential Loads in Natural Gas Networks

Natural gas maximal load delivery for multi-contingency analysis


A python binding for crfsuite

Negation Scope Detection for Twitter Sentiment Analysis

Empirical Methods in Natural Language Processing

Automatically Tagging Constructions of Causation and Their Slot-Fillers

Transactions of the Association for Computational Linguistics

Toward a Standardized and More Accurate Indonesian Part-of-Speech Tagging

nala: text mining natural language mutation mentions

Sentence-Level Resampling for Named Entity Recognition

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

Beyond Query-Oriented Highlighting: Investigating the Effect of Snippet Text Highlighting in Search User Behavior

Computational intelligence and neuroscience

CMNEROne at SemEval-2022 Task 11: Code-Mixed Named Entity Recognition by leveraging multilingual data

AI pptX: Robust Continuous Learning for Document Generation with AI Insights.


Automatically Track Radiosonde Launches using RTLSDR


The reference P4 software switch

Heavy-Hitter Detection Entirely in the Data Plane

A survey on data plane programming with P4: Fundamentals, advances, and applied research

P4-IPsec: Site-to-Site and Host-to-Site VPN with IPsec in P4-Based SDN

P4-MACsec: Dynamic Topology Monitoring and Data Layer Protection with MACsec in P4-SDN

In-Network Volumetric DDoS Victim Identification Using Programmable Commodity Switches

IEEE Transactions on Network and Service Management

Tracking Normalized Network Traffic Entropy to Detect DDoS Attacks in P4

QROUTE: An Efficient Quality of Service (QoS) Routing Scheme for Software-Defined Overlay Networks

Gauntlet: Finding Bugs in Compilers for Programmable Packet Processing

FastReact: In-Network Control and Caching for Industrial Control Networks using Programmable Data Planes

Random Linear Network Coding on Programmable Switches


Audiocraft is a library for audio processing and generation with deep learning. It features the state-of-the-art EnCodec audio compressor / tokenizer, along with MusicGen, a simple and controllable music generation LM with textual and melodic conditioning.

MusicLM: Generating Music From Text

Simple and Controllable Music Generation

AudioGen: Textually Guided Audio Generation

AudioLDM 2: Learning Holistic Audio Generation with Self-supervised Pretraining

CodePlan: Repository-level Coding using LLMs and Planning

Masked Audio Generation using a Single Non-Autoregressive Transformer

Natural language guidance of high-fidelity text-to-speech with synthetic
  annotations

An HCI-Centric Survey and Taxonomy of Human-Generative-AI Interactions

Moshi: a speech-text foundation model for real-time dialogue

Stable Audio Open


Single Image Crowd Counting via MCNN (Unofficial Implementation)

Single-Image Crowd Counting via Multi-Column Convolutional Neural Network

Learning Spatial Awareness to Improve Crowd Counting

Misplaced Trust: Measuring the Interference of Machine Learning in Human Decision-Making

International Workshop on Continual Semi-Supervised Learning: Introduction, Benchmarks and Baselines


LexiLaw - 中文法律大模型

Large Language Models in Law: A Survey

LawBench: Benchmarking Legal Knowledge of Large Language Models

PanGu-π: Enhancing Language Model Architectures via Nonlinearity Compensation

A Survey on Large Language Models for Critical Societal Domains:
  Finance, Healthcare, and Law

LAiW: A Chinese Legal Large Language Models Benchmark (A Technical Report)

AviationGPT: A Large Language Model for the Aviation Domain

BLADE: Enhancing Black-box Large Language Models with Small
  Domain-Specific Models

LawLuo: A Chinese Law Firm Co-run by LLM Agents

Exploring the Nexus of Large Language Models and Legal Systems: A Short
  Survey


A prototype of soft contract verification for an untyped functional language

Soft contract verification

International Conference on Functional Programming

Relatively Complete Counterexamples for Higher-Order Programs

Soft contract verification for higher-order stateful programs

Symposium on Principles of Programming Languages

Higher-order symbolic execution for contract verification and refutation


The ARTIC field bioinformatics pipeline

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

bioRxiv : the preprint server for biology

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing

Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient

SARS-CoV-2 Infection in Captive Hippos (Hippopotamus amphibius), Belgium

Animals : an open access journal from MDPI

Rapid genomic surveillance of SARS-CoV-2 in a dense urban community of Kathmandu Valley using sewage samples

