Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

Opportunities and challenges in long-read sequencing data analysis

Illuminating the dark side of the human transcriptome with long read transcript sequencing

Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus

A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi

The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes

Profiles of phenolics and their synthetic pathways in Asparagus officinalis L.


This repo hosts the code and models of "Masked Autoencoders that Listen".

Masked Autoencoders that Listen

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

Global birdsong embeddings enable superior transfer learning for bioacoustic classification

SemantiCodec: An Ultra Low Bitrate Semantic Audio Codec for General
  Sound

Music Consistency Models

Reverse the auditory processing pathway: Coarse-to-fine audio reconstruction from fMRI


piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School

piRNA-mediated regulation of transposon alternative splicing in the soma and germ line

The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility

Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification

An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells

Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation

Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements


PyTorch implementation for SDEdit: Image Synthesis and Editing with Stochastic Differential Equations

GLIDE: Towards Photorealistic Image Generation and Editing with Text-Guided Diffusion Models

SDEdit: Guided Image Synthesis and Editing with Stochastic Differential Equations

Null-text Inversion for Editing Real Images using Guided Diffusion Models

On Distillation of Guided Diffusion Models

Diffusion Models for Adversarial Purification

EGSDE: Unpaired Image-to-Image Translation via Energy-Guided Stochastic Differential Equations

TF-ICON: Diffusion-Based Training-Free Cross-Domain Image Composition

The Devil's Advocate: Shattering the Illusion of Unexploitable Data using Diffusion Models

Accelerating Diffusion Models for Inverse Problems through Shortcut Sampling

SAMScore: A Semantic Structural Similarity Metric for Image Translation Evaluation


Fast, efficient RNA-Seq metrics for quality control and process optimization

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

Transcript expression-aware annotation improves rare variant interpretation

PRMD: an integrated database for plant RNA modifications

RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts

Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients

Neutrophil profiles of pediatric COVID-19 and multisystem inflammatory syndrome in children

caAtlas: An immunopeptidome atlas of human cancer

Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients

Nimodipine Exerts Beneficial Effects on the Rat Oligodendrocyte Cell Line OLN-93


A TensorFlow implementation of this Nvidia paper: https://arxiv.org/pdf/1604.07316.pdf with some changes

End to End Learning for Self-Driving Cars

Scalable End-to-End Autonomous Vehicle Testing via Rare-event Simulation

A Low-cost Fault Corrector for Deep Neural Networks through Range Restriction

The art and practice of data science pipelines

Autonomous Driving in Reality with Reinforcement Learning and Image Translation

Delicar: A Smart Deep Learning Based Self Driving Product Delivery Car in Perspective of Bangladesh

A Little Fog for a Large Turn

Workshop on Applications of Computer Vision

Supporting Safety Analysis of Image-processing DNNs through Clustering-based Approaches

Towards a Change Taxonomy for Machine Learning Systems


Mostly deprecated. See https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries

Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline

De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences

Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies

Reduced Genome of the Gut Symbiotic Bacterium “Candidatus Benitsuchiphilus tojoi” Provides Insight Into Its Possible Roles in Ecology and Adaptation of the Host Insect

Genome Sequencing of Hericium coralloides by a Combination of PacBio RS II and Next-Generation Sequencing Platforms

Draft Genome Sequence of Putative 2-Methylisoborneol-Producing Pseudanabaena yagii Strain GIHE-NHR1, Isolated from the North Han River in South Korea.


Neighborhood Attention Extension. Bringing attention to a neighborhood near you!

Neighborhood Attention Transformer

Dilated Neighborhood Attention Transformer

All-In-One Metrical And Functional Structure Analysis With Neighborhood Attentions on Demixed Audio

Faster Neighborhood Attention: Reducing the O(n^2) Cost of Self
  Attention at the Threadblock Level


Code for the paper "Adversarially Regularized Autoencoders  (ICML 2018)" by Zhao, Kim, Zhang, Rush and LeCun

Adversarially Regularized Autoencoders

Adversarially Regularized Autoencoders for Generating Discrete Structures.

Enhance Long Text Understanding via Distilled Gist Detector from Abstractive Summarization


Bayesian Convolutional Neural Network with Variational Inference based on Bayes by Backprop in PyTorch.

Weight Uncertainty in Neural Networks

Variational Dropout and the Local Reparameterization Trick

A Comprehensive guide to Bayesian Convolutional Neural Network with Variational Inference

Uncertainty Estimations by Softplus normalization in Bayesian Convolutional Neural Networks with Variational Inference

ProbAct: A Probabilistic Activation Function for Deep Neural Networks


Python wrapper for OpenJTalk

Non-autoregressive Error Correction for CTC-based ASR with Phone-conditioned Masked LM

Dict-TTS: Learning to Pronounce with Prior Dictionary Knowledge for Text-to-Speech

Phoneme-aware Encoding for Prefix-tree-based Contextual ASR

MID-Attribute Speaker Generation Using Optimal-Transport-Based Interpolation of Gaussian Mixture Models


Lucid library adapted for PyTorch

Similarity and Matching of Neural Network Representations

Robust Feature-Level Adversaries are Interpretability Tools

A Unifying Principle for the Functional Organization of Visual Cortex

bioRxiv : the preprint server for biology

TorchEsegeta: Framework for Interpretability and Explainability of Image-based Deep Learning Models

DORA: Exploring Outlier Representations in Deep Neural Networks

Pruning for Feature-Preserving Circuits in CNNs

Visualizing the Diversity of Representations Learned by Bayesian Neural Networks

The Missing Curve Detectors of InceptionV1: Applying Sparse Autoencoders
  to InceptionV1 Early Vision

Feature Accentuation: Revealing 'What' Features Respond to in Natural
  Images

Improve Convolutional Neural Network Pruning by Maximizing Filter Variety


A library for debugging/inspecting machine learning classifiers and explaining their predictions

DeepHateExplainer: Explainable Hate Speech Detection in Under-resourced Bengali Language

Leveraging contextual embeddings and self-attention neural networks with bi-attention for sentiment analysis

Journal of Intelligent Information Systems

Classifying variety of customer's online engagement for churn prediction with mixed-penalty logistic regression

TSInterpret: A unified framework for time series interpretability

Unreasonable Effectiveness of Rule-Based Heuristics in Solving Russian SuperGLUE Tasks


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)


IPFS Papers (not specs)

Towards Blockchain-based Auditable Storage and Sharing of IoT Data

Droplet: Decentralized Authorization and Access Control for Encrypted Data Streams

A Decentralized Model for Spatial Data Digital Rights Management

ISPRS International Journal of Geo-Information

d-MABE: Distributed Multilevel Attribute-Based EMR Management and Applications

A Blockchain-Based e-Government Service for Quantity Surveyors


SMAC: The StarCraft Multi-Agent Challenge

QMIX: Monotonic Value Function Factorisation for Deep Multi-Agent Reinforcement Learning

The StarCraft Multi-Agent Challenge

A survey and critique of multiagent deep reinforcement learning

Learning Implicit Credit Assignment for Cooperative Multi-Agent Reinforcement Learning

Contrasting Centralized and Decentralized Critics in Multi-Agent Reinforcement Learning

Cooperative Exploration for Multi-Agent Deep Reinforcement Learning

Deep Implicit Coordination Graphs for Multi-agent Reinforcement Learning

Plan Better Amid Conservatism: Offline Multi-Agent Reinforcement Learning with Actor Rectification

Tesseract: Tensorised Actors for Multi-Agent Reinforcement Learning


A Web API that provides a family of lightweight interfaces for accessing Environmental Data resources.


A collection of tools for painting super-resolution images

Single-molecule localization microscopy

Simultaneous orientation and 3D localization microscopy with a Vortex point spread function

Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard

Rapid and efficient C-terminal labeling of nanobodies for DNA-PAINT

Toward Absolute Molecular Numbers in DNA-PAINT

Super-resolved visualization of single DNA-based tension sensors in cell adhesion

Quantification of Strand Accessibility in Biostable DNA Origami with Single-Staple Resolution

Principles of RNA recruitment to viral ribonucleoprotein condensates in a segmented dsRNA virus

nanoTRON: a Picasso module for MLP-based classification of super-resolution data

Super-resolution imaging and quantitative analysis of microtubule arrays in model neurons show that epothilone D increases the density but decreases the length and straightness of microtubules in axon-like processes


Bayesian optimisation & Reinforcement Learning library developped by Huawei Noah's Ark Lab

HEBO Pushing The Limits of Sample-Efficient Hyperparameter Optimisation

Tree-Structured Parzen Estimator: Understanding Its Algorithm Components and Their Roles for Better Empirical Performance

High-Dimensional Bayesian Optimisation with Variational Autoencoders and Deep Metric Learning

Saute RL: Almost Surely Safe Reinforcement Learning Using State Augmentation

Toward real-world automated antibody design with combinatorial Bayesian optimization

PFNs4BO: In-Context Learning for Bayesian Optimization

AntBO: Towards Real-World Automated Antibody Design with Combinatorial Bayesian Optimisation

Model-Based Offline Reinforcement Learning with Pessimism-Modulated Dynamics Belief

Are we Forgetting about Compositional Optimisers in Bayesian Optimisation?

Are Random Decompositions all we need in High Dimensional Bayesian Optimisation?


De novo assembler for single molecule sequencing reads using repeat graphs

Assembly of long, error-prone reads using repeat graphs

metaFlye: scalable long-read metagenome assembly using repeat graphs

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

Assembly of long error-prone reads using de Bruijn graphs

Efficient assembly of nanopore reads via highly accurate and intact error correction

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

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

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

HASLR: Fast Hybrid Assembly of Long Reads

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche


Pytorch implementation of BERT4Rec and Netflix VAE.

