3D force-directed graph component using ThreeJS/WebGL

VICE: Visual Identification and Correction of Neural Circuit Errors

WikiDataSets: Standardized sub-graphs from Wikidata

How To Quantify a Genetic Firewall? A Polarity‐Based Metric for Genetic Code Engineering

Chembiochem : a European journal of chemical biology

Contributions to Representation Learning with Graph Autoencoders and Applications to Music Recommendation


Tools to work with Allen Inst CCF data in matlab

Distributed coding of choice, action and engagement across the mouse brain

A tool for analyzing electrode tracks from slice histology

Rapid suppression and sustained activation of distinct cortical regions for a delayed sensory-triggered motor response

Distance-tuned neurons drive specialized path integration calculations in medial entorhinal cortex

Corticothalamic feedback sculpts visual spatial integration in mouse thalamus

Distributed correlates of visually-guided behavior across the mouse brain

Organization of feedback projections to mouse primary visual cortex

An adaptable, reusable, and light implant for chronic Neuropixels probes

bioRxiv : the preprint server for biology

Histological E-data Registration in rodent Brain Spaces

Top-down modulation of the retinal code via histaminergic neurons of the hypothalamus


Riemannian Adaptive Optimization Methods with pytorch optim

Geoopt: Riemannian Optimization in PyTorch

Mixed-curvature Variational Autoencoders

Graph Geometry Interaction Learning

Pseudo-Riemannian Graph Convolutional Networks

Symmetric Spaces for Graph Embeddings: A Finsler-Riemannian Approach

FisheyeHDK: Hyperbolic Deformable Kernel Learning for Ultra-Wide Field-of-View Image Recognition

Time Series Alignment with Global Invariances

Hybridizing Euclidean and Hyperbolic Similarities for Attentively Refining Representations in Semantic Segmentation of Remote Sensing Images

IEEE Geoscience and Remote Sensing Letters

ICLR 2021 Challenge for Computational Geometry & Topology: Design and Results


MyoSuite is a collection of environments/tasks to be solved by musculoskeletal models simulated with the MuJoCo physics engine and wrapped in the OpenAI gym API.

MyoSuite -- A contact-rich simulation suite for musculoskeletal motor control

RoboHive: A Unified Framework for Robot Learning

Seizing Serendipity: Exploiting the Value of Past Success in Off-Policy Actor-Critic

Natural and Robust Walking using Reinforcement Learning without Demonstrations in High-Dimensional Musculoskeletal Models

MuscleVAE: Model-Based Controllers of Muscle-Actuated Characters

Growing Q-Networks: Solving Continuous Control Tasks with Adaptive
  Control Resolution

Self Model for Embodied Intelligence: Modeling Full-Body Human Musculoskeletal System and Locomotion Control with Hierarchical Low-Dimensional Representation


StarDist - Object Detection with Star-convex Shapes

Cell Detection with Star-convex Polygons

Medical Image Computing and Computer-Assisted Intervention

Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy

Workshop on Applications of Computer Vision

A shift in lung macrophage composition is associated with COVID-19 severity and recovery

Non-invasive scoring of cellular atypia in keratinocyte cancers in 3D LC-OCT images using Deep Learning

Software tools for 3D nuclei segmentation and quantitative analysis in multicellular aggregates

Computational and structural biotechnology journal

Bubble identification from images with machine learning methods

StarDist Image Segmentation Improves Circulating Tumor Cell Detection

NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scale

Nuclei Instance Segmentation and Classification in Histopathology Images with Stardist

2022 IEEE International Symposium on Biomedical Imaging Challenges (ISBIC)

Different approaches to Imaging Mass Cytometry data analysis


Training neural network potentials

TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials

Pre-training via Denoising for Molecular Property Prediction

Machine Learning Coarse-Grained Potentials of Protein Thermodynamics

Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs

NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics

Journal of chemical information and modeling

TensorNet: Cartesian Tensor Representations for Efficient Learning of Molecular Potentials

Fractional Denoising for 3D Molecular Pre-training

TorchMD-Net 2.0: Fast Neural Network Potentials for Molecular Simulations

NNP/MM: Accelerating molecular dynamics simulations with machine learning potentials and molecular mechanic

Self-Consistency Training for Hamiltonian Prediction


Finds SNP sites from a multi-FASTA alignment file

Genome-Wide Variation in Potyviruses

Global phylogeography and evolutionary history of Shigella dysenteriae type 1

RdRp mutations are associated with SARS-CoV-2 genome evolution

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Information about variations in multiple copies of bacterial 16S rRNA genes may aid in species identification

Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes

Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation

Molecular characterization of carbapenem-resistant and virulent plasmids in Klebsiella pneumoniae from patients with bloodstream infections in China

Population Structure of Multidrug-Resistant Klebsiella oxytoca within Hospitals across the United Kingdom and Ireland Identifies Sharing of Virulence and Resistance Genes with K. pneumoniae


[NeurIPS'22] PointNeXt: Revisiting PointNet++ with Improved Training and Scaling Strategies

Meta Architecture for Point Cloud Analysis

Applying Plain Transformers to Real-World Point Clouds

Multi-task 3D building understanding with multi-modal pretraining

S2O: Static to Openable Enhancement for Articulated 3D Objects


KaHyPar (Karlsruhe Hypergraph Partitioning) is a multilevel hypergraph partitioning framework providing direct k-way and recursive bisection based partitioning algorithms that compute solutions of very high quality.

High-Quality Hypergraph Partitioning

Improving Coarsening Schemes for Hypergraph Partitioning by Exploiting Community Structure

Network Flow-Based Refinement for Multilevel Hypergraph Partitioning

Memetic Multilevel Hypergraph Partitioning

Advanced Flow-Based Multilevel Hypergraph Partitioning

Multilevel Acyclic Hypergraph Partitioning

Evolutionary n -Level Hypergraph Partitioning With Adaptive Coarsening

IEEE Transactions on Evolutionary Computation

Multilevel Hypergraph Partitioning with Vertex Weights Revisited

K-SpecPart: Supervised Embedding Algorithms and Cut Overlay for Improved Hypergraph Partitioning


iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Retrospective detection of asymptomatic monkeypox virus infections among male sexual health clinic attendees in Belgium

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

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

Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing

Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic

A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples

SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City

Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda

Genomic stability of self-inactivating rabies

Genomic Surveillance of Monkeypox Virus, Minas Gerais, Brazil, 2022

The Isolated in Utero Environment Is Conducive to the Emergence of RNA and DNA Virus Variants


Waymo Open Dataset

The Waymo Open Sim Agents Challenge

LET-3D-AP: Longitudinal Error Tolerant 3D Average Precision for Camera-Only 3D Detection

3D Cascade RCNN: High Quality Object Detection in Point Clouds

USB: Universal-Scale Object Detection Benchmark

trajdata: A Unified Interface to Multiple Human Trajectory Datasets

VectorFlow: Combining Images and Vectors for Traffic Occupancy and Flow Prediction

Ridon Vehicle: Drive-by-Wire System for Scaled Vehicle Platform and Its Application on Behavior Cloning


A repository for leveraging Self-Sovereign Identity in applications

Privacy and Trust Redefined in Federated Machine Learning

Machine Learning and Knowledge Extraction

A Distributed Trust Framework for Privacy-Preserving Machine Learning

Syft 0.5: A Platform for Universally Deployable Structured Transparency


Segmentation models with pretrained backbones. Keras and TensorFlow Keras.

U-Net: Convolutional Networks for Biomedical Image Segmentation

Pyramid Scene Parsing Network

LinkNet: Exploiting Encoder Representations for Efficient Semantic Segmentation

Visual Communications and Image Processing

SLEAP: A deep learning system for multi-animal pose tracking

Multimodal Self-Supervised Learning for Medical Image Analysis

Automated Detection and Classification of Oral Lesions Using Deep Learning to Detect Oral Potentially Malignant Disorders

Continual Adaptation of Visual Representations via Domain Randomization and Meta-learning

The Devil is in the Margin: Margin-based Label Smoothing for Network Calibration

Red-GAN: Attacking class imbalance via conditioned generation. Yet another medical imaging perspective

ExplAIn: Explanatory artificial intelligence for diabetic retinopathy diagnosis


Lasagne recipes: examples, IPython notebooks, ...

Membership Inference Attacks against Machine Learning Models

Machine Learning Models that Remember Too Much

Feature Learning for Chord Recognition: The Deep Chroma Extractor

Learning to Teach

Learning What Data to Learn

Quantitatively Evaluating GANs With Divergences Proposed for Training

Texture Synthesis Using Shallow Convolutional Networks with Random Filters

Recognizing Birds from Sound - The 2018 BirdCLEF Baseline System

Super-resolution Using Constrained Deep Texture Synthesis


Automatically create Faiss knn indices with the most optimal similarity search parameters.

