ENMTools R Package

Climate change and the future restructuring of Neotropical anuran biodiversity

Potential distributions of Bacillus anthracis and Bacillus cereus biovar anthracis causing anthrax in Africa

Potential migratory routes of Urania boisduvalii (Lepidoptera: Uraniidae) among host plant populations

Diversity and Distributions: A journal of biological invasions and biodiversity

Predicting Distribution of the Asian Longhorned Beetle, Anoplophora glabripennis (Coleoptera: Cerambycidae) and Its Natural Enemies in China

Climate change may induce connectivity loss and mountaintop extinction in Central American forests

Modeling and mapping the habitat suitability and the potential distribution of Arboviruses vectors in Morocco

Potentially suitable habitats of Daodi goji berry in China under climate change

Potential Distribution of the Biocontrol Agent Toxorhynchites rutilus By 2070.

Journal of the American Mosquito Control Association

Linking Habitat and Associated Abiotic Conditions to Predict Fish Hotspots Distribution Areas within La Paz Bay: Evaluating Marine Conservation Areas

Prediction of Suitable Habitat Distribution of Cryptosphaeria pullmanensis in the World and China under Climate Change


Use the HYSPLIT model from inside R and do more with it

Marine and terrestrial influences on ice nucleating particles during continuous springtime measurements in an Arctic oilfield location

Summertime surface PM1 aerosol composition and size by source region at the Lampedusa island in the central Mediterranean Sea

Chemical composition and source apportionment of atmospheric aerosols on the Namibian coast

Combining Regulatory Instruments and Low-Cost Sensors to Quantify the Effects of 2020 California Wildfires on PM2.5 in San Joaquin Valley


Automatic fingering generator for piano scores

Score Difficulty Analysis for Piano Performance Education based on Fingering

Optimizing piano practice with a utility-based scaffold

Combining piano performance dimensions for score difficulty classification

Piano Fingering with Reinforcement Learning

Passive Haptic Rehearsal for Accelerated Piano Skill Acquisition


A versatile simulation and optimization platform for power-system planning and operations.


Emissions Modeling Framework (EMF)


Count bases in BAM/CRAM files

Canine SARS-CoV-2 infection

Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer

Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma

Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer

Circulating tumour cells from patients with colorectal cancer have cancer stem cell hallmarks in ex vivo culture

Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma

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

Neoantigen quality predicts immunoediting in survivors of pancreatic cancer

Multiplex PCR and Next Generation Sequencing for the Non-Invasive Detection of Bladder Cancer


Signature Analysis and Visualization for Single-Cell RNA-seq

Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis

TAK1 deficiency promotes liver injury and tumorigenesis via ferroptosis and macrophage cGAS-STING signalling

An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability

SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance

Interactive, integrated analysis of single-cell transcriptomic and phylogenetic data with PhyloVision


An R package  making it easy to query, preview, download and preprocess multiple kinds of spatial data  via R. All beta.

Mammals adjust diel activity across gradients of urbanization

A Machine Learning Based Downscaling Approach to Produce High Spatio-Temporal Resolution Land Surface Temperature of the Antarctic Dry Valleys from MODIS Data


pytorch implementation for "PointNet: Deep Learning on Point Sets for 3D Classification and Segmentation"  https://arxiv.org/abs/1612.00593

Laser-Based People Detection and Obstacle Avoidance for a Hospital Transport Robot

InOR-Net: Incremental 3-D Object Recognition Network for Point Cloud Representation

Duodepth: Static Gesture Recognition Via Dual Depth Sensors

International Conference on Information Photonics

Explaining Deep Neural Networks for Point Clouds using Gradient-based Visualisations

Gesture Recognition with Keypoint and Radar Stream Fusion for Automated Vehicles

Crystal structure identification with 3D convolutional neural networks
  with application to high-pressure phase transitions in SiO_2


RocketQA, dense retrieval for information retrieval and question answering, including both Chinese and English state-of-the-art models.

RocketQA: An Optimized Training Approach to Dense Passage Retrieval for Open-Domain Question Answering

ColBERTv2: Effective and Efficient Retrieval via Lightweight Late Interaction

RocketQAv2: A Joint Training Method for Dense Passage Retrieval and Passage Re-ranking

Dense Text Retrieval Based on Pretrained Language Models: A Survey

PAIR: Leveraging Passage-Centric Similarity Relation for Improving Dense Passage Retrieval

Meeting of the Association for Computational Linguistics

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

DuReader_retrieval: A Large-scale Chinese Benchmark for Passage Retrieval from Web Search Engine

UniMS-RAG: A Unified Multi-source Retrieval-Augmented Generation for Personalized Dialogue Systems

DORIS-MAE: Scientific Document Retrieval using Multi-level Aspect-based Queries

Large Language Models as Source Planner for Personalized Knowledge-grounded Dialogue


[ICLR 2022] Official implementation of the paper "DAB-DETR: Dynamic Anchor Boxes are Better Queries for DETR"

DINO: DETR with Improved DeNoising Anchor Boxes for End-to-End Object Detection

DN-DETR: Accelerate DETR Training by Introducing Query DeNoising

Mask DINO: Towards A Unified Transformer-based Framework for Object Detection and Segmentation

To Make Yourself Invisible with Adversarial Semantic Contours


Keras implementation of a CNN network for age and gender estimation

Efficient facial representations for age, gender and identity recognition in organizing photo albums using multi-output ConvNet

Bias, awareness, and ignorance in deep-learning-based face recognition

Improving Borderline Adulthood Facial Age Estimation through Ensemble Learning

Robustness, Evaluation and Adaptation of Machine Learning Models in the Wild

Active Assessment of Prediction Services as Accuracy Surface Over Attribute Combinations


Semi Supervised Learning for Medical Image Segmentation, a collection of literature reviews and code implementations.

