A list projects to make emergency ventilators in response to COVID-19, focusing on free-libre open source

Low-tech solutions for the COVID19 supply chain crisis

Partially RepRapable automated open source bag valve mask-based ventilator

How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles

Can Open Source Hardware Mechanical Ventilator (OSH-MVs) initiatives help cope with the COVID-19 health crisis? Taxonomy and state of the art

Emergency Blower-Based Ventilator with Novel-Designed Ventilation Sensor and Actuator

Overcoming supply disruptions during pandemics by utilizing found hardware for open source gentle ventilation

Open ventilator evaluation framework: A synthesized database of regulatory requirements and technical standards for emergency use ventilators from Australia, Canada, UK, and US

Frugal Innovation: Enabling Mechanical Ventilation During Coronavirus Disease 2019 Pandemic in Resource-Limited Settings

The HEV Ventilator.

Evidence-Based Considerations for the Design of an Open-Source Ventilator: A Systematic Review


semantic similarity framework for knowledge graph

A survey of ontology learning techniques and applications

Database : the journal of biological databases and curation

Semantic similarity and machine learning with ontologies

Sematch: Semantic Entity Search from Knowledge Graph

A Comparison of Document Similarity Algorithms


Large-scale, multi-GPU capable, kernel solver

Kernel methods through the roof: handling billions of points efficiently

Efficient Hyperparameter Tuning for Large Scale Kernel Ridge Regression

Neural Tangent Kernel: A Survey

Fast Region Proposal Learning for Object Detection for Robotics

Ada-BKB: Scalable Gaussian Process Optimization on Continuous Domains by Adaptive Discretization

Triggerless data acquisition pipeline for Machine Learning based statistical anomaly detection


LexNLP by LexPredict

LexNLP: Natural language processing and information extraction for legal and regulatory texts

Extracting Outcomes from Appellate Decisions in US State Courts

eyecite: A tool for parsing legal citations

The Case for a Linked Data Research Engine for Legal Scholars

CaseGNN: Graph Neural Networks for Legal Case Retrieval with Text-Attributed Graphs


Differential expression analysis for single-cell RNA-seq data.

Emerging Roles of Airway Epithelial Cells in Idiopathic Pulmonary Fibrosis

Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b‐mediated chromatin demethylation

Single cell RNA sequencing reveals distinct clusters of Irf8-expressing pulmonary conventional dendritic cells

Lineage Commitment of Dermal Fibroblast Progenitors is Mediated by Chromatin De-repression.

bioRxiv : the preprint server for biology

Immunogenomic profile at baseline predicts host susceptibility to clinical malaria


A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage

A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system

A high-quality reference genome of wild Cannabis sativa

Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm

High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy

A chromosome-level genome assembly for the beet armyworm (Spodoptera exigua) using PacBio and Hi-C sequencing

Systematic Comparison of the Performances of De Novo Genome Assemblers for Oxford Nanopore Technology Reads From Piroplasm

Frontiers in cellular and infection microbiology

A High-quality Draft Genome Assembly of Sinella curviseta: A Soil Model Organism (Collembola)

The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes)

A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data


Next generation sequencing reads de novo assembler.

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)

Prevalence and Genetic Diversity of Listeria monocytogenes Isolated From Retail Pork in Wuhan, China

Molecular Characteristics of Brucella Isolates Collected From Humans in Hainan Province, China

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Population Genomic Approaches for Weed Science

The Gut Microbiota Determines the High-Altitude Adaptability of Tibetan Wild Asses (Equus kiang) in Qinghai-Tibet Plateau

GAAP: A Genome Assembly + Annotation Pipeline

Development of Sequence-Tagged Site Marker Set for Identification of J, JS, and St Sub-genomes of Thinopyrum intermedium in Wheat Background

The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean


PyTorch implementation of VALL-E(Zero-Shot Text-To-Speech), Reproduced Demo https://lifeiteng.github.io/valle/index.html

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

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

CLaM-TTS: Improving Neural Codec Language Model for Zero-Shot
  Text-to-Speech

Fewer-Token Neural Speech Codec with Time-Invariant Codes

Acoustic BPE for Speech Generation with Discrete Tokens

Transduce and Speak: Neural Transducer for Text-to-Speech with Semantic Token Prediction

Speech Slytherin: Examining the Performance and Efficiency of Mamba for Speech Separation, Recognition, and Synthesis

TraceableSpeech: Towards Proactively Traceable Text-to-Speech with
  Watermarking

Codec Does Matter: Exploring the Semantic Shortcoming of Codec for Audio Language Model

Improving Language Model-Based Zero-Shot Text-to-Speech Synthesis with Multi-Scale Acoustic Prompts


OpenSTL: A Comprehensive Benchmark of Spatio-Temporal Predictive Learning

Convolutional LSTM Network: A Machine Learning Approach for Precipitation Nowcasting

PredRNN: Recurrent Neural Networks for Predictive Learning using Spatiotemporal LSTMs

Visual attention network

Memory In Memory: A Predictive Neural Network for Learning Higher-Order Non-Stationarity from Spatiotemporal Dynamics

PredRNN: A Recurrent Neural Network for Spatiotemporal Predictive Learning

Disentangling Physical Dynamics from Unknown Factors for Unsupervised Video Prediction

HorNet: Efficient High-Order Spatial Interactions with Recursive Gated Convolutions

SimVP: Simpler yet Better Video Prediction

Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning

Efficient Multi-order Gated Aggregation Network


Nvidia Semantic Segmentation monorepo

PointPainting: Sequential Fusion for 3D Object Detection

Hierarchical Multi-Scale Attention for Semantic Segmentation

Improving Semantic Segmentation via Video Propagation and Label Relaxation

DeepFusion: Lidar-Camera Deep Fusion for Multi-Modal 3D Object Detection

PandaSet: Advanced Sensor Suite Dataset for Autonomous Driving

SDCNet: Video Prediction Using Spatially-Displaced Convolution

SemSegMap – 3D Segment-based Semantic Localization

Simple and Efficient Architectures for Semantic Segmentation

Vision-based Large-scale 3D Semantic Mapping for Autonomous Driving Applications

Contour-Aware Equipotential Learning for Semantic Segmentation


A standardized Python API with necessary preprocessing, machine learning and explainability tools to facilitate graph-analytics in computational pathology.

Hierarchical Graph Representations in Digital Pathology

Quantifying Explainers of Graph Neural Networks in Computational Pathology

Learning Whole-Slide Segmentation from Inexact and Incomplete Labels using Tissue Graphs

HistoCartography: A Toolkit for Graph Analytics in Digital Pathology

Explainable AI for Bioinformatics: Methods, Tools, and Applications


Official codebase used to develop Vision Transformer, SigLIP, MLP-Mixer, LiT and more.

Scaling Vision Transformers

How to train your ViT? Data, Augmentation, and Regularization in Vision Transformers

PaLI: A Jointly-Scaled Multilingual Language-Image Model

LiT: Zero-Shot Transfer with Locked-image text Tuning

Sigmoid Loss for Language Image Pre-Training

Knowledge distillation: A good teacher is patient and consistent

Better plain ViT baselines for ImageNet-1k

FlexiViT: One Model for All Patch Sizes

UViM: A Unified Modeling Approach for Vision with Learned Guiding Codes

Image Captioners Are Scalable Vision Learners Too


Long read based human genomic structural variation detection with cuteSV

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

Long Read based Human Genomic Structural Variation Detection with cuteSV

Structural Variant Detection from Long-Read Sequencing Data with cuteSV.

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

Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology

Regenotyping structural variants through an accurate force-calling method

Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq


Seawater carbonate chemistry with R


For managing 2P imaging datasets from preprocessing to activity trace extraction

Hippocampal place codes are gated by behavioral engagement

Dopamine differentially modulates the size of projection neuron ensembles in the intact and dopamine-depleted striatum

Cognitive experience alters cortical involvement in goal-directed navigation

A cell-type-specific error-correction signal in the posterior parietal cortex

Scaling of information in large neural populations reveals signatures of information-limiting correlations

Cognitive experience alters cortical involvement in navigation decisions


A code for generating fake spectra from a cosmological simulation

Trident: A Universal Tool for Generating Synthetic Absorption Spectra from Astrophysical Simulations

An emulator for the Lyman-α forest

Journal of Cosmology and Astroparticle Physics

The Effect of AGN Heating on the Low-redshift Lyα Forest

An emulator for the Lyman-α forest in beyond-ΛCDM cosmologies

Massive neutrinos and degeneracies in Lyman-alpha forest simulations

Simulating the carbon footprint of galactic haloes

Monthly Notices of the Royal Astronomical Society

Characterizing Protoclusters and Protogroups at z ∼ 2.5 Using Lyα Tomography

The Low-redshift Lyα Forest as a Constraint for Models of AGN Feedback

A Multi-Fidelity Emulator for the Lyman-α Forest Flux Power Spectrum

A neural network emulator for the Lyman-α forest 1D flux power spectrum


Energy performance and Carbon emissions Assessment and Monitoring tool (Lluís Bosch, Lluís Corominas, IWA, Wacclim project, GIZ)


A bayesian pipeline for detecting stochastic backgrounds with LISA.

Cosmology with the Laser Interferometer Space Antenna

Mapping the gravitational-wave sky with LISA: a Bayesian spherical harmonic approach

Monthly notices of the Royal Astronomical Society

LISA Detectability of a Stochastic Gravitational Wave Background from Unresolved White Dwarf Binaries in the LMC


A modern Python utility library for climate data collection and management


R scripts for an indicator on long-term trends in groundwater levels in B.C. published on Environmental Reporting BC


RH 1.5D

On the generation of solar spicules and Alfvénic waves

Characterization and formation of on-disk spicules in the Ca II K and Mg II k spectral lines

Semi-empirical model atmospheres for the chromosphere of the sunspot penumbra and umbral flashes

Statistical Study of Chromospheric Evaporation in Impulsive Phase of Solar Flares

An optically thin view of the flaring chromosphere: non-thermal widths in a chromospheric condensation during an X-class solar flare

Understanding the Duration of Solar and Stellar Flares at Various Wavelengths


Repository for mini-projects in the Data science for Sustainable development project


Python client to interface with the NSF NOIRLab's Astro Data Lab Science Platform.