BERT4Rec: Sequential Recommendation with Bidirectional Encoder Representations from Transformer

Variational Autoencoders for Collaborative Filtering

Knowledge Transfer via Pre-training for Recommendation: A Review and Prospect

A Systematic Review and Replicability Study of BERT4Rec for Sequential Recommendation

From Implicit to Explicit feedback: A deep neural network for modeling sequential behaviours and long-short term preferences of online users

Rethinking Cross-Domain Sequential Recommendation under Open-World Assumptions

SLMRec: Empowering Small Language Models for Sequential Recommendation


A library for running membership inference attacks against ML models

Membership Inference Attacks against Machine Learning Models

Differential Privacy Protection Against Membership Inference Attack on Machine Learning for Genomic Data

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

Accurate Differentially Private Deep Learning on the Edge

IEEE Transactions on Parallel and Distributed Systems

Data Provenance via Differential Auditing


R package plspm

Multigroup Analysis using SmartPLS: Step-by-Step Guidelines for Business Research

Hidden danger: Unexpected scenario in the vector-parasite dynamics of leishmaniases in the Brazil side of triple border (Argentina, Brazil and Paraguay)

Contrasting responses of soil microbial biomass and extracellular enzyme activity along an elevation gradient on the eastern Qinghai-Tibetan Plateau

Plant-Soil Mediated Effects of Long-Term Warming on Soil Nematodes of Alpine Meadows on the Qinghai–Tibetan Plateau

Analyzing Word Embedding Through Structural Equation Modeling

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

Consistent time allocation fraction to vegetation green-up versus senescence across northern ecosystems despite recent climate change


[NeurIPS 2022] Denoising Diffusion Restoration Models -- Official Code Repository

Denoising Diffusion Restoration Models

GibbsDDRM: A Partially Collapsed Gibbs Sampler for Solving Blind Inverse Problems with Denoising Diffusion Restoration

Unsupervised Vocal Dereverberation with Diffusion-Based Generative Models

OmniSSR: Zero-shot Omnidirectional Image Super-Resolution using Stable
  Diffusion Model

DMPlug: A Plug-in Method for Solving Inverse Problems with Diffusion Models

Principled Probabilistic Imaging using Diffusion Models as Plug-and-Play
  Priors

Benchmarking the Fairness of Image Upsampling Methods


Tools for manipulating sequence graphs in the GFA and rGFA formats

A draft human pangenome reference

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

基因组蛋白质组与生物信息学报

The design and construction of reference pangenome graphs

Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana

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

A Chromosome Level Genome Assembly of a Winter Turnip Rape (Brassica rapa L.) to Explore the Genetic Basis of Cold Tolerance

RGFA: powerful and convenient handling of assembly graphs

Fast sequence to graph alignment using the graph wavefront algorithm

Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data

Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression


FairFace: Face Attribute Dataset for Balanced Race, Gender, and Age

Social Biases through the Text-to-Image Generation Lens

Fairness Testing: A Comprehensive Survey and Analysis of Trends

Canonical Saliency Maps: Decoding Deep Face Models

Class Attribute Inference Attacks: Inferring Sensitive Class Information by Diffusion-Based Attribute Manipulations

Comparing Deep Neural Nets with UMAP Tour


R Scripts to analyze deep lab cut point data and related data

Deep learning-based behavioral analysis reaches human accuracy and is capable of outperforming commercial solutions

Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology

Deep learning based behavioral analysis enables high precision rodent tracking and is capable of outperforming commercial solutions

Sensory conflict disrupts circadian rhythms in the sea anemone Nematostella vectensis

Lockbox enrichment facilitates manipulative and cognitive activities for mice


Code for ICLR 2020 paper "VL-BERT: Pre-training of Generic Visual-Linguistic Representations".

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

FashionBERT: Text and Image Matching with Adaptive Loss for Cross-modal Retrieval

InterBERT: Vision-and-Language Interaction for Multi-modal Pretraining

Unsupervised Vision-and-Language Pre-training Without Parallel Images and Captions

Probing Contextual Language Models for Common Ground with Visual Representations

Probing Text Models for Common Ground with Visual Representations

Leveraging Visual Knowledge in Language Tasks: An Empirical Study on Intermediate Pre-training for Cross-modal Knowledge Transfer

ICAF: Iterative Contrastive Alignment Framework for Multimodal Abstractive Summarization


flexible barcode and adapter removal

Flexbar 3.0 – SIMD and multicore parallelization

Simultaneous sequencing of genetic and epigenetic bases in DNA

Genome-wide analysis of the Dof gene family in durian reveals fruit ripening-associated and cultivar-dependent Dof transcription factors

De novo assembly of Persea americana cv. ‘Hass’ transcriptome during fruit development

Homeostatic plasticity fails at the intersection of autism-gene mutations and a novel class of common genetic modifiers

A gene expression signature in HER2+ breast cancer patients related to neoadjuvant chemotherapy resistance, overall survival, and disease-free survival

De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources

Mkt1 is required for RNAi-mediated silencing and establishment of heterochromatin in fission yeast

Identification of Novel Placentally Expressed Aspartic Proteinase in Humans

International journal of molecular sciences

mRNA expression and DNA methylation analysis of the inhibitory mechanism of H2O2 on the proliferation of A549 cells


Pronounced as "musician", musicnn is a set of pre-trained deep convolutional neural networks for music audio tagging.

musicnn: Pre-trained convolutional neural networks for music audio tagging

Learning Audio Embeddings with User Listening Data for Content-Based Music Recommendation

Cross-Modal Music-Video Recommendation: A Study of Design Choices

Analysis of Feature Representations for Anomalous Sound Detection

International Conference on Agents and Artificial Intelligence

Mood Classification Using Listening Data

Towards Musically Meaningful Explanations Using Source Separation

A Multimodal Single-Branch Embedding Network for Recommendation in Cold-Start and Missing Modality Scenarios

Fonts That Fit the Music: A Multimodal Design Trend Analysis of Lyric Videos


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

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

Anchor-based Plain Net for Mobile Image Super-Resolution

Collapsible Linear Blocks for Super-Efficient Super Resolution

Neural Network Quantization with AI Model Efficiency Toolkit (AIMET)

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


[CVPR2020] BiFuse: Monocular 360 Depth Estimation via Bi-Projection Fusion

HoHoNet: 360 Indoor Holistic Understanding with Latent Horizontal Features

Monocular spherical depth estimation with explicitly connected weak layout cues

Distortion-Aware Self-Supervised 360° Depth Estimation from A Single Equirectangular Projection Image


Coronavirus (COVID-19) UK Historical Data

Covid-19: Open-Data Resources for Monitoring, Modeling, and Forecasting the Epidemic

Open Data Resources for Fighting COVID-19

Testing and tracking in the UK: A dynamic causal modelling study

COVID-19 incidence and R decreased on the Isle of Wight after the launch of the Test, Trace, Isolate programme

Tracking and tracing in the UK: a dynamic causal modelling study

Visualising the Evolution of English Covid-19 Cases with Topological Data Analysis Ball Mapper


Prune a model while finetuning or training.

Movement Pruning: Adaptive Sparsity by Fine-Tuning

Train Large, Then Compress: Rethinking Model Size for Efficient Training and Inference of Transformers

Block Pruning For Faster Transformers

Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

What Matters In The Structured Pruning of Generative Language Models?

SwiftPruner: Reinforced Evolutionary Pruning for Efficient Ad Relevance

Data Pruning for Efficient Model Pruning in Neural Machine Translation

Findings of the Association for Computational Linguistics: EMNLP 2023


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

SliceGPT: Compress Large Language Models by Deleting Rows and Columns

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

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


A Python package to efficiently simulate non-Markovian open quantum systems with process tensors.

Efficient non-Markovian quantum dynamics using time-evolving matrix product operators

Non-Markovian quantum processes: Complete framework and efficient characterization

Exploiting the Causal Tensor Network Structure of Quantum Processes to Efficiently Simulate Non-Markovian Path Integrals

Efficient Exploration of Hamiltonian Parameter Space for Optimal Control of Non-Markovian Open Quantum Systems

Efficient real-time path integrals for non-Markovian spin-boson models


CARLA: A Python Library to Benchmark Algorithmic Recourse and Counterfactual Explanation Algorithms

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

Explaining Machine Learning Classifiers through Diverse Counterfactual Explanations

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

Explanations based on the Missing: Towards Contrastive Explanations with Pertinent Negatives

Actionable Recourse in Linear Classification

Proceedings of the Conference on Fairness, Accountability, and Transparency

FACE: Feasible and Actionable Counterfactual Explanations

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

Learning Model-Agnostic Counterfactual Explanations for Tabular Data

Towards Realistic Individual Recourse and Actionable Explanations in Black-Box Decision Making Systems

Getting a CLUE: A Method for Explaining Uncertainty Estimates

Inverse Classification for Comparison-based Interpretability in Machine Learning


Java tools for analyzing Drop-seq data

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

6th European Congress of Immunology, 1-4 September 2021, Virtual meeting.

Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease

A single-cell survey of Drosophila blood

Cell type prioritization in single-cell data

Single Cell Analysis Reveals Immune Cell-Adipocyte Crosstalk Regulating the Transcription of Thermogenic Adipocytes

HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations

Systematic comparative analysis of single cell RNA-sequencing methods

Insights into variation in meiosis from 31,228 human sperm genomes


Fast Fourier Transform-accelerated Interpolation-based  t-SNE (FIt-SNE)

Dimensionality reduction for visualizing single-cell data using UMAP

A high-bias, low-variance introduction to Machine Learning for physicists

Efficient Algorithms for t-distributed Stochastic Neighborhood Embedding

Heavy-tailed kernels reveal a finer cluster structure in t-SNE visualisations

MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2019, PT I

The Tumor Suppressor Role of Zinc Finger Protein 671 (ZNF671) in Multiple Tumors Based on Cancer Single-Cell Sequencing

Randomized Near Neighbor Graphs, Giant Components, and Applications in Data Science

Improving the Effectiveness and Efficiency of Stochastic Neighbour Embedding with Isolation Kernel

Embedding Functional Brain Networks in Low Dimensional Spaces Using Manifold Learning Techniques

SG-t-SNE-Π: Swift Neighbor Embedding of Sparse Stochastic Graphs


Thermal energy components for the Open Energy Modeling Framework (oemof).