Semi-supervised Learning for Network-Based Cardiac MR Image Segmentation

Medical Image Computing and Computer-Assisted Intervention

Deep Adversarial Networks for Biomedical Image Segmentation Utilizing Unannotated Images

Efficient Semi-supervised Gross Target Volume of Nasopharyngeal Carcinoma Segmentation via Uncertainty Rectified Pyramid Consistency

Semi-Supervised Brain Lesion Segmentation with an Adapted Mean Teacher Model

Semi-Supervised Medical Image Segmentation via Cross Teaching between CNN and Transformer

Mutual Consistency Learning for Semi-supervised Medical Image Segmentation

Learning with Limited Annotations: A Survey on Deep Semi-Supervised Learning for Medical Image Segmentation

Local and Global Structure-Aware Entropy Regularized Mean Teacher Model for 3D Left Atrium Segmentation

Uncertainty guided semi-supervised segmentation of retinal layers in OCT images

Exploring Smoothness and Class-Separation for Semi-supervised Medical Image Segmentation


A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum

Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients

Diversity of Mycobacterium tuberculosis across Evolutionary Scales

Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses

Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms

Population Bottlenecks and Intra-host Evolution During Human-to-Human Transmission of SARS-CoV-2

Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO

Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand

Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)

LoLoPicker: detecting low allelic-fraction variants from low-quality cancer samples


FUNGuild: parsing OTUs into functional guilds

Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System

Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed

Soil depth and grassland origin cooperatively shape microbial community co‐occurrence and function

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Build Your Own Mushroom Soil: Microbiota Succession and Nutritional Accumulation in Semi-Synthetic Substratum Drive the Fructification of a Soil-Saprotrophic Morel

Microbiota dysbiosis in honeybee (Apis mellifera L.) larvae infected with brood diseases and foraging bees exposed to agrochemicals

Application of Manure Rather Than Plant-Origin Organic Fertilizers Alters the Fungal Community in Continuous Cropping Tobacco Soil

Diversity and Communities of Fungal Endophytes from Four Pinus Species in Korea

Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions

Mycology&#58 An International Journal on Fungal Biology

How Tillage and Crop Rotation Change the Distribution Pattern of Fungi


SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

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

Dexamethasone modulates immature neutrophils and interferon programming in severe COVID-19

A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data

Characterizing dedifferentiation of thyroid cancer by integrated analysis

Alginate oligosaccharides improve germ cell development and testicular microenvironment to rescue busulfan disrupted spermatogenesis

Single-cell Transcriptome Profiling reveals Dermal and Epithelial cell fate decisions during Embryonic Hair Follicle Development

Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets

Single-cell dissection of cellular and molecular features underlying human cervical squamous cell carcinoma initiation and progression

Single-cell atlas of keratoconus corneas revealed aberrant transcriptional signatures and implicated mechanical stretch as a trigger for keratoconus pathogenesis


Python tools for the Regional Ocean Modeling System (ROMS)


RoutingKit is a C++ library that provides advanced route planning functionality.

Scalable and Congestion-aware Routing for Autonomous Mobility-on-Demand via Frank-Wolfe Optimization

Faster and Better Nested Dissection Orders for Customizable Contraction Hierarchies

Efficient Route Planning with Temporary Driving Bans, Road Closures, and Rated Parking Areas

Simulating the Impact of Dynamic Rerouting on Metropolitan-scale Traffic Systems

Fast, Exact and Scalable Dynamic Ridesharing

More Hierarchy in Route Planning Using Edge Hierarchies

Fast Many-to-Many Routing for Ridesharing with Multiple Pickup and Dropoff Locations

A Fast and Tight Heuristic for A* in Road Networks

Nearest-Neighbor Queries in Customizable Contraction Hierarchies and Applications

Efficient Non-Learning Similar Subtrajectory Search


NCCL Tests

Evaluating Modern GPU Interconnect: PCIe, NVLink, NV-SLI, NVSwitch and GPUDirect

IEEE Transactions on Parallel and Distributed Systems

Daydream: Accurately Estimating the Efficacy of Optimizations for DNN Training

Performance Analysis of Deep Learning Workloads on Leading-edge Systems

Multi-node Bert-pretraining: Cost-efficient Approach

DeAR: Accelerating Distributed Deep Learning with Fine-Grained All-Reduce Pipelining

A Hardware Evaluation Framework for Large Language Model Inference

Srifty: Swift and Thrifty Distributed Training on the Cloud

USP: A Unified Sequence Parallelism Approach for Long Context Generative AI

Using machine learning to model the training scalability of convolutional neural networks on clusters of GPUs


Implementation of Graph Convolutional Networks in TensorFlow

Semi-Supervised Classification with Graph Convolutional Networks

A Comprehensive Survey on Graph Neural Networks

IEEE transactions on neural networks and learning systems

Graph Neural Networks: A Review of Methods and Applications

Revisiting Semi-Supervised Learning with Graph Embeddings

Deep Learning on Graphs: A Survey

FastGCN: Fast Learning with Graph Convolutional Networks via Importance Sampling

Beyond Homophily in Graph Neural Networks: Current Limitations and Effective Designs

Graph Neural Networks Exponentially Lose Expressive Power for Node Classification

Graph Representation Learning via Graphical Mutual Information Maximization

AM-GCN: Adaptive Multi-channel Graph Convolutional Networks


Unofficial pytorch implementation for Self-critical Sequence Training for Image Captioning. and others.

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

How Much Can CLIP Benefit Vision-and-Language Tasks?

On Hallucination and Predictive Uncertainty in Conditional Language Generation

Adversarial Inference for Multi-Sentence Video Description

Mitigating Gender Bias in Captioning Systems

Exact Adversarial Attack to Image Captioning via Structured Output Learning with Latent Variables

Bayesian Attention Modules

UMIC: An Unreferenced Metric for Image Captioning via Contrastive Learning

A Better Variant of Self-Critical Sequence Training


[EMNLP'23, ACL'24] To speed up LLMs' inference and enhance LLM's perceive of key information, compress the prompt and KV-Cache, which achieves up to 20x compression with minimal performance loss.

LongLLMLingua: Accelerating and Enhancing LLMs in Long Context Scenarios via Prompt Compression

LLMLingua: Compressing Prompts for Accelerated Inference of Large Language Models

LLMLingua-2: Data Distillation for Efficient and Faithful Task-Agnostic
  Prompt Compression

MInference 1.0: Accelerating Pre-filling for Long-Context LLMs via Dynamic Sparse Attention

Unifying Demonstration Selection and Compression for In-Context Learning

KV Cache Compression, But What Must We Give in Return? A Comprehensive Benchmark of Long Context Capable Approaches


Django-based clone of Amazon's Mechanical Turk service running in your local environment.