The Dark Energy Survey Data Release 2

The Astrophysical Journal Supplement Series

An empirical model of the Gaia DR3 selection function

Deep Synoptic Array Science: A Massive Elliptical Host Among Two Galaxy-cluster Fast Radio Bursts

Linking Extragalactic Transients and Their Host Galaxy Properties: Transient Sample, Multiwavelength Host Identification, and Database Construction

Jupyter-Enabled Astrophysical Analysis Using Data-Proximate Computing Platforms

Deep Drilling in the Time Domain with DECam: Survey Characterization


A C++/python library for source modeling in gamma astronomy

Gamma-Ray Flares in the Long-term Light Curve of 3C 454.3

Galactic gamma-ray and neutrino emission from interacting cosmic-ray nuclei

Multi wavelength study of 4C+28.07

Possible TeV Gamma-Ray Binary Origin of HESS J1828–099

Spectral Modeling of Flares in Long-term Gamma-Ray Light Curve of PKS 0903-57

Gamma-ray flares and broadband spectral study of PKS 0402-362

Hadronic re-acceleration at the Crab pulsar wind termination shock as a source of PeV gamma-rays

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

Exploring the Emission Mechanisms of Mrk 180 with Long-term X-Ray and γ-Ray Data


An Extendible (General) Continual Learning Framework based on Pytorch - official codebase of Dark Experience for General Continual Learning

Overcoming catastrophic forgetting in neural networks

Learning without Forgetting

iCaRL: Incremental Classifier and Representation Learning

Gradient Episodic Memory for Continual Learning

Continual Learning Through Synaptic Intelligence

Progressive Neural Networks

Efficient Lifelong Learning with A-GEM

Large Scale Incremental Learning

Learning a Unified Classifier Incrementally via Rebalancing

Gradient based sample selection for online continual learning


Code for the General Lake Model

A multi-lake comparative analysis of the General Lake Model (GLM): Stress-testing across a global observatory network

Differential Responses of Maximum Versus Median Chlorophyll-ato Air Temperature and Nutrient Loads in an Oligotrophic Lake Over 31 Years


A python package and a set of shell commands to handle GTF files

OLOGRAM: determining significance of total overlap length between genomic regions sets

Explore, edit and leverage genomic annotations using Python GTF toolkit

OLOGRAM-MODL: mining enriched n-wise combinations of genomic features with Monte Carlo and dictionary learning


Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109

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

Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling

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

Yet Another ICU Benchmark: A Flexible Multi-Center Framework for Clinical ML


Many-body dispersion library

Long-range dispersion-inclusive machine learning potentials for structure search and optimization of hybrid organic-inorganic interfaces

Ab Initio Evaluation of Henry Coefficients Using Importance Sampling

Journal of chemical theory and computation

libMBD: A general-purpose package for scalable quantum many-body dispersion calculations


BESST - scaffolder for genomic assemblies

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Assembly scaffolding with PE-contaminated mate-pair libraries

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools

Genome scaffolding with PE-contaminated mate-pair libraries


SIDH Library is a fast and portable software library that implements state-of-the-art supersingular isogeny cryptographic schemes. The chosen parameters aim to provide security against attackers running a large-scale quantum computer, and security against classical algorithms.

SIDH on ARM: Faster Modular Multiplications for Faster Post-Quantum Supersingular Isogeny Key Exchange

IACR Transactions on Cryptographic Hardware and Embedded Systems

Supersingular Curves You Can Trust

New Techniques for SIDH-based NIKE

Cold Boot Attacks on the Supersingular Isogeny Key Encapsulation (SIKE) Mechanism

Faulty isogenies: a new kind of leakage

An Alternative Approach for Computing Discrete Logarithms in Compressed SIDH.


HLS based Deep Neural Network Accelerator Library for Xilinx Ultrascale+ MPSoCs

A Survey of FPGA-Based Neural Network Accelerator

Best of Both Worlds: AutoML Codesign of a CNN and its Hardware Accelerator

EDD: Efficient Differentiable DNN Architecture and Implementation Co-search for Embedded AI Solutions

A Systematic Assessment of Embedded Neural Networks for Object Detection

IEEE International Conference on Emerging Technologies and Factory Automation

GPT4AIGChip: Towards Next-Generation AI Accelerator Design Automation via Large Language Models

Energy and Performance Trade-Off Optimization in Heterogeneous Computing via Reinforcement Learning

Dynamic Temperature Management of Near-Sensor Processing for Energy-Efficient High-Fidelity Imaging

Analysis and Optimization of I/O Cache Coherency Strategies for SoC-FPGA Device

CodeX: Bit-Flexible Encoding for Streaming-based FPGA Acceleration of DNNs

Effective Algorithm-Accelerator Co-design for AI Solutions on Edge Devices


Spatial Sparse Convolution Library

Superpoint Transformer for 3D Scene Instance Segmentation

D3Net: A Unified Speaker-Listener Architecture for 3D Dense Captioning and Visual Grounding

Green Hierarchical Vision Transformer for Masked Image Modeling

Robo3D: Towards Robust and Reliable 3D Perception against Corruptions

Towards Efficient 3D Object Detection with Knowledge Distillation

PonderV2: Pave the Way for 3D Foundation Model with A Universal Pre-training Paradigm

Deep Learning of Preconditioners for Conjugate Gradient Solvers in Urban Water Related Problems

MarS3D: A Plug-and-Play Motion-Aware Model for Semantic Segmentation on Multi-Scan 3D Point Clouds

StereoVoxelNet: Real-Time Obstacle Detection Based on Occupancy Voxels from a Stereo Camera Using Deep Neural Networks

TorchSparse++: Efficient Training and Inference Framework for Sparse Convolution on GPUs


A library for directly calling PyTorch ML models from Fortran.

Interpretable multiscale Machine Learning-Based Parameterizations of Convection for ICON


phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

Short-chain alkanes fuel mussel and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps

phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes

Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2

Sugars dominate the seagrass rhizosphere

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf

Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis

Microbial Diversity of Co-occurring Heterotrophs in Cultures of Marine Picocyanobacteria


Pyro models of SARS-CoV-2 variants

Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness

medRxiv : the preprint server for health sciences

Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection

Early warning of emerging infectious diseases based on multimodal data

Biophysical principles predict fitness of SARS-CoV-2 variants


TensorFlow code for the neural network presented in the paper: "code2vec: Learning Distributed Representations of Code"

Adversarial Examples for Models of Code

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

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

A Literature Study of Embeddings on Source Code

GraphCode2Vec: Generic Code Embedding via Lexical and Program Dependence Analyses

Testing Neural Program Analyzers

The Best of Both Worlds: Combining Learned Embeddings with Engineered Features for Accurate Prediction of Correct Patches

On using distributed representations of source code for the detection of C security vulnerabilities

A Source Code Similarity Based on Siamese Neural Network

Using Distributed Representation of Code for Bug Detection


A Java library for Paillier partially homomorphic encryption.

TimeCrypt: Encrypted Data Stream Processing at Scale with Cryptographic Access Control

Homomorphic-Encrypted Volume Rendering

IEEE transactions on visualization and computer graphics


Debugging, monitoring and visualization for Python Machine Learning and Data Science

DeepDiagnosis: Automatically Diagnosing Faults and Recommending Actionable Fixes in Deep Learning Programs

VizSeq: A Visual Analysis Toolkit for Text Generation Tasks

Empirical Methods in Natural Language Processing

A System for Real-Time Interactive Analysis of Deep Learning Training

PROCEEDINGS OF THE ACM SIGCHI SYMPOSIUM ON ENGINEERING INTERACTIVE COMPUTING SYSTEMS (EICS'19)


SAM with text prompt

Neural Parametric Gaussians for Monocular Non-Rigid Object Reconstruction

DreamEdit: Subject-driven Image Editing

SuFIA: Language-Guided Augmented Dexterity for Robotic Surgical
  Assistants

Compositional Text-to-Image Generation with Dense Blob Representations

RB-Modulation: Training-Free Personalization of Diffusion Models using
  Stochastic Optimal Control

Concept Weaver: Enabling Multi-Concept Fusion in Text-to-Image Models

Text-driven Affordance Learning from Egocentric Vision

Can Foundation Models Reliably Identify Spatial Hazards? A Case Study on
  Curb Segmentation


An R package for multivariate adaptive shrinkage.

Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus

A genome-wide multiphenotypic association analysis identified candidate genes and gene ontology shared by four common risky behaviors

The statistical practice of the GTEx Project: from single to multiple tissues


RAPPOR: Privacy-Preserving Reporting Algorithms

Practical Locally Private Heavy Hitters

Local Differential Privacy: a tutorial

ARA: Aggregated RAPPOR and Analysis for Centralized Differential Privacy

Local Differentially Private Fuzzy Counting in Stream Data Using Probabilistic Data Structures

IEEE Transactions on Knowledge and Data Engineering


The Bitcoin Fungibility Framework

Adoption and Actual Privacy of Decentralized CoinJoin Implementations in Bitcoin

Pinpointing and Measuring Wasabi and Samourai CoinJoins in the Bitcoin Ecosystem.

BaseSAP: Modular Stealth Address Protocol for Programmable Blockchains

Heuristics for Detecting CoinJoin Transactions on the Bitcoin Blockchain


A tool for exploring large trees in the browser

CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants

Taxonium, a web-based tool for exploring large phylogenetic trees

Identifying SARS-CoV-2 regional introductions and transmission clusters in real time

Tracking and curating putative SARS-CoV-2 recombinants with RIVET

Treenome Browser: co-visualization of enormous phylogenies and millions of genomes


Python implementation of Empirical Mode Decompoisition (EMD) method

The role of seasonality in the spread of COVID-19 pandemic

EMD: Empirical Mode Decomposition and Hilbert-Huang Spectral Analyses in Python

EntropyHub: An open-source toolkit for entropic time series analysis

MFDFA: Efficient multifractal detrended fluctuation analysis in python

Predicting the Dynamics of the COVID-19 Pandemic in the United States Using Graph Theory-Based Neural Networks

International journal of environmental research and public health

Fluctuations of water quality time series in rivers follow superstatistics

Spiking activity in the visual thalamus is coupled to pupil dynamics across temporal scales

Hilbert–Huang Transform Analysis of Quasiperiodic Oscillations in MAXI J1820+070

The cyclic behaviour in the N–S asymmetry of sunspots and solar plages for the period 1910 to 1937 using data from Ebro catalogues

Machine learning approach for early onset dementia neurobiomarker using EEG network topology features


[CVPR 2023 Best Paper Award] Planning-oriented Autonomous Driving

Planning-oriented Autonomous Driving

Generalized Predictive Model for Autonomous Driving

Vista: A Generalizable Driving World Model with High Fidelity and Versatile Controllability

DualAD: Disentangling the Dynamic and Static World for End-to-End
  Driving


Application for inferring subclonal composition and evolution from whole-genome sequencing data.

Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

A community effort to create standards for evaluating tumor subclonal reconstruction

Quantifying the influence of mutation detection on tumour subclonal reconstruction

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer

Cellular and molecular architecture of hematopoietic stem cells and progenitors in genetic models of bone marrow failure

A Bayesian Nonparametric Model for Inferring Subclonal Populations from Structured DNA Sequencing Data

Exact inference under the perfect phylogeny model


Training models for basecalling Oxford Nanopore reads

Latest techniques to study DNA methylation

Recent advances in the detection of base modifications using the Nanopore sequencer

Nanopore Base Calling on the Edge

Dynamic Pooling Improves Nanopore Base Calling Accuracy

RNA dataset generated by Taiyaki

Zenodo (CERN European Organization for Nuclear Research)


[ECCV 2022] ByteTrack: Multi-Object Tracking by Associating Every Detection Box

Detection Recovery in Online Multi-Object Tracking with Sparse Graph Tracker

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

Continuous Human Action Recognition for Human-machine Interaction: A Review

LettuceMOT: A dataset of lettuce detection and tracking with re-identification of re-occurred plants for agricultural robots

Bag of Tricks for Domain Adaptive Multi-Object Tracking


HTSeq is a Python library to facilitate processing and analysis of data from  high-throughput sequencing (HTS) experiments.

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples

Spinal Cord Injury Induces Permanent Reprogramming of Microglia into a Disease-Associated State Which Contributes to Functional Recovery

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

Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy

Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation

Isolation of Anaerobic Bromate-Reducing Bacteria Using Different Carbon Sources and Transcriptomic Insights From Klebsiella variicola Glu3

Maize ZmLAZ1-3 gene negatively regulates drought tolerance in transgenic Arabidopsis

Transcriptomics reveals the molecular regulation of Chinese medicine formula on improving bone quality in broiler

Enhanced Bioremediation Potential of Shewanella decolorationis RNA Polymerase Mutants and Evidence for Novel Azo Dye Biodegradation Pathways


A basecaller for Oxford Nanopore Technologies' sequencers

Performance of neural network basecalling tools for Oxford Nanopore sequencing

Computational methods for 16S metabarcoding studies using Nanopore sequencing data

Computational and structural biotechnology journal

Helix: Algorithm/Architecture Co-design for Accelerating Nanopore Genome Base-calling


Original Implementation of Prompt Tuning from Lester, et al, 2021

SuperGLUE: A Stickier Benchmark for General-Purpose Language Understanding Systems

The Power of Scale for Parameter-Efficient Prompt Tuning

Overcoming Catastrophic Forgetting in Zero-Shot Cross-Lingual Generation

Two-stage LLM Fine-tuning with Less Specialization and More Generalization


A tree-based federated learning system (MLSys 2023)

Towards Open Federated Learning Platforms: Survey and Vision from Technical and Legal Perspectives

Histogram-Based Federated XGBoost using Minimal Variance Sampling for Federated Tabular Data

International Conference on Fog and Mobile Edge Computing

UniFed: All-In-One Federated Learning Platform to Unify Open-Source Frameworks

A Federated Learning Benchmark on Tabular Data: Comparing Tree-Based Models and Neural Networks

A collaborative ensemble construction method for federated random forest


DeepSphere: a graph-based spherical CNN (PyTorch)

DeepSphere: Efficient spherical convolutional neural network with HEALPix sampling for cosmological applications

DeepSphere: a graph-based spherical CNN

A neural simulation-based inference approach for characterizing the Galactic Center γ-ray excess

DeepSphere: towards an equivariant graph-based spherical CNN

Inferring dark matter substructure with astrometric lensing beyond the power spectrum

DeepSphere: a graph-based spherical CNN (ICLR'20 spotlight)


An implementation of CycleGan using TensorFlow

Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks

Cross-Domain Car Detection Using Unsupervised Image-to-Image Translation: From Day to Night

International Joint Conference on Neural Network

Unsupervised domain adaptation for mobile semantic segmentation based on cycle consistency and feature alignment

Anomaly Generation Using Generative Adversarial Networks in Host-Based Intrusion Detection

Ubiquitous Computing, Electronics & Mobile Communication Conference

Can Synthetic Data Improve Object Detection Results for Remote Sensing Images?

Primary Tumor and Inter-Organ Augmentations for Supervised Lymph Node Colon Adenocarcinoma Metastasis Detection


EvoloPy toolbox provides classical and recent nature-inspired metaheuristic for the global optimization.

EvoloPy: An Open-source Nature-inspired Optimization Framework in Python

PROCEEDINGS OF THE 8TH INTERNATIONAL JOINT CONFERENCE ON COMPUTATIONAL INTELLIGENCE, VOL 1: ECTA

Swarm Intelligence Algorithms in Text Document Clustering with Various Benchmarks

Opytimizer: A Nature-Inspired Python Optimizer

A New Metaheuristic Approach to Solving Benchmark Problems: Hybrid Salp Swarm Jaya Algorithm

Computers, materials & continua/Computers, materials & continua (Print)


Distributed, Versioned, Image-oriented Dataservice

A connectome of a learning and memory center in the adult Drosophila brain

TDat: An Efficient Platform for Processing Petabyte-Scale Whole-Brain Volumetric Images

NeuTu: Software for Collaborative, Large-Scale, Segmentation-Based Connectome Reconstruction

DVID: Distributed Versioned Image-Oriented Dataservice

The Brain Observatory Storage Service and Database (BossDB): A Cloud-Native Approach for Petascale Neuroscience Discovery

Analyzing Image Segmentation for Connectomics

Large-Scale Electron Microscopy Image Segmentation in Spark

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

Large-scale EM Analysis of the Drosophila Antennal Lobe with Automatically Computed Synapse Point Clouds


Open clone of OpenAI's unreleased WebText dataset scraper. This version uses pushshift.io files instead of the API for speed.

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

Pre-trained models for natural language processing: A survey

Activation Addition: Steering Language Models Without Optimization

Teaching Arithmetic to Small Transformers

ApplicaAI at SemEval-2020 Task 11: On RoBERTa-CRF, Span CLS and Whether Self-Training Helps Them

Taken out of context: On measuring situational awareness in LLMs

Scaling Distributed Deep Learning Workloads beyond the Memory Capacity with KARMA

Evaluating the Robustness of Discrete Prompts

Collective response to the media coverage of COVID-19 Pandemic on Reddit and Wikipedia

Conformal Nucleus Sampling


The SP800-90B_EntropyAssessment C++package implements the min-entropy assessment methods included in Special Publication 800-90B.

A Fully Digital True Random Number Generator With Entropy Source Based in Frequency Collapse

FastZIP: Faster and More Secure Zero-Interaction Pairing

International Conference on Mobile Systems, Applications, and Services

Random number generation from a quantum tunneling diode

On Entropy and Bit Patterns of Ring Oscillator Jitter

Multiplexing quantum tunneling diodes for random number generation


Deformable Convolutional Networks

Deformable Convolutional Networks

R-FCN: Object Detection via Region-based Fully Convolutional Networks

DOTA: A Large-scale Dataset for Object Detection in Aerial Images

Deformable ConvNets v2: More Deformable, Better Results

Simple Baselines for Human Pose Estimation and Tracking

MVOR: A Multi-view RGB-D Operating Room Dataset for 2D and 3D Human Pose Estimation

EAGLE: Large-scale Vehicle Detection Dataset in Real-World Scenarios using Aerial Imagery

Towards Interpretable R-CNN by Unfolding Latent Structures

Adaptive Precision Training: Quantify Back Propagation in Neural Networks with Fixed-point Numbers


Interval data structure

GIGGLE: a search engine for large-scale integrated genome analysis

A distinct class of antioxidant response elements is consistently activated in tumors with NRF2 mutations

Nucleosomes effectively shield DNA from radiation damage in living cells

Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

Scalable approaches for functional analyses of whole-genome sequencing non-coding variants

Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin

Genome Informatics 2016


Tevatron - A flexible toolkit for neural retrieval research and development.

Dense Passage Retrieval for Open-Domain Question Answering

Dense Text Retrieval Based on Pretrained Language Models: A Survey

Fine-Tuning LLaMA for Multi-Stage Text Retrieval

Tevatron: An Efficient and Flexible Toolkit for Dense Retrieval

Improving Query Representations for Dense Retrieval with Pseudo Relevance Feedback: A Reproducibility Study

DataLab: A Platform for Data Analysis and Intervention

Sparsifying Sparse Representations for Passage Retrieval by Top-k Masking

The tale of two MS MARCO -- and their unfair comparisons

Towards Best Practices for Training Multilingual Dense Retrieval Models

An Encoder Attribution Analysis for Dense Passage Retriever in Open-Domain Question Answering

Proceedings of the 2nd Workshop on Trustworthy Natural Language Processing (TrustNLP 2022)


MIT Cheetah I Implementation

GenLoco: Generalized Locomotion Controllers for Quadrupedal Robots

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

WoLF: the Whole-body Locomotion Framework for Quadruped Robots

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


SALMONN: Speech Audio Language Music Open Neural Network

SALMONN: Towards Generic Hearing Abilities for Large Language Models

Explainable Multimodal Emotion Reasoning

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

video-SALMONN: Speech-Enhanced Audio-Visual Large Language Models

AffectGPT: Dataset and Framework for Explainable Multimodal Emotion
  Recognition


Tools to Calculate Climate Targets for Financial Portfolios


A climate4R package for data access


This repository contains code and datasets related to entity/knowledge papers from the VERT (Versatile Entity Recognition & disambiguation Toolkit) project, by the Knowledge Computing group at Microsoft Research Asia (MSRA).