Genomics of postvaccination SARS‐CoV‐2 infections during the Delta dominated second wave of COVID‐19 pandemic, from Mumbai Metropolitan Region (MMR), India


Tools for detecting DNA modifications from single molecule, real-time sequencing data

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

DNAModAnnot: a R toolbox for DNA modification filtering and annotation

Adenine methylation is very scarce in the Drosophila genome and not erased by the ten-eleven translocation dioxygenase


Scientific analysis of nanoscale materials imaging data

Recent advances and applications of deep learning methods in materials science

Deep learning in electron microscopy

Feature extraction via similarity search: application to atom finding and denoising in electron and scanning probe microscopy imaging

Advanced structural and chemical imaging

USID and Pycroscopy -- Open frameworks for storing and analyzing spectroscopic and imaging data

A Processing and Analytics System for Microscopy Data Workflows: The Pycroscopy Ecosystem of Packages

Advances in Electron Microscopy with Deep Learning


Patch-level verification for Bundler

Towards Measuring Supply Chain Attacks on Package Managers for Interpreted Languages

Cleaning the NVD: Comprehensive Quality Assessment, Improvements, and Analyses

Measuring and Preventing Supply Chain Attacks on Package Managers.


ROS-Industrial Universal Robots support (https://wiki.ros.org/universal_robot)

Inverse Kinematics with Forward Dynamics Solvers for Sampled Motion Tracking

Virtual Forward Dynamics Models for Cartesian Robot Control

Improving Haptic Response for Contextual Human Robot Interaction


HighFive - Header-only C++ HDF5 interface

On the Effectiveness of Weight-Encoded Neural Implicit 3D Shapes

Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors

Phoebe: a high-performance framework for solving phonon and electron Boltzmann transport equations

Phoebe: a collection of Phonon and Electron Boltzmann Equation solvers


FlexFlow Serve: Low-Latency, High-Performance LLM Serving

Unity: Accelerating DNN Training Through Joint Optimization of Algebraic Transformations and Parallelization

USENIX Symposium on Operating Systems Design and Implementation

Towards Efficient Generative Large Language Model Serving: A Survey from Algorithms to Systems

SpecInfer: Accelerating Large Language Model Serving with Tree-based Speculative Inference and Verification

Understanding LLMs: A Comprehensive Overview from Training to Inference

Minions: Accelerating Large Language Model Inference with Adaptive and
  Collective Speculative Decoding

FlexLLM: A System for Co-Serving Large Language Model Inference and Parameter-Efficient Finetuning


Official git repository for Biopython (originally converted from CVS)

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

A deep learning approach to programmable RNA switches

The evolution of a counter-defense mechanism in a virus constrains its host range

Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes

Amplification of overlapping DNA amplicons in a single-tube multiplex PCR for targeted next-generation sequencing of BRCA1 and BRCA2

An integrated pipeline for mammalian genetic screening

The Big Effects of Short-term Efforts: Mentorship and Code Integration in Open Source Scientific Software

Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity

Revealing data leakage in protein interaction benchmarks

Establishing comprehensive quaternary structural proteomes from genome sequence


AudioGPT: Understanding and Generating Speech, Music, Sound, and Talking Head

Fast-MD: Fast Multi-Decoder End-to-End Speech Translation with Non-Autoregressive Hidden Intermediates

GAMA: A Large Audio-Language Model with Advanced Audio Understanding and
  Complex Reasoning Abilities


Emissions Modeling Framework (EMF)


Library for unit extraction - fork of quantulum for python3

ACES: Translation Accuracy Challenge Sets for Evaluating Machine Translation Metrics

Measurement Extraction with Natural Language Processing: A Review

Findings of the Association for Computational Linguistics: EMNLP 2022

CQE: A Comprehensive Quantity Extractor


Code and documents of LongLoRA and LongAlpaca (ICLR 2024 Oral)

LongLoRA: Efficient Fine-tuning of Long-Context Large Language Models

AcademicGPT: Empowering Academic Research

3D-RPE: Enhancing Long-Context Modeling Through 3D Rotary Position
  Encoding


Fast audio data augmentation in PyTorch. Inspired by audiomentations. Useful for deep learning.