FinQA: A Dataset of Numerical Reasoning over Financial Data

ConvFinQA: Exploring the Chain of Numerical Reasoning in Conversational Finance Question Answering

Collecting Verified COVID-19 Question Answer Pairs

Empirical Methods in Natural Language Processing

Laughter Synthesis: Combining Seq2seq modeling with Transfer Learning

Analysis and Assessment of Controllability of an Expressive Deep Learning-based TTS system

OpenRT: An Open-source Framework for Reasoning Over Tabular Data

Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations)

Meeting the Needs of Low-Resource Languages: The Value of Automatic Alignments via Pretrained Models

Machine Translation Believability

VizAI : Selecting Accurate Visualizations of Numerical Data

Building OCR/NER Test Collections

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


Read coverage calculator for metagenomics

SARS-CoV-2 RNA monitoring in wastewater as a potential early warning system for COVID-19 transmission in the community: A temporal case study

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travellers

Identification of mobile genetic elements with geNomad

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

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

Wildfire-dependent changes in soil microbiome diversity and function

A catalogue of 1,167 genomes from the human gut archaeome

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

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes

bioRxiv : the preprint server for biology

METABOLIC: High-throughput profiling of microbial genomes for functional traits, biogeochemistry, and community-scale metabolic networks


A disease diagnosis and treatment recommendation system based on big data mining and cloud computing

Fine-grained Event Categorization with Heterogeneous Graph Convolutional Networks

Encoding Conversation Context for Neural Keyphrase Extraction from Microblog Posts

North American Chapter of the Association for Computational Linguistics

Building a comprehensive syntactic and semantic corpus of Chinese clinical texts

Prosody leaks into the memories of words

Neural Networks for Negation Cue Detection in Chinese

Proceedings of the Workshop Computational Semantics Beyond Events and Roles

MUSIED: A Benchmark for Event Detection from Multi-Source Heterogeneous Informal Texts


[ECCV 2022] This is the official implementation of BEVFormer, a camera-only framework for autonomous driving perception, e.g., 3D object detection and semantic map segmentation.

BEVFormer: Learning Bird's-Eye-View Representation from Multi-Camera Images via Spatiotemporal Transformers

BEVFormer v2: Adapting Modern Image Backbones to Bird's-Eye-View Recognition via Perspective Supervision

UniSim: A Neural Closed-Loop Sensor Simulator

Delving into the Devils of Bird's-eye-view Perception: A Review, Evaluation and Recipe

NeuRAD: Neural Rendering for Autonomous Driving

DFA3D: 3D Deformable Attention For 2D-to-3D Feature Lifting

LightSim: Neural Lighting Simulation for Urban Scenes

Are NeRFs ready for autonomous driving? Towards closing the
  real-to-simulation gap

Multi-View Attentive Contextualization for Multi-View 3D Object
  Detection


nuScenes: A multimodal dataset for autonomous driving

Scalability in Perception for Autonomous Driving: Waymo Open Dataset

Center-based 3D Object Detection and Tracking

Multimodal Virtual Point 3D Detection

VISTA: Boosting 3D Object Detection via Dual Cross-VIew SpaTial Attention

Robo3D: Towards Robust and Reliable 3D Perception against Corruptions

FP8 versus INT8 for efficient deep learning inference

It's All Around You: Range-Guided Cylindrical Network for 3D Object Detection

Optimizing LiDAR Placements for Robust Driving Perception in Adverse
  Conditions

Real-Aug: Realistic Scene Synthesis for LiDAR Augmentation in 3D Object Detection


A Very Low-Bitrate Codec for Speech Compression

Efficient Neural Audio Synthesis

SoundStream: An End-to-End Neural Audio Codec

High Fidelity Neural Audio Compression

Wavenet based low rate speech coding

Generative Speech Coding with Predictive Variance Regularization

End-to-End Neural Speech Coding for Real-Time Communications

Latent-Domain Predictive Neural Speech Coding

Language-Codec: Reducing the Gaps Between Discrete Codec Representation
  and Speech Language Models

CQNV: A combination of coarsely quantized bitstream and neural vocoder for low rate speech coding

An Intra-BRNN and GB-RVQ Based END-TO-END Neural Audio Codec


Open-source platform for model predictive control (MPC) in buildings.


Aave Protocol Version 1.0 - Decentralized Lending Pools

Quantifying Blockchain Extractable Value: How dark is the forest?

Attacking the DeFi Ecosystem with Flash Loans for Fun and Profit

The Decentralized Financial Crisis

On the Just-In-Time Discovery of Profit-Generating Transactions in DeFi Protocols

An Empirical Study of DeFi Liquidations: Incentives, Risks, and Instabilities

SoK: Decentralized Finance (DeFi) Attacks

CeFi vs. DeFi -- Comparing Centralized to Decentralized Finance

SoK: Lending Pools in Decentralized Finance

Flashot: A Snapshot of Flash Loan Attack on DeFi Ecosystem

Perpetual Contract NFT as Collateral for DeFi Composability


a distributed Hyperband implementation on Steroids

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

BOHB: Robust and Efficient Hyperparameter Optimization at Scale

NAS-Bench-101: Towards Reproducible Neural Architecture Search

Benchmark and Survey of Automated Machine Learning Frameworks

Well-tuned Simple Nets Excel on Tabular Datasets

Learning Search Space Partition for Black-box Optimization using Monte Carlo Tree Search

Tabular Benchmarks for Joint Architecture and Hyperparameter Optimization

HPOBench: A Collection of Reproducible Multi-Fidelity Benchmark Problems for HPO

Neural Ensemble Search for Uncertainty Estimation and Dataset Shift

HEBO Pushing The Limits of Sample-Efficient Hyperparameter Optimisation


PyTorch - FID calculation with proper image resizing and quantization steps [CVPR 2022]

On Aliased Resizing and Surprising Subtleties in GAN Evaluation

Pros and Cons of GAN Evaluation Measures: New Developments

Generative Novel View Synthesis with 3D-Aware Diffusion Models

Erasing Concepts from Diffusion Models

ATISS: Autoregressive Transformers for Indoor Scene Synthesis

I^2SB: Image-to-Image Schrödinger Bridge

Soft Truncation: A Universal Training Technique of Score-based Diffusion Model for High Precision Score Estimation

Consistent View Synthesis with Pose-Guided Diffusion Models

Rickrolling the Artist: Injecting Backdoors into Text Encoders for Text-to-Image Synthesis