Few-NERD: A Few-Shot Named Entity Recognition Dataset

CAN-NER: Convolutional Attention Network for Chinese Named Entity Recognition

GRN: Gated Relation Network to Enhance Convolutional Neural Network for Named Entity Recognition

Enhanced Meta-Learning for Cross-lingual Named Entity Recognition with Minimal Resources

Decomposed Meta-Learning for Few-Shot Named Entity Recognition

Single-/Multi-Source Cross-Lingual NER via Teacher-Student Learning on Unlabeled Data in Target Language

UniTrans: Unifying Model Transfer and Data Transfer for Cross-Lingual Named Entity Recognition with Unlabeled Data

AdvPicker: Effectively Leveraging Unlabeled Data via Adversarial Discriminator for Cross-Lingual NER

Prompt-Based Metric Learning for Few-Shot NER

Time for aCTIon: Automated Analysis of Cyber Threat Intelligence in the Wild


SpQR: A Sparse-Quantized Representation for Near-Lossless LLM Weight Compression

A Comprehensive Evaluation of Quantization Strategies for Large Language
  Models


Multichannel Igor Electrophysiology Suite

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

The Neurodata Without Borders ecosystem for neurophysiological data science

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

Multimodal cell type correspondence by intersectional mFISH in intact tissues

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

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


Notebooks and documentation for AI-for-Earth-managed datasets on Azure


dataset and code for 2016 paper "Learning a Driving Simulator"

DeepTest: Automated Testing of Deep-Neural-Network-driven Autonomous Cars

Deep Predictive Coding Networks for Video Prediction and Unsupervised Learning

Learning a Driving Simulator

Predicting Scene Parsing and Motion Dynamics in the Future

Autonomous Driving with Deep Learning: A Survey of State-of-Art Technologies

Deep Learning Based Motion Planning For Autonomous Vehicle Using Spatiotemporal LSTM Network

Road Context-aware Intrusion Detection System for Autonomous Cars

ARTDL: Adaptive Random Testing for Deep Learning Systems

Practical Issues of Action-conditioned Next Image Prediction


Particle-resolved stochastic atmospheric aerosol model

Chemistry Across Multiple Phases (CAMP) version 1.0: An integrated multi-phase chemistry model


Functional connectomics spanning multiple areas of mouse visual cortex

Binary and analog variation of synapses between cortical pyramidal neurons

Oligodendrocyte precursor cells ingest axons in the mouse neocortex

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

CAVE: Connectome Annotation Versioning Engine

bioRxiv : the preprint server for biology


Python module for stochastic residential occupancy behavior for both building and district energy simulations.

A Markov Process Approach to Ensemble Control of Smart Buildings


Structural variation caller using third generation sequencing

Accurate detection of complex structural variations using single molecule sequencing

SVIM: structural variant identification using mapped long reads

Detection of mosaic and population-level structural variants with Sniffles2

Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer

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

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv

Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle

Correction of a Factor VIII genomic inversion with designer-recombinases

Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef


A Bayesian inference software package for end-to-end fitting and interpretation of electromagnetic transients

On the diversity of magnetar-driven kilonovae

Monthly notices of the Royal Astronomical Society

1100 days in the life of the supernova 2018ibb -- The best pair-instability supernova candidate, to date

A generalized semi-analytic model for magnetar-driven supernovae

Redback: A Bayesian inference software package for electromagnetic transients

Tidal Disruption Events through the Lens of the Cooling Envelope Model


Modular image processing pipelines with Python. Built for Astronomy.

Two temperate super-Earths transiting a nearby late-type M dwarf

prose: A Python framework for modular astronomical images processing

Monthly Notices of the Royal Astronomical Society

HST/WFC3 transmission spectroscopy of the cold rocky planet TRAPPIST-1h

Validation of 13 Hot and Potentially Terrestrial TESS Planets

A super-Earth and a mini-Neptune near the 2:1 MMR straddling the radius valley around the nearby mid-M dwarf TOI-2096

SPECULOOS Northern Observatory: Searching for Red Worlds in the Northern Skies

TOI-3235 b: A Transiting Giant Planet around an M4 Dwarf Star

TESS discovery of a sub-Neptune orbiting a mid-M dwarf TOI-2136

A 1.55 R⊕ habitable-zone planet hosted by TOI-715, an M4 star near the ecliptic South Pole

TOI-1442 b and TOI-2445 b: Two potentially rocky ultra-short period planets around M dwarfs


The Ferret program from NOAA/PMEL


B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation

Likelihood-Based Inference of B Cell Clonal Families

Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation

Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data

Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage

Tracing Antibody Repertoire Evolution by Systems Phylogeny

Using B cell receptor lineage structures to predict affinity

Inference of B cell clonal families using heavy/light chain pairing information

Diversity and Function of Maternal HIV-1-Specific Antibodies at the Time of Vertical Transmission

A diverse collection of B cells responded to HIV infection in infant BG505


A lazy-grounding Answer-Set Programming system

Degrees of Laziness in Grounding: Effects of Lazy-Grounding Strategies on ASP Solving

Neural Program Repair with Program Dependence Analysis and Effective Filter Mechanism

Exploiting Partial Knowledge in Declarative Domain-Specific Heuristics for ASP

Specifying and Exploiting Non-Monotonic Domain-Specific Declarative Heuristics in Answer Set Programming

Conflict Generalisation in ASP: Learning Correct and Effective Non-Ground Constraints


Python Active-subspaces Utility Library

Learning nonlinear level sets for dimensionality reduction in function approximation

Sequential Learning of Active Subspaces

Active Manifolds: A non-linear analogue to Active Subspaces

Multi-fidelity data fusion through parameter space reduction with applications to automotive engineering

Multi‐fidelity data fusion for the approximation of scalar functions with low intrinsic dimensionality through active subspaces

Accelerating Derivative-Free Optimization with Dimension Reduction and Hyperparameter Learning


Neurosynth core tools

Movie viewing elicits rich and reliable brain state dynamics

Topographic gradients of intrinsic dynamics across neocortex

Large-scale resting state network correlates of cognitive impairment in Parkinson's disease and related dopaminergic deficits

Intrinsic connectivity reveals functionally distinct cortico-hippocampal networks in the human brain

Activation network mapping for integration of heterogeneous fMRI findings

A Precuneal Causal Loop Mediates External and Internal Information Integration in the Human Brain

Information-Restricted Neural Language Models Reveal Different Brain Regions' Sensitivity to Semantics, Syntax and Context

Molecular signatures of cognition and affect

Transitions between cognitive topographies: contributions of network structure, neuromodulation, and disease

Large-scale functional coactivation patterns reflect the structural connectivity of the medial prefrontal cortex

Social cognitive and affective neuroscience


SourceXtractor++, the next generation SExtractor

Constraining the physical properties of the first lensed z∼10-16 galaxy candidates with JWST

Aging of galaxies along the morphological sequence, marked by bulge growth and disk quenching

Euclid. I. Overview of the Euclid mission

Euclid preparation. XXV. The Euclid Morphology Challenge -- Towards model-fitting photometry for billions of galaxies

HAL (Le Centre pour la Communication Scientifique Directe)

Euclid preparation

A SPectroscopic survey of biased halos In the Reionization Era (ASPIRE):
  JWST Discovers an Overdensity around a Metal Absorption-selected Galaxy at
  z∼5.5


Large suite of N-body simulations

Constraining M ν with the bispectrum. Part I. Breaking parameter degeneracies

Journal of Cosmology and Astroparticle Physics

Constraining M ν with the bispectrum. Part II. The information content of the galaxy bispectrum monopole

Nearest neighbour distributions: New statistical measures for cosmological clustering

A Lagrangian perturbation theory in the presence of massive neutrinos

Learning neutrino effects in Cosmology with Convolutional Neural Networks

Anisotropic halo assembly bias and redshift-space distortions

What can we learn by combining the skew spectrum and the power spectrum?

Effective halo model: Creating a physical and accurate model of the matter power spectrum and cluster counts

Weighing neutrinos with the halo environment

Clustering in massive neutrino cosmologies via Eulerian Perturbation Theory


Build and train Lipschitz constrained networks: TensorFlow implementation of k-Lipschitz layers

Achieving robustness in classification using optimal transport with hinge regularization

White Paper Machine Learning in Certified Systems

Pay attention to your loss: understanding misconceptions about 1-Lipschitz neural networks

Existence, Stability and Scalability of Orthogonal Convolutional Neural Networks

DP-SGD Without Clipping: The Lipschitz Neural Network Way

Robust One-Class Classification with Signed Distance Function using 1-Lipschitz Neural Networks

The Rise of Open Science: Tracking the Evolution and Perceived Value of Data and Methods Link-Sharing Practices

On the explainable properties of 1-Lipschitz Neural Networks: An Optimal Transport Perspective


Large language models (LLMs) made easy, EasyLM is a one stop solution for pre-training, finetuning, evaluating and serving LLMs in JAX/Flax.

LLaMA: Open and Efficient Foundation Language Models

Llama 2: Open Foundation and Fine-Tuned Chat Models

The False Promise of Imitating Proprietary LLMs

Camels in a Changing Climate: Enhancing LM Adaptation with Tulu 2

Focused Transformer: Contrastive Training for Context Scaling

Lemur: Harmonizing Natural Language and Code for Language Agents

Learning to (Learn at Test Time): RNNs with Expressive Hidden States

Multilingual Mathematical Autoformalization

Self Information Update for Large Language Models through Mitigating Exposure Bias

Structured Packing in LLM Training Improves Long Context Utilization


C++17 Library for analysis, compilation/synthesis, and optimization of quantum circuits

An Open-Source, Industrial-Strength Optimizing Compiler for Quantum Programs

Automatic generation of Grover quantum oracles for arbitrary data structures

Using ZDDs in the Mapping of Quantum Circuits

Optimizing quantum circuit synthesis for permutations using recursion


DeepWalk - Deep Learning for Graphs

DeepWalk: Online Learning of Social Representations

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

Revisiting Semi-Supervised Learning with Graph Embeddings

A Survey on Network Embedding

Heterogeneous Information Network Embedding for Recommendation

Network Representation Learning: A Survey

Inductive Representation Learning on Temporal Graphs

Graph Self-Supervised Learning: A Survey

Representation Learning for Attributed Multiplex Heterogeneous Network

A Comprehensive Survey on Pretrained Foundation Models: A History from BERT to ChatGPT

Graph-based Semi-supervised Learning: A Comprehensive Review


Essential Routines for Fundamental Astronomy. Maintainers: @eteq @mhvk @sergiopasra

Gammapy - A prototype for the CTA science tools

Towards new solutions for scientific computing: the case of Julia

The BlueMUSE data reduction pipeline: lessons learned from MUSE and first design choices

Software and Cyberinfrastructure for Astronomy VII


Fn Flow Server

No Provisioned Concurrency: Fast RDMA-codesigned Remote Fork for Serverless Computing

Serverless Workflows with Durable Functions and Netherite

Standards‐based modeling and deployment of serverless function orchestrations using BPMN and TOSCA

Efficiency in the serverless cloud paradigm: A survey on the reusing and approximation aspects

Efficiency in the Serverless Cloud Computing Paradigm: A Survey Study.