Redshift fitting for spectroperfectionism

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar, and APOGEE-2 Data

The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: measurement of the BAO and growth rate of structure of the luminous red galaxy sample from the anisotropic correlation function between redshifts 0.6 and 1

Monthly Notices of the Royal Astronomical Society

The Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: Large-scale structure catalogues for cosmological analysis

The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: large-scale structure catalogues and measurement of the isotropic BAO between redshift 0.6 and 1.1 for the Emission Line Galaxy Sample

Validation of the Scientific Program for the Dark Energy Spectroscopic Instrument

The wide-field, multiplexed, spectroscopic facility WEAVE: Survey design, overview, and simulated implementation

The Spectroscopic Data Processing Pipeline for the Dark Energy Spectroscopic Instrument

Target Selection and Validation of DESI Emission Line Galaxies

CGM 2 I: The Extent of the Circumgalactic Medium Traced by Neutral Hydrogen

The DESI Survey Validation: Results from Visual Inspection of Bright Galaxies, Luminous Red Galaxies, and Emission-line Galaxies


A Large Quadcopter Swarm

Swarm Robotic Behaviors and Current Applications

A Fleet of Miniature Cars for Experiments in Cooperative Driving

Distributed Planning for Serving Cooperative Tasks with Time Windows: A Game Theoretic Approach

Decision-Making Among Bounded Rational Agents

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

M-SET: Multi-Drone Swarm Intelligence Experimentation with Collision Avoidance Realism


Julia package for tensor contractions and related operations

Hand-waving and interpretive dance: an introductory course on tensor networks

Journal of Physics A: Mathematical and Theoretical

Developments in the Tensor Network — from Statistical Mechanics to Quantum Entanglement

QuantumInformation.jl—A Julia package for numerical computation in quantum information theory

TeNeS: Tensor network solver for quantum lattice systems

Numerical evaluation of spin foam amplitudes beyond simplices

Highly Accurate Electronic Structure of Metallic Solids from Coupled-Cluster Theory with Nonperturbative Triple Excitations.


OpenEmbedded/Yocto layer for RISC-V Architecture


ILVR: Conditioning Method for Denoising Diffusion Probabilistic Models (ICCV 2021 Oral)

Diffusion Posterior Sampling for General Noisy Inverse Problems

Improving Diffusion Models for Inverse Problems using Manifold Constraints

EGSDE: Unpaired Image-to-Image Translation via Energy-Guided Stochastic Differential Equations

DOLCE: A Model-Based Probabilistic Diffusion Framework for Limited-Angle CT Reconstruction

GibbsDDRM: A Partially Collapsed Gibbs Sampler for Solving Blind Inverse Problems with Denoising Diffusion Restoration

Manifold Preserving Guided Diffusion

Pyramidal Denoising Diffusion Probabilistic Models

CycleNet: Rethinking Cycle Consistency in Text-Guided Diffusion for Image Manipulation

DOLPH: Diffusion Models for Phase Retrieval


scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis

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

基因组蛋白质组与生物信息学报

Deep Learning in Single-Cell Analysis

Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning

scRNA‐seq data analysis method to improve analysis performance


Hyperbolic Graph Convolutional Networks in PyTorch.

Graph Attention Networks

Poincaré Embeddings for Learning Hierarchical Representations

Hyperbolic Graph Convolutional Neural Networks

Hyperbolic Neural Networks

Discrete-time Temporal Network Embedding via Implicit Hierarchical Learning in Hyperbolic Space

Fully Hyperbolic Neural Networks

Hyperbolic Graph Neural Networks: A Review of Methods and Applications

κHGCN: Tree-likeness Modeling via Continuous and Discrete Curvature Learning

Pseudo-Riemannian Graph Convolutional Networks

Link Prediction without Graph Neural Networks


List of surgical tool datasets organised by task.

Kvasir-Instrument: Diagnostic and therapeutic tool segmentation dataset in gastrointestinal endoscopy

Data-Driven Visual Tracking in Retinal Microsurgery

Medical Image Computing and Computer-Assisted Intervention

Cataract-101-Video Dataset of 101 Cataract Surgeries

PROCEEDINGS OF THE 9TH ACM MULTIMEDIA SYSTEMS CONFERENCE (MMSYS'18)

Robotic Endoscope Control Via Autonomous Instrument Tracking


Official Repo for Ground-aware Monocular 3D Object Detection for Autonomous Driving / YOLOStereo3D: A Step Back to 2D for Efficient Stereo 3D Detection

Objects are Different: Flexible Monocular 3D Object Detection

MonoDTR: Monocular 3D Object Detection with Depth-Aware Transformer

OBMO: One Bounding Box Multiple Objects for Monocular 3D Object Detection

Star-Convolution for Image-Based 3D Object Detection

IEEE International Conference on Robotics and Automation


Sorted A-Prolog with Consistency Restoring rules.

Syntactic Conditions for Antichain Property in Consistency Restoring Prolog

Introducing Computer Science to High School Students Through Logic Programming

onlineSPARC: A Programming Environment for Answer Set Programming

A Preliminary Data-driven Analysis of Common Errors Encountered by Novice SPARC Programmers


An open-source implementation of SEAL for link prediction in open graph benchmark (OGB) datasets.

Link Prediction Based on Graph Neural Networks

Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning

Learning from Counterfactual Links for Link Prediction

Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction

Algorithm and System Co-design for Efficient Subgraph-based Graph Representation Learning

Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking

Revisiting Link Prediction: A Data Perspective

SUREL+: Moving from Walks to Sets for Scalable Subgraph-based Graph Representation Learning

Link Prediction without Graph Neural Networks


Microbial Populations as Clusters Of Gene Transfer

Meta Analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology

Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria

Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives


Identifying Blue Large Amplitude Pulsators from Gaia DR2 & ZTF DR3

Monthly notices of the Royal Astronomical Society

AT 2021loi: A Bowen Fluorescence Flare with a Rebrightening Episode Occurring in a Previously Known AGN

Automated SpectroPhotometric Image REDuction (ASPIRED) -- A Python-based spectral data reduction toolkit

Rapidly Evolving Transients in Archival ZTF Public Alerts


Linear mixed model for genomic analyses.

The germline genetic component of drug sensitivity in cancer cell lines

Length variation in short tandem repeats affects gene expression in natural populations of Arabidopsis thaliana

LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies

Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS

Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis

Gene-environment interactions using a Bayesian whole genome regression model

Adaptive protein evolution through length variation in short tandem repeats


An Automated Scanning Transmission Electron Microscope Guided by Sparse Data Analytics

Towards Automating Structural Discovery in Scanning Transmission Electron Microscopy

Towards Augmented Microscopy with Reinforcement Learning-Enhanced Workflows

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

Probe microscopy is all you need

Machine Learning: Science and Technology


The official repo of NBC & SpatialNet for multichannel speech separation, denoising, and dereverberation

SpatialNet: Extensively Learning Spatial Information for Multichannel Joint Speech Separation, Denoising and Dereverberation

Multichannel Long-Term Streaming Neural Speech Enhancement for Static and Moving Speakers

Multi-Channel Narrow-Band Deep Speech Separation with Full-Band Permutation Invariant Training

Multichannel Speech Separation with Narrow-band Conformer

NBC2: Multichannel Speech Separation with Revised Narrow-band Conformer


A knowledge graph and a set of tools for drug repurposing

Strategies for Pre-training Graph Neural Networks

Building a knowledge graph to enable precision medicine

SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization

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

A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective

Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery

Few-shot link prediction via graph neural networks for Covid-19 drug-repurposing

SMORE: Knowledge Graph Completion and Multi-hop Reasoning in Massive Knowledge Graphs

Probabilistic Entity Representation Model for Reasoning over Knowledge Graphs

Knowledge Graphs Meet Multi-Modal Learning: A Comprehensive Survey


Toward Multimodal Image-to-Image Translation

Mode Seeking Generative Adversarial Networks for Diverse Image Synthesis

Normalized Diversification

On the Evaluation of Conditional GANs

Physics-informed GANs for Coastal Flood Visualization

Generating Physically-Consistent Satellite Imagery for Climate Visualizations

Generative Transition Mechanism to Image-to-Image Translation via Encoded Transformation


Code and papers for the Siena Galaxy Atlas (SGA-2020).

unWISE tomography of Planck CMB lensing

Journal of Cosmology and Astroparticle Physics

unWISE Coadds: The Five-year Data Set

Publications of the Astronomical Society of the Pacific

Constraining the baryon abundance with the kinematic Sunyaev-Zel'dovich effect: Projected-field detection using Planck, WMAP, and unWISE

Cross-correlation of Planck CMB lensing with DESI-like LRGs

Characterizing the target selection pipeline for the Dark Energy Spectroscopic Instrument Bright Galaxy Survey

Siena Galaxy Atlas 2020

Baryon acoustic oscillations in the projected cross-correlation function between the eBOSS DR16 quasars and photometric galaxies from the DESI Legacy Imaging Surveys

Constraining the galaxy-halo connection of infrared-selected unWISE galaxies with galaxy clustering and galaxy-CMB lensing power spectra


A Tensorflow implementation of QANet for machine reading comprehension

Character-Aware Neural Language Models

How Much Reading Does Reading Comprehension Require? A Critical Investigation of Popular Benchmarks

Neural Arabic Question Answering

DRCD: a Chinese Machine Reading Comprehension Dataset

The art and practice of data science pipelines

EQuANt (Enhanced Question Answer Network)


Access and analyze historical weather and climate data with Python.