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


Komondor Wireless Networks Simulator

Wi-Fi Meets ML: A Survey on Improving IEEE 802.11 Performance With Machine Learning

Potential and pitfalls of Multi-Armed Bandits for decentralized Spatial Reuse in WLANs

Journal of Network and Computer Applications

Dynamic Channel Bonding in Spatially Distributed High-Density WLANs

Spatial Reuse in IEEE 802.11ax WLANs

To overlap or not to overlap: Enabling Channel Bonding in High-Density WLANs

Komondor: a Wireless Network Simulator for Next-Generation High-Density WLANs

Usage of Network Simulators in Machine-Learning-Assisted 5G/6G Networks

On the Performance of the Spatial Reuse Operation in IEEE 802.11ax WLANs

Machine Learning for Performance Prediction of Channel Bonding in Next-Generation IEEE 802.11 WLANs

Experimental Evaluation of Interactive Edge/Cloud Virtual Reality Gaming
  over Wi-Fi using Unity Render Streaming


Program for the analysis and visualization of whole-slide images in digital pathology

1399 H&E-stained sentinel lymph node sections of breast cancer patients: the CAMELYON dataset

The importance of stain normalization in colorectal tissue classification with convolutional networks

A Fast and Refined Cancer Regions Segmentation Framework in Whole-slide Breast Pathological Images

Deep Learning Methods for Lung Cancer Segmentation in Whole-Slide Histopathology Images—The ACDC@LungHP Challenge 2019

Resolution-agnostic tissue segmentation in whole-slide histopathology images with convolutional neural networks

Development and evaluation of a deep neural network for histologic classification of renal cell carcinoma on biopsy and surgical resection slides

Automated detection of cribriform growth patterns in prostate histology images

Convolutional Neural Networks for the Evaluation of Chronic and Inflammatory Lesions in Kidney Transplant Biopsies

Improving Prostate Cancer Detection with Breast Histopathology Images

Deep Learning-Based Recognition of Different Thyroid Cancer Categories Using Whole Frozen-Slide Images

Frontiers in bioengineering and biotechnology


Extensive de-novo TE Annotator

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

A platinum standard pan-genome resource that represents the population structure of Asian rice

Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline

Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry

The 3D architecture of the pepper genome and its relationship to function and evolution

A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Differences in activity and stability drive transposable element variation in tropical and temperate maize

Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks

High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres

SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding


Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

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

The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design

Biochemical and biophysical research communications

Chest imaging representing a COVID-19 positive rural U.S. population

Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia

Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

medRxiv : the preprint server for health sciences

Characterization of the Immune Resistance of Severe Acute Respiratory Syndrome Coronavirus 2 Mu Variant and the Robust Immunity Induced by Mu Infection

Genomic epidemiology of COVID-19 in care homes in the east of England

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

Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador


LoFreq Star: Sensitive variant calling from sequencing data

Variant profiling of evolving prokaryotic populations

Emergence of a Reassortant 2.3.4.4b Highly Pathogenic H5N1 Avian Influenza Virus Containing H9N2 PA Gene in Burkina Faso, West Africa, in 2021

Evolutionary Dynamics of H5 Highly Pathogenic Avian Influenza Viruses (Clade 2.3.4.4B) Circulating in Bulgaria in 2019–2021

Carnivore protoparvovirus 1 (CPV-2 and FPV) Circulating in Wild Carnivores and in Puppies Illegally Imported into North-Eastern Italy

Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets

Emergence and Persistent Circulation of Highly Pathogenic Avian Influenza Virus A (H5N8) in Kosovo, May 2021–May 2022

Identification of Dobrava-Belgrade Virus in Apodemus flavicollis from North-Eastern Italy during Enhanced Mortality


RL Environments in JAX

Discovering Evolution Strategies via Meta-Black-Box Optimization

VMAS: A Vectorized Multi-Agent Simulator for Collective Robot Learning

Discovering Attention-Based Genetic Algorithms via Meta-Black-Box Optimization

JaxMARL: Multi-Agent RL Environments in JAX

Jumanji: a Diverse Suite of Scalable Reinforcement Learning Environments in JAX

Large Language Models As Evolution Strategies

Pgx: Hardware-Accelerated Parallel Game Simulators for Reinforcement Learning

XLand-MiniGrid: Scalable Meta-Reinforcement Learning Environments in JAX

Gymnasium: A Standard Interface for Reinforcement Learning Environments

JAX-LOB: A GPU-Accelerated limit order book simulator to unlock large scale reinforcement learning for trading


machine learning with logical rules in Python

Counterfactual Phenotyping with Censored Time-to-Events

Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining

Computer-Assisted Creation of Boolean Search Rules for Text Classification in the Legal Domain

NetRCA: An Effective Network Fault Cause Localization Algorithm

Shapley-based Explainable AI for Clustering Applications in Fault Diagnosis and Prognosis

Computing Rule-Based Explanations of Machine Learning Classifiers using Knowledge Graphs

Rule-based Out-Of-Distribution Detection

PubMed-Scale Chemical Concept Embeddings Reconstruct Physical Protein Interaction Networks

Frontiers in research metrics and analytics

Intelligent Tools to Monitor, Control and Predict Wastewater Reclamation and Reuse

Beyond explaining: XAI-based Adaptive Learning with SHAP Clustering for
  Energy Consumption Prediction


High-speed Large Language Model Serving on PCs with Consumer-grade GPUs

PowerInfer: Fast Large Language Model Serving with a Consumer-grade GPU

ReLU Strikes Back: Exploiting Activation Sparsity in Large Language Models

Turbo Sparse: Achieving LLM SOTA Performance with Minimal Activated Parameters

PowerInfer-2: Fast Large Language Model Inference on a Smartphone

Faster and Lighter LLMs: A Survey on Current Challenges and Way Forward


Performance-portable geometric search library

ArborX: A Performance Portable Geometric Search Library

Simulating Hydrodynamics in Cosmology with CRK-HACC

A single-tree algorithm to compute the Euclidean minimum spanning tree on GPUs

Fast tree-based algorithms for DBSCAN for low-dimensional data on GPUs

Proceedings of the 52nd International Conference on Parallel Processing

PANDORA: A Parallel Dendrogram Construction Algorithm for Single Linkage Clustering on GPU

Revising Apetrei's bounding volume hierarchy construction algorithm to
  allow stackless traversal


A CV toolkit for my papers.