Flock: A Low-Cost Streaming Query Engine on FaaS Platforms


An extension of LPeg that supports labeled failures

Syntax error recovery in parsing expression grammars

Error Reporting in Parsing Expression Grammars

Automatic Syntax Error Reporting and Recovery in Parsing Expression Grammars

Error recovery in parsing expression grammars through labeled failures and its implementation based on a parsing machine

Journal of Visual Languages and Computing


Paddle Large Scale Classification Tools，supports ArcFace, CosFace, PartialFC, Data Parallel + Model Parallel. Model includes ResNet, ViT, Swin, DeiT, CaiT, FaceViT, MoCo, MAE, ConvMAE, CAE.

An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

ArcFace: Additive Angular Margin Loss for Deep Face Recognition

IEEE Transactions on Pattern Analysis and Machine Intelligence

Training data-efficient image transformers & distillation through attention

CosFace: Large Margin Cosine Loss for Deep Face Recognition

Context Autoencoder for Self-Supervised Representation Learning

Token Merging: Your ViT But Faster

Partial FC: Training 10 Million Identities on a Single Machine

ConvMAE: Masked Convolution Meets Masked Autoencoders


Sequential Monte Carlo in python

Waste-free Sequential Monte Carlo

On backward smoothing algorithms

The Normal-Generalised Gamma-Pareto Process: A Novel Pure-Jump Lévy Process with Flexible Tail and Jump-Activity Properties

Iterated INLA for State and Parameter Estimation in Nonlinear Dynamical
  Systems

Bayesian Windkessel calibration using optimized 0D surrogate models


Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics

Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models

State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs


Python package for automatic tree crown delineation based on the Detectron2 implementation of Mask R-CNN

Accurate delineation of individual tree crowns in tropical forests from aerial RGB imagery using Mask R-CNN


Yet another Japanese morphological analyzer

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

A clinical specific BERT developed using a huge Japanese clinical text corpus

WeChat Neural Machine Translation Systems for WMT21

The NiuTrans Machine Translation Systems for WMT20

Empirical Methods in Natural Language Processing

fugashi, a Tool for Tokenizing Japanese in Python

The NiuTrans Machine Translation Systems for WMT21

An Empirical Study of Generating Texts for Search Engine Advertising

North American Chapter of the Association for Computational Linguistics

Breaking the Representation Bottleneck of Chinese Characters: Neural Machine Translation with Stroke Sequence Modeling

Improving Japanese-to-English Neural Machine Translation by Paraphrasing the Target Language

Japanese to English/Chinese/Korean Datasets for Translation Quality Estimation and Automatic Post-Editing


CAMISIM: Simulating metagenomes and microbial communities

CAMISIM: simulating metagenomes and microbial communities

Terabase-scale metagenome coassembly with MetaHipMer

MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities


한국어 자연어처리를 위한 파이썬 라이브러리입니다. 단어 추출/ 토크나이저 / 품사판별/ 전처리의 기능을 제공합니다.

Machine Learning-Based Prediction of Korean Triage and Acuity Scale Level in Emergency Department Patients

Towards standardizing Korean Grammatical Error Correction: Datasets and Annotation

Keyword Extraction Algorithm for Classifying Smoking Status from Unstructured Bilingual Electronic Health Records Based on Natural Language Processing

Exploring acceptance of autonomous vehicle policies using KeyBERT and SNA: Targeting engineering students


An easy-to-use Python framework to generate adversarial jailbreak prompts.

AutoDAN: Generating Stealthy Jailbreak Prompts on Aligned Large Language Models

EasyJailbreak: A Unified Framework for Jailbreaking Large Language
  Models

Protecting Your LLMs with Information Bottleneck


A python library for Argo data beginners and experts


Explain, analyze, and visualize NLP language models. Ecco creates interactive visualizations directly in Jupyter notebooks explaining the behavior of Transformer-based language models (like GPT2, BERT, RoBERTA, T5, and T0).

AMMUS : A Survey of Transformer-based Pretrained Models in Natural Language Processing

Ecco: An Open Source Library for the Explainability of Transformer Language Models

Meeting of the Association for Computational Linguistics

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

GPT-D: Inducing Dementia-related Linguistic Anomalies by Deliberate Degradation of Artificial Neural Language Models

GeMI: interactive interface for transformer-based Genomic Metadata Integration

Database : the journal of biological databases and curation


Distributed Communication-Optimal Matrix-Matrix Multiplication Algorithm

DISTAL: the distributed tensor algebra compiler

Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation

TAMM: Tensor Algebra for Many-body Methods

Efficiently Parallelizable Strassen-Based Multiplication of a Matrix by its Transpose


A novel machine learning pipeline to analyse spatial transcriptomics data

stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues

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

Deep Learning in Single-Cell Analysis

Combining single-cell sequencing and spatial transcriptome sequencing to identify exosome-related features of glioblastoma and constructing a prognostic model to identify BARD1 as a potential therapeutic target for GBM patients


Peptide-MHC I binding affinity prediction

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

MHCflurry: open-source class I MHC binding affinity prediction

MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing.

Predicting Antigen Presentation—What Could We Learn From a Million Peptides?

Sparse-Input Neural Networks for High-dimensional Nonparametric Regression and Classification

DeepLigand: accurate prediction of MHC class I ligands using peptide embedding

An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer

Computational cancer neoantigen prediction: current status and recent advances

Characterization of SARS-CoV-2 viral diversity within and across hosts

Predicting Peptide-MHC Binding Affinities with Imputed Training Data


Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations

Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

Computational and structural biotechnology journal

CTCF and transcription influence chromatin structure re-configuration after mitosis

Activity-dependent regulome of human GABAergic neurons reveals new patterns of gene regulation and neurological disease heritability

KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress

IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia

SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease

Mapping cis-regulatory elements in human neurons links psychiatric disease heritability and activity-regulated transcriptional programs

3D genome organization links non-coding disease-associated variants to genes

Frontiers in cell and developmental biology

hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context

Zenodo (CERN European Organization for Nuclear Research)


Bidirectional LSTM-CRF and ELMo for Named-Entity Recognition, Part-of-Speech Tagging and so on.

Deep contextualized word representations

Recurrent Neural Network Grammars

Ludwig: a type-based declarative deep learning toolbox

Aspect and Opinion Terms Extraction Using Double Embeddings and Attention Mechanism for Indonesian Hotel Reviews

Domain adaptation for part-of-speech tagging of noisy user-generated text

A Lightweight Recurrent Network for Sequence Modeling

PheneBank: a literature-based database of phenotypes


Natural Language Toolkit for Malaysian language, https://malaya.readthedocs.io/

Pre-training Polish Transformer-based Language Models at Scale

Sentiment analysis of informal Malay tweets with deep learning

IAES International Journal of Artificial Intelligence (IJ-AI)

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

COOL, a Context Outlooker, and its Application to Question Answering and other Natural Language Processing Tasks


Bioinformatics code libraries and scripts

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea

Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity

Transcriptional Landscape of Small Non-coding RNAs in Somatic and Gonadal Tissues of Brachyuran Crabs (Genus Eriocheir and Portunus)


keras implement of transformers for humans

ZLPR: A Novel Loss for Multi-label Classification

ELECTRA is a Zero-Shot Learner, Too

DACPGTN: Drug ATC Code Prediction Method Based on Graph Transformer Network for Drug Discovery

Development and Application of Knowledge Graphs for the Injection Molding Process

A Polyphone BERT for Polyphone Disambiguation in Mandarin Chinese


MicaSense RedEdge and Altum image processing tutorials

Vegetation monitoring using multispectral sensors – best practices and lessons learned from high latitudes

High-Throughput Phenotyping Enabled Genetic Dissection of Crop Lodging in Wheat

Tree Species Classification and Health Status Assessment for a Mixed Broadleaf-Conifer Forest with UAS Multispectral Imaging

Retrieval of Crop Variables from Proximal Multispectral UAV Image Data Using PROSAIL in Maize Canopy

Evaluation of Unoccupied Aircraft System (UAS) Remote Sensing Reflectance Retrievals for Water Quality Monitoring in Coastal Waters

Identifying the Optimal Radiometric Calibration Method for UAV-Based Multispectral Imaging

Development of an Open-Source Thermal Image Processing Software for Improving Irrigation Management in Potato Crops (Solanum tuberosum L.)

Assessing The Performance of YOLOv5 Algorithm for Detecting Volunteer Cotton Plants in Corn Fields at Three Different Growth Stages

An initial exploration of vicarious and in-scene calibration techniques for small unmanned aircraft systems

Detecting Sorghum Plant and Head Features from Multispectral UAV Imagery


An interactional aerodynamics and acoustics solver for multirotor aircraft and wind energy

High-Fidelity Modeling of Multirotor Aerodynamic Interactions for Aircraft Design

Modeling Multirotor Aerodynamic Interactions Through the Vortex Particle Method

Development of a Vortex Particle Code for the Modeling of Wake Interaction in Distributed Propulsion

On the Scope of Lagrangian Vortex Methods for Two-Dimensional Flow Simulations and the POD Technique Application for Data Storing and Analyzing


pvcompare is a model for comparing the benefits of different PV technologies in local energy systems in different energy supply scenarios.