LAION-5B: An open large-scale dataset for training next generation image-text models

ImageBind-LLM: Multi-modality Instruction Tuning

BioReader: a Retrieval-Enhanced Text-to-Text Transformer for Biomedical Literature

Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing

An Empirical Evaluation of Columnar Storage Formats

Automating Nearest Neighbor Search Configuration with Constrained Optimization

X&Fuse: Fusing Visual Information in Text-to-Image Generation

OpenStreetView-5M: The Many Roads to Global Visual Geolocation

Stark: Social Long-Term Multi-Modal Conversation with Persona Commonsense Knowledge

Document-Level Abstractive Summarization


Extract 3D contacts (.pairs) from sequencing alignments

Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase

Pairtools: From sequencing data to chromosome contacts

Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs

Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML

Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers

Order and stochasticity in the folding of individual Drosophila genomes

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos


Llama中文社区，Llama3在线体验和微调模型已开放，实时汇总最新Llama3学习资料，已将所有代码更新适配Llama3，构建最好的中文Llama大模型，完全开源可商用

LLaMA: Open and Efficient Foundation Language Models

Llama 2: Open Foundation and Fine-Tuned Chat Models

LoRA: Low-Rank Adaptation of Large Language Models

Knowledgeable Preference Alignment for LLMs in Domain-specific Question Answering

ChatRadio-Valuer: A Chat Large Language Model for Generalizable Radiology Report Generation Based on Multi-institution and Multi-system Data

Assistive Large Language Model Agents for Socially-Aware Negotiation
  Dialogues

UniOQA: A Unified Framework for Knowledge Graph Question Answering with Large Language Models


Run the PACTA analysis on EQ & CB portfolios


A PyTorch Implementation of Single Shot MultiBox Detector

Very Deep Convolutional Networks for Large-Scale Image Recognition

SSD: Single Shot MultiBox Detector

CutMix: Regularization Strategy to Train Strong Classifiers with Localizable Features

Receptive Field Block Net for Accurate and Fast Object Detection

Learning Loss for Active Learning

Small Object Detection using Context and Attention

Interpolation-based semi-supervised learning for object detection

Entropy-based Active Learning for Object Detection with Progressive Diversity Constraint

URBAN-i: From urban scenes to mapping slums, transport modes, and pedestrians in cities using deep learning and computer vision

Environment and Planning B: Urban Analytics and City Science

Post-training Quantization with Multiple Points: Mixed Precision without Mixed Precision


Python API to access the Copernicus Climate Data Store (CDS)

OpenForecast v2: Development and Benchmarking of the First National-Scale Operational Runoff Forecasting System in Russia

Impact of mobility restrictions on NO2 concentrations in key Latin American cities during the first wave of the COVID-19 pandemic

Identifying the Causes of Pyrocumulonimbus (PyroCb)

Pyrocast: a Machine Learning Pipeline to Forecast Pyrocumulonimbus (PyroCb) Clouds


Open Drug Discovery Toolkit

Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field

Development of a Protein-Ligand Extended Connectivity (PLEC) Fingerprint and Its Application for Binding Affinity Predictions.

Structure-based protein–ligand interaction fingerprints for binding affinity prediction

Open-Source Machine Learning in Computational Chemistry


Climate indices for drought monitoring

A quantitative evaluation of the issue of drought definition: a source of disagreement in future drought assessments

Effects of dry spells on soil moisture and yield anomalies at a montane managed grassland site: A lysimeter climate experiment

Projected changes in synoptic circulations over Europe and their implications for summer precipitation: A CMIP6 perspective

Drought dynamics in the East European Plain for the period 1980-2018


This repository hosts the tracker for issues pertaining to GO annotations.

The Gene Ontology Resource: 20 years and still GOing strong

A GO catalogue of human DNA-binding transcription factors

Categorizing Sequences of Concern by Function To Better Assess Mechanisms of Microbial Pathogenesis


Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins

PrimeDesign software for rapid and simplified design of prime editing guide RNAs

A Cas9 with PAM recognition for adenine dinucleotides

Ex vivo prime editing of patient haematopoietic stem cells rescues sickle-cell disease phenotypes after engraftment in mice

Designing and executing prime editing experiments in mammalian cells

Zenodo (CERN European Organization for Nuclear Research)

A humanized knockin mouse model of Duchenne muscular dystrophy and its correction by CRISPR-Cas9 therapeutic gene editing

Development of a Self-Restricting CRISPR-Cas9 System to Reduce Off-Target Effects

Molecular therapy. Methods & clinical development

Correction of a urea cycle defect after ex vivo gene editing of human hepatocytes

Molecular therapy : the journal of the American Society of Gene Therapy

Rora Regulates Neutrophil Migration and Activation in Zebrafish

PAM-Flexible Genome Editing with an Engineered Chimeric Cas9


Force-directed graph layout using velocity Verlet integration.

A Deep Generative Model for Graph Layout

IEEE transactions on visualization and computer graphics

FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis

The Role of Hub Neurons in Modulating Cortical Dynamics

Comparative Evaluation of Bipartite, Node-Link, and Matrix-Based Network Representations

CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic

Quantitative Comparison of Statistical Methods for Analyzing Human Metabolomics Data

Is embodied interaction beneficial? A study on navigating network visualizations

DiVA: A Scalable, Interactive and Customizable Visual Analytics Platform for Information Diffusion on Large Networks

Graph visualization of dark web hyperlinks and their feature analysis

International Journal of Networking and Computing

Grounding force-directed network layouts with latent space models


Port of OpenAI's Whisper model in C/C++

Robust Speech Recognition via Large-Scale Weak Supervision

DungeonMaker: Embedding Tangible Creation and Destruction in Hybrid Board Games through Personal Fabrication Technology

Proceedings of the CHI Conference on Human Factors in Computing Systems

Real-Time Multimodal Cognitive Assistant for Emergency Medical Services


Home of the dionaea honeypot

A Survey of Honeypots and Honeynets for Internet of Things, Industrial Internet of Things, and Cyber-Physical Systems

Prevalence of IoT Protocols in Telescopeand Honeypot Measurements

PHOENI2X – A European Cyber Resilience Framework With Artificial-Intelligence-Assisted Orchestration, Automation & Response Capabilities for Business Continuity and Recovery, Incident Response, and Information Exchange

What are Attackers after on IoT Devices? An approach based on a multi-phased multi-faceted IoT honeypot ecosystem and data clustering

Honeypot Implementation in a Cloud Environment

HoneyGPT: Breaking the Trilemma in Terminal Honeypots with Large Language Model

URSID: Using formalism to Refine attack Scenarios for vulnerable Infrastructure Deployment


Entity Linker solution

Scalable Zero-shot Entity Linking with Dense Entity Retrieval

Neural Entity Linking: A Survey of Models Based on Deep Learning

Efficient One-Pass End-to-End Entity Linking for Questions

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

KILM: Knowledge Injection into Encoder-Decoder Language Models

How can voting mechanisms improve the robustness and generalizability of toponym disambiguation?

TempEL: Linking Dynamically Evolving and Newly Emerging Entities

Reveal the Unknown: Out-of-Knowledge-Base Mention Discovery with Entity Linking

TABi: Type-Aware Bi-Encoders for Open-Domain Entity Retrieval

A Transformational Biencoder with In-Domain Negative Sampling for Zero-Shot Entity Linking

Findings of the Association for Computational Linguistics: ACL 2022


Next-generation radio interferometric imaging.

Sparse Image Reconstruction for the SPIDER Optical Interferometric Telescope

PHOTOPTICS: PROCEEDINGS OF THE 9TH INTERNATIONAL CONFERENCE ON PHOTONICS, OPTICS AND LASER TECHNOLOGY

Distributed and parallel sparse convex optimization for radio interferometry with PURIFY

w-Stacking w-projection hybrid algorithm for wide-field interferometric imaging: implementation details and improvements

Publications of the Astronomical Society of Australia

Scalable Bayesian uncertainty quantification with data-driven priors for radio interferometric imaging

Load balancing for distributed interferometric image reconstruction


Meteorology Simulator

Parameters for PITRI Precipitation Temporal Disaggregation over continental US, Mexico, and southern Canada, 1981-2013

On the Sensitivity of Future Hydrology in the Colorado River to the Selection of the Precipitation Partitioning Method


Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments

Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life

Distribution and Implications of Haloarchaeal Plasmids Disseminated in Self-Encoded Plasmid Vesicles


General purpose unsupervised sentence representations

SemEval-2017 Task 1: Semantic Textual Similarity Multilingual and Crosslingual Focused Evaluation

Meeting of the Association for Computational Linguistics

Unsupervised Learning of Sentence Embeddings using Compositional n-Gram Features

North American Chapter of the Association for Computational Linguistics

Simple Unsupervised Keyphrase Extraction using Sentence Embeddings

Boosting Neural Machine Translation with Similar Translations

Improving Neural Conversational Models with Entropy-Based Data Filtering

Transfer Learning and Sentence Level Features for Named Entity Recognition on Tweets

Empirical Methods in Natural Language Processing

Better Word Embeddings by Disentangling Contextual n-Gram Information

Obtaining Better Static Word Embeddings Using Contextual Embedding Models

KFU NLP Team at SMM4H 2019 Tasks: Want to Extract Adverse Drugs Reactions from Tweets? BERT to The Rescue

SOCIAL MEDIA MINING FOR HEALTH APPLICATIONS (#SMM4H) WORKSHOP & SHARED TASK

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


Automated 3D cell detection in very large images

A deep learning algorithm for 3D cell detection in whole mouse brain image datasets

Multisensory coding of angular head velocity in the retrosplenial cortex

Brain-wide analysis of the supraspinal connectome reveals anatomical correlates to functional recovery after spinal injury

The retrosplenial cortex combines internal and external cues to encode head velocity during navigation


[vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium

Peptide–MHC Class I Tetramers Can Fail To Detect Relevant Functional T Cell Clonotypes and Underestimate Antigen-Reactive T Cell Populations

Inferring the T cell repertoire dynamics of healthy individuals

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

Predicting recognition between T cell receptors and epitopes using contextualized motifs

Mtb HLA-E tetramer sorted CD8+ T-cells have a diverse TCR repertoire


Tools for processing 2P recordings

Suite2p: beyond 10,000 neurons with standard two-photon microscopy

Negative feedback control of neuronal activity by microglia

Accurate quantification of astrocyte and neurotransmitter fluorescence dynamics for single-cell and population-level physiology

Robustness of Spike Deconvolution for Neuronal Calcium Imaging

The Journal of neuroscience : the official journal of the Society for Neuroscience

Two-photon calcium imaging of the medial prefrontal cortex and hippocampus without cortical invasion

HNCcorr: A Novel Combinatorial Approach for Cell Identification in Calcium-Imaging Movies

Arousal regulates frequency tuning in primary auditory cortex

Behaviorally relevant decision coding in primary somatosensory cortex neurons

Neural signatures of auditory hypersensitivity following acoustic trauma

Robustness of spike deconvolution for calcium imaging of neural spiking


R functions to perform and display Google Trends queries

Real Time Influenza Monitoring Using Hospital Big Data in Combination with Machine Learning Methods: Comparison Study (Preprint)

Calibration of Google Trends Time Series

International Conference on Information and Knowledge Management

Using web search queries to monitor influenza-like illness: an exploratory retrospective analysis, Netherlands, 2017/18 influenza season

Monitoring of cherry flowering phenology with Google Trends

Impact of the Coronavirus Disease on Micronutrient Search Trends and Interest in Global Population: A Worldwide Google Trend Analysis

PREPRINT: Using digital epidemiology methods to monitor influenza-like illness in the Netherlands in real-time: the 2017-2018 season

Predicting Day-Ahead Stock Returns using Search Engine Query Volumes: An Application of Gradient Boosted Decision Trees to the S&P 100


Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic

FAIR Data Point: A FAIR-Oriented Approach for Metadata Publication

The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data

Towards FAIR protocols and workflows: The OpenPREDICT case study


A list of all named GANs!