ResNeSt: Split-Attention Networks

Context Encoding for Semantic Segmentation

Co-Occurrent Features in Semantic Segmentation

Deep TEN: Texture Encoding Network

Region Mutual Information Loss for Semantic Segmentation

Linear Semantics in Generative Adversarial Networks

Extracting Semantic Knowledge from GANs with Unsupervised Learning

Refining Semantic Segmentation with Superpixel by Transparent Initialization and Sparse Encoder

Adaptive Context Encoding Module for Semantic Segmentation

SSSegmenation: An Open Source Supervised Semantic Segmentation Toolbox Based on PyTorch


Medusa: Simple Framework for Accelerating LLM Generation with Multiple Decoding Heads

Medusa: Simple LLM Inference Acceleration Framework with Multiple Decoding Heads

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

SnapKV: LLM Knows What You are Looking for Before Generation

Efficient Interactive LLM Serving with Proxy Model-based Sequence Length
  Prediction

BiTA: Bi-Directional Tuning for Lossless Acceleration in Large Language Models


Text-prompted Generative Audio Model - With the ability to clone voices

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

AudioLM: a Language Modeling Approach to Audio Generation


An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer’s disease

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria

Phenome-wide analysis of Taiwan Biobank reveals novel glycemia-related loci and genetic risks for diabetes

Statin therapy inhibits fatty acid synthase via dynamic protein modifications

Zenodo (CERN European Organization for Nuclear Research)

Relationships among Fecal, Air, Oral, and Tracheal Microbial Communities in Pigs in a Respiratory Infection Disease Model

A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach

Development of Toehold Switches as a Novel Ribodiagnostic Method for West Nile Virus

High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species


Detect 6-DOF grasp poses in point clouds

Grasp Pose Detection in Point Clouds

High precision grasp pose detection in dense clutter

ACRONYM: A Large-Scale Grasp Dataset Based on Simulation

DGCM-Net: Dense Geometrical Correspondence Matching Network for Incremental Experience-Based Robotic Grasping


Port of Google's language-detection library to Python.

Reformulating Unsupervised Style Transfer as Paraphrase Generation

Mapping languages: the Corpus of Global Language Use

Language Tags Matter for Zero-Shot Neural Machine Translation

Abusive content detection in transliterated Bengali-English social media corpus

Proceedings of the Fifth Workshop on Computational Approaches to Linguistic Code-Switching

CODA-19: Using a Non-Expert Crowd to Annotate Research Aspects on 10,000+ Abstracts in the COVID-19 Open Research Dataset

Cross-lingual sentiment classification in low-resource Bengali language

A Large Parallel Corpus of Full-Text Scientific Articles

Exploring Media Bias and Toxicity in South Asian Political Discourse

The Geography of Taste: Using Yelp to Study Urban Culture

ISPRS International Journal of Geo-Information

Social Sensing of Heatwaves


Machine Learning toolbox for Humans

A Roadmap for HEP Software and Computing R&D for the 2020s

Strategic Plan for a Scientific Software Innovation Institute (S2I2) for High Energy Physics

Disk storage management for LHCb based on Data Popularity estimator

Machine learning and multivariate goodness of fit

Reproducible Experiment Platform


XLNet: Generalized Autoregressive Pretraining for Language Understanding

Pre-trained models for natural language processing: A survey

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing

Green AI

Revisiting Few-sample BERT Fine-tuning

A Survey on Text Classification: From Shallow to Deep Learning

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

Fake news detection based on news content and social contexts: a transformer-based approach

International Journal of Data Science and Analytics

Towards Generalizable Neuro-Symbolic Systems for Commonsense Question Answering

Improving Constituency Parsing with Span Attention


CnOCR: Awesome Chinese/English OCR Python toolkits based on PyTorch. It comes with 20+ well-trained models for different application scenarios and can be used directly after installation. 【基于 PyTorch/MXNet 的中文/英文 OCR Python 包。】

PEIT: Bridging the Modality Gap with Pre-trained Models for End-to-End Image Translation

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

Understanding Privacy Over-collection in WeChat Sub-app Ecosystem


StyleTTS 2: Towards Human-Level Text-to-Speech through Style Diffusion and Adversarial Training with Large Speech Language Models

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

XTTS: a Massively Multilingual Zero-Shot Text-to-Speech Model

Phoneme-Level BERT for Enhanced Prosody of Text-to-Speech with Grapheme Predictions

ZMM-TTS: Zero-shot Multilingual and Multispeaker Speech Synthesis Conditioned on Self-supervised Discrete Speech Representations

XPhoneBERT: A Pre-trained Multilingual Model for Phoneme Representations for Text-to-Speech

Autoregressive Diffusion Transformer for Text-to-Speech Synthesis

Bayesian Parameter-Efficient Fine-Tuning for Overcoming Catastrophic
  Forgetting

EmpathyEar: An Open-source Avatar Multimodal Empathetic Chatbot


Dataset distribution for Seurat

Deep learning tackles single-cell analysis A survey of deep learning for scRNA-seq analysis

Human genetics uncovers MAP3K15 as an obesity-independent therapeutic target for diabetes

Cell type hierarchy reconstruction via reconciliation of multi-resolution cluster tree

Multi-modal quantification of pathway activity with MAYA

FlexDotPlot: a universal and modular dot plot visualization tool for complex multifaceted data

Is your data alignable? Principled and interpretable alignability testing and integration of single-cell data

Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error

Single-cell Multi-view Clustering via Community Detection with Unknown Number of Clusters


NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

Accurate detection of complex structural variations using single molecule sequencing

Technology dictates algorithms: Recent developments in read alignment

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

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

The human origin recognition complex is essential for pre-RC assembly, mitosis, and maintenance of nuclear structure

Long-read sequencing in human genetics

Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes

Study of complex structural variations of X-linked deafness-2 based on single-molecule sequencing

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


Fuzzy String Matching in Python

Large Language Model as Attributed Training Data Generator: A Tale of Diversity and Bias

Words are all you need? Language as an approximation for human similarity judgments

DRG-LLaMA : tuning LLaMA model to predict diagnosis-related group for hospitalized patients

CAT-LM Training Language Models on Aligned Code And Tests

Revisiting non-English Text Simplification: A Unified Multilingual Benchmark

WangLab at MEDIQA-Chat 2023: Clinical Note Generation from Doctor-Patient Conversations using Large Language Models

CodeLMSec Benchmark: Systematically Evaluating and Finding Security Vulnerabilities in Black-Box Code Language Models

DE-COP: Detecting Copyrighted Content in Language Models Training Data

Automatically Generating Scenarios from a Text Corpus: A Case Study on Electric Vehicles

A comprehensive analysis of acknowledgement texts in Web of Science: a case study on four scientific domains


Laser Odometry and Mapping (Loam) is a realtime method for state estimation and mapping using a 3D lidar.