AudioCLIP: Extending CLIP to Image, Text and Audio

Adaptive Representations of Sound for Automatic Insect Recognition

R-Spin: Efficient Speaker and Noise-invariant Representation Learning with Acoustic Pieces

Audio Denoising for Robust Audio Fingerprinting

Contrastive Learning from Synthetic Audio Doppelgangers


A pure-Rust implementation of Bulletproofs using Ristretto.

RoFL: Robustness of Secure Federated Learning

Bulletproofs+: Shorter Proofs for a Privacy-Enhanced Distributed Ledger

Retrofitting a two-way peg between blockchains

Zef: Low-latency, Scalable, Private Payments

Privacy-Preserving Decentralized Exchange Marketplaces


The ThingML modelling language

From things' modeling language (ThingML) to things' machine learning (ThingML2)

Proceedings of the 23rd ACM/IEEE International Conference on Model Driven Engineering Languages and Systems: Companion Proceedings

Supporting AI Engineering on the IoT Edge through Model-Driven TinyML

Annual International Computer Software and Applications Conference

Data Analytics and Machine Learning Methods, Techniques and Tool for Model-Driven Engineering of Smart IoT Services

International Conference on Software Engineering

MDE4QAI: Towards Model-Driven Engineering for Quantum Artificial Intelligence

Runtime Monitoring for Executable DSLs

Towards a secure API client generator for IoT devices

ML-Quadrat & DriotData: A Model-Driven Engineering Tool and a Low-Code Platform for Smart IoT Services


Python IRF builder

Reconstruction of stereoscopic CTA events using deep learning with CTLearn

Physics Performance of the Large Size Telescope prototype of the Cherenkov Telescope Array

Deep-learning-driven event reconstruction applied to simulated data from a single Large-Sized Telescope of CTA

Interpolation of Instrument Response Functions for the Cherenkov Telescope Array in the Context of pyirf

Performance update of an event-type based analysis for the Cherenkov Telescope Array


Julia solvers for systems of nonlinear equations and mixed complementarity problems

OVERT: An Algorithm for Safety Verification of Neural Network Control Policies for Nonlinear Systems

Optimal noise-canceling networks

Analysis of Theoretical and Numerical Properties of Sequential Convex Programming for Continuous-Time Optimal Control

Initialisation of a hybrid AC/DC power system for harmonic stability analysis using a power flow formulation

Particle Swarm Optimization-based co-state initialization for low-thrust minimum-fuel trajectory optimization

Pixel Arrays: A fast and elementary method for solving nonlinear systems

Order conditions for exponential integrators

MatsubaraFunctions.jl: An equilibrium Green's function library in the Julia programming language


Link Discovery Framework for Metric Spaces.

CovidPubGraph: A FAIR Knowledge Graph of COVID-19 Publications

Zenodo (CERN European Organization for Nuclear Research)

LIMES: A Framework for Link Discovery on the Semantic Web

On the Effect of Geometries Simplification on Geo-spatial Link Discovery

MaskLink: Efficient Link Discovery for Spatial Relations via Masking Areas

A Comparative Evaluation of Geospatial Semantic Web Frameworks for Cultural Heritage

Three-dimensional Geospatial Interlinking with JedAI-spatial

Duplicate Detection as a Service

COBALT: A Content-Based Similarity Approach for Link Discovery over Geospatial Knowledge Graphs

Application of Open-Source Software in Knowledge Graph Construction


Grammars written for ANTLR v4; expectation that the grammars are free of actions.

Superion: Grammar-Aware Greybox Fuzzing

Mapping Language to Code in Programmatic Context

9.6 Million Links in Source Code Comments: Purpose, Evolution, and Decay

Darwinian data structure selection

Code-based Vulnerability Detection in Node.js Applications: How far are we?

Syntax error recovery in parsing expression grammars

HSTREAM: A directive-based language extension for heterogeneous stream computing

Does Python Smell Like Java? Tool Support for Design Defect Discovery in Python

A Declarative Extension of Parsing Expression Grammars for Recognizing Most Programming Languages

Nez: practical open grammar language


Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

Dsuite - fast D-statistics and related admixture evidence from VCF files

Adaptive and maladaptive introgression in grapevine domestication

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

Genomic analyses provide insights into sex differentiation of tetraploid strawberry (Fragaria moupinensis)


Optimize and assist planning your garden


A formal verifier and analysis tool for Solidity Smart Contracts

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

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

A Comparative Evaluation of Automated Analysis Tools for Solidity Smart Contracts