Explainable Multi-Agent Recommendation System for Energy-Efficient Decision Support in Smart Homes


Multiplexed Shotgun Genotyping

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species

A compartmentalized signaling network mediates crossover control in meiosis

A Major Locus Controls a Genital Shape Difference Involved in Reproductive Isolation Between Drosophila yakuba and Drosophila santomea

Hybrid dysgenesis in Drosophila virilis results in clusters of mitotic recombination and loss-of-heterozygosity but leaves meiotic recombination unaltered

Olfactory sensory neuron population expansions influence projection neuron adaptation and enhance odour tracking


Technology agnostic long read analysis pipeline for transcriptomes

Accurate isoform discovery with IsoQuant using long reads

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

bioRxiv : the preprint server for biology

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


Generating Vectors for DBpedia Entities via Word2Vec and Wikipedia Dumps. Questions? https://gitter.im/idio-opensource/Lobby

Wikipedia2Vec: An Efficient Toolkit for Learning and Visualizing the Embeddings of Words and Entities from Wikipedia

Knowledge Graph Embeddings and Explainable AI

Automatic distractor generation for multiple-choice English vocabulary questions

Research and practice in technology enhanced learning

Benchmark for Complex Answer Retrieval

Entity Commonsense Representation for Neural Abstractive Summarization

Efficient Text Classification Using Tree-structured Multi-linear Principal Component Analysis

New Embedded Representations and Evaluation Protocols for Inferring Transitive Relations

International ACM SIGIR Conference on Research and Development in Information Retrieval

An Automated Approach for Identification of Non-Functional Requirements using Word2Vec Model

International Journal of Advanced Computer Science and Applications

Predicting the Argumenthood of English Prepositional Phrases

A Comparison of Word Embeddings and N-gram Models for DBpedia Type and Invalid Entity Detection


Multi-Turn Response Selection for Chatbots with Deep Attention Matching Network

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

One Time of Interaction May Not Be Enough: Go Deep with an Interaction-over-Interaction Network for Response Selection in Dialogues

Meeting of the Association for Computational Linguistics

Proactive Human-Machine Conversation with Explicit Conversation Goals

What does BERT know about books, movies and music? Probing BERT for Conversational Recommendation

RECSYS 2020: 14TH ACM CONFERENCE ON RECOMMENDER SYSTEMS

IART: Intent-aware Response Ranking with Transformers in Information-seeking Conversation Systems

Discovering Dialog Structure Graph for Open-Domain Dialog Generation

Learning to Expand: Reinforced Pseudo-relevance Feedback Selection for Information-seeking Conversations


Exoplanet detection in RVs with DNest4 and GPs

Decoding the radial velocity variations of HD 41248 with ESPRESSO

Improving circumbinary planet detections by fitting their binary's apsidal precession

The SOPHIE search for northern extrasolar planets XVIII. Six new cold Jupiters, including one of the most eccentric exoplanet orbits

Scheduling strategies for the ESPRESSO follow-up of TESS targets

Monthly Notices of the Royal Astronomical Society

Scheduling ESPRESSO follow-up of TESS Targets. I. Myopic versus non-myopic sampling

Confronting compositional confusion through the characterisation of the sub-Neptune orbiting HD 77946


:bullettrain_front: Fast orthogonal polynomial transforms :surfer:

Fast algorithms using orthogonal polynomials

Fast and backward stable transforms between spherical harmonic expansions and bivariate Fourier series

A sparse spectral method on triangles

A fast and accurate algorithm for spherical harmonic analysis on HEALPix grids with applications to the cosmic microwave background radiation

Polynomial and rational measure modifications of orthogonal polynomials via infinite-dimensional banded matrix factorizations

Fast associated classical orthogonal polynomial transforms


Repository for all spatial data.

Assessing OpenStreetMap Data Using Intrinsic Quality Indicators: An Extension to the QGIS Processing Toolbox

Hepatitis B vaccination coverage across India: exploring the spatial heterogeneity and contextual determinants

Long-term trends in air quality in major cities in the UK and India: a view from space

Proximal and contextual correlates of childhood stunting in India: A geo-spatial analysis

Disaggregated analysis of birth averted due to family planning use in India: An evidence from NFHS-4 (2015–16)


Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Bakta: Rapid & standardized annotation of bacterial genomes via alignment-free sequence identification

Genomic Analysis Reveals New Integrative Conjugal Elements and Transposons in GBS Conferring Antimicrobial Resistance

Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis

Genomics of Tenacibaculum Species in British Columbia, Canada

Real-time genomic epidemiologic investigation of a multispecies plasmid-associated hospital outbreak of NDM-5-producing Enterobacterales infections

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

Genomic Epidemiologic Investigation of a Multispecies Hospital Outbreak of NDM-5-Producing Enterobacterales Infections

medRxiv : the preprint server for health sciences

StAP1 phage: an effective tool for treating methicillin-resistant Staphylococcus aureus infections

Emergence of High-Level Gentamicin Resistance in Streptococcus agalactiae Hypervirulent Serotype IV ST1010 (CC452) Strains by Acquisition of a Novel Integrative and Conjugative Element


AquaCrop-OSPy: Python implementation of AquaCrop-OS

AquaCrop-OS: An open source version of FAO’s crop water productivity model

AquaCrop-OSPy: Bridging the gap between research and practice in crop-water modeling


Beta-RecSys: Build, Evaluate and Tune Automated Recommender Systems

Neural Graph Collaborative Filtering

PROCEEDINGS OF THE 42ND INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL (SIGIR '19)

BERT4Rec: Sequential Recommendation with Bidirectional Encoder Representations from Transformer

KGAT: Knowledge Graph Attention Network for Recommendation

Personalized Top-N Sequential Recommendation via Convolutional Sequence Embedding

Variational Autoencoders for Collaborative Filtering

A Simple Convolutional Generative Network for Next Item Recommendation

Collaborative Memory Network for Recommendation Systems

Representing and Recommending Shopping Baskets with Complementarity, Compatibility and Loyalty

International Conference on Information and Knowledge Management

BETA-Rec: Build, Evaluate and Tune Automated Recommender Systems


The windpowerlib is a library to model the output of wind turbines and farms.

A Novel Power Curve Prediction Method for Horizontal-Axis Wind Turbines Using Artificial Neural Networks


Developer repository for the LATTE code

Enabling particle applications for exascale computing platforms

The international journal of high performance computing applications

Next generation extended Lagrangian first principles molecular dynamics

Quantum-Based Molecular Dynamics Simulations Using Tensor Cores

Quantum perturbation theory using Tensor cores and a deep neural network

Density-matrix based Extended Lagrangian Born-Oppenheimer Molecular Dynamics

Bringing discrete-time Langevin splitting methods into agreement with thermodynamics

Graph-based Quantum Response Theory and Shadow Born-Oppenheimer Molecular Dynamics

Shadow Energy Functionals and Potentials in Born-Oppenheimer Molecular Dynamics

A fast, dense Chebyshev solver for electronic structure on GPUs

Hybrid programming-model strategies for GPU offloading of electronic structure calculation kernels


Tutorials, examples, discussions, research proposals, and other resources related to fuzzing

An Empirical Study of OSS-Fuzz Bugs

RULF: Rust Library Fuzzing via API Dependency Graph Traversal

Evaluating Synthetic Bugs

IvySyn: Automated Vulnerability Discovery in Deep Learning Frameworks

Hopper: Interpretative Fuzzing for Libraries

FuzzingDriver: the Missing Dictionary to Increase Code Coverage in Fuzzers

Prompt Fuzzing for Fuzz Driver Generation

Homo in Machina: Improving Fuzz Testing Coverage via Compartment Analysis


Mobility as a Service API - data model, tests, and validation


Rayleigh: Pseudo-spectral MHD

Equatorially trapped convection in a rapidly rotating shallow shell

Constraining Global Solar Models through Helioseismic Analysis

Perspectives on Reproducibility and Sustainability of Open-Source Scientific Software from Seven Years of the Dedalus Project

MagIC v5.10: a two-dimensional message-passing interface (MPI) distribution for pseudo-spectral magnetohydrodynamics simulations in spherical geometry

Dataset for ApJ Letter: Confinement of the Solar Tachocline by Dynamo Action in the Radiative Interior

Zenodo (CERN European Organization for Nuclear Research)

Simulation data-set for ApJ Article: "Confinement of the Solar Tachocline by a Non-Axisymmetric Dynamo"


A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

Sustainable data analysis with Snakemake

Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Using prototyping to choose a bioinformatics workflow management system

uap: reproducible and robust HTS data analysis

Recent Advances in Data Engineering for Networking

Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology

A sustainable infrastructure concept for improved accessibility, reusability, and archival of research software

MolSSI and BioExcel Workflow Workshop 2018 Report

Converting Biomedical Text Annotated Resources into FAIR Research Objects with an Open Science Platform

The bdpar Package: Big Data Pipelining Architecture for R


Designing a Practical Degradation Model for Deep Blind Image Super-Resolution (ICCV, 2021) (PyTorch) - We released the training code!

SwinIR: Image Restoration Using Swin Transformer

DiffBIR: Towards Blind Image Restoration with Generative Diffusion Prior

Real-World Blind Super-Resolution via Feature Matching with Implicit High-Resolution Priors

Solving Diffusion ODEs with Optimal Boundary Conditions for Better Image Super-Resolution


Feature Pyramid and Hierarchical Boosting Network for Pavement Crack Detection

Defect Detection Methods for Industrial Products Using Deep Learning Techniques: A Review

Advances in deep learning methods for pavement surface crack detection and identification with visible light visual images

Developing a Free and Open-Source Semi-Automated Building Exterior Crack Inspection Software for Construction and Facility Managers

Image2PCI -- A Multitask Learning Framework for Estimating Pavement Condition Indices Directly from Images

DepthCrackNet: A Deep Learning Model for Automatic Pavement Crack Detection


MOODS: Motif Occurrence Detection Suite

Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation

Non-coding germline GATA3 variants alter chromatin topology and contribute to pathogenesis of acute lymphoblastic leukemia


The official code repo of "HTS-AT: A Hierarchical Token-Semantic Audio Transformer for Sound Classification and Detection"

Speech Commands: A Dataset for Limited-Vocabulary Speech Recognition

Large-scale Contrastive Language-Audio Pretraining with Feature Fusion and Keyword-to-Caption Augmentation

Cross-modal Prompts: Adapting Large Pre-trained Models for Audio-Visual Downstream Tasks

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


Public release of the TransCoder research project https://arxiv.org/pdf/2006.03511.pdf

Unsupervised Translation of Programming Languages

Execution-based Code Generation using Deep Reinforcement Learning

Syntax and Domain Aware Model for Unsupervised Program Translation

On ML-Based Program Translation: Perils and Promises

A Novel Approach for Automatic Program Repair using Round-Trip Translation with Large Language Models


Fast Global Registration

Fast Global Registration

A New Outlier Removal Strategy Based on Reliability of Correspondence Graph for Fast Point Cloud Registration

A Maximum Feasible Subsystem for Globally Optimal 3D Point Cloud Registration

Evolutionary Multitasking With Solution Space Cutting for Point Cloud Registration


A toolbox for worst-case validation of autonomous policies

A Survey of Algorithms for Black-Box Safety Validation of Cyber-Physical Systems

Finding Failures in High-Fidelity Simulation using Adaptive Stress Testing and the Backward Algorithm

How Do We Fail? Stress Testing Perception in Autonomous Vehicles


An R package implementing the UMAP dimensionality reduction method.

UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

Visualizing Large-scale and High-dimensional Data

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

Inferring and perturbing cell fate regulomes in human brain organoids

Structural and functional characterization of G protein–coupled receptors with deep mutational scanning

DeepACP: A Novel Computational Approach for Accurate Identification of Anticancer Peptides by Deep Learning Algorithm

Age-associated changes in lineage composition of the enteric nervous system regulate gut health and disease

Clustering with UMAP: Why and How Connectivity Matters

DeepT3_4: A Hybrid Deep Neural Network Model for the Distinction Between Bacterial Type III and IV Secreted Effectors

A transcriptome atlas of the mouse iris at single-cell resolution defines cell types and the genomic response to pupil dilation


Library for Bayesian inference via sequential Monte Carlo for quantum parameter estimation.

Hamiltonian Learning and Certification Using Quantum Resources

Quantum Hamiltonian learning using imperfect quantum resources

Accelerated randomized benchmarking

Quantum model averaging


software tools for haplotype assembly from sequence data

Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga

Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing

Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers

Efficient long single molecule sequencing for cost effective and accurate sequencing, haplotyping, and de novo assembly

HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data.

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


Repository containing experimentation platform on how to train, infer on wav2vec2 models.

CLSRIL-23: Cross Lingual Speech Representations for Indic Languages

Code Switched and Code Mixed Speech Recognition for Indic languages


Package for evaluating word embeddings

Learning General Purpose Distributed Sentence Representations via Large Scale Multi-task Learning

How to evaluate word embeddings? On importance of data efficiency and simple supervised tasks

A comparative evaluation and analysis of three generations of Distributional Semantic Models

Learning Numeral Embeddings

Word Similarity Datasets for Thai: Construction and Evaluation

Regional Differences in Information Privacy Concerns After the Facebook-Cambridge Analytica Data Scandal

Computer Supported Cooperative Work (CSCW)

Improving the state-of-the-art in Thai semantic similarity using distributional semantics and ontological information

Can language models learn analogical reasoning? Investigating training objectives and comparisons to human performance

Gating Mechanisms for Combining Character and Word-level Word Representations: An Empirical Study

Word Embedding Binarization with Semantic Information Preservation

International Conference on Computational Linguistics


Platform for direct visualization, analysis and reporting of soil organic carbon predictions and changes over time.


An automatic ML model optimization tool.

Multi-Modal Emotion recognition on IEMOCAP Dataset using Deep Learning

Auptimizer - an Extensible, Open-Source Framework for Hyperparameter Tuning

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


Generally Applicable Atomic-Charge Dependent London Dispersion Correction

Assessing Conformer Energies using Electronic Structure and Machine Learning Methods

International Journal of Quantum Chemistry

High‐throughput screening of spin states for transition metal complexes with spin‐polarized extended tight‐binding methods

CO Adsorption on the Surface of MgO from Periodic Coupled-Cluster Theory with Local Natural Orbitals: Adding to the Consensus

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


fastPM - A N-body Particle Mesh solver that scales

Learning to predict the cosmological structure formation

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

FastPM: a new scheme for fast simulations of dark matter and haloes

Iterative initial condition reconstruction

Large-scale dark matter simulations

Living Reviews in Computational Astrophysics

ICE-COLA: towards fast and accurate synthetic galaxy catalogues optimizing a quasi-N-body method

Cosmological reconstruction from galaxy light: neural network based light-matter connection

Journal of Cosmology and Astroparticle Physics

Halo bias in Lagrangian Space: Estimators and theoretical predictions

TARDIS. I. A Constrained Reconstruction Approach to Modeling the z ∼ 2.5 Cosmic Web Probed by Lyα Forest Tomography

A fast particle-mesh simulation of non-linear cosmological structure formation with massive neutrinos

Precision tests of CO and [CII] power spectra models against simulated intensity maps


CFE is a conceptual rainfall-runoff model with an implementation of the Basic Model Interface.

Comprehensive Analysis of the NOAA National Water Model: A Call for Heterogeneous Formulations and Diagnostic Model Selection

Journal of Geophysical Research: Atmospheres


Brain-inspired Cognitive Intelligence Engine (BrainCog) is a brain-inspired spiking neural network based platform for Brain-inspired Artificial Intelligence and simulating brains at multiple scales. The long term goal of BrainCog is to provide a comprehensive theory and system to decode the mechanisms and principles of human intelligence and its evolution, and develop artificial brains for brain-inspired conscious living AI in future Human-AI symbiotic Society.

Solving the spike feature information vanishing problem in spiking deep Q network with potential based normalization

Enhancing Efficient Continual Learning with Dynamic Structure Development of Spiking Neural Networks

Multi-compartment Neuron and Population Encoding improved Spiking Neural Network for Deep Distributional Reinforcement Learning

A brain-inspired intention prediction model and its applications to humanoid robot

TIM: An Efficient Temporal Interaction Module for Spiking Transformer

DPSNN: A Differentially Private Spiking Neural Network with Temporal Enhanced Pooling


The code of multi-attention deepfake detection

Multi-attentional Deepfake Detection

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

Block shuffling learning for Deepfake Detection


R functions for processing individual tree TLS point clouds

Estimation of Forest Growing Stock Volume with UAV Laser Scanning Data: Can It Be Done without Field Data?


SenseAct: A computational framework for developing real-world robot learning tasks

Benchmarking Reinforcement Learning Algorithms on Real-World Robots

Setting up a Reinforcement Learning Task with a Real-World Robot

A Survey on Reproducibility by Evaluating Deep Reinforcement Learning Algorithms on Real-World Robots

Reproducibility of Machine Learning: Terminology, Recommendations and Open Issues


A scene text recognition toolbox based on PyTorch

An End-to-End Trainable Neural Network for Image-Based Sequence Recognition and Its Application to Scene Text Recognition

ASTER: An Attentional Scene Text Recognizer with Flexible Rectification

IEEE transactions on pattern analysis and machine intelligence

Robust Scene Text Recognition with Automatic Rectification

Towards Accurate Scene Text Recognition with Semantic Reasoning Networks

Rosetta: Large scale system for text detection and recognition in images

On Recognizing Texts of Arbitrary Shapes with 2D Self-Attention

Revisiting Classification Perspective on Scene Text Recognition


AEC Challenge

ICASSP 2022 Acoustic Echo Cancellation Challenge

AECMOS: A Speech Quality Assessment Metric for Echo Impairment

F-T-LSTM based Complex Network for Joint Acoustic Echo Cancellation and Speech Enhancement

ICASSP 2023 Acoustic Echo Cancellation Challenge

Acoustic Echo Cancellation using Residual U-Nets

Real-time speech enhancement with dynamic attention span


Machine learning for transportation data imputation and prediction.

A Bayesian tensor decomposition approach for spatiotemporal traffic data imputation

Transportation Research Part C: Emerging Technologies

Bayesian Temporal Factorization for Multidimensional Time Series Prediction

Spatial-temporal traffic speed patterns discovery and incomplete data recovery via SVD-combined tensor decomposition

A nonconvex low-rank tensor completion model for spatiotemporal traffic data imputation

Low-Rank Autoregressive Tensor Completion for Spatiotemporal Traffic Data Imputation

Missing traffic data imputation and pattern discovery with a Bayesian augmented tensor factorization model

Filling the G_ap_s: Multivariate Time Series Imputation by Graph Neural Networks

Scalable low-rank tensor learning for spatiotemporal traffic data imputation

PriSTI: A Conditional Diffusion Framework for Spatiotemporal Imputation

Dynamic Collaborative Filtering Based on User Preference Drift and Topic Evolution


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


Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia

IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella

Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors

Prevalence of hypervirulent and carbapenem-resistant Klebsiella pneumoniae under divergent evolutionary patterns

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

Global Trends in Proteome Remodeling of the Outer Membrane Modulate Antimicrobial Permeability in Klebsiella pneumoniae

Characterization of phage resistance and phages capable of intestinal decolonization of carbapenem-resistant Klebsiella pneumoniae in mice


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

Eidetic 3D LSTM: A Model for Video Prediction and Beyond

International Conference on Learning Representations

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


Machine Learning for High Energy Physics.

Machine Learning in High Energy Physics Community White Paper

Test of lepton universality in b → s ℓ^+ ℓ^- decays

Analysis of neutral B-meson decays into two muons

Reweighting with Boosted Decision Trees

Amplitude analysis of B^0_s→ K^0_S K^±π^∓ decays

Measurement of CP violation in B^0→ D^*± D^∓ decays

Updated measurement of time-dependent
    CP
-violating observables in
    B ^0_s→ J/ψ K^+ K^-
 decays

Robust Jet Classifiers through Distance Correlation

Observation of the semileptonic decay
    B^+→ ppμ^+ν_μ

Search for the doubly charmed baryon
    _cc^+
 in the
    _c^+π^-π^+
 final state


The code to reproduce results from paper "MultiFiT: Efficient Multi-lingual Language Model Fine-tuning" https://arxiv.org/abs/1909.04761

A Corpus for Multilingual Document Classification in Eight Languages

Don't Use English Dev: On the Zero-Shot Cross-Lingual Evaluation of Contextual Embeddings

Semi-supervised Contextual Historical Text Normalization

Meeting of the Association for Computational Linguistics


Single-level and multi-level mediation analyses for any kind of data, with bootstrap-based significance testing. Neuroimaging-oriented functions allow for mediation effect parametric mapping (mapping of mediation effects across the brain) and multivariate mediation.