RTAB-Map as an open-source lidar and visual simultaneous localization and mapping library for large-scale and long-term online operation

Self-supervised Learning of LiDAR Odometry for Robotic Applications

Large-Scale LiDAR SLAM with Factor Graph Optimization on High-Level Geometric Features

Point wise or Feature wise? Benchmark Comparison of Public Available LiDAR Odometry Algorithms in Urban Canyons

Study of the Effect of Exploiting 3D Semantic Segmentation in LiDAR Odometry

Mapping of Sparse 3D Data using Alternating Projection

Can generalised relative pose estimation solve sparse 3D registration?

Advanced Algorithms of Collision Free Navigation and Flocking for Autonomous UAVs

SEGMENT-BASED LIDAR ODOMETRY FOR LESS STRUCTURED OUTDOOR SCENE

The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciences


SenseTime Research platform for single object tracking, implementing algorithms like SiamRPN and SiamMask.

SiamRPN++: Evolution of Siamese Visual Tracking with Very Deep Networks

Rotation Equivariant Siamese Networks for Tracking

Fast Visual Object Tracking using Ellipse Fitting for Rotated Bounding Boxes

Few-Shot Backdoor Attacks on Visual Object Tracking

SiamMan: Siamese Motion-aware Network for Visual Tracking

Tackling Occlusion in Siamese Tracking with Structured Dropouts

Robust Visual Object Tracking with Two-Stream Residual Convolutional Networks

Siamese Tracking with Lingual Object Constraints

An Analysis of Object Representations in Deep Visual Trackers


Photorealistic Text-to-Image Diffusion Models with Deep Language Understanding

DPM-Solver++: Fast Solver for Guided Sampling of Diffusion Probabilistic Models

Adversarial Diffusion Distillation

Exploiting Diffusion Prior for Real-World Image Super-Resolution

VideoCrafter1: Open Diffusion Models for High-Quality Video Generation

Show-1: Marrying Pixel and Latent Diffusion Models for Text-to-Video Generation

Holistic Evaluation of Text-To-Image Models

DatasetDM: Synthesizing Data with Perception Annotations Using Diffusion Models

TextDiffuser: Diffusion Models as Text Painters

RichDreamer: A Generalizable Normal-Depth Diffusion Model for Detail Richness in Text-to-3D


InVEST®: models that map and value the goods and services from nature that sustain and fulfill human life.

Mapping the benefits of nature in cities with the InVEST software


Shared repository for open-sourced projects from the Google AI Language team.

Natural Questions: A Benchmark for Question Answering Research

Transactions of the Association for Computational Linguistics

REALM: Retrieval-Augmented Language Model Pre-Training

What Makes Good In-Context Examples for GPT-3?

Latent Retrieval for Weakly Supervised Open Domain Question Answering

Sparse, Dense, and Attentional Representations for Text Retrieval

Time-Aware Language Models as Temporal Knowledge Bases

Fusion of Detected Objects in Text for Visual Question Answering

Canine: Pre-training an Efficient Tokenization-Free Encoder for Language Representation

Thieves on Sesame Street! Model Extraction of BERT-based APIs

Compositional Generalization and Natural Language Variation: Can a Semantic Parsing Approach Handle Both?


The GitHub repository for the paper "Informer" accepted by AAAI 2021.

Informer: Beyond Efficient Transformer for Long Sequence Time-Series Forecasting

TS2Vec: Towards Universal Representation of Time Series

TCCT: Tightly-coupled convolutional transformer on time series forecasting

PromptCast: A New Prompt-based Learning Paradigm for Time Series Forecasting

The Capacity and Robustness Trade-off: Revisiting the Channel Independent Strategy for Multivariate Time Series Forecasting

Dish-TS: A General Paradigm for Alleviating Distribution Shift in Time Series Forecasting

A Survey on Time-Series Pre-Trained Models

Ti-MAE: Self-Supervised Masked Time Series Autoencoders

Online Metro Origin-Destination Prediction via Heterogeneous Information Aggregation

FormerTime: Hierarchical Multi-Scale Representations for Multivariate Time Series Classification


Equivariant Steerable CNNs Library for Pytorch https://quva-lab.github.io/escnn/

Steerable CNNs

General E(2)-Equivariant Steerable CNNs

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

A Program to Build E(N)-Equivariant Steerable CNNs

International Conference on Learning Representations

Equivariant Reinforcement Learning under Partial Observability


Chinese version of CLIP which achieves Chinese cross-modal retrieval and representation generation.

AutoAugment: Learning Augmentation Policies from Data

Chinese CLIP: Contrastive Vision-Language Pretraining in Chinese

GlyphDraw: Seamlessly Rendering Text with Intricate Spatial Structures in Text-to-Image Generation

MCFEND: A Multi-source Benchmark Dataset for Chinese Fake News Detection

PEA-Diffusion: Parameter-Efficient Adapter with Knowledge Distillation in non-English Text-to-Image Generation


ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data

ENIGMA HALFpipe: Interactive, reproducible, and efficient analysis for resting-state and task-based fMRI data

ENIGMA’s simple seven: Recommendations to enhance the reproducibility of resting-state fMRI in traumatic brain injury

Neuroimaging-based classification of PTSD using data-driven computational approaches: A multisite big data study from the ENIGMA-PGC PTSD consortium

Intrusive Traumatic Re-Experiencing Domain: Functional Connectivity Feature Classification by the ENIGMA PTSD Consortium

Biological psychiatry global open science


Strelka2 germline and somatic small variant caller

Strelka2: fast and accurate calling of germline and somatic variants

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Curated variation benchmarks for challenging medically relevant autosomal genes

Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival

The clonal evolution of metastatic colorectal cancer

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

Low-burden TP53 mutations in CLL: clinical impact and clonal evolution within the context of different treatment options

Strelka2: Fast and accurate variant calling for clinical sequencing applications

Analysis pipelines for cancer genome sequencing in mice


An R package that assists with the setup and operation of a collection of soil data summary, comparison, and evaluation reports. These reports are primarily used by USDA-NRCS soil scientists in both initial and update mapping.


offline/online spike sorting. Un logiciel de gauche qui ne fait pas d'amalgame entre la classe et la coquetterie.