Repository for the GA4GH phenopacket schema

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

The RD‐Connect Genome‐Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases

GeneBreaker: Variant simulation to improve the diagnosis of Mendelian rare genetic diseases


A pytorch adversarial library for attack and defense methods on images and graphs

Graph Structure Learning for Robust Graph Neural Networks

Adversarial Attack and Defense on Graph Data: A Survey

GNNGuard: Defending Graph Neural Networks against Adversarial Attacks

Node Similarity Preserving Graph Convolutional Networks

Graph Information Bottleneck

DeepRobust: A PyTorch Library for Adversarial Attacks and Defenses

Adversarial Attacks and Defenses on Graphs: A Review and Empirical Study

Elastic Graph Neural Networks

Adversarial Attacks and Defenses in Images, Graphs and Text: A Review

Are Defenses for Graph Neural Networks Robust?


Bias Auditing & Fair ML Toolkit

Retiring Adult: New Datasets for Fair Machine Learning

Aequitas: A Bias and Fairness Audit Toolkit

Amazon SageMaker Clarify: Machine Learning Bias Detection and Explainability in the Cloud

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

Conference on Fairness, Accountability and Transparency

Turning the Tables: Biased, Imbalanced, Dynamic Tabular Datasets for ML Evaluation

Dealing with Bias and Fairness in Data Science Systems: A Practical Hands-on Tutorial

Building Trustworthy AI Solutions: A Case for Practical Solutions for Small Businesses

IEEE Transactions on Artificial Intelligence

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

The Right Tool for the Job: Open-Source Auditing Tools in Machine Learning

Data quality dimensions for fair AI


Deep learning with spiking neural networks (SNNs) in PyTorch.

Spiking Neural Networks and Their Applications: A Review

Spiking Recurrent Neural Networks Represent Task-Relevant Neural Sequences in Rule-Dependent Computation

mlGeNN: accelerating SNN inference using GPU-enabled neural networks


Fast and embedded solvers for nonlinear optimal control

The control toolbox — An open-source C++ library for robotics, optimal and model predictive control

Simulation, Modeling, and Programming for Autonomous Robots


Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

The tuatara genome reveals ancient features of amniote evolution

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

Antarctic blackfin icefish genome reveals adaptations to extreme environments

Reference genome and demographic history of the most endangered marine mammal, the vaquita

Genomic basis of homoploid hybrid speciation within chestnut trees

Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions

Recent evolution in Rattus norvegicus is shaped by declining effective population size


A biplot based on ggplot2

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

Gut microbial composition in patients with psoriasis

Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio)

Phenotypic plasticity and genetic control in colorectal cancer evolution

Brain composition in Heliconius butterflies, post-eclosion growth and experience dependent neuropil plasticity

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

Brain Composition in Godyris zavaleta, a Diurnal Butterfly, Reflects an Increased Reliance on Olfactory Information

Soil texture and environmental conditions influence the biogeochemical responses of soils to drought and flooding

Phenomic and Physiological Analysis of Salinity Effects on Lettuce

Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota


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

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

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

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

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

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

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


Official repository of open data MassBank records

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species

MS2Tox Machine Learning Tool for Predicting the Ecotoxicity of Unidentified Chemicals in Water by Nontarget LC-HRMS

S1 | MASSBANK | NORMAN Compounds in MassBank


【PyTorch】Easy-to-use,Modular and Extendible package of deep-learning based CTR models.

Wide & Deep Learning for Recommender Systems

An Overview of Multi-Task Learning in Deep Neural Networks

DeepFM: A Factorization-Machine based Neural Network for CTR Prediction

Deep Interest Network for Click-Through Rate Prediction

Neural Factorization Machines for Sparse Predictive Analytics

Deep & Cross Network for Ad Click Predictions

xDeepFM: Combining Explicit and Implicit Feature Interactions for Recommender Systems

Deep Interest Evolution Network for Click-Through Rate Prediction

Modeling Task Relationships in Multi-task Learning with Multi-gate Mixture-of-Experts

Attentional Factorization Machines: Learning the Weight of Feature Interactions via Attention Networks


OpenFOAM-preCICE adapter

preCICE v2: A sustainable and user-friendly coupling library

FEniCS-preCICE: Coupling FEniCS to other Simulation Software

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

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

Gym-preCICE: Reinforcement Learning Environments for Active Flow Control


Laplace approximations for Deep Learning.