Software for analyzing high dimensional dose-response data

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow

Assessment of developmental neurotoxicity induced by chemical mixtures using an adverse outcome pathway concept

Environmental health : a global access science source

A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip® and the TGx-DDI Transcriptomic Biomarker in Human HepaRG™ Cell Cultures

The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization

Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action

Mining toxicogenomic data for dose-responsive pathways: implications in advancing next-generation risk assessment


Minotour API, web and client code

minoTour, real-time monitoring and analysis for nanopore sequencers

Barcode aware adaptive sampling for GridION and PromethION Oxford Nanopore sequencers

A framework for real-time monitoring, analysis and adaptive sampling of viral amplicon nanopore sequencing

Real-time monitoring and analysis of SARS-CoV-2 nanopore sequencing with minoTour


statistical models of forest carbon potential and risks


事件小分队论文笔记

Interactive Grounded Language Acquisition and Generalization in a 2D World

ECONET: Effective Continual Pretraining of Language Models for Event Temporal Reasoning

Clinical Temporal Relation Extraction with Probabilistic Soft Logic Regularization and Global Inference

What is Event Knowledge Graph: A Survey

Effective Distant Supervision for Temporal Relation Extraction


Modelling jetted Active Galactic Nuclei radiative processes with python

VHE gamma-ray detection of FSRQ QSO B1420+326 and modeling of its enhanced broadband state in 2020

agnpy: An open-source python package modelling the radiative processes of jetted active galactic nuclei

Precession-induced Variability in AGN Jets and OJ 287

Multiwavelength study of the gravitationally lensed blazar QSO B0218+357 between 2016 and 2020

Non-thermal radiation from dual jet interactions in supermassive black hole binaries


Creative Commons Attribution 4.0 International

Medical action ontology

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

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research

DDIEM: drug database for inborn errors of metabolism

Phenopacket-tools: Building and validating GA4GH Phenopackets

The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease.

medRxiv : the preprint server for health sciences


Trait-Driven Models of Ecology and Evolution :evergreen_tree:


Algorithms for Quantitative Pedology


A toolset for profiling alternative splicing events in RNA-Seq data.

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

An alternative splicing event amplifies evolutionary differences between vertebrates

The changing paradigm of intron retention: regulation, ramifications and recipes

Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing

Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons


The UppASD package is a simulation tool for atomistic spin dynamics and Monte Carlo simulations of Heisenberg spin systems.

Self-induced spin glass state in elemental and crystalline neodymium

Thermally induced magnetic order from glassiness in elemental neodymium

Theory of magnon diffuse scattering in scanning transmission electron microscopy

Skyrmions as quasiparticles: Free energy and entropy

Spin wave excitations of magnetic metalorganic materials

Influence of nonlocal damping on magnon properties of ferromagnets

Unveiling the impact of temperature on magnon diffuse scattering detection in the transmission electron microscope


Tools for working with BUS files

Modular, efficient and constant-memory single-cell RNA-seq preprocessing

IL-1-driven stromal–neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies

Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data Alignment

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT

Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

BUSZ: compressed BUS files


Python utility to estimate, compare, and reweight RNA energetics across many secondary structure algorithms.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses

bioRxiv : the preprint server for biology

Deep learning models for predicting RNA degradation via dual crowdsourcing

RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning

Ribonanza: deep learning of RNA structure through dual crowdsourcing

RNA structure landscape ofS. cerevisiaeintrons


Brain signature patterns, atlases of regions, and meta-analysis masks for neuroimaging data analysis.

A neuromarker for drug and food craving distinguishes drug users from non-users

An fMRI-Based Brain Marker of Individual Differences in Delay Discounting

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

Brain Structural Changes During Juvenile Fibromyalgia: Relationships With Pain, Fatigue, and Functional Disability

Arthritis & rheumatology (Hoboken, N.J.)

Healthcare experience affects pain‐specific responses to others' suffering in the anterior insula

Evoked pain intensity representation is distributed across brain systems: A multistudy mega-analysis

Odor imagery but not perception drives risk for food cue reactivity and increased adiposity


A OpenMMLAB toolbox  for human pose estimation, skeleton-based action recognition, and action synthesis.

Spatial Temporal Graph Convolutional Networks for Skeleton-Based Action Recognition

Graph Embedded Pose Clustering for Anomaly Detection

Vision-based Human Fall Detection Systems using Deep Learning: A Review

Predictively encoded graph convolutional network for noise-robust skeleton-based action recognition

HA-ViD: A Human Assembly Video Dataset for Comprehensive Assembly Knowledge Understanding

Graph Neural Network based Child Activity Recognition

Recognition of Rare Low-Moral Actions Using Depth Data


A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

Clustering of single-cell multi-omics data with a multimodal deep learning method

Deep Learning in Single-Cell Analysis

Single Cell Self-Paced Clustering with Transcriptome Sequencing Data

International journal of molecular sciences

Single-cell data clustering based on sparse optimization and low-rank matrix factorization


Tools for multi-label classification problems.

On Data Augmentation for Extreme Multi-label Classification

A Survey on Extreme Multi-label Learning


R package to access DoRothEA's regulons

ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination

BACH1 deficiency prevents neointima formation and maintains the differentiated phenotype of vascular smooth muscle cells by regulating chromatin accessibility

Single-Cell Analysis Identify Transcription Factor BACH1 as a Master Regulator Gene in Vascular Cells During Aging

Gene Expression Monotonicity across Bladder Cancer Stages Informs on the Molecular Pathogenesis and Identifies a Prognostic Eight-Gene Signature


This project contains command line tools to perform rigid, affine and non-linear registration of nifti or analyse images as well as utilities

An automated framework for localization, segmentation and super-resolution reconstruction of fetal brain MRI

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning

NODEO: A Neural Ordinary Differential Equation Based Optimization Framework for Deformable Image Registration

Automated White Matter Hyperintensity Segmentation Using Bayesian Model Selection: Assessment and Correlations with Cognitive Change

Evaluation of MRI-derived surrogate signals to model respiratory motion

Biomedical physics & engineering express

AutoProstate: Towards Automated Reporting of Prostate MRI for Prostate Cancer Assessment Using Deep Learning

Diffusion tensor driven image registration: a deep learning approach

Presumed small vessel disease, imaging and cognition markers in the Alzheimer’s Disease Neuroimaging Initiative

Substantially thinner internal granular layer and reduced molecular layer surface in the cerebellar cortex of the Tc1 mouse model of down syndrome – a comprehensive morphometric analysis with active staining contrast-enhanced MRI

Treatment reduces the incidence of newly appearing multiple sclerosis lesions evolving into chronic active, slowly expanding lesions: A retrospective analysis


Mamba SSM architecture

Mamba: Linear-Time Sequence Modeling with Selective State Spaces

Transformers are SSMs: Generalized Models and Efficient Algorithms
  Through Structured State Space Duality

xLSTM: Extended Long Short-Term Memory

MambaByte: Token-free Selective State Space Model

ZigMa: A DiT-style Zigzag Mamba Diffusion Model

StableSSM: Alleviating the Curse of Memory in State-space Models through Stable Reparameterization

Decision Mamba: Reinforcement Learning via Sequence Modeling with
  Selective State Spaces

RankMamba: Benchmarking Mamba's Document Ranking Performance in the Era of Transformers

Exploring the Capability of Mamba in Speech Applications

MambaLRP: Explaining Selective State Space Sequence Models


COIN-OR Linear Programming Solver

Design and implementation of a modular interior-point solver for linear optimization

ROC++: Robust Optimization in C++

Learning to Reformulate for Linear Programming

Preprocessing and cutting planes with conflict graphs

From an Interior Point to a Corner Point: Smart Crossover

Linear programming feedrate optimization - Adaptive path sampling and feedrate override

The International Journal of Advanced Manufacturing Technology

2-neighborly 0/1-polytopes of dimension 7

Monoidal strengthening of simple ��-polyhedral disjunctive cuts


Perceptual Quality Estimator for speech and audio

High Fidelity Neural Audio Compression

ViSQOL v3: An Open Source Production Ready Objective Speech and Audio Metric

UniAudio: An Audio Foundation Model Toward Universal Audio Generation

Objective Measures of Perceptual Audio Quality Reviewed: An Evaluation of Their Application Domain Dependence

IEEE/ACM Transactions on Audio, Speech, and Language Processing

Assessment of QoE for Video and Audio in WebRTC Applications Using Full-Reference Models

Can You See Me Now? A Measurement Study of Zoom, Webex, and Meet

PROCEEDINGS OF THE 2021 ACM INTERNET MEASUREMENT CONFERENCE, IMC 2021

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

APCodec: A Neural Audio Codec with Parallel Amplitude and Phase Spectrum
  Encoding and Decoding

Perceptual Evaluation of 360 Audiovisual Quality and Machine Learning Predictions

InSE-NET: A Perceptually Coded Audio Quality Model based on CNN


Beautiful visualizations of how language differs among document types.

Scattertext: a Browser-Based Tool for Visualizing how Corpora Differ

Generalized word shift graphs: a method for visualizing and explaining pairwise comparisons between texts

Evaluation of Automatic Speech Recognition for Conversational Speech in Dutch, English and German: What Goes Missing?