SpikeInterface, a unified framework for spike sorting

SpikeForest, reproducible web-facing ground-truth validation of automated neural spike sorters

Compatibility Evaluation of Clustering Algorithms for Contemporary Extracellular Neural Spike Sorting

From End to End: Gaining, Sorting, and Employing High-Density Neural Single Unit Recordings

NeuSort: An Automatic Adaptive Spike Sorting Approach with Neuromorphic Models

Early classification of Alzheimer's disease phenotype based on hippocampal electrophysiology in the TgF344-AD rat model


End-to-end neural table-text understanding models.

Well-Read Students Learn Better: On the Importance of Pre-training Compact Models

TAPAS: Weakly Supervised Table Parsing via Pre-training

Understanding tables with intermediate pre-training

TableFormer: Robust Transformer Modeling for Table-Text Encoding

MATE: Multi-view Attention for Table Transformer Efficiency

Open Domain Question Answering over Tables via Dense Retrieval

Capturing Row and Column Semantics in Transformer Based Question Answering over Tables

AIT-QA: Question Answering Dataset over Complex Tables in the Airline Industry

Large Language Models(LLMs) on Tabular Data: Prediction, Generation, and
  Understanding -- A Survey

Table-based Fact Verification with Salience-aware Learning


PASA software

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

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

A bird’s white-eye view on avian sex chromosome evolution

A draft genome, resequencing, and metabolomes reveal the genetic background and molecular basis of the nutritional and medicinal properties of loquat (Eriobotrya japonica (Thunb.) Lindl)

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

bioRxiv : the preprint server for biology

The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution

The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies

Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

Gossypium purpurascens genome provides insight into the origin and domestication of upland cotton


PyTorch deep learning models for document classification

Regularizing and Optimizing LSTM Language Models

DocBERT: BERT for Document Classification

Rethinking Complex Neural Network Architectures for Document Classification

North American Chapter of the Association for Computational Linguistics

Document Classification for COVID-19 Literature

Stance Prediction for Contemporary Issues: Data and Experiments

Exploring the Limits of Simple Learners in Knowledge Distillation for Document Classification with DocBERT

Workshop on Representation Learning for NLP

SUMSUM@FNS-2020 Shared Task

Efficient Document Image Classification Using Region-Based Graph Neural Network

Showing Your Work Doesn't Always Work

From Sentiment Annotations to Sentiment Prediction through Discourse Augmentation


Extensible Combinatorial Optimization Learning Environments

Ecole: A Gym-like Library for Machine Learning in Combinatorial Optimization Solvers

Learning To Cut By Looking Ahead: Cutting Plane Selection via Imitation Learning


Run Keras models in the browser, with GPU support using WebGL

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

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

Applied intelligence (Dordrecht, Netherlands)

Towards Understanding the Faults of JavaScript-Based Deep Learning Systems

Proceedings of the 37th IEEE/ACM International Conference on Automated Software Engineering

Approach for Improving User Interface Based on Gesture Recognition

Live Emoji: Semantic Emotional Expressiveness of 2D Live Animation


all kinds of text classification models and more with deep learning

BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding

Neural Machine Translation by Jointly Learning to Align and Translate

Bag of Tricks for Efficient Text Classification

A Sensitivity Analysis of (and Practitioners' Guide to) Convolutional Neural Networks for Sentence Classification

FRAGE: Frequency-Agnostic Word Representation

Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation


A Neo4j backed ontology store

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

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

DataMed – an open source discovery index for finding biomedical datasets

Journal of the American Medical Informatics Association : JAMIA

The SPARC DRC: Building a Resource for the Autonomic Nervous System Community

An overview of graph databases and their applications in the biomedical domain

Database : the journal of biological databases and curation

COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database

ChemRxiv : the preprint server for chemistry

A Biomedical Knowledge Graph System to Propose Mechanistic Hypotheses for Real-World Environmental Health Observations: Cohort Study and Informatics Application

AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures


Isaac Gym Reinforcement Learning Environments

Isaac Gym: High Performance GPU-Based Physics Simulation For Robot Learning

AMP

DeXtreme: Transfer of Agile In-hand Manipulation from Simulation to Reality

DoReMi: Grounding Language Model by Detecting and Recovering from Plan-Execution Misalignment

Causal Reinforcement Learning: A Survey

From Data-Fitting to Discovery: Interpreting the Neural Dynamics of Motor Control through Reinforcement Learning

LARG, Language-based Automatic Reward and Goal Generation

Entity-Centric Reinforcement Learning for Object Manipulation from
  Pixels


An efficient implementation of the Double Description Method

A Formal Disproof of Hirsch Conjecture

Computational aspects of relaxation complexity: possibilities and limitations

A FAIR File Format for Mathematical Software


R We There Yet?

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses

Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi

An in silico comparison of reduced-representation and sequence-capture protocols for phylogenomics


RIVET is a tool for Topological Data Analysis, in particular two-parameter persistent homology.

Scalar Field Comparison with Topological Descriptors: Properties and Applications for Scientific Visualization

Persistent Homology Analysis for Materials Research and Persistent Homology Software: HomCloud

BrainIAK: The Brain Imaging Analysis Kit

Stability of 2-Parameter Persistent Homology

Fast Minimal Presentations of Bi-graded Persistence Modules

Koszul Complexes and Relative Homological Algebra of Functors Over Posets

Characterizing the Latent Space of Molecular Deep Generative Models with Persistent Homology Metrics

Topological Data Analysis on Simple English Wikipedia Articles

The Degree-Rips Complexes of an Annulus with Outliers

The bifiltration of a relation and extended Dowker duality


:robot: The MoveIt motion planning framework

A Composable Framework for Policy Design, Learning, and Transfer Toward Safe and Efficient Industrial Insertion