Image Segmentation Using Deep Learning: A Survey

A Review on Generative Adversarial Networks: Algorithms, Theory, and Applications

PacGAN: The power of two samples in generative adversarial networks

Biometrics recognition using deep learning: a survey

CapsuleGAN: Generative Adversarial Capsule Network

Deep learning in electron microscopy

Machine Learning: Science and Technology

Adversarial Training in Affective Computing and Sentiment Analysis: Recent Advances and Perspectives

Semi-Supervised Learning for Seismic Impedance Inversion Using Generative Adversarial Networks

Applications of Generative Adversarial Networks in Anomaly Detection: A Systematic Literature Review

Dialectical GAN for SAR Image Translation: From Sentinel-1 to TerraSAR-X


Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

Molecular and functional variation in iPSC-derived sensory neurons

LeafCutter: annotation-free quantification of RNA splicing

Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci

High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report

Implications of Antigen Selection on T Cell-Based Immunotherapy

Integrative Proteogenomics for Differential Expression and Splicing Variation in a DM1 Mouse Model


腾讯高性能分布式图计算框架Plato

Graph Neural Networks: A Review of Methods and Applications

Nebula Graph: An open source distributed graph database

A Distributed Multi-GPU System for Large-Scale Node Embedding at Tencent

A Systematic Review of Deep Graph Neural Networks: Challenges, Classification, Architectures, Applications & Potential Utility in Bioinformatics

WindGP: Efficient Graph Partitioning on Heterogenous Machines


Developed to power Conveyal's web-based interface for scenario planning and land-use/transport accessibility analysis, R5 is our routing engine for multimodal (transit/bike/walk/car) networks with a particular focus on public transit

Travel times and transfers in public transport: Comprehensive accessibility analysis based on Pareto-optimal journeys

Computers, Environment and Urban Systems

BEAM: The Modeling Framework for Behavior, Energy, Autonomy & Mobility

Half-(head)way there: Comparing two methods to account for public transport waiting time in accessibility indicators

Environment and Planning B: Urban Analytics and City Science


Unofficial Parallel WaveGAN (+ MelGAN & Multi-band MelGAN & HiFi-GAN & StyleMelGAN) with Pytorch

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

WaveGrad: Estimating Gradients for Waveform Generation

A Survey on Neural Speech Synthesis

Recent Developments on ESPnet Toolkit Boosted by Conformer

Voice Transformer Network: Sequence-to-Sequence Voice Conversion Using Transformer with Text-to-Speech Pretraining

WaveFake: A Data Set to Facilitate Audio Deepfake Detection

iSTFTNet: Fast and Lightweight Mel-Spectrogram Vocoder Incorporating Inverse Short-Time Fourier Transform

Audiodec: An Open-Source Streaming High-Fidelity Neural Audio Codec

IEEE International Conference on Acoustics, Speech, and Signal Processing

Emotion Intensity and its Control for Emotional Voice Conversion

IEEE Transactions on Affective Computing

The 2020 ESPnet Update: New Features, Broadened Applications, Performance Improvements, and Future Plans


Example RISC-V Out-of-Order/Superscalar Processor Performance Core and MSS Model


a truly censorship-resistant alternative to Twitter that has a chance of working

Bluesky and the AT Protocol: Usable Decentralized Social Media

Exploring the Nostr Ecosystem: A Study of Decentralization and
  Resilience


Text-Prompted Generative Audio Model

Neural Codec Language Models are Zero-Shot Text to Speech Synthesizers

AudioLM: a Language Modeling Approach to Audio Generation

A review of deep learning techniques for speech processing

InternGPT: Solving Vision-Centric Tasks by Interacting with ChatGPT Beyond Language

BASE TTS: Lessons from building a billion-parameter Text-to-Speech model
  on 100K hours of data

WavJourney: Compositional Audio Creation with Large Language Models

The VoicePrivacy 2024 Challenge Evaluation Plan

From Discrete Tokens to High-Fidelity Audio Using Multi-Band Diffusion

Speaker anonymization using neural audio codec language models

Vec-Tok Speech: speech vectorization and tokenization for neural speech generation


FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

Fast and accurate de novo genome assembly from long uncorrected reads

Phased diploid genome assembly with single-molecule real-time sequencing

Multi-platform discovery of haplotype-resolved structural variation in human genomes

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm

De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities

Chromosome conformation capture resolved near complete genome assembly of broomcorn millet

The chromosome-level wintersweet (Chimonanthus praecox) genome provides insights into floral scent biosynthesis and flowering in winter


Differentiable ODE solvers with full GPU support and O(1)-memory backpropagation.

Neural Ordinary Differential Equations

Latent ODEs for Irregularly-Sampled Time Series

Augmented Neural ODEs

Score-based Generative Modeling in Latent Space

Neural Controlled Differential Equations for Irregular Time Series

On Neural Differential Equations

Voicebox: Text-Guided Multilingual Universal Speech Generation at Scale

On Robustness of Neural Ordinary Differential Equations

Augmenting physical models with deep networks for complex dynamics forecasting

Neural SDEs as Infinite-Dimensional GANs


an imagenet example in torch.

OverFeat: Integrated Recognition, Localization and Detection using Convolutional Networks

Learning Deep Representations of Fine-grained Visual Descriptions

Parametric Exponential Linear Unit for Deep Convolutional Neural Networks

Comparative Study of Deep Learning Software Frameworks

PowerAI DDL

Efficient Training of Convolutional Neural Nets on Large Distributed Systems


ETNA – Time-Series Library

DeepAR: Probabilistic Forecasting with Autoregressive Recurrent Networks

Temporal Fusion Transformers for Interpretable Multi-horizon Time Series Forecasting

N-BEATS: Neural basis expansion analysis for interpretable time series forecasting

A Time Series is Worth 64 Words: Long-term Forecasting with Transformers

Deep State Space Models for Time Series Forecasting


cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

Raincloud plots: a multi-platform tool for robust data visualization

DeepC: predicting 3D genome folding using megabase-scale transfer learning

NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform

No Evidence That Frontal Eye Field tDCS Affects Latency or Accuracy of Prosaccades

Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints

The Distribution and Spread of Susceptible and Resistant Neisseria gonorrhoeae Across Demographic Groups in a Major Metropolitan Center

Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

Screening and Identification of Potential Biomarkers in Hepatitis B Virus-Related Hepatocellular Carcinoma by Bioinformatics Analysis

Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions


Survival analysis built on top of scikit-learn

An Efficient Training Algorithm for Kernel Survival Support Vector Machines

Novel artificial intelligence machine learning approaches to precisely predict survival and site-specific recurrence in cervical cancer: A multi-institutional study

Neural Fine-Gray: Monotonic neural networks for competing risks


Text-to-3D & Image-to-3D & Mesh Exportation with NeRF + Diffusion.

DreamFusion: Text-to-3D using 2D Diffusion

ProlificDreamer: High-Fidelity and Diverse Text-to-3D Generation with Variational Score Distillation

Score Jacobian Chaining: Lifting Pretrained 2D Diffusion Models for 3D Generation

DreamGaussian: Generative Gaussian Splatting for Efficient 3D Content Creation

Latent-NeRF for Shape-Guided Generation of 3D Shapes and Textures

Magic123: One Image to High-Quality 3D Object Generation Using Both 2D and 3D Diffusion Priors

RealFusion 360° Reconstruction of Any Object from a Single Image

Objaverse-XL: A Universe of 10M+ 3D Objects

DreamAvatar: Text-and-Shape Guided 3D Human Avatar Generation via Diffusion Models

Scalable 3D Captioning with Pretrained Models


Julia package to run Dynamic Power System simulations. Part of the Scalable Integrated Infrastructure Planning Initiative at the National Renewable Energy Lab.

Revisiting Power Systems Time-domain Simulation Methods and Models

PowerDynamics.jl—An experimentally validated open-source package for the dynamical analysis of power grids

PowerSimulationsDynamics.jl -- An Open Source Modeling Package for Modern Power Systems with Inverter-Based Resources


RNA Velocity generalized through dynamical modeling

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

Targeted pharmacological therapy restores β-cell function for diabetes remission

Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice

Regionally distinct trophoblast regulate barrier function and invasion in the human placenta

A transcriptional cross species map of pancreatic islet cells

Pax6 limits the competence of developing cerebral cortical cells to respond to inductive intercellular signals

Endothelial versus pronephron fate decision is modulated by the transcription factors Cloche/Npas4l, Tal1, and Lmo2

Calcium-dependent transcriptional changes in human pancreatic islet cells reveal functional diversity in islet cell subtypes (Retracted article. See AUG, 2023)

Fusion-negative rhabdomyosarcoma 3D organoids to predict effective drug combinations: A proof-of-concept on cell death inducers

Single-cell trajectory analysis reveals a CD9 positive state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug-resistant states


TRAM is an open-source platform designed to advance research into automating the mapping of cyber threat intelligence reports to MITRE ATT&CK®.

Cybersecurity Threat Hunting and Vulnerability Analysis Using a Neo4j Graph Database of Open Source Intelligence

TTPXHunter: Actionable Threat Intelligence Extraction as TTPs from Finished Cyber Threat Reports

APT-MMF: An advanced persistent threat actor attribution method based on multimodal and multilevel feature fusion

Semantic Ranking for Automated Adversarial Technique Annotation in
  Security Text


DARPA Challenges Sets for Linux, Windows, and macOS

NEUZZ: Efficient Fuzzing with Neural Program Smoothing

Magma: A Ground-Truth Fuzzing Benchmark

Proceedings of the ACM on Measurement and Analysis of Computing Systems

Adaptive Grey-Box Fuzz-Testing with Thompson Sampling

Proceedings of the 11th ACM Workshop on Artificial Intelligence and Security

Improving Grey-Box Fuzzing by Modeling Program Behavior

Evolutionary Mutation-based Fuzzing as Monte Carlo Tree Search

Top of the Heap: Efficient Memory Error Protection for Many Heap Objects


TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data

T cell fate and clonality inference from single-cell transcriptomes

T Cell Receptor Profiling in Type 1 Diabetes

Revealing Clonal Responses of Tumor-Reactive T-Cells Through T Cell Receptor Repertoire Analysis

Opposing immune and genetic forces shape oncogenic programs in synovial sarcoma


IEA Task 43: pre-construction energy estimate data standard repository


Elegant parsing in Java and Scala - lightweight, easy-to-use, powerful.