Conference on Natural Language Processing

Predicting gender and age categories in English conversations using lexical, non-lexical, and turn-taking features


The git repository for the TT-Toolbox

Tensor Decompositions for Signal Processing Applications: From two-way to multiway component analysis

Tensorizing Neural Networks

Tensor Networks for Dimensionality Reduction and Large-scale Optimization: Part 2 Applications and Future Perspectives

Foundations and Trends® in Machine Learning

Alternating minimal energy methods for linear systems in higher dimensions. Part II: Faster algorithm and application to nonsymmetric systems

Era of Big Data Processing: A New Approach via Tensor Networks and Tensor Decompositions

Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains

Extension of PCA to Higher Order Data Structures: An Introduction to Tensors, Tensor Decompositions, and Tensor PCA

Computation of extreme eigenvalues in higher dimensions using block tensor train format

Polynomial Chaos Expansion of random coefficients and the solution of stochastic partial differential equations in the Tensor Train format

Simultaneous state-time approximation of the chemical master equation using tensor product formats


Simple text to phones converter for multiple languages

Unsupervised Speech Recognition

End-to-End Adversarial Text-to-Speech

UnivNet: A Neural Vocoder with Multi-Resolution Spectrogram Discriminators for High-Fidelity Waveform Generation

UniSpeech: Unified Speech Representation Learning with Labeled and Unlabeled Data

SC-GlowTTS: an Efficient Zero-Shot Multi-Speaker Text-To-Speech Model

DeepSinger: Singing Voice Synthesis with Data Mined From the Web

Towards End-to-end Unsupervised Speech Recognition

Guided-TTS 2: A Diffusion Model for High-quality Adaptive Text-to-Speech with Untranscribed Data

Denoising Text to Speech with Frame-Level Noise Modeling

ALICE: An open-source tool for automatic measurement of phoneme, syllable, and word counts from child-centered daylong recordings


YACCLAB: Yet Another Connected Components Labeling Benchmark

Toward reliable experiments on the performance of Connected Components Labeling algorithms

Connected Components Labeling on DRAGs

International Conference on Pattern Recognition

Parallel Algorithm for Connected-Component Analysis Using CUDA

Efficient Source Finding for Radio Interferometric Images

An Efficient Connected-Component Labeling Algorithm for 3-D Binary Images

IEEE Open Journal of the Computer Society

A Heuristic-Based Decision Tree for Connected Components Labeling of 3D Volumes: Implementation and Reproducibility Notes

Reproducible Research in Pattern Recognition


A repository in development for a solar powered network of servers that host a distributed web platform. Project by Tega Brain, Alex Nathanson and Benedetta Piantella. Supported by Eyebeam, Mozilla, and CS&S


CRSLab is an open-source toolkit for building Conversational Recommender System (CRS).

Advances and Challenges in Conversational Recommender Systems: A Survey

Towards Unified Conversational Recommender Systems via Knowledge-Enhanced Prompt Learning

CRSLab: An Open-Source Toolkit for Building Conversational Recommender System

C2-CRS: Coarse-to-Fine Contrastive Learning for Conversational Recommender System

A Unified Multi-task Learning Framework for Multi-goal Conversational Recommender Systems

User-Centric Conversational Recommendation with Multi-Aspect User Modeling

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

A Large Language Model Enhanced Conversational Recommender System

Improving Conversational Recommendation Systems via Counterfactual Data Simulation

INSPIRED2: An Improved Dataset for Sociable Conversational Recommendation


Direct Sparse Odometry

Direct Sparse Odometry

ORB-SLAM3: An Accurate Open-Source Library for Visual, Visual–Inertial, and Multimap SLAM

Direct Sparse Visual-Inertial Odometry using Dynamic Marginalization

IEEE International Conference on Robotics and Automation

Good Feature Matching: Toward Accurate, Robust VO/VSLAM With Low Latency

Good Feature Selection for Least Squares Pose Optimization in VO/VSLAM

Sparse2Dense: From direct sparse odometry to dense 3D reconstruction

SDVL: Efficient and Accurate Semi-Direct Visual Localization

Automated Indoor Image Localization to Support a Post-Event Building Assessment

3D reconstruction from spherical images: A review of techniques, applications, and prospects

UAV-Borne Mapping Algorithms for Low-Altitude and High-Speed Drone Applications


Luminaire is a python package that provides ML driven solutions for monitoring time series data.

Building an Automated and Self-Aware Anomaly Detection System

Root Cause Detection Among Anomalous Time Series Using Temporal State Alignment

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


Specification and reference implementation of the TCN Protocol for decentralized, privacy-preserving contact tracing.

Decentralized Privacy-Preserving Proximity Tracing

Epione: Lightweight Contact Tracing with Strong Privacy

Apps Against the Spread: Privacy Implications and User Acceptance of COVID-19-Related Smartphone Apps on Three Continents

Proceedings of the 2021 CHI Conference on Human Factors in Computing Systems

Tackling COVID-19 through Responsible AI Innovation: Five Steps in the Right Direction

COVI White Paper

Asymmetric Private Set Intersection with Applications to Contact Tracing and Private Vertical Federated Machine Learning

A review of information security aspects of the emerging COVID-19 contact tracing mobile phone applications

PCT-TEE: Trajectory-based Private Contact Tracing System with Trusted Execution Environment

Listening to Bluetooth Beacons for Epidemic Risk Mitigation

ACOUSTIC-TURF: Acoustic-based Privacy-Preserving COVID-19 Contact
  Tracing


A PyTorch-based library for semi-supervised learning (NeurIPS'21)

FlexMatch: Boosting Semi-Supervised Learning with Curriculum Pseudo Labeling

FreeMatch: Self-adaptive Thresholding for Semi-supervised Learning

SoftMatch: Addressing the Quantity-Quality Trade-off in Semi-supervised Learning

Masked Autoencoders are Robust Data Augmentors

Diffusion Models and Semi-Supervised Learners Benefit Mutually with Few Labels

The Perils of Learning From Unlabeled Data: Backdoor Attacks on Semi-supervised Learning

Boosting Semi-Supervised Learning with Contrastive Complementary Labeling

Boosting Semi-Supervised Learning by bridging high and low-confidence predictions


QCD for Intel Xeon Phi and Xeon processors

Λ_c →Λ^*(1520) form factors from lattice QCD and improved analysis of the Λ_b →Λ^*(1520) and Λ_b →Λ_c^*(2595,2625) form factors

Practical Implementation of Lattice QCD Simulation on SIMD Machines with Intel AVX-512

Charm-baryon semileptonic decays and the strange Λ^* resonances: New insights from lattice QCD

Twisted mass gauge ensembles at physical values of the light, strange and charm quark masses

Practical Implementation of Lattice QCD Simulation on Intel Xeon Phi Knights Landing

Accelerating Twisted Mass LQCD with QPhiX

Twisted mass ensemble generation on GPU machines

Optimizing shift selection in multilevel Monte Carlo for disconnected diagrams in lattice QCD

Gradient-flow scale setting with N_f=2+1+1 Wilson-clover twisted-mass fermions


PyBullet CartPole and Quadrotor environments—with CasADi symbolic a priori dynamics—for learning-based control and RL

Safe Learning in Robotics: From Learning-Based Control to Safe Reinforcement Learning

Safe-Control-Gym: A Unified Benchmark Suite for Safe Learning-Based Control and Reinforcement Learning in Robotics

Multi-Step Model Predictive Safety Filters: Reducing Chattering by Increasing the Prediction Horizon


DESI 2024 III: Baryon Acoustic Oscillations from Galaxies and Quasars

Optimal Reconstruction of Baryon Acoustic Oscillations for DESI 2024

ELG Spectroscopic Systematics Analysis of the DESI Data Release 1


Evaluate layer and volume potentials accurately. Solve integral equations.

Optimization of fast algorithms for global Quadrature by Expansion using target-specific expansions

Simulation of Multiscale Hydrophobic Lipid Dynamics via Efficient Integral Equation Methods

High-order finite element–integral equation coupling on embedded meshes

Adjoint-based control of three dimensional Stokes droplets


Core of Py-ORBIT code

Resonance identification studies at the CERN PS

Modeling Transverse Space Charge effects in IOTA with pyORBIT

Space Charge Driven Resonances in the CERN PS


Parallel Programming with Python and Charm++

Performance Evaluation of Python Parallel Programming Models: Charm4Py and mpi4py

pPython for Parallel Python Programming


xOpera orchestrator compliant with TOSCA YAML v1.3 in the making

SODALITE@RT: Orchestrating Applications on Cloud-Edge Infrastructures

Containerization for High Performance Computing Systems: Survey and Prospects

IEEE Transactions on Software Engineering

Static Analysis of Infrastructure as Code: a Survey

2022 IEEE 19th International Conference on Software Architecture Companion (ICSA-C)

Automated Application Deployment on Multi-Access Edge Computing: A Survey

A Declarative Modelling Framework for the Deployment and Management of Blockchain Applications

Modeling Different Deployment Variants of a Composite Application in a Single Declarative Deployment Model


Matrix-free Measurement Mitigation

Scalable Mitigation of Measurement Errors on Quantum Computers

Observation of the non-Hermitian skin effect and Fermi skin on a digital quantum computer

Efficient quantum readout-error mitigation for sparse measurement outcomes of near-term quantum devices

Simulating Majorana zero modes on a noisy quantum processor

Enhancing quantum utility: Simulating large-scale quantum spin chains on superconducting quantum computers

Teaching Qubits to Sing: Mission Impossible?


Atmospheric fluid dynamics solver optimized for GPUs.

Revisiting the Phase Curves of WASP-43b: Confronting Re-analyzed Spitzer Data with Cloudy Atmospheres

Three-dimensional Circulation Driving Chemical Disequilibrium in WASP-43b

THOR 2.0: Major Improvements to the Open-source General Circulation Model

The Astrophysical Journal Supplement Series

Cloudy and Cloud-free Thermal Phase Curves with PICASO: Applications to WASP-43b

Examining NHD vs QHD in the GCM THOR with non-grey radiative transfer for the hot Jupiter regime


Theano-based implementation of Deep Q-learning

Playing Atari with Deep Reinforcement Learning

Weight Normalization: A Simple Reparameterization to Accelerate Training of Deep Neural Networks

Unmasking Clever Hans predictors and assessing what machines really learn

Adversarial Attacks on Neural Network Policies

Revisiting the Softmax Bellman Operator: New Benefits and New Perspective

Revisiting the Softmax Bellman Operator: Theoretical Properties and Practical Benefits.


Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions

hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update

Simulation studies, 3D QSAR and molecular docking on a point mutation of protein kinase B with flavonoids targeting ovarian Cancer

My Cancer Genome: Coevolution of Precision Oncology and a Molecular Oncology Knowledgebase

Unraveling the Mystery: Next Generation Sequencing Sheds Light on Neuroblastoma Pathogenesis and Targeted Therapies

Frontiers in bioscience (Landmark edition)


Rainbow is all you need! A step-by-step tutorial from DQN to Rainbow

Dueling Network Architectures for Deep Reinforcement Learning

Prioritized Experience Replay

A Distributional Perspective on Reinforcement Learning

Noisy Networks for Exploration


A general purpose, write-back block cache for Linux.