Hippocampal GABA enables inhibitory control over unwanted thoughts

Brain lesions disrupting addiction map to a common human brain circuit

Reorganization of brain networks and its association with general cognitive performance over the adult lifespan

Multiple brain networks mediating stimulus-pain relationships in humans

Human Extinction Learning Is Accelerated by an Angiotensin Antagonist via Ventromedial Prefrontal Cortex and Its Connections With Basolateral Amygdala

Brain structure is linked to the association between family environment and behavioral problems in children in the ABCD study

The Immediate and Sustained Positive Effects of Meditation on Resilience Are Mediated by Changes in the Resting Brain

What Is the Link Between Attention-Deficit/Hyperactivity Disorder and Sleep Disturbance? A Multimodal Examination of Longitudinal Relationships and Brain Structure Using Large-Scale Population-Based Cohorts

Severe nausea and vomiting in pregnancy: psychiatric and cognitive problems and brain structure in children

The morphometry of left cuneus mediating the genetic regulation on working memory


Python library to access Gene Expression Omnibus Database (GEO)

GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA

GeMI: interactive interface for transformer-based Genomic Metadata Integration

Database : the journal of biological databases and curation

IL-1β Induces SOCS2 Expression in Human Dendritic Cells

International journal of molecular sciences


A Python 3 Bitcoin blockchain parser

Knowledge Discovery in Cryptocurrency Transactions: A Survey

Steganographic Analysis of Blockchains

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

Illicit Activity Detection in Bitcoin Transactions using Timeseries Analysis

International Journal of Advanced Computer Science and Applications


Official outputs from the RDA DMP Common Standards WG

Data Management Planning: How Requirements and Solutions are Beginning to Converge

Open government data and environmental science: a federal Canadian perspective

Machine-Actionable Data Management Plans: A Knowledge Retrieval Approach to Automate the Assessment of Funders’ Requirements

Making Data Management Plans Machine Actionable: Templates and Tools

Data Management in Distributed, Federated Research Infrastructures: The Case of EPOS


Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

Machine learning for metagenomics: methods and tools

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

funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model

Prebiotic Driven Increases in IL-17A Do Not Prevent Campylobacter jejuni Colonization of Chickens

Differences between the Leaf Mycobiome of Coffea arabica and Wild Coffee Species and Their Modulation by Caffeine/Chlorogenic Acid Content

Galacto-oligosaccharides fed during gestation increase Rotavirus A specific antibodies in sow colostrum, modulate the microbiome, and reduce infectivity in neonatal piglets in a commercial farm setting


Apache Tomcat

A Manually-Curated Dataset of Fixes to Vulnerabilities of Open-Source Software

An In-depth Study of Java Deserialization Remote-Code Execution Exploits and Vulnerabilities

ACM Transactions on Software Engineering and Methodology

Guiding Greybox Fuzzing with Mutation Testing

Proceedings of the 32nd ACM SIGSOFT International Symposium on Software Testing and Analysis

On the Relationship between Self-Admitted Technical Debt Removals and Technical Debt Measures

Predicting technical debt from commit contents: reproduction and extension with automated feature selection

Using Distributed Representation of Code for Bug Detection

Quick remedy commits and their impact on mining software repositories

Automated Self-Admitted Technical Debt Tracking at Commit-Level: A Language-independent Approach


3.8% and 18.3% on CIFAR-10 and CIFAR-100

Wide Residual Networks

Learn To Pay Attention

Neural Attention Distillation: Erasing Backdoor Triggers from Deep Neural Networks

Regularizing Deep Neural Networks by Noise: Its Interpretation and Optimization

Decorrelated Batch Normalization

Shakedrop Regularization for Deep Residual Learning

Regularizing CNNs with Locally Constrained Decorrelations

Iterative Normalization: Beyond Standardization towards Efficient Whitening

Approximating the Gradient of Cross-Entropy Loss Function

Hybrid Discriminative-Generative Training via Contrastive Learning


Magic Copy is a Chrome extension that uses Meta's Segment Anything Model to extract a foreground object from an image and copy it to the clipboard.

Black-box Targeted Adversarial Attack on Segment Anything (SAM)

Segment Anything Meets Universal Adversarial Perturbation


Systemic is a C library for modeling exoplanetary radial velocities, with an R binding and a full GUI IDE.

The Solar Neighborhood XLIX: Nine Giant Planets Orbiting Nearby K Dwarfs, and the CHIRON Spectrograph's Radial Velocity Performance

A High-Precision NIR Survey for RV Variable Low-Mass Stars

Magellan/PFS Radial Velocities of GJ 9827, a Late K dwarf at 30 pc with Three Transiting Super-Earths


The Cannon 2: Compressed sensing edition

Isochrone ages for ∼3 million stars with the second Gaia data release

Monthly Notices of the Royal Astronomical Society

CHEMICAL TAGGING CAN WORK: IDENTIFICATION OF STELLAR PHASE-SPACE STRUCTURES PURELY BY CHEMICAL-ABUNDANCE SIMILARITY

Spectroscopy of the Young Stellar Association Price-Whelan 1: Origin in the Magellanic Leading Arm and Constraints on the Milky Way Hot Halo

Combined APOGEE-GALAH stellar catalogues using the Cannon

Kinetic Tomography. II. A Second Method for Mapping the Velocity Field of the Milky Way Interstellar Medium and a Comparison with Spiral Structure Models


Doing simple retrieval from LLM models at various context lengths to measure accuracy

The Llama 3 Herd of Models

Long Context Compression with Activation Beacon

LongAlign: A Recipe for Long Context Alignment of Large Language Models

BABILong: Testing the Limits of LLMs with Long Context
  Reasoning-in-a-Haystack

Make Your LLM Fully Utilize the Context

The Chronicles of RAG: The Retriever, the Chunk and the Generator

NeedleBench: Can LLMs Do Retrieval and Reasoning in 1 Million Context Window?

Extending Llama-3's Context Ten-Fold Overnight

Needle In A Multimodal Haystack

ThinK: Thinner Key Cache by Query-Driven Pruning


A circuit toolkit

Design Automation and Design Space Exploration for Quantum Computers

Logic Synthesis for Quantum Computing

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

Late Breaking Results: Reinforcement Learning for Scalable Logic Optimization with Graph Neural Networks


Convert 10x BAM files to the original FASTQs compatible with 10x pipelines

DISCO: a database of Deeply Integrated human Single-Cell Omics data

GepLiver: an integrative liver expression atlas spanning developmental stages and liver disease phases

Telomemore enables single-cell analysis of cell cycle and chromatin condensation


ACM Multimedia2020 University-1652: A Multi-view Multi-source Benchmark for Drone-based Geo-localization :helicopter: annotates 1652 buildings in 72 universities around the world.

Random Erasing Data Augmentation

Fine-tuning CNN Image Retrieval with No Human Annotation

Dual-path Convolutional Image-Text Embeddings with Instance Loss

ACM Transactions on Multimedia Computing, Communications, and Applications

Understanding Image Retrieval Re-Ranking: A Graph Neural Network Perspective

Multiple-environment Self-adaptive Network for Aerial-view Geo-localization

MuirBench: A Comprehensive Benchmark for Robust Multi-image
  Understanding

Visual and Object Geo-localization: A Comprehensive Survey

Towards Natural Language-Guided Drones: GeoText-1652 Benchmark with Spatially Relation Matching


Compute FID scores with PyTorch.

Contrastive Learning for Unpaired Image-to-Image Translation

Are GANs Created Equal? A Large-Scale Study

Scaling Autoregressive Models for Content-Rich Text-to-Image Generation

T2I-Adapter: Learning Adapters to Dig out More Controllable Ability for Text-to-Image Diffusion Models

ILVR: Conditioning Method for Denoising Diffusion Probabilistic Models

AdaBelief Optimizer: Adapting Stepsizes by the Belief in Observed Gradients

On Aliased Resizing and Surprising Subtleties in GAN Evaluation

Come-Closer-Diffuse-Faster: Accelerating Conditional Diffusion Models for Inverse Problems through Stochastic Contraction

GAN Compression: Efficient Architectures for Interactive Conditional GANs

Neural Actor: Neural Free-view Synthesis of Human Actors with Pose Control


Creative Commons Attribution 4.0 International

Project's architecture documentation


a CLI that provides a generic automation layer for assessing the security of ML models

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

Conference on Fairness, Accountability and Transparency

secml-malware: Pentesting Windows Malware Classifiers with Adversarial EXEmples in Python

Exploring Naming Conventions (and Defects) of Pre-trained Deep Learning Models in Hugging Face and Other Model Hubs

Testing autonomous vehicles and AI: perspectives and challenges from
  cybersecurity, transparency, robustness and fairness

AI Security Threats against Pervasive Robotic Systems: A Course for Next Generation Cybersecurity Workforce


R package hyperSpec can now be found at https://github.com/r-hyperspec/hyperSpec

Implementing the CRISPR/Cas9 Technology in Eucalyptus Hairy Roots Using Wood-Related Genes

Raman Spectroscopy-Based Measurements of Single-Cell Phenotypic Diversity in Microbial Populations

Low biodegradability of dissolved organic matter from Southeast Asian peat-draining rivers

Journal of Geophysical Research: Biogeosciences

Revealing the Chemical Composition of Birch Pollen Grains by Raman Spectroscopic Imaging

Diffuse reflectance spectroscopy characterises the functional chemistry of soil organic carbon in agricultural soils

Methane Production Rate during Anoxic Litter Decomposition Depends on Si Mass Fractions, Nutrient Stoichiometry, and Carbon Quality

Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition


A semidefinite program solver for the conformal bootstrap.

TASI Lectures on the Conformal Bootstrap

A Semidefinite Program Solver for the Conformal Bootstrap

Carving out OPE space and precise O(2) model critical exponents

Scaling the semidefinite program solver SDPB

Weizmann Lectures on the Numerical Conformal Bootstrap

The Gross-Neveu-Yukawa archipelago

autoboot: a generator of bootstrap equations with global symmetry

Bootstrapping mixed correlators in ��=4 Super Yang-Mills.