Syntax error recovery in parsing expression grammars

Automatic Syntax Error Reporting and Recovery in Parsing Expression Grammars


On the Tool Manipulation Capability of Open-source Large Language Models

Use of LLMs for Illicit Purposes: Threats, Prevention Measures, and Vulnerabilities

Comprehensive Assessment of Jailbreak Attacks Against LLMs

Breaking Down the Defenses: A Comparative Survey of Attacks on Large
  Language Models


DNS Tunneling: A Deep Learning based Lexicographical Detection Approach

Identifying DNS-tunneled traffic with predictive models

A Study of Newly Observed Hostnames and DNS Tunneling in the Wild

DNS tunneling Detection Using Elasticsearch

IOP Conference Series: Materials Science and Engineering

A Lightweight Adaptable DNS Channel for Covert Data Transmission


Creative Commons Attribution Share Alike 4.0 International

This book will be an undergraduate textbook written in the univalent style, taking advantage of the presence of symmetry in the logic at an early stage.

Synthetic fibered (∞,1)-category theory

On Small Types in Univalent Foundations

Central H-spaces and banded types

Eilenberg-MacLane spaces and stabilisation in homotopy type theory

On symmetries of spheres in univalent foundations

Delooping cyclic groups with lens spaces in homotopy type theory

Limits and exponentiable functors in simplicial homotopy type theory

Delooping generated groups in homotopy type theory

Domain Theory in Constructive and Predicative Univalent Foundations


Finding duplicate images made easy!

Searching for MobileNetV3

DataComp: In search of the next generation of multimodal datasets

The Privacy Onion Effect: Memorization is Relative

No "Zero-Shot" Without Exponential Data: Pretraining Concept Frequency
  Determines Multimodal Model Performance

Perfusion Quantification from Endoscopic Videos: Learning to Read Tumor Signatures

Privacy Side Channels in Machine Learning Systems

Students Parrot Their Teachers: Membership Inference on Model Distillation

CE-Dedup: Cost-Effective Convolutional Neural Nets Training based on Image Deduplication

Placental Vessel Segmentation and Registration in Fetoscopy: Literature Review and MICCAI FetReg2021 Challenge Findings

DiffusionLight: Light Probes for Free by Painting a Chrome Ball


Pool-based active learning in Python

modAL: A modular active learning framework for Python

libact: Pool-based Active Learning in Python

Goldilocks: Just-Right Tuning of BERT for Technology-Assisted Review

Heuristic Stopping Rules For Technology-Assisted Review

Proceedings of the 21st ACM Symposium on Document Engineering

A Lagrangian Duality Approach to Active Learning

Active Feature Selection for the Mutual Information Criterion

TARexp: A Python Framework for Technology-Assisted Review Experiments

Proceedings of the 45th International ACM SIGIR Conference on Research and Development in Information Retrieval

TAR on Social Media: A Framework for Online Content Moderation

Re-Benchmarking Pool-Based Active Learning for Binary Classification

A Reproducibility Study of Goldilocks: Just-Right Tuning of BERT for TAR


fastFM: A Library for Factorization Machines

Content-aware Neural Hashing for Cold-start Recommendation

PROCEEDINGS OF THE 43RD INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL (SIGIR '20)

HitFraud: A Broad Learning Approach for Collective Fraud Detection in Heterogeneous Information Networks

Modeling Game Avatar Synergy and Opposition through Embedding in Multiplayer Online Battle Arena Games


Toolkit for working with RADIANCE for the ray-trace modeling of Bifacial Photovoltaics

The 2020 photovoltaic technologies roadmap

Validation of Bifacial Photovoltaic Simulation Software against Monitoring Data from Large-Scale Single-Axis Trackers and Fixed Tilt Systems in Denmark


Line based ATR Engine based on OCRopy

Optical character recognition with neural networks and post-correction with finite state methods

International Journal on Document Analysis and Recognition (IJDAR)

Comparison of OCR Accuracy on Early Printed Books using the Open Source Engines Calamari and OCRopus

Journal for Language Technology and Computational Linguistics

FAWA: Fast Adversarial Watermark Attack on Optical Character Recognition (OCR) Systems

How Much Data Do You Need? About the Creation of a Ground Truth for Black Letter and the Effectiveness of Neural OCR

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

Mixed Model OCR Training on Historical Latin Script for Out-of-the-Box Recognition and Finetuning

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

On the Accuracy of CRNNs for Line-Based OCR: A Multi-Parameter Evaluation

Proceedings of the 5th International Workshop on Reading Music Systems


phy: interactive visualization and manual spike sorting of large-scale ephys data

Single-trial neural dynamics are dominated by richly varied movements

Distributed coding of choice, action and engagement across the mouse brain

Cortical pattern generation during dexterous movement is input-driven

The neurons that restore walking after paralysis

Chronically-implanted Neuropixels probes enable high yield recordings in freely moving mice

Sensory coding and the causal impact of mouse cortex in a visual decision

Bidirectional perisomatic inhibitory plasticity of a Fos neuronal network

The sifting of visual information in the superior colliculus

An increase of inhibition drives the developmental decorrelation of neural activity

Cerebellar involvement in an evidence-accumulation decision-making task


Dynamic analysis framework for JavaScript

Towards Runtime Monitoring of Node.js and Its Application to the Internet of Things

Gelato: Feedback-driven and Guided Security Analysis of Client-side Web Applications

Automatic Root Cause Quantification for Missing Edges in JavaScript Call Graphs (Extended Version)


Dense Passage Retriever - is a set of tools and models for open domain Q&A task.

Dense Passage Retrieval for Open-Domain Question Answering

Approximate Nearest Neighbor Negative Contrastive Learning for Dense Text Retrieval

Retrieval-Augmented Generation for Large Language Models: A Survey

ColBERTv2: Effective and Efficient Retrieval via Lightweight Late Interaction

Generate rather than Retrieve: Large Language Models are Strong Context Generators

MKQA: A Linguistically Diverse Benchmark for Multilingual Open Domain Question Answering

Knowledge Guided Text Retrieval and Reading for Open Domain Question Answering

Relevance-guided Supervision for OpenQA with ColBERT

End-to-End Training of Neural Retrievers for Open-Domain Question Answering

On the Risk of Misinformation Pollution with Large Language Models


ANTARES Visualizations


Cutadapt removes adapter sequences from sequencing reads

Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer

RNA stores tau reversibly in complex coacervates

Supermeres are functional extracellular nanoparticles replete with disease biomarkers and therapeutic targets

The Implication of Early Chromatin Changes in X Chromosome Inactivation

The CASC15 Long Intergenic Noncoding RNA Locus Is Involved in Melanoma Progression and Phenotype Switching

The Journal of investigative dermatology

Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies

miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy

A simple guide to de novo transcriptome assembly and annotation

Reprogramming the antigen specificity of B cells using genome-editing technologies

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


Multi-layer Recurrent Neural Networks (LSTM, GRU, RNN) for character-level language models in Torch

Generating Sequences With Recurrent Neural Networks

AdaComp : Adaptive Residual Gradient Compression for Data-Parallel Distributed Training

Music transcription modelling and composition using deep learning

SYSTRAN's Pure Neural Machine Translation Systems

Recurrent Neural Networks Hardware Implementation on FPGA

Teaching Arithmetic to Small Transformers

Deep Learning at Scale and at Ease

Optimizing seed inputs in fuzzing with machine learning

Confidence through Attention

Learning to Capitalize with Character-Level Recurrent Neural Networks: An Empirical Study

Empirical Methods in Natural Language Processing


Python Blob Detector and Source Finder

Unveiling the rarest morphologies of the LOFAR Two-metre Sky Survey radio source population with self-organised maps

CHANG-ES XII: A LOFAR and VLA view of the edge-on star-forming galaxy NGC 3556

The eROSITA Final Equatorial-Depth Survey (eFEDS): LOFAR view of brightest cluster galaxies and AGN feedback

Astronomy and Astrophysics - Deep LOFAR 150 MHz imaging of the Boötes field: Unveiling the faint low-frequency sky

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

HAL (Le Centre pour la Communication Scientifique Directe)

Evolutionary Map of the Universe (EMU): A pilot search for diffuse, non-thermal radio emission in galaxy clusters with the Australian SKA Pathfinder

Radio source-component association for the LOFAR Two-metre Sky Survey with region-based convolutional neural networks

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

The contribution of non-central radio galaxies to AGN feedback in rich galaxy clusters

Monthly Notices of the Royal Astronomical Society

A search for intercluster filaments with LOFAR and eROSITA


Code for building ConceptNet from raw data.

KG-BART: Knowledge Graph-Augmented BART for Generative Commonsense Reasoning

Augmenting End-to-End Dialog Systems with Commonsense Knowledge

EVALution 1.0: an Evolving Semantic Dataset for Training and Evaluation of Distributional Semantic Models

Proceedings of the 4th Workshop on Linked Data in Linguistics: Resources and Applications

CSKG: The CommonSense Knowledge Graph

Dimensions of Commonsense Knowledge

Assessing Demographic Bias in Named Entity Recognition

Neuro-Symbolic Procedural Planning with Commonsense Prompting

Mutual-Enhanced Incongruity Learning Network for Multi-Modal Sarcasm Detection

THIRTY-SEVENTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, VOL 37 NO 8

KACE: Generating Knowledge Aware Contrastive Explanations for Natural Language Inference

Meeting of the Association for Computational Linguistics

What's Missing: A Knowledge Gap Guided Approach for Multi-hop Question Answering


An instance of KG Hub to produce a knowledge graph for COVID-19 response.