Bayesian Deep Learning via Subnetwork Inference

Adapting the Linearised Laplace Model Evidence for Modern Deep Learning

Laplace Redux -- Effortless Bayesian Deep Learning

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

NeuralEF: Deconstructing Kernels by Deep Neural Networks

Scalable Bayesian Inference in the Era of Deep Learning: From Gaussian
  Processes to Deep Neural Networks

Evaluating Bayesian deep learning for radio galaxy classification


Quantus is an eXplainable AI toolkit for responsible evaluation of neural network explanations

Quantus: An Explainable AI Toolkit for Responsible Evaluation of Neural Network Explanations and Beyond

NoiseGrad: Enhancing Explanations by Introducing Stochasticity to Model Weights

Optimizing Explanations by Network Canonization and Hyperparameter Search

Sanity Checks Revisited: An Exploration to Repair the Model Parameter Randomisation Test

A Fresh Look at Sanity Checks for Saliency Maps


An Open-source Toolkit for LLM Development

LLaMA-Adapter: Efficient Fine-tuning of Language Models with Zero-init Attention

LIMA: Less Is More for Alignment

SPHINX: The Joint Mixing of Weights, Tasks, and Visual Embeddings for Multi-modal Large Language Models

SPHINX-X: Scaling Data and Parameters for a Family of Multi-modal Large
  Language Models

Visual Autoregressive Modeling: Scalable Image Generation via Next-Scale
  Prediction

Autoregressive Model Beats Diffusion: Llama for Scalable Image Generation

Composite Backdoor Attacks Against Large Language Models

Alleviating Distortion in Image Generation via Multi-Resolution Diffusion Models

TEAL: Tokenize and Embed ALL for Multi-modal Large Language Models

TerDiT: Ternary Diffusion Models with Transformers


James Webb Space Telescope PSF simulation tool

The chemical enrichment in the early Universe as probed by JWST via direct metallicity measurements at z~8

JexoSim: a time-domain simulator of exoplanet transit spectroscopy with JWST

Monthly notices of the Royal Astronomical Society

Active Galactic Nuclei Selection and Demographics: A New Age with JWST/MIRI

Constrained Reference Star Differential Imaging: Enabling High-Fidelity Imagery of Highly Structured Circumstellar Disks

The Near Infrared Imager and Slitless Spectrograph for JWST. V. Kernel Phase Imaging and Data Analysis

Transiting Exoplanet Yields for the Roman Galactic Bulge Time Domain Survey Predicted from Pixel-level Simulations

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

Frontiers in Astronomy and Space Sciences

Quantifying the Escape of Lyα at z ≈ 5–6: A Census of Lyα Escape Fraction with Hα-emitting Galaxies Spectroscopically Confirmed by JWST and VLT/MUSE

The Astrophysical Journal Supplement Series

PDRs4All. V. Modelling the dust evolution across the illuminated edge of the Orion Bar

Quantifying the escape of Lyα at z≈ 5-6: a census of Lyα escape fraction with Hα emitting galaxies spectroscopically confirmed by JWST and VLT/MUSE


PyTorch code for EMNLP 2019 paper "LXMERT: Learning Cross-Modality Encoder Representations from Transformers".

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

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

Behind the Scene: Revealing the Secrets of Pre-trained Vision-and-Language Models

Learning to Model and Ignore Dataset Bias with Mixed Capacity Ensembles

Deep Multi-modal Fusion of Image and Non-image Data in Disease Diagnosis and Prognosis: A Review

Separating Skills and Concepts for Novel Visual Question Answering

Automatic Generation of Contrast Sets from Scene Graphs: Probing the Compositional Consistency of GQA

Reasoning over Vision and Language: Exploring the Benefits of Supplemental Knowledge

Probing Contextual Language Models for Common Ground with Visual Representations


Automatic White Matter Bundle Segmentation

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

An overview of deep learning in medical imaging focusing on MRI

TractSeg - Fast and accurate white matter tract segmentation

Combined tract segmentation and orientation mapping for bundle-specific tractography

Prevalence of white matter pathways coming into a single white matter voxel orientation: The bottleneck issue in tractography

Tract orientation mapping for bundle-specific tractography

Population-based tract-to-region connectome of the human brain and its hierarchical topology