Error Characterization, Mitigation, and Recovery in Flash-Memory-Based Solid-State Drives

Errors in Flash-Memory-Based Solid-State Drives: Analysis, Mitigation, and Recovery

Nova-LSM: A Distributed, Component-based LSM-tree Key-value Store

SIGMOD '21: PROCEEDINGS OF THE 2021 INTERNATIONAL CONFERENCE ON MANAGEMENT OF DATA

ECI-Cache

Proceedings of the ACM on Measurement and Analysis of Computing Systems

Flashield: a Key-value Cache that Minimizes Writes to Flash


A PyTorch implementation of NeRF (Neural Radiance Fields) that reproduces the results.

NeRF: Representing Scenes as Neural Radiance Fields for View Synthesis

NeuS: Learning Neural Implicit Surfaces by Volume Rendering for Multi-view Reconstruction

Volume Rendering of Neural Implicit Surfaces

KITTI-360: A Novel Dataset and Benchmarks for Urban Scene Understanding in 2D and 3D

Nerfstudio: A Modular Framework for Neural Radiance Field Development

Point-Based Neural Rendering with Per-View Optimization

HDR-NeRF: High Dynamic Range Neural Radiance Fields

ReLU Fields: The Little Non-linearity That Could

Special Interest Group on Computer Graphics and Interactive Techniques Conference Proceedings

R2L: Distilling Neural Radiance Field to Neural Light Field for Efficient Novel View Synthesis

Voxurf: Voxel-based Efficient and Accurate Neural Surface Reconstruction


MCMC sample analysis, kernel densities, plotting, and GUI

A NICER View of PSR J0030+0451: Millisecond Pulsar Parameter Estimation

A NICER View of the Massive Pulsar PSR J0740+6620 Informed by Radio Timing and XMM-Newton Spectroscopy

GetDist: a Python package for analysing Monte Carlo samples

Cobaya: code for Bayesian analysis of hierarchical physical models

Journal of Cosmology and Astroparticle Physics

Modelling and interpreting spectral energy distributions of galaxies with BEAGLE

Monthly Notices of the Royal Astronomical Society

Cluster Cosmology Constraints from the 2500 deg2 SPT-SZ Survey: Inclusion of Weak Gravitational Lensing Data from Magellan and the Hubble Space Telescope

Early dark energy does not restore cosmological concordance

Probing the interaction between dark matter and dark energy in the presence of massive neutrinos

Echo of interactions in the dark sector

Constraining early dark energy with large-scale structure


Torch implementation of neural style algorithm

Arbitrary Style Transfer in Real-time with Adaptive Instance Normalization

A Neural Algorithm of Artistic Style

A Learned Representation For Artistic Style

Demystifying Neural Style Transfer

Artistic Style Transfer for Videos

Artistic Style Transfer for Videos and Spherical Images

International Journal of Computer Vision

Laplacian-Steered Neural Style Transfer

PROCEEDINGS OF THE 2017 ACM MULTIMEDIA CONFERENCE (MM'17)

Multimodal Style Transfer via Graph Cuts

A Deep-Learning-Based Geological Parameterization for History Matching Complex Models

Makeup like a superstar: Deep Localized Makeup Transfer Network


PAIR.withgoogle.com and friend's work on interpretability methods

Visualizing and Measuring the Geometry of BERT

Patchscopes: A Unifying Framework for Inspecting Hidden Representations of Language Models

Visualizing Linguistic Diversity of Text Datasets Synthesized by Large Language Models


Error-bounded Lossy Data Compressor (for floating-point/integer datasets)

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

LFZip: Lossy compression of multivariate floating-point time series data via improved prediction

Revisiting Huffman Coding: Toward Extreme Performance on Modern GPU Architectures

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

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


min(DALL·E) is a fast, minimal port of DALL·E Mini to PyTorch

StoryDALL-E: Adapting Pretrained Text-to-Image Transformers for Story Continuation

GenEval: An Object-Focused Framework for Evaluating Text-to-Image Alignment

Detecting Euphemisms with Literal Descriptions and Visual Imagery

Getting it Right: Improving Spatial Consistency in Text-to-Image Models


The official home of climt, a Python based climate modelling toolkit.

sympl (v. 0.4.0) and climt (v. 0.15.3) – towards a flexible framework for building model hierarchies in Python

Effects of Ozone Levels on Climate Through Earth History


Global shoreline mapping tool from satellite imagery

CoastSat: A Google Earth Engine-enabled Python toolkit to extract shorelines from publicly available satellite imagery

Interannual Response of Reef Islands to Climate-Driven Variations in Water Level and Wave Climate

A 1.2 Billion Pixel Human-Labeled Dataset for Data-Driven Classification of Coastal Environments

Large regional variability in coastal erosion caused by ENSO

Training data for: CoastSat image classification

Zenodo (CERN European Organization for Nuclear Research)

Time-series of shoreline change along the Pacific Rim

Time-series of shoreline change for the Klamath River Littoral Cell (California)


Trained models & code to predict toxic comments on all 3 Jigsaw Toxic Comment Challenges. Built using ⚡ Pytorch Lightning and  Transformers. For access to our API, please email us at contact@unitary.ai.

Automated Hate Speech Detection and the Problem of Offensive Language

The RefinedWeb Dataset for Falcon LLM: Outperforming Curated Corpora with Web Data, and Web Data Only

A General Language Assistant as a Laboratory for Alignment

Racial Bias in Hate Speech and Abusive Language Detection Datasets

OpenAssistant Conversations -- Democratizing Large Language Model Alignment

A Gentle Introduction to Conformal Prediction and Distribution-Free Uncertainty Quantification

Fine-tuning Aligned Language Models Compromises Safety, Even When Users Do Not Intend To!

DataComp: In search of the next generation of multimodal datasets

Predictability and Surprise in Large Generative Models

Pretraining Language Models with Human Preferences


PyBullet Gymnasium environments for single and multi-agent reinforcement learning of quadcopter control

Neural Lander: Stable Drone Landing Control Using Learned Dynamics

International Conference on Robotics and Automation

Learning to Fly -- a Gym Environment with PyBullet Physics for Reinforcement Learning of Multi-agent Quadcopter Control

Flightmare: A Flexible Quadrotor Simulator

The Role of Physics-Based Simulators in Robotics

Annual Review of Control, Robotics, and Autonomous Systems

Hamiltonian-based Neural ODE Networks on the SE(3) Manifold For Dynamics Learning and Control

Autonomous Drone Racing: A Survey

An Introduction to Multi-Agent Reinforcement Learning and Review of its Application to Autonomous Mobility

A Reinforcement Learning Environment for Multi-Service UAV-enabled Wireless Systems

IEEE International Conference on Pervasive Computing and Communications

Intelligent Position Controller for Unmanned Aerial Vehicles (UAV) Based on Supervised Deep Learning


Algorithm to texture 3D reconstructions from multi-view stereo images

Monitor Cotton Budding Using SVM and UAV Images

How to Build a 2D and 3D Aerial Multispectral Map?—All Steps Deeply Explained

3D Reconstruction of Temples in the Special Region of Yogyakarta By Using Close-Range Photogrammetry

Initialization and Alignment for Adversarial Texture Optimization


Application Layer DoS attack simulator

SDN-Assisted Network-Based Mitigation of Slow DDoS Attacks

Two-Stage Intelligent Model for Detecting Malicious DDoS Behavior

Generator of Slow Denial-of-Service Cyber Attacks

Trusted Multi-Domain DDoS Detection Based on Federated Learning

Using a Neural Network to Detect Anomalies given an N-gram Profile


de novo sequence assembler using string graphs

A global reference for human genetic variation

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

Exploring Genome Characteristics and Sequence Quality Without a Reference

RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi

Readjoiner: a fast and memory efficient string graph-based sequence assembler

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

Whole-Genome Sequence of the Metastatic PC3 and LNCaP Human Prostate Cancer Cell Lines


A list of useful payloads and bypass for Web Application Security and Pentest/CTF

Code Injection Attacks in Wireless-Based Internet of Things (IoT): A Comprehensive Review and Practical Implementations

EWVHunter: Grey-Box Fuzzing with Knowledge Guide on Embedded Web Front-Ends

Can You Accept LaTeX Files from Strangers? Ten Years Later


EasyPQP: Simple library generation for OpenSWATH

Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant

High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe

DIAproteomics: A multi-functional data analysis pipeline for data-independent-acquisition proteomics and peptidomics

Clinical and pulmonary function analysis in long-COVID revealed that long-term pulmonary dysfunction is associated with vascular inflammation pathways and metabolic syndrome


Experimental paradigm functions.

Auditory Brainstem Responses to Continuous Natural Speech in Human Listeners

The Parallel Auditory Brainstem Response

Exposing distinct subcortical components of the auditory brainstem response evoked by continuous naturalistic speech

Reading instruction causes changes in category-selective visual cortex


Energy Rating Index (ERI) calculation via OpenStudio/EnergyPlus.


Optimized Computation of Tight Focusing of Short Pulses Using Mapping to Periodic Space

High Performance Implementation of Boris Particle Pusher on DPC++. A First Look at oneAPI

ML-Based Analysis of Particle Distributions in High-Intensity Laser Experiments: Role of Binning Strategy

Optimized routines for event generators in QED-PIC codes

Optimized event generator for strong-field QED simulations within the hi-χ framework


Open-sourced codes for MiniGPT-4 and MiniGPT-v2 (https://minigpt-4.github.io, https://minigpt-v2.github.io/)

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

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

Visual Adversarial Examples Jailbreak Aligned Large Language Models

Understanding LLMs: A Comprehensive Overview from Training to Inference

Safety Fine-Tuning at (Almost) No Cost: A Baseline for Vision Large
  Language Models

X-IQE: eXplainable Image Quality Evaluation for Text-to-Image Generation with Visual Large Language Models

Sparkles: Unlocking Chats Across Multiple Images for Multimodal Instruction-Following Models

Safety of Multimodal Large Language Models on Images and Text

PhD: A Prompted Visual Hallucination Evaluation Dataset

Shadowcast: Stealthy Data Poisoning Attacks Against Vision-Language
  Models