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response

CODO: An Ontology for Collection and Analysis of Covid-19 Data

PROCEEDINGS OF THE 12TH INTERNATIONAL JOINT CONFERENCE ON KNOWLEDGE DISCOVERY, KNOWLEDGE ENGINEERING AND KNOWLEDGE MANAGEMENT (KEOD), VOL 2

Covid-on-the-Web: Knowledge Graph and Services to Advance COVID-19 Research

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Healthcare Knowledge Graph Construction: State-of-the-art, open issues, and opportunities

Towards an ML-based semantic IoT for pandemic management: A survey of enabling technologies for COVID-19

Biomedical Knowledge Graph Refinement with Embedding and Logic Rules

An open source knowledge graph ecosystem for the life sciences

KG-Hub -- Building and Exchanging Biological Knowledge Graphs

Does tetanus vaccination contribute to reduced severity of the COVID-19 infection?


GPU-based Onion Hash generator

Classifying Illegal Activities on Tor Network Based on Web Textual Contents

Conference of the European Chapter of the Association for Computational Linguistics

Identifying and characterizing Sybils in the Tor network

How Do Tor Users Interact With Onion Services?

Anomalous keys in Tor relays


Library for Digital Pathology Image Processing

HistoCartography: A Toolkit for Graph Analytics in Digital Pathology

Development and Validation of a Machine Learning Model for Detection and Classification of Tertiary Lymphoid Structures in Gastrointestinal Cancers

AI slipping on tiles: data leakage in digital pathology

Quantification of the Immune Content in Neuroblastoma: Deep Learning and Topological Data Analysis in Digital Pathology

International journal of molecular sciences

Development and interpretation of a pathomics-driven ensemble model for predicting the response to immunotherapy in gastric cancer

Interpretable histopathology-based prediction of disease relevant features in Inflammatory Bowel Disease biopsies using weakly-supervised deep learning


A Python framework for performing information retrieval experiments, building on http://terrier.org/

Declarative Experimentation in Information Retrieval using PyTerrier

International Conference on the Theory of Information Retrieval

Dense Text Retrieval Based on Pretrained Language Models: A Survey

Deep Reinforced Query Reformulation for Information Retrieval

Overview of the TREC 2022 NeuCLIR Track

A Survey on Asking Clarification Questions Datasets in Conversational Systems


Run LLMs at home, BitTorrent-style. Fine-tuning and inference up to 10x faster than offloading

Challenges and Applications of Large Language Models

Petals: Collaborative Inference and Fine-tuning of Large Models

Understanding LLMs: A Comprehensive Overview from Training to Inference

Distributed Inference and Fine-tuning of Large Language Models Over The Internet

The Ultimate Guide to Fine-Tuning LLMs from Basics to Breakthroughs: An Exhaustive Review of Technologies, Research, Best Practices, Applied Research Challenges and Opportunities


Open-source evaluation toolkit of large vision-language models (LVLMs), support 160+ VLMs, 50+ benchmarks

MMBench: Is Your Multi-modal Model an All-around Player?

SEED-Bench-2: Benchmarking Multimodal Large Language Models

When Do We Not Need Larger Vision Models?

VLMEvalKit: An Open-Source Toolkit for Evaluating Large Multi-Modality
  Models

xGen-MM (BLIP-3): A Family of Open Large Multimodal Models

MINT-1T: Scaling Open-Source Multimodal Data by 10x: A Multimodal
  Dataset with One Trillion Tokens

SEED-Bench-2-Plus: Benchmarking Multimodal Large Language Models with
  Text-Rich Visual Comprehension

MMBench-Video: A Long-Form Multi-Shot Benchmark for Holistic Video Understanding

GMAI-MMBench: A Comprehensive Multimodal Evaluation Benchmark Towards
  General Medical AI

Rethinking Overlooked Aspects in Vision-Language Models


pyKT: A Python Library to Benchmark Deep Learning based Knowledge Tracing Models

Enhancing Deep Knowledge Tracing with Auxiliary Tasks

simpleKT: A Simple But Tough-to-Beat Baseline for Knowledge Tracing

Towards Robust Knowledge Tracing Models via k-Sparse Attention

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


The Push programming language and the PushGP genetic programming system implemented in Clojure.

Problem-solving benefits of down-sampled lexicase selection

Lexicase Selection of Specialists

Comparing and Combining Lexicase Selection and Novelty Search

Lexicase Selection at Scale

Proceedings of the Genetic and Evolutionary Computation Conference Companion

Stochastic synthesis of recursive functions made easy with bananas, lenses, envelopes and barbed wire

Genetic Programming and Evolvable Machines

Population Diversity Leads to Short Running Times of Lexicase Selection

Optimizing LLVM Pass Sequences with Shackleton: A Linear Genetic Programming Framework


Tool for robust segmentation of >100 important anatomical structures in CT and MR images

A large annotated medical image dataset for the development and evaluation of segmentation algorithms

SegVol: Universal and Interactive Volumetric Medical Image Segmentation

SA-Med2D-20M Dataset: Segment Anything in 2D Medical Imaging with 20 Million masks

TotalSegmentator MRI: Sequence-Independent Segmentation of 59 Anatomical Structures in MR images

Segmentation of 71 Anatomical Structures Necessary for the Evaluation of Guideline-Conforming Clinical Target Volumes in Head and Neck Cancers

LNQ Challenge 2023: Learning Mediastinal Lymph Node Segmentation with a Probabilistic Lymph Node Atlas


cluster data collected from production clusters in Alibaba for cluster management research

Learning Scheduling Algorithms for Data Processing Clusters

TPP: Transparent Page Placement for CXL-Enabled Tiered-Memory

SoCC - Wukong: a scalable and locality-enhanced framework for serverless parallel computing

From Cloud to Edge: A First Look at Public Edge Platforms

esDNN: Deep Neural Network Based Multivariate Workload Prediction in Cloud Computing Environments

Characterizing Co-located Datacenter Workloads: An Alibaba Case Study

Tailored Learning-Based Scheduling for Kubernetes-Oriented Edge-Cloud System

Adaptive Prediction Models for Data Center Resources Utilization Estimation

IEEE Transactions on Network and Service Management

ThermoSim: Deep learning based framework for modeling and simulation of thermal-aware resource management for cloud computing environments

In Search of a Fast and Efficient Serverless DAG Engine


Gives criticality score for an open source project

An Empirical Study on the Use of Static Analysis Tools in Open Source Embedded Software

Towards a Critical Open-Source Software Database

Lessons from the Long Tail: Analysing Unsafe Dependency Updates across Software Ecosystems


microbiome R package

The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia

microViz: an R package for microbiome data visualization and statistics

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls

Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar

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

Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3)

Transport to the Slaughterhouse Affects the Salmonella Shedding and Modifies the Fecal Microbiota of Finishing Pigs

Animals : an open access journal from MDPI

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study

High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community

Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells in vitro


PyTorch implementation of adversarial attacks [torchattacks]

Torchattacks: A PyTorch Repository for Adversarial Attacks

WaveCNet: Wavelet Integrated CNNs to Suppress Aliasing Effect for Noise-Robust Image Classification

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

Scattering Model Guided Adversarial Examples for SAR Target Recognition: Attack and Defense

A Unified Wasserstein Distributional Robustness Framework for Adversarial Training

Indicators of Attack Failure: Debugging and Improving Optimization of Adversarial Examples

Minimum Noticeable Difference-Based Adversarial Privacy Preserving Image Generation

Probing the Purview of Neural Networks via Gradient Analysis

Comparing the Robustness of Modern No-Reference Image- and Video-Quality Metrics to Adversarial Attacks

Perturbation Towards Easy Samples Improves Targeted Adversarial Transferability

Delving into Deep Image Prior for Adversarial Defense: A Novel Reconstruction-based Defense Framework


Hydrological modeling


Extensible specification for representing and uniquely identifying biological sequence variation

GA4GH: International policies and standards for data sharing across genomic research and healthcare

The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

Development and application of a computable genotype model in the GA4GH Variation Representation Specification


:round_pushpin: Repel overlapping text labels away from each other in your ggplot2 figures.

QKI is a critical pre-mRNA alternative splicing regulator of cardiac myofibrillogenesis and contractile function

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells

rigrag: high-resolution mapping of genic targeting preferences during HIV-1 integration in vitro and in vivo

Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions

Sex-Specific Relationship between the Cardiorespiratory Fitness and Plasma Metabolite Patterns in Healthy Humans—Results of the KarMeN Study

Power of inclusion: Enhancing polygenic prediction with admixed individuals

Genetic Diversity and Pedigree Analysis of Red Currant Germplasm

Transient acetaldehyde production by SO2-producing Saccharomyces cerevisiae promotes the survival of Oenococcus oeni during co-fermentation

Between Raetia Secunda and the dutchy of Bavaria: Exploring patterns of human movement and diet


Collaborative editing in any app

Real Differences between OT and CRDT in Correctness and Complexity for Consistency Maintenance in Co-Editors

Proceedings of the ACM on Human-Computer Interaction

Real Differences between OT and CRDT under a General Transformation Framework for Consistency Maintenance in Co-Editors

Real Differences between OT and CRDT in Building Co-Editing Systems and Real World Applications

Real Differences between OT and CRDT for Co-Editors


GA4GH Variation Representation Python Implementation

The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

Development and application of a computable genotype model in the GA4GH Variation Representation Specification


Antimicrobial Resistance Identification By Assembly

Rapid Methods for Antimicrobial Resistance Diagnostics

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

Comparison of classical multi-locus sequence typing software for next-generation sequencing data

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

Genome plasticity favours double chromosomal Tn4401b-blaKPC-2 transposon insertion in the Pseudomonas aeruginosa ST235 clone

Genome-Based Analysis of Enterococcus faecium Bacteremia Associated with Recurrent and Mixed-Strain Infection

Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory

Epidemiological and Molecular Characterization of an Invasive Group A Streptococcus emm32.2 Outbreak

First Report and Comparative Genomics Analysis of a blaOXA-244-Harboring Escherichia coli Isolate Recovered in the American Continent

Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance


This repository contains the source code for the paper First Order Motion Model for Image Animation

Motion Representations for Articulated Animation

Long Video Generation with Time-Agnostic VQGAN and Time-Sensitive Transformer

Generating Videos with Dynamics-aware Implicit Generative Adversarial Networks

StyleInV: A Temporal Style Modulated Inversion Network for Unconditional Video Generation

Compressing Video Calls using Synthetic Talking Heads

NARRATE: A Normal Assisted Free-View Portrait Stylizer

DF40: Toward Next-Generation Deepfake Detection

Improved First-Order Motion Model of Image Animation with Enhanced Dense Motion and Repair Ability

PriorityCut: Occlusion-guided Regularization for Warp-based Image Animation


Neural machine translation and sequence learning using TensorFlow

Self-Attention with Relative Position Representations

Semantic Neural Machine Translation using AMR

Transactions of the Association for Computational Linguistics

Boosting Neural Machine Translation with Similar Translations

Guided Alignment Training for Topic-Aware Neural Machine Translation

Towards Automating Code Review Activities

Contextual Handling in Neural Machine Translation: Look Behind, Ahead and on Both Sides

European Association for Machine Translation Conferences/Workshops

Transfer Learning in Multilingual Neural Machine Translation with Dynamic Vocabulary

Multilingual Neural Machine Translation for Zero-Resource Languages

Revisiting Multi-Domain Machine Translation

Zenodo (CERN European Organization for Nuclear Research)

OpenNMT System Description for WNMT 2018: 800 words/sec on a single-core CPU

NEURAL MACHINE TRANSLATION AND GENERATION


Diem’s mission is to build a trusted and innovative financial network that empowers people and businesses around the world.

BFT Protocol Forensics

How do programmers use unsafe rust?

Proceedings of the ACM on Programming Languages

Bottlenecks in Blockchain Consensus Protocols

Memory-Safety Challenge Considered Solved? An In-Depth Study with All Rust CVEs

Block-STM: Scaling Blockchain Execution by Turning Ordering Curse to a Performance Blessing

Characterizing EOSIO Blockchain

Twins: BFT Systems Made Robust

Strengthened Fault Tolerance in Byzantine Fault Tolerant Replication

On Exploiting Transaction Concurrency To Speed Up Blockchains

BigBFT: A Multileader Byzantine Fault Tolerance Protocol for High Throughput


Accelerated BLAST compatible local sequence aligner.

Altered gut microbial profile is associated with abnormal metabolism activity of Autism Spectrum Disorder

Depletion of acetate-producing bacteria from the gut microbiota facilitates cognitive impairment through the gut-brain neural mechanism in diabetic mice

Structural and Functional Annotation of Eukaryotic Genomes with GenSAS

Methods in molecular biology (Clifton, N.J.)

A simple guide to de novo transcriptome assembly and annotation

A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism

Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese

Residual chlorine disrupts the microbial communities and spreads antibiotic resistance in freshwater

SARS-like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

Carbapenemases on the move: it’s good to be on ICEs

A pilot exploration of multi-omics research of gut microbiome in major depressive disorders


Astropy package for region handling

astroquery: An Astronomical Web-Querying Package in Python

SRG/eROSITA and XMM-Newton observations of Vela Jr

Searching for X-ray counterparts of degree-wide TeV halos around middle-aged pulsars with SRG/eROSITA

G189.6+03.3: The first complete X-ray view provided by SRG/eROSITA

S 308 and other X-ray emitting bubbles around Wolf-Rayet stars


Creative Commons Attribution 4.0 International

The consensus GEM for Saccharomyces cerevisiae

De novo biosynthesis of rubusoside and rebaudiosides in engineered yeasts

Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast

Genome-scale modeling of yeast metabolism: retrospectives and perspectives

Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production

Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity

Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model

standard-GEM: standardization of open-source genome-scale metabolic models

Author Correction: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models

Saccharomyces cerevisiae as a Host for Chondroitin Production


CodeXGLUE

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

No more fine-tuning? an experimental evaluation of prompt tuning in code intelligence

Proceedings of the 30th ACM Joint European Software Engineering Conference and Symposium on the Foundations of Software Engineering

ReGVD: Revisiting Graph Neural Networks for Vulnerability Detection

NatGen: Generative pre-training by "Naturalizing" source code

CoSQA: 20,000+ Web Queries for Code Search and Question Answering

Multilingual training for Software Engineering

ReCode: Robustness Evaluation of Code Generation Models

StructCoder: Structure-Aware Transformer for Code Generation

Memorization and Generalization in Neural Code Intelligence Models

ERNIE-Code: Beyond English-Centric Cross-lingual Pretraining for Programming Languages


An open-source implementation of the AlphaGoZero algorithm

Mastering Chess and Shogi by Self-Play with a General Reinforcement Learning Algorithm

Accelerating Self-Play Learning in Go

Explain Your Move: Understanding Agent Actions Using Focused Feature Saliency


PV Analysis Tools in Python

Robust PV Degradation Methodology and Application

OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)

Validation of the PVLife model using 3 million module-years of live site data

Quantifying Soiling Loss Directly From PV Yield

PV degradation methodology comparison — A basis for a standard

Signal Processing on PV Time-Series Data: Robust Degradation Analysis Without Physical Models

Review of open source tools for PV modeling

Performance Comparison of Clipping Detection Techniques in AC Power Time Series

Overcoming Communications Outages in Inverter Downtime Analysis


Coq is a formal proof management system. It provides a formal language to write mathematical definitions, executable algorithms and theorems together with an environment for semi-interactive development of machine-checked proofs.

Coq Coq correct! verification of type checking and erasure for Coq, in Coq

QED at Large: A Survey of Engineering of Formally Verified Software

Foundations and Trends® in Programming Languages

Mtac2: typed tactics for backward reasoning in Coq

The Marriage of Univalence and Parametricity

Beyond Notations: Hygienic Macro Expansion for Theorem Proving Languages

LL(1) Parsing with Derivatives and Zippers

Validating Mathematical Structures

Complete Bidirectional Typing for the Calculus of Inductive Constructions

Computable analysis and notions of continuity in Coq

The Trusted Computing Base of the CompCert Verified Compiler


Autograd automatically differentiates native Torch code

Automatic differentiation in machine learning: a survey

Theano: A Python framework for fast computation of mathematical expressions

AutoGraph: Imperative-style Coding with Graph-based Performance

Perturbation confusion in forward automatic differentiation of higher-order functions


Eukaryotic Genome Annotation Pipeline

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

bioRxiv : the preprint server for biology

Malassezia vespertilionis sp. nov.: a new cold-tolerant species of yeast isolated from bats

Persoonia - Molecular Phylogeny and Evolution of Fungi

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats

Raphidocelis subcapitata (=Pseudokirchneriella subcapitata) provides an insight into genome evolution and environmental adaptations in the Sphaeropleales

De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust

Characterization of Aspergillus niger Isolated from the International Space Station

Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure

Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris


A platform for collecting and disseminating data for the Sustainable Development Goal global indicators.


(Formerly Solium) Code quality & Security Linter for Solidity

Assessing Smart Contracts Security Technical Debts

Continuous and Secure Integration Framework for Smart Contracts

Static Application Security Testing (SAST) Tools for Smart Contracts: How Far Are We?


A Python Library for Self Organizing Map (SOM)

Machine Learning in Astronomy: a practical overview

Co-occurrence of Fe and P stress in natural populations of the marine diazotroph Trichodesmium

PS1-STRM: neural network source classification and photometric redshift catalogue for PS1 3π DR1

Monthly Notices of the Royal Astronomical Society

Horizon-AGN virtual observatory -- 2: Template-free estimates of galaxy
  properties from colours

Data-Driven Design: Exploring new Structural Forms using Machine Learning and Graphic Statics

Circulation patterns in the Gulf of Finland from daily to seasonal timescales

Tellus A: Dynamic Meteorology and Oceanography

Extracting Frequent Sequential Patterns of Forest Landscape Dynamics in Fenhe River Basin, Northern China, from Landsat Time Series to Evaluate Landscape Stability

SuSi: Supervised Self-Organizing Maps for Regression and Classification in Python

Assessment of Astronomical Images Using Combined Machine-learning Models

An Unsupervised Data-Driven Model to Classify Gait Patterns in Children with Cerebral Palsy


COSMIC (Compact Object Synthesis and Monte Carlo Investigation Code)

COSMIC Variance in Binary Population Synthesis

A Census of Blue Stragglers in Gaia DR2 Open Clusters as a Test of Population Synthesis and Mass Transfer Physics

Observational signatures of the black hole mass distribution in the galactic center

Journal of Cosmology and Astroparticle Physics

Detectability of gravitational waves from a population of inspiralling black holes in Milky Way-mass galaxies

Monthly notices of the Royal Astronomical Society

Understanding the progenitor formation galaxies of merging binary black holes

Mapping progenitors of binary black holes and neutron stars with binary population synthesis


Main development repository for TinyOS (an OS for embedded, wireless devices).

A Beaconless Asymmetric Energy-Efficient Time Synchronization Scheme for Resource-Constrained Multi-Hop Wireless Sensor Networks

Towards Touch-to-Access Device Authentication Using Induced Body Electric Potentials

MOBICOM'19: PROCEEDINGS OF THE 25TH ANNUAL INTERNATIONAL CONFERENCE ON MOBILE COMPUTING AND NETWORKING

A Comprehensive Study on LPWANs With a Focus on the Potential of LoRa/LoRaWAN Systems

IEEE Communications Surveys and Tutorials

Performance Analysis of Time Synchronization Protocols in Wireless Sensor Networks

D-Box: DMA-enabled Compartmentalization for Embedded Applications

Proceedings 2022 Network and Distributed System Security Symposium

Link quality estimation for arbitrary packet sizes over wireless links using packet reception events

International Journal of Communication Systems

Design Considerations for Low Power Internet Protocols

A protocol architecture for energy efficient and pervasive eHealth systems

IEEE-EMBS International Conference on Biomedical and Health Informatics

Development and Validation of an ISA100.11a Simulation Model for Accurate Industrial WSN Planning and Deployment

Clock Skew Compensation Algorithm Immune to Floating-Point Precision Loss


Rapid fuzzy string matching in Python using various string metrics

MELHISSA: a multilingual entity linking architecture for historical press articles

Zenodo (CERN European Organization for Nuclear Research)

ARQMath Lab: An Incubator for Semantic Formula Search in zbMATH Open?