Detecting microstructural deviations in individuals with deep diffusion MRI tractometry

Fiber tractography bundle segmentation depends on scanner effects, vendor effects, acquisition resolution, diffusion sampling scheme, diffusion sensitization, and bundle segmentation workflow

Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation


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

SuperPoint: Self-Supervised Interest Point Detection and Description

Navigating to Objects Specified by Images

Semi-Supervised Keypoint Detector and Descriptor for Retinal Image Matching

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

Self-Calibrating Anomaly and Change Detection for Autonomous Inspection Robots

Towards View-invariant and Accurate Loop Detection Based on Scene Graph


R package: Methods that Apply to Rows and Columns of Matrices (and to Vectors)

CopywriteR: DNA copy number detection from off-target sequence data

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

Single Cell Imaging of Nuclear Architecture Changes

Frontiers in cell and developmental biology

Inter- and Intra-Scanner Variability of Automated Brain Volumetry on Three Magnetic Resonance Imaging Systems in Alzheimer’s Disease and Controls

Defining the Influence of the A12.2 Subunit on Transcription Elongation and Termination by RNA Polymerase I In Vivo

Multidimensional well-being of US households at a fine spatial scale using fused household surveys


Enrico helps you with your Fermi data analysis

The Blazar PG 1553+113 as a Binary System of Supermassive Black Holes

Multiwaveband quasi-periodic oscillation in the blazar 3C 454.3

Monthly Notices of the Royal Astronomical Society

Enrico : a Python package to simplify Fermi-LAT analysis

High-energy Gamma-Ray Activity from V404 Cygni Detected by AGILE during the 2015 June Outburst

THE GAMMA-RAY SOURCE AGL J2241+4454 AS THE POSSIBLE COUNTERPART OF MWC 656

AGILE, Fermi, Swift, and GASP/WEBT multi-wavelength observations of the high-redshift blazar 4C +71.07 in outburst

The mid-2016 flaring activity of the flat spectrum radio quasar PKS 2023-07

X-ray and Gamma-ray Variability of NGC 1275


POT : Python Optimal Transport

Optimal Transport for structured data with application on graphs

Wasserstein Weisfeiler-Lehman Graph Kernels

Optimal Transport for Multi-source Domain Adaptation under Target Shift

Community Detection on Networks with Ricci Flow

Fused Gromov-Wasserstein distance for structured objects: theoretical foundations and mathematical properties

Wasserstein Discriminant Analysis

Partial Optimal Transport with Applications on Positive-Unlabeled Learning

Fairness Violations and Mitigation under Covariate Shift

Proceedings of the 2021 ACM Conference on Fairness, Accountability, and Transparency

A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors

Matching Code and Law: Achieving Algorithmic Fairness with Optimal Transport


Circuit IR Compilers and Tools

ScaleHLS: A New Scalable High-Level Synthesis Framework on Multi-Level Intermediate Representation

HIR: An MLIR-based Intermediate Representation for Hardware Accelerator Description

Bridging Control-Centric and Data-Centric Optimization

Proceedings of the 21st ACM/IEEE International Symposium on Code Generation and Optimization

Verilog-to-PyG -- A Framework for Graph Learning and Augmentation on RTL Designs

Allo: A Programming Model for Composable Accelerator Design

Proceedings of the ACM on Programming Languages

Compiler Infrastructure for Specializing Domain-Specific Memory Templates

An Intermediate Representation for Composable Typed Streaming Dataflow Designs

Trireme: Exploring Hierarchical Multi-Level Parallelism for Domain Specific Hardware Acceleration

Platform-Aware FPGA System Architecture Generation based on MLIR

A Toolchain for Streaming Dataflow Accelerator Designs for Big Data Analytics: Defining an IR for Composable Typed Streaming Dataflow Designs


R-CNN: Regions with Convolutional Neural Network Features

Region-Based Convolutional Networks for Accurate Object Detection and Segmentation

Taking a Deeper Look at Pedestrians

AttentionNet: Aggregating Weak Directions for Accurate Object Detection

Context-aware CNNs for person head detection

Practices and Applications of Convolutional Neural Network-Based Computer Vision Systems in Animal Farming: A Review

LOGO-Net: Large-scale Deep Logo Detection and Brand Recognition with Deep Region-based Convolutional Networks