OPE coefficients in Argyres-Douglas theories

The Regge bootstrap, from linear to non-linear trajectories


Python implementation of the TT-Toolbox

Exponential Machines

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

Tensor Train decomposition on TensorFlow (T3F)

Approximation and sampling of multivariate probability distributions in the tensor train decomposition

Sobol Tensor Trains for Global Sensitivity Analysis

Calculating vibrational spectra of molecules using tensor train decomposition.

Ergodic Exploration Using Tensor Train: Applications in Insertion Tasks

Solution of the Fokker-Planck equation by cross approximation method in the tensor train format

tntorch: Tensor Network Learning with PyTorch

Iterative Power Algorithm for Global Optimization with Quantics Tensor Trains.

Journal of chemical theory and computation


EasyTransfer is designed to make the development of transfer learning in NLP applications easier.

Kaleido-BERT: Vision-Language Pre-training on Fashion Domain

FashionBERT: Text and Image Matching with Adaptive Loss for Cross-modal Retrieval

AdaBERT: Task-Adaptive BERT Compression with Differentiable Neural Architecture Search

Deep Transfer Learning for Automatic Speech Recognition: Towards Better Generalization

Meta-KD: A Meta Knowledge Distillation Framework for Language Model Compression across Domains

Meta Fine-Tuning Neural Language Models for Multi-Domain Text Mining

EasyNLP: A Comprehensive and Easy-to-use Toolkit for Natural Language Processing

EasyTransfer -- A Simple and Scalable Deep Transfer Learning Platform for NLP Applications


Starlink Software Collection

AST: A library for modelling and manipulating coordinate systems

Preservation through modernisation: The software of the H1 experiment at HERA

Phase-resolved spectroscopy of Gaia14aae: line emission from near the white dwarf surface

Monthly notices of the Royal Astronomical Society

SDSS J124043.01+671034.68: the partially burned remnant of a low-mass white dwarf that underwent thermonuclear ignition?

The General Single-Dish Data format: A retrospective


A Python library for amortized Bayesian workflows using generative neural networks.

BayesFlow: Learning complex stochastic models with invertible neural networks

Amortized Bayesian model comparison with evidential deep learning

Detecting Model Misspecification in Amortized Bayesian Inference with Neural Networks

JANA: Jointly Amortized Neural Approximation of Complex Bayesian Models

A General Integrative Neurocognitive Modeling Framework to Jointly Describe EEG and Decision-making on Single Trials

BayesFlow: Amortized Bayesian Workflows With Neural Networks

Neural superstatistics for Bayesian estimation of dynamic cognitive models


A differentiable bridge between phase space and Fock space

A Quadratic Speedup in the Optimization of Noisy Quantum Optical Circuits

A Quantum Optical Recurrent Neural Network for Online Processing of Quantum Times Series

Seeding Gaussian boson samplers with single photons for enhanced state generation


The prime repository for state-of-the-art Multilingual Question Answering research and development.

Learning Cross-Lingual IR from an English Retriever

MuMuQA: Multimedia Multi-Hop News Question Answering via Cross-Media Knowledge Extraction and Grounding

UDAPDR: Unsupervised Domain Adaptation via LLM Prompting and Distillation of Rerankers

Rethinking the Role of Token Retrieval in Multi-Vector Retrieval

QACHECK: A Demonstration System for Question-Guided Multi-Hop Fact-Checking

Towards Robust Neural Retrieval with Source Domain Synthetic Pre-Finetuning

International Conference on Computational Linguistics

Moving Beyond Downstream Task Accuracy for Information Retrieval Benchmarking

PrimeQA: The Prime Repository for State-of-the-Art Multilingual Question Answering Research and Development


ReFT: Representation Finetuning for Language Models

UltraFeedback: Boosting Language Models with High-quality Feedback

A Primer on the Inner Workings of Transformer-based Language Models

pyvene: A Library for Understanding and Improving PyTorch Models via
  Interventions

Towards Incremental Learning in Large Language Models: A Critical Review


Code for our ICCV 2021 Paper "OadTR: Online Action Detection with Transformers".

Video-Based Automatic Baby Motion Analysis for Early Neurological Disorder Diagnosis: State of the Art and Future Directions

Continual Transformers: Redundancy-Free Attention for Online Inference

Efficient Online Processing with Deep Neural Networks


Pytorch implementation for "Decoupled attention network for text recognition".

Decoupled Attention Network for Text Recognition

Text Recognition in the Wild: A Survey

Recognition of Handwritten Chinese Text by Segmentation: A Segment-Annotation-Free Approach

Revisiting Scene Text Recognition: A Data Perspective

Reciprocal Feature Learning via Explicit and Implicit Tasks in Scene Text Recognition


Estimate recombination rates from population genetic data

The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat

Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus

Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape


The official codes for "PMC-LLaMA: Towards Building Open-source Language Models for Medicine"

LLaMA: Open and Efficient Foundation Language Models

Leveraging Biomolecule and Natural Language through Multi-Modal
  Learning: A Survey

Large Language Models for Medicine: A Survey

Hippocrates: An Open-Source Framework for Advancing Large Language
  Models in Healthcare

RaTEScore: A Metric for Radiology Report Generation


official code repo for paper "CogView2: Faster and Better Text-to-Image Generation via Hierarchical Transformers"

CogView: Mastering Text-to-Image Generation via Transformers

Toward Verifiable and Reproducible Human Evaluation for Text-to-Image Generation

Auditing Gender Presentation Differences in Text-to-Image Models


Classical molecular simulation code

Exploring the Potential of a Highly Scalable Metal-Organic Framework CALF-20 for Selective Gas Adsorption at Low Pressure

Correlation between structure and dynamics of CO2 confined in Mg-MOF-74 and the role of inter-crystalline space: A molecular dynamics simulation study

Quantifying the Uncertainty of Force Field Selection on Adsorption Predictions in MOFs

Journal of Chemical Theory and Computation


Lung medical image analysis and visualisation software for Matlab.

CT image segmentation for inflamed and fibrotic lungs using a multi-resolution convolutional neural network

Spectral graph theory efficiently characterizes ventilation heterogeneity in lung airway networks

Tapering Analysis of Airways with Bronchiectasis

A Fissure-Aided Registration Approach for Automatic Pulmonary Lobe Segmentation Using Deep Learning

Quantitative Analysis of Radiation-Associated Parenchymal Lung Change

In Silico Ventilation Within the Dose-Volume is Predictive of Lung Function Post-radiation Therapy in Patients with Lung Cancer

Evaluation of automated airway morphological quantification for assessing fibrosing lung disease

Development of a Multi-Task Learning V-Net for Pulmonary Lobar Segmentation on Computed Tomography and Application to Diseased Lungs

Right Ventricular and Pulmonary Computed Tomography Assessments in Paradoxical Low-Flow Low-Gradient Aortic Stenosis Undergoing Transcatheter Aortic Valve Replacement

Structural heart : the journal of the Heart Team


A modular PyTorch library for optical flow estimation using neural networks

FlowNet: Learning Optical Flow with Convolutional Networks

PWC-Net: CNNs for Optical Flow Using Pyramid, Warping, and Cost Volume

RAFT: Recurrent All-Pairs Field Transforms for Optical Flow

Volumetric Correspondence Networks for Optical Flow

Displacement-Invariant Matching Cost Learning for Accurate Optical Flow Estimation

DCVNet: Dilated Cost Volume Networks for Fast Optical Flow


Implements the Tsetlin Machine, Coalesced Tsetlin Machine, Convolutional Tsetlin Machine, Regression Tsetlin Machine, and Weighted Tsetlin Machine, with support for continuous features, drop clause, Type III Feedback, focused negative sampling, multi-task classifier, autoencoder, literal budget, and one-vs-one multi-class classifier. TMU is written in Python with wrappers for C and CUDA-based clause evaluation and updating.

The regression Tsetlin machine: a novel approach to interpretable nonlinear regression

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

Tsetlin Machine Embedding: Representing Words Using Logical Expressions

Learning Minimalistic Tsetlin Machine Clauses with Markov Boundary-Guided Pruning


The Pile is a large, diverse, open source language modelling data set that consists of many smaller datasets combined together.

The Pile: An 800GB Dataset of Diverse Text for Language Modeling

A Survey on Data Selection for Language Models

Understanding LLMs: A Comprehensive Overview from Training to Inference

Taken out of context: On measuring situational awareness in LLMs

Datasheet for the Pile

JUWELS Booster -- A Supercomputer for Large-Scale AI Research

Generalization v.s. Memorization: Tracing Language Models' Capabilities Back to Pretraining Data


NequIP is a code for building E(3)-equivariant interatomic potentials

E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials

Towards universal neural network potential for material discovery applicable to arbitrary combination of 45 elements

Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations

Fast Uncertainty Estimates in Deep Learning Interatomic Potentials

Complexity of many-body interactions in transition metals via machine-learned force fields from the TM23 data set

DPA-2: Towards a universal large atomic model for molecular and material simulation

Data efficiency and extrapolation trends in neural network interatomic potentials

Physics-Inspired Neural Graph ODE for Long-term Dynamical Simulation

Beyond MD17: the reactive xxMD dataset

Performance Assessment of Universal Machine Learning Interatomic
  Potentials: Challenges and Directions for Materials' Surfaces


Barnes-Hut t-SNE

A method for the generation of human stem cell-derived alpha cells

Ventricular-Subventricular Zone Contact by Glioblastoma is Not Associated with Molecular Signatures in Bulk Tumor Data

Self-Supervised Learning from Web Data for Multimodal Retrieval

RETRACTED ARTICLE: AKT3-mediated IWS1 phosphorylation promotes the proliferation of EGFR-mutant lung adenocarcinomas through cell cycle-regulated U2AF2 RNA splicing

The Stars of the HETDEX Survey. I. Radial Velocities and Metal-poor Stars from Low-resolution Stellar Spectra

PixelSNE: Visualizing Fast with Just Enough Precision via Pixel-Aligned Stochastic Neighbor Embedding

Stochastic cluster embedding

T-SNE Is Not Optimized to Reveal Clusters in Data

SG-t-SNE-Π: Swift Neighbor Embedding of Sparse Stochastic Graphs


LabStreamingLayer super repository comprising submodules for LSL and associated apps.