BELB: a Biomedical Entity Linking Benchmark

Towards Automated Accessibility Report Generation for Mobile Apps

Train & Constrain: Phonologically Informed Tongue-Twister Generation
  from Topics and Paraphrases

KGrEaT: A Framework to Evaluate Knowledge Graphs via Downstream Tasks

Twenty-four years of empirical research on trust in AI: a bibliometric review of trends, overlooked issues, and future directions

BELHD: improving biomedical entity linking with homonym disambiguation


Time series Timeseries Deep Learning Machine Learning Python Pytorch  fastai | State-of-the-art Deep Learning library  for Time Series and Sequences in Pytorch / fastai

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

Time Series Classification from Scratch with Deep Neural Networks: A Strong Baseline

LSTM Fully Convolutional Networks for Time Series Classification

InceptionTime: Finding AlexNet for time series classification

Multivariate LSTM-FCNs for Time Series Classification

Neural networks : the official journal of the International Neural Network Society

A Transformer-based Framework for Multivariate Time Series Representation Learning

A Time Series is Worth 64 Words: Long-term Forecasting with Transformers

ROCKET: exceptionally fast and accurate time series classification using random convolutional kernels

TabTransformer: Tabular Data Modeling Using Contextual Embeddings

MiniRocket: A Very Fast (Almost) Deterministic Transform for Time Series Classification


Matlab toolbox for Geometry Processing.

Orientation-boosted Voxel Nets for 3D Object Recognition

ZoomOut: Spectral Upsampling for Efficient Shape Correspondence

Globally Consistent Normal Orientation for Point Clouds by Regularizing the Winding-Number Field

Global rigid registration of CT to video in laparoscopic liver surgery

International Journal of Computer Assisted Radiology and Surgery

Designing Volumetric Truss Structures

Information decomposition of multichannel EMG to map functional interactions in the distributed motor system

A Smoothness Energy without Boundary Distortion for Curved Surfaces

Complementary dynamics

Wavelet-based Heat Kernel Derivatives: Towards Informative Localized Shape Analysis

Non-Isometric Shape Matching via Functional Maps on Landmark-Adapted Bases


enviroCar Android Application


Qbsolv,a decomposing solver, finds a minimum value of a large quadratic unconstrained binary optimization (QUBO) problem by splitting it into pieces solved either via a D-Wave system or a classical tabu solver.   (Note that qbsolv by default uses its internal classical solver.  Access to a D-Wave system must be arranged separately.)

Traffic flow optimization using a quantum annealer

Graph Partitioning using Quantum Annealing on the D-Wave System

A Hybrid Solution Method for the Capacitated Vehicle Routing Problem Using a Quantum Annealer

Open source software in quantum computing

A Tutorial on Formulating and Using QUBO Models

Nonnegative/Binary matrix factorization with a D-Wave quantum annealer

Prime factorization algorithm based on parameter optimization of Ising model

Calculation of molecular vibrational spectra on a quantum annealer

Journal of chemical theory and computation

Towards Prediction of Financial Crashes with a D-Wave Quantum Computer

Hybrid quantum annealing via molecular dynamics


Scientist friendly Python toolbox for processing 2D satellite Earth observation data.

Operational algorithm for ice–water classification on dual-polarized RADARSAT-2 images

Sea ice cover in Isfjorden and Hornsund, Svalbard (2000–2014) from remote sensing data

Open-source feature-tracking algorithm for sea ice drift retrieval from Sentinel-1 SAR imagery

Nansat: a Scientist-Orientated Python Package for Geospatial Data Processing

Sea ice drift from Sentinel-1 SAR imagery using open source feature tracking


A high-performance topological machine learning toolbox in Python

giotto-tda: A Topological Data Analysis Toolkit for Machine Learning and Data Exploration.

On the stability of persistent entropy and new summary functions for topological data analysis

Learning Hyperbolic Representations of Topological Features

Topic Modeling With Topological Data Analysis

Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing

Topological Methods in Machine Learning: A Tutorial for Practitioners

Homological Time Series Analysis of Sensor Signals from Power Plants


A tool for light curve extraction from the TESS FFIs.

eleanor: An Open-source Tool for Extracting Light Curves from the TESS Full-frame Images

Publications of the Astronomical Society of the Pacific

The μ Tau Association: A 60 Myr Old Coeval Group at 150 pc from the Sun

A search for young exoplanets in Sectors 1-5 of the TESS full-frame images

TOI-3984 A b and TOI-5293 A b: Two Temperate Gas Giants Transiting Mid-M Dwarfs in Wide Binary Systems

TFAW survey - I. Wavelet-based denoising of K2 light curves. Discovery and validation of two new Earth-sized planets in K2 campaign 1

Detection and characterization of planets orbiting oscillating red-giant stars with NASA's TESS mission

A Comparative Study of TESS Light-curve Extraction Methods Applied to Blazars


Graph-based alignment (Hierarchical Graph FM index)

Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes

The transcriptional reprograming and functional identification of WRKY family members in pepper’s response to Phytophthora capsici infection

Vargas: heuristic-free alignment for assessing linear and graph read aligners

In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales

Differences in Leaf Morphology and Related Gene Expression between Diploid and Tetraploid Birch (Betula pendula)

International journal of molecular sciences

Unveiling inflammatory and prehypertrophic cell populations as key contributors to knee cartilage degeneration in osteoarthritis using multi-omics data integration

Blastospores from Metarhizium anisopliae and Metarhizium rileyi Are Not Always as Virulent as Conidia Are towards Spodoptera frugiperda Caterpillars and Use Different Infection Mechanisms

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plantNepenthes gracilis

Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation

Whole-Genome Sequence of Entomortierella parvispora E1425, a Mucoromycotan Fungus Associated with Burkholderiaceae-Related Endosymbiotic Bacteria


Specification documents for the P4Runtime control-plane API

The Programmable Data Plane: Abstractions, Architectures, Algorithms, and Applications

QuIP: A P4 Quantum Internet Protocol Prototyping Framework

IEEE Journal on Selected Areas in Communications

P4R-Type: A Verified API for P4 Control Plane Programs

Proceedings of the ACM on Programming Languages


Bergen Layered Ocean Model

Ocean biogeochemistry in the Norwegian Earth System Model version 2 (NorESM2)


Agent Learning Framework https://alf.readthedocs.io

Hierarchical Reinforcement Learning By Discovering Intrinsic Options

Learning to Synthesize Programs as Interpretable and Generalizable Policies

TAAC: Temporally Abstract Actor-Critic for Continuous Control

Mutual Information-based State-Control for Intrinsically Motivated Reinforcement Learning


:memo: A text file containing 479k English words for all your dictionary/word-based projects e.g: auto-completion / autosuggestion

Calculated avoidance: Math anxiety predicts math avoidance in effort-based decision-making

Fast and general density peaks clustering

Controllable Open-ended Question Generation with A New Question Type Ontology

Practical Volume-Based Attacks on Encrypted Databases

Preparing Bengali-English Code-Mixed Corpus for Sentiment Analysis of Indian Languages

Named Entity Recognition and Hashtag Decomposition to Improve the Classification of Tweets

International Conference on Computational Linguistics

Differentially Private Histograms in the Shuffle Model from Fake Users

Selecting Seed Words for Wordle using Character Statistics

Analyzing the Quality of Twitter Data Streams

Information systems frontiers : a journal of research and innovation

Fast and Exact Outlier Detection in Metric Spaces: A Proximity Graph-based Approach


Wide Neural Networks of Any Depth Evolve as Linear Models Under Gradient Descent

Scientific Machine Learning through Physics-Informed Neural Networks: Where we are and What's next

Neural Tangents: Fast and Easy Infinite Neural Networks in Python

Provably efficient machine learning for quantum many-body problems

The large learning rate phase of deep learning: the catapult mechanism

Dataset Distillation with Infinitely Wide Convolutional Networks

Explaining Neural Scaling Laws

Infinite attention: NNGP and NTK for deep attention networks

Bayesian Deep Ensembles via the Neural Tangent Kernel

Stable ResNet


Astronomy and astrophysics core library

The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package

SWE-bench: Can Language Models Resolve Real-World GitHub Issues?

Python Leap Second Management and Implementation of Precise Barycentric Correction (barycorrpy)

Hypothesis: A new approach to property-based testing

On the Detection of Exomoons Transiting Isolated Planetary-mass Objects

Prediction and Verification of Parker Solar Probe Solar Wind Sources at 13.3 R_⊙

CodeR: Issue Resolving with Multi-Agent and Task Graphs

CSST forecast: impact from non-Gaussian covariances and requirements on systematics-control

Fast Period Searches Using the Lomb-Scargle Algorithm on Graphics Processing Units for Large Datasets and Real-Time Applications

A Dataset for Learning University STEM Courses at Scale and Generating Questions at a Human Level

Proceedings of the AAAI Conference on Artificial Intelligence


Extensible, Efficient Quantum Algorithm Design for Humans.

Variational quantum eigensolver with fewer qubits

Solving quantum statistical mechanics with variational autoregressive networks and quantum circuits

Secure quantum computing for healthcare sector: A short analysis

Tensor Network Circuit Simulation at Exascale

QAOA.jl: Toolkit for the Quantum and Mean-Field Approximate Optimization Algorithms


Image augmentation for machine learning experiments.