Pedestrian Models for Autonomous Driving Part I: Low-Level Models, From Sensing to Tracking

IEEE Transactions on Intelligent Transportation Systems

Analysing domain shift factors between videos and images for object detection

Double Attention-based Multimodal Neural Machine Translation with Semantic Image Regions

European Association for Machine Translation Conferences/Workshops

Una Revisión Sistemática de Métodos para Localizar Automáticamente Objetos en Imágenes

Revista Iberoamericana de Automática e Informática industrial


Repository for the Framework for Accessing Changes To Sea-level (FACTS)


ModBus Measurement Daemon - simple reading of data from ModBus meters and grid inverters


Data Reduction for Astronomy from Gemini Observatory North and South

Mining S-PLUS for Metal-poor Stars in the Milky Way

SPLUS J142445.34–254247.1: An r-process–enhanced, Actinide-boost, Extremely Metal-poor Star Observed with GHOST

PASSAGES: The Wide-ranging, Extreme Intrinsic Properties of Planck-selected, Lensed Dusty Star-forming Galaxies

DRAGONS -- A Quick Overview


Fermi-LAT Python Analysis Framework

Fermipy: An open-source Python package for analysis of Fermi-LAT Data

Gammapy - A prototype for the CTA science tools

GeV–TeV Counterparts of SS 433/W50 from Fermi-LAT and HAWC Observations

MADHAT: Model-Agnostic Dark Halo Analysis Tool

Testing the dark matter subhalo hypothesis of the gamma-ray source 3FGL J2212.5+0703

The contribution of winds from star clusters to the Galactic cosmic-ray population

K2 Optical Emission from OJ 287 and Other γ-Ray Blazars on Hours-to-weeks Timescales from 2014 to 2018

Nonthermal Radiation of the Extreme TeV Blazar 1ES 0229+200 from Electromagnetic Cascades on Infrared Photon Field

Constraints on dark matter and astrophysics from tomographic γ-ray cross-correlations

LST-1 observations of an enormous flare of BL Lacertae in 2021

Proceedings of 38th International Cosmic Ray Conference — PoS(ICRC2023)


The BGP swiss army knife of networking

ARTEMIS: Neutralizing BGP Hijacking within a Minute

Routing Centralization Across Domains via SDN: A Model and Emulation Framework for BGP Evolution

Evaluating the Effect of Centralization on Routing Convergence on a Hybrid BGP-SDN Emulation Framework

Supercharge me: Boost Router Convergence with SDN

Isolario: a Do-ut-des Approach to Improve the Appeal of BGP Route Collecting


An open-source application for biological image analysis

Anthelmintic drug discovery: target identification, screening methods and the role of open science

BioCoder: a benchmark for bioinformatics code generation with large language models

CellProfiler plugins -- an easy image analysis platform integration for containers and Python tools

OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control

A fully automated deep learning pipeline for high-throughput colony segmentation and classification

Epigenetic silencing of HTATIP2 in glioblastoma contributes to treatment resistance by enhancing nuclear translocation of the DNA repair protein MPG.


Learning Chinese Character style with conditional GAN

Conditional Image Synthesis With Auxiliary Classifier GANs

Unsupervised Cross-Domain Image Generation

Generating Handwritten Chinese Characters using CycleGAN

Workshop on Applications of Computer Vision

DG-Font: Deformable Generative Networks for Unsupervised Font Generation

GANwriting: Content-Conditioned Generation of Styled Handwritten Word Images

Learning to Write Stylized Chinese Characters by Reading a Handful of Examples

Few-shot Compositional Font Generation with Dual Memory

Few-shot Font Generation with Localized Style Representations and Factorization

Look Closer to Supervise Better: One-Shot Font Generation via Component-Based Discriminator

CF-Font: Content Fusion for Few-shot Font Generation


Code to compute the XP-CLR statistic to infer natural selection

Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding

The Plant journal : for cell and molecular biology

Genome-Wide Association Study Reveals Complex Genetic Architecture of Cadmium and Mercury Accumulation and Tolerance Traits in Medicago truncatula

Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach

Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

Genome resequencing reveals independent domestication and breeding improvement of naked oat

Metabolite-based genome-wide association studies enable the dissection of the genetic bases of flavonoids, betaine and spermidine in wolfberry (Lycium).

The genomic history and global migration of a windborne pest