Detecting and Quantifying Mind Wandering during Simulated Driving

Validating Deep Neural Networks for Online Decoding of Motor Imagery Movements from EEG Signals

Walking through Architectural Spaces: The Impact of Interior Forms on Human Brain Dynamics

Understanding Minds in Real-World Environments: Toward a Mobile Cognition Approach

A Riemannian Modification of Artifact Subspace Reconstruction for EEG Artifact Handling

Breeze: Sharing Biofeedback Through Wearable Technologies

PROCEEDINGS OF THE 2018 CHI CONFERENCE ON HUMAN FACTORS IN COMPUTING SYSTEMS (CHI 2018)

Optical imaging and spectroscopy for the study of the human brain: status report

Real-time synthesis of imagined speech processes from minimally invasive recordings of neural activity

Decoding Movement From Electrocorticographic Activity: A Review

Mobile Brain/Body Imaging (MoBI) of Physical Interaction with Dynamically Moving Objects


An Open-Source Package for Textual Adversarial Attack.

OpenAttack: An Open-source Textual Adversarial Attack Toolkit

Triggerless Backdoor Attack for NLP Tasks with Clean Labels

On Robustness and Bias Analysis of BERT-based Relation Extraction

Rethinking Textual Adversarial Defense for Pre-Trained Language Models

InterroLang: Exploring NLP Models and Datasets through Dialogue-based Explanations

Disentangled Contrastive Learning for Learning Robust Textual Representations

Distinguishing Non-natural from Natural Adversarial Samples for More Robust Pre-trained Language Model

RMLM: A Flexible Defense Framework for Proactively Mitigating Word-level Adversarial Attacks

Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

HAT4RD: Hierarchical Adversarial Training for Rumor Detection in Social Media

Rumor Detection on Social Media with Hierarchical Adversarial Training


Official repository for "SimpleTOD: A Simple Language Model for Task-Oriented Dialogue"

Knowledge-Aware Graph-Enhanced GPT-2 for Dialogue State Tracking

Controllable Dialogue Simulation with In-Context Learning

Diable: Efficient Dialogue State Tracking as Operations on Tables

JoTR: A Joint Transformer and Reinforcement Learning Framework for Dialog Policy Learning


An open-source impl. of Large Reconstruction Models

LRM: Large Reconstruction Model for Single Image to 3D

CRM: Single Image to 3D Textured Mesh with Convolutional Reconstruction
  Model

MVDiffusion++: A Dense High-resolution Multi-view Diffusion Model for
  Single or Sparse-view 3D Object Reconstruction

VFusion3D: Learning Scalable 3D Generative Models from Video Diffusion Models

VideoMV: Consistent Multi-View Generation Based on Large Video
  Generative Model

ComboVerse: Compositional 3D Assets Creation Using Spatially-Aware
  Diffusion Guidance

ZeroShape: Regression-based Zero-shot Shape Reconstruction

MVD^2: Efficient Multiview 3D Reconstruction for Multiview Diffusion

GVGEN: Text-to-3D Generation with Volumetric Representation

ThemeStation: Generating Theme-Aware 3D Assets from Few Exemplars


A versatile aligning pipeline for bisulfite sequencing data

Introduction to Single-Cell DNA Methylation Profiling Methods

Integrating Epigenomics into the Understanding of Biomedical Insight

Epigenetics and Early Life Stress: Experimental Brood Size Affects DNA Methylation in Great Tits (Parus major)


A toolbox for improving metagenome-assembled genomes.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage

Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis

Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings


Project OCELoT: an Open, Collaborative Evaluation Leaderboard of Translations

Findings of the 2020 Conference on Machine Translation (WMT20)

Empirical Methods in Natural Language Processing

Findings of the 2021 Conference on Machine Translation (WMT21)

compare-mt: A Tool for Holistic Comparison of Language Generation Systems

Findings of the 2023 Conference on Machine Translation (WMT23): LLMs Are Here but Not Quite There Yet

Proceedings of the Eighth Conference on Machine Translation


DeepLab-ResNet rebuilt in TensorFlow

Incremental Learning Techniques for Semantic Segmentation

Towards Image Understanding from Deep Compression without Decoding

Knowledge Distillation for Incremental Learning in Semantic Segmentation

Adversarial Learning and Self-Teaching Techniques for Domain Adaptation in Semantic Segmentation

Panoramic Robust PCA for Foreground-Background Separation on Noisy, Free-Motion Camera Video

GeneSIS-RT: Generating Synthetic Images for training Secondary Real-world Tasks

Unsupervised Domain Adaptation with Multiple Domain Discriminators and Adaptive Self-Training

Multi-Scale, Class-Generic, Privacy-Preserving Video


Binarized Neural Network (BNN) for pytorch

Xcel-RAM: Accelerating Binary Neural Networks in High-Throughput SRAM Compute Arrays

Discretization Based Solutions for Secure Machine Learning Against Adversarial Attacks

Improving Noise Tolerance of Mixed-Signal Neural Networks

Combinatorial Attacks on Binarized Neural Networks

ASTERYX: A model-Agnostic SaT-basEd appRoach for sYmbolic and score-based eXplanations

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

Always-On 674uW @ 4GOP/s Error Resilient Binary Neural Networks with Aggressive SRAM Voltage Scaling on a 22nm IoT End-Node

Mirror Descent View for Neural Network Quantization

Exploring the Back Alleys: Analysing The Robustness of Alternative Neural Network Architectures against Adversarial Attacks


中文法律对话语言模型

Large Language Models in Law: A Survey

LawBench: Benchmarking Legal Knowledge of Large Language Models

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

AviationGPT: A Large Language Model for the Aviation Domain

LawGPT: A Chinese Legal Knowledge-Enhanced Large Language Model

Leveraging Large Language Models for Relevance Judgments in Legal Case
  Retrieval

MING-MOE: Enhancing Medical Multi-Task Learning in Large Language Models
  with Sparse Mixture of Low-Rank Adapter Experts


Excimontec is an open-source KMC simulation software package for modeling the optoelectronic processes in organic semiconductor materials and devices, such as OPVs, OLEDs, and more.

Theoretical description of charge transport in disordered organic semiconductors

Developing understanding of organic photovoltaic devices: kinetic Monte Carlo models of geminate and non-geminate recombination, charge transport and charge extraction

Simulating charge transport in organic semiconductors and devices: a review

Reports on progress in physics. Physical Society (Great Britain)

Advances in modeling the physics of disordered organic electronic devices

Handbook of Organic Materials for Electronic and Photonic Devices

Excimontec v1.0: An Open-Source Software Tool for Kinetic Monte Carlo Simulations of Organic Electronic Devices


A repository for maintaing the fave-align and fave-extract toolkits

A Web Application for Automated Dialect Analysis

North American Chapter of the Association for Computational Linguistics

Boomer Peak or Gen X Cliff? From SVS to LBMS in Georgia English

Dialect levelling and Cockney diphthong shift reversal in South East England: the case of the Debden Estate

Predicting TED Talk Ratings from Language and Prosody

goose-fronting in Received Pronunciation across time: A trend study


Jack the Reader

Utilizing BERT for Aspect-Based Sentiment Analysis via Constructing Auxiliary Sentence

Making Neural QA as Simple as Possible but not Simpler

NLProlog: Reasoning with Weak Unification for Question Answering in Natural Language

Context-Guided BERT for Targeted Aspect-Based Sentiment Analysis

SubjQA: A Dataset for Subjectivity and Review Comprehension

Jack the Reader - A Machine Reading Framework


Parameterizing neural power spectra into periodic & aperiodic components.

Decomposing age effects in EEG alpha power

Automated EEG mega-analysis I: Spectral and amplitude characteristics across studies

Regional healthy brain activity, glioma occurrence and symptomatology

Impaired spatial learning and suppression of sharp wave ripples by cholinergic activation at the goal location

L-dopa treatment increases oscillatory power in the motor cortex of Parkinson's disease patients

Resting state activity and connectivity of the nucleus basalis of Meynert and globus pallidus in Lewy body dementia and Parkinson's disease dementia

Alteration of Excitation/Inhibition Imbalance in the Hippocampus and Amygdala of Drug-Resistant Epilepsy Patients Treated with Acute Vagus Nerve Stimulation

Developmental trajectories of EEG aperiodic and periodic power: Implications for understanding the timing of thalamocortical development during infancy

bioRxiv : the preprint server for biology

Test-retest reliability of spectral parameterization by 1/fcharacterization usingSpecParam

Vestibular loss disrupts visual reactivity in the alpha EEG rhythm


DataComp: In search of the next generation of multimodal datasets

The Devil is in the Details: A Deep Dive into the Rabbit Hole of Data Filtering

Blind Baselines Beat Membership Inference Attacks for Foundation Models

Variance Alignment Score: A Simple But Tough-to-Beat Data Selection
  Method for Multimodal Contrastive Learning

CLIPLoss and Norm-Based Data Selection Methods for Multimodal Contrastive Learning


General Toolkit for Modeling Radial Velocity Data

RadVel: The Radial Velocity Modeling Toolkit

Publications of the Astronomical Society of the Pacific

Age Determination in Upper Scorpius with Eclipsing Binaries

Masses and compositions of three small planets orbiting the nearby M dwarf L231-32 (TOI-270) and the M dwarf radius valley

Monthly Notices of the Royal Astronomical Society

Three’s Company: An Additional Non-transiting Super-Earth in the Bright HD 3167 System, and Masses for All Three Planets

Four Sub-Saturns with Dissimilar Densities: Windows into Planetary Cores and Envelopes

The CARMENES Search for Exoplanets around M Dwarfs: A Low-mass Planet in the Temperate Zone of the Nearby K2-18

zeus: a PYTHON implementation of ensemble slice sampling for efficient Bayesian parameter inference

Monthly notices of the Royal Astronomical Society

K2-66b and K2-106b: Two Extremely Hot Sub-Neptune-size Planets with High Densities

New Insights on Planet Formation in WASP-47 from a Simultaneous Analysis of Radial Velocities and Transit Timing Variations

Two Small Transiting Planets and a Third Body Orbiting HD 106315