Albumentations: fast and flexible image augmentations

AutoML: A survey of the state-of-the-art

The ApolloScape Open Dataset for Autonomous Driving and Its Application

IEEE transactions on pattern analysis and machine intelligence

DeepPoseKit, a software toolkit for fast and robust animal pose estimation using 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

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

Domain Randomization and Pyramid Consistency: Simulation-to-Real Generalization without Accessing Target Domain Data

SLEAP: A deep learning system for multi-animal pose tracking

Scenic: a language for scenario specification and scene generation

Programming Language Design and Implementation

Cross-domain Face Presentation Attack Detection via Multi-domain Disentangled Representation Learning


Brave's Rust-based adblock engine

Who Funds Misinformation? A Systematic Analysis of the Ad-related Profit Routines of Fake News Sites

Blocked or Broken? Automatically Detecting When Privacy Interventions Break Websites


A Python nearest neighbor descent for approximate nearest neighbors

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

A General Framework For Detecting Anomalous Inputs to DNN Classifiers

LANNS: A Web-Scale Approximate Nearest Neighbor Lookup System

K-Nearest Neighbor Approximation Via the Friend-of-a-Friend Principle

TopoAct: Exploring the Shape of Activations in Deep Learning

Empirical complexity of comparator-based nearest neighbor descent

An Efficient Content-based Time Series Retrieval System

A Survey on Efficient Processing of Similarity Queries over Neural Embeddings

Fast Single-Core K-Nearest Neighbor Graph Computation

CEnt: An Entropy-based Model-agnostic Explainability Framework to Contrast Classifiers' Decisions


Official home of genome aligner based upon notion of Cactus graphs

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Cactus: Algorithms for genome multiple sequence alignment

A comparative genomics multitool for scientific discovery and conservation

HAL: a hierarchical format for storing and analyzing multiple genome alignments

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

Cactus Graphs for Genome Comparisons

Research in Computational Molecular Biology

Sequence tube maps: making graph genomes intuitive to commuters

A paternal bias in germline mutation is widespread in amniotes and can arise independently of cell division numbers

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

SegAlign: A Scalable GPU-Based Whole Genome Aligner

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


Provides analysis for the MPAS components of E3SM

Statistical Generation of Ocean Forcing With Spatiotemporal Variability for Ice Sheet Models


Solar thermal power/fuel station performance simulation and optimisation using Modelica. Read a paper about our project: https://is.gd/solth


PyTorch implementation of Advantage Actor Critic (A2C), Proximal Policy Optimization (PPO), Scalable trust-region method for deep reinforcement learning using Kronecker-factored approximation (ACKTR) and Generative Adversarial Imitation Learning (GAIL).

Proximal Policy Optimization Algorithms

Reward Constrained Policy Optimization

Character Controllers Using Motion VAEs

Embodied Intelligence via Learning and Evolution

Automatic Data Augmentation for Generalization in Deep Reinforcement Learning

Decentralized Structural-RNN for Robot Crowd Navigation with Deep Reinforcement Learning

An Exploration of Embodied Visual Exploration

Why Generalization in RL is Difficult: Epistemic POMDPs and Implicit Partial Observability

Evolving Curricula with Regret-Based Environment Design

Evolution Gym: A Large-Scale Benchmark for Evolving Soft Robots


a lightweight db framework for exploring genetic variation.

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy

Genomic analysis of a spinal muscular atrophy (SMA) discordant family identifies a novel mutation in TLL2, an activator of growth differentiation factor 8 (myostatin): a case report

A flexible computational pipeline for research analyses of unsolved clinical exome cases


A small speech recognizer

Preech: A System for Privacy-Preserving Speech Transcription

Prϵϵch: A System for Privacy-Preserving Speech Transcription

PROCEEDINGS OF THE 29TH USENIX SECURITY SYMPOSIUM

VGPN: Voice-Guided Pointing Robot Navigation for Humans

NUVA: A Naming Utterance Verifier for Aphasia Treatment

Challenges of Artificial Intelligence -- From Machine Learning and Computer Vision to Emotional Intelligence

ASTER: Automatic Speech Recognition System Accessibility Testing for Stutterers


Java time series machine learning tools in a Weka compatible toolkit

The great multivariate time series classification bake off: a review and experimental evaluation of recent algorithmic advances

The Canonical Interval Forest (CIF) Classifier for Time Series Classification

Scalable Dictionary Classifiers for Time Series Classification

The Temporal Dictionary Ensemble (TDE) Classifier for Time Series Classification

MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2020, PT I

A tale of two toolkits, report the third: on the usage and performance of HIVE-COTE v1.0.

A Review and Evaluation of Elastic Distance Functions for Time Series Clustering

Monash University, UEA, UCR Time Series Extrinsic Regression Archive

The FreshPRINCE: A Simple Transformation Based Pipeline Time Series Classifier

A tale of two toolkits, report the first: benchmarking time series classification algorithms for correctness and efficiency

Forecasting with sktime: Designing sktime's New Forecasting API and Applying It to Replicate and Extend the M4 Study


Objax is a machine learning framework that provides an Object Oriented layer for JAX.

Opacus: User-Friendly Differential Privacy Library in PyTorch

AdaMatch: A Unified Approach to Semi-Supervised Learning and Domain Adaptation

Equinox: neural networks in JAX via callable PyTrees and filtered transformations

Handcrafted Backdoors in Deep Neural Networks

FedJAX: Federated learning simulation with JAX

An Attack on InstaHide: Is Private Learning Possible with Instance Encoding?

GPJax: A Gaussian Process Framework in JAX

Reconciling AI Performance and Data Reconstruction Resilience for Medical Imaging

Dynamic Online Ensembles of Basis Expansions


4 bits quantization of LLaMA using GPTQ

LLaMA: Open and Efficient Foundation Language Models

A Survey of Large Language Models

GPTQ: Accurate Post-Training Quantization for Generative Pre-trained Transformers

The case for 4-bit precision: k-bit Inference Scaling Laws

Compressing LLMs: The Truth is Rarely Pure and Never Simple

Do Emergent Abilities Exist in Quantized Large Language Models: An Empirical Study

EfficientQAT: Efficient Quantization-Aware Training for Large Language
  Models

EasyQuant: An Efficient Data-free Quantization Algorithm for LLMs


Implementations of recent research prototypes/demonstrations using MONAI.

UNETR: Transformers for 3D Medical Image Segmentation

Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images

Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis

UNetFormer: A Unified Vision Transformer Model and Pre-Training Framework for 3D Medical Image Segmentation

SwinUNETR-V2: Stronger Swin Transformers with Stagewise Convolutions for 3D Medical Image Segmentation

MEDICAL IMAGE COMPUTING AND COMPUTER ASSISTED INTERVENTION, MICCAI 2023, PT IV

Attention-based CT scan interpolation for lesion segmentation of colorectal liver metastases

Medical Imaging 2023: Biomedical Applications in Molecular, Structural, and Functional Imaging

Building Universal Foundation Models for Medical Image Analysis with Spatially Adaptive Networks


Semantics of C in K

Exploring C semantics and pointer provenance

Understanding GCC Builtins to Develop Better Tools

Deductive Verification of Programs with Underspecified Semantics by Model Extraction.

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


Multi-language suite for high-performance solvers of differential equations and scientific machine learning (SciML) components. Ordinary differential equations (ODEs), stochastic differential equations (SDEs), delay differential equations (DDEs), differential-algebraic equations (DAEs), and more in Julia.

Universal Differential Equations for Scientific Machine Learning

On Neural Differential Equations

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

An examination of school reopening strategies during the SARS-CoV-2 pandemic

medRxiv : the preprint server for health sciences

Bifurcation Analysis of Bogdanov-Takens Bifurcations in Delay Differential Equations

D-ꞵ-hydroxybutyrate stabilizes hippocampal CA3-CA1 circuit during acute insulin resistance

bioRxiv : the preprint server for biology


A python library for decision tree visualization and model interpretation.

Customized Monte Carlo Tree Search for LLVM/Polly's Composable Loop Optimization Transformations

Explainable AI for engineering design: A unified approach of systems engineering and component-based deep learning

Clinical decision support tool for breast cancer recurrence prediction using SHAP value in cooperative game theory

SHARCS: Shared Concept Space for Explainable Multimodal Learning

From exemplar to copy: the scribal appropriation of a Hadewijch manuscript computationally explored

Identification of Pediatric Bacterial Gastroenteritis From Blood Counts and Interviews Based on Machine Learning

Strategizing University Rank Improvement using Interpretable Machine Learning and Data Visualization


Brain Dynamics Programming in Python

BrainPy: a flexible, integrative, efficient, and extensible framework towards general-purpose brain dynamics programming

A Just-In-Time Compilation Approach for Neural Dynamics Simulation

A differentiable brain simulator bridging brain simulation and brain-inspired computing

A Differentiable Approach to Multi-scale Brain Modeling


The Visualization Multitool for Molecular Epidemiology and Bioinformatics

MicrobeTrace: Retooling molecular epidemiology for rapid public health response

Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis

Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters

The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002–2020)

Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study

Molecular Epidemiology of the HIV-1 Subtype B Sub-Epidemic in Bulgaria

HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations

High Genetic Diversity of HIV-1 and Active Transmission Clusters among Male-to-Male Sexual Contacts (MMSCs) in Zhuhai, China


MII makes low-latency and high-throughput inference possible, powered by DeepSpeed.

A Survey of Large Language Models

DeepSpeed- Inference: Enabling Efficient Inference of Transformer Models at Unprecedented Scale

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

DeepSpeed-FastGen: High-throughput Text Generation for LLMs via MII and DeepSpeed-Inference

LoongServe: Efficiently Serving Long-context Large Language Models with
  Elastic Sequence Parallelism

Applications of Large Scale Foundation Models for Autonomous Driving

A Survey of Time Series Foundation Models: Generalizing Time Series
  Representation with Large Language Model

Fiddler: CPU-GPU Orchestration for Fast Inference of Mixture-of-Experts
  Models

Enabling Efficient Batch Serving for LMaaS via Generation Length
  Prediction

Slice-Level Scheduling for High Throughput and Load Balanced LLM Serving


Python package for studying large scale structure, cosmology, and galaxy evolution using N-body simulations and halo models

Introducing decorated HODs: modelling assembly bias in the galaxy–halo connection

Monthly Notices of the Royal Astronomical Society

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: N-body mock challenge for galaxy clustering measurements

Generating synthetic cosmological data with GalSampler

The Outer Stellar Mass of Massive Galaxies: A Simple Tracer of Halo Mass with Scatter Comparable to Richness and Reduced Projection Effects

A Short Research Note on Calculating Exact Distribution Functions and Random Sampling for the 3D NFW Profile

An Empirical Model For Intrinsic Alignments: Insights From Cosmological Simulations