Towards self-adaptable robots: from programming to training machines

CircuitBot: Learning to Survive with Robotic Circuit Drawing


QML: Quantum Machine Learning

Machine Learning Force Fields

Data‐Driven Materials Science: Status, Challenges, and Perspectives

Machine Learning for Electronically Excited States of Molecules

FCHL revisited: faster and more accurate quantum machine learning

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

On the role of gradients for machine learning of molecular energies and forces

Operators in quantum machine learning: Response properties in chemical space

IMPRESSION -- Prediction of NMR Parameters for 3-dimensional chemical structures using Machine Learning with near quantum chemical accuracy

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

Machine learning and excited-state molecular dynamics

Machine Learning: Science and Technology


Mobility, an open-source library for mobility modelisation


A Python package for exploring and analysing genetic variation data

Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms

Genome-wide divergence among invasive populations of Aedes aegypti in California

Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus

Genomic consequences of domestication of the Siamese fighting fish

An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

Radiation with reticulation marks the origin of a major malaria vector

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

Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses

A deep learning framework for characterization of genotype data

Evidence of Local Extinction and Reintroduction of Aedes aegypti in Exeter, California

A multiplexed plant-animal SNP array for selective breeding and species conservation applications


The General Game Playing Base Package

Ludii -- The Ludemic General Game System

Ludii as a Competition Platform

An Empirical Evaluation of Two General Game Systems: Ludii and RBG

Enhancing Playout Policy Adaptation for General Game Playing

Data Archiving and Networked Services (DANS)


Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies

Genetic diversity fuels gene discovery for tobacco and alcohol use

Causal effects of gut microbiota on diabetic retinopathy: A Mendelian randomization study

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

GWAS of serum ALT and AST reveals an association of SLC30A10 Thr95Ile with hypermanganesemia symptoms

The role of vitamin C in pneumonia and COVID-19 infection in adults with European ancestry: a Mendelian randomisation study

Genome-wide association study meta-analysis of suicide death and suicidal behavior

Graves’ Disease and Rheumatoid Arthritis: A Bidirectional Mendelian Randomization Study

Host genetic factors of COVID-19 susceptibility and disease severity in a Thai population

Loci for insulin processing and secretion provide insight into type 2 diabetes risk


Facet calibration for LOFAR

A radio ridge connecting two galaxy clusters in a filament of the cosmic web

Gentle reenergization of electrons in merging galaxy clusters

LOFAR discovery of an ultra-steep radio halo and giant head–tail radio galaxy in Abell 1132

Monthly Notices of the Royal Astronomical Society

A LOFAR study of non-merging massive galaxy clusters

LOFAR discovery of a double radio halo system in Abell 1758 and radio/X-ray study of the cluster pair

Radio observations of the merging galaxy cluster Abell 520

LOFAR discoveryof radio emission in MACS J0717.5+3745

First evidence of diffuse ultra-steep-spectrum radio emission surrounding the cool core of a cluster

LOFAR observations of X-ray cavity systems

Monthly notices of the Royal Astronomical Society

Investigation of the cosmic ray population and magnetic field strength in the halo of NGC 891


WannierTools: An open-source software package for novel topological materials. Full documentation:

Nodal-chain metals

Irvsp: To obtain irreducible representations of electronic states in the VASP

Three-component fermions with surface Fermi arcs in tungsten carbide

Transition between strong and weak topological insulator in ZrTe5 and HfTe5

Phonon-induced topological transition to a type-II Weyl semimetal

Topological semimetal to insulator quantum phase transition in the Zintl compounds B a 2 X (X =Si ,Ge )

Topologically nontrivial electronic states in CaSn3

Observation of surface Fermi arcs in altermagnetic Weyl semimetal CrSb


VIMA: General Robot Manipulation with Multimodal Prompts

Synergies Between Affordance and Geometry: 6-DoF Grasp Detection via Implicit Representations

SORNet: Spatial Object-Centric Representations for Sequential Manipulation

Optical Flow Estimation for Spiking Camera

NViSII: A Scriptable Tool for Photorealistic Image Generation

Appearance-Driven Automatic 3D Model Simplification


EU's  Type-Approving vehicle simulator predicting NEDC CO2 emissions from WLTP


A trusty face analysis research platform developed by Tencent Youtu Lab

AdaFace: Quality Adaptive Margin for Face Recognition

SDD-FIQA: Unsupervised Face Image Quality Assessment with Similarity Distribution Distance

DCFace: Synthetic Face Generation with Dual Condition Diffusion Model

CR-FIQA: Face Image Quality Assessment by Learning Sample Relative Classifiability

Consistent Instance False Positive Improves Fairness in Face Recognition

Evaluation-oriented Knowledge Distillation for Deep Face Recognition

Privacy-Preserving Face Recognition with Learnable Privacy Budgets in Frequency Domain

Sibling-Attack: Rethinking Transferable Adversarial Attacks against Face Recognition

DuetFace: Collaborative Privacy-Preserving Face Recognition via Channel Splitting in the Frequency Domain

Proceedings of the 30th ACM International Conference on Multimedia

DifFIQA: Face Image Quality Assessment Using Denoising Diffusion Probabilistic Models


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

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

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

SpeechLM: Enhanced Speech Pre-Training with Unpaired Textual Data

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

WavLLM: Towards Robust and Adaptive Speech Large Language Model

The YiTrans Speech Translation System for IWSLT 2022 Offline Shared Task

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

Robust Automatic Speech Recognition via WavAugment Guided Phoneme Adversarial Training


Pytorch implementation of FlowNet 2.0: Evolution of Optical Flow Estimation with Deep Networks

Deep High-Resolution Representation Learning for Human Pose Estimation

Simple Baselines for Human Pose Estimation and Tracking

Tracking Objects as Points

Efficient Semantic Video Segmentation with Per-frame Inference

ISINet: An Instance-Based Approach for Surgical Instrument Segmentation

Learning to Relight Portrait Images via a Virtual Light Stage and Synthetic-to-Real Adaptation

Adversarial Attacks for Optical Flow-Based Action Recognition Classifiers

Real-Time End-to-End Action Detection with Two-Stream Networks

Differentiable Visual Computing


Open-source implementations of OpenAI Gym MuJoCo environments for use with the OpenAI Gym Reinforcement Learning Research Platform.

Memory-based Deep Reinforcement Learning for POMDPs

Leveraging exploration in off-policy algorithms via normalizing flows

Efficient Continuous Control with Double Actors and Regularized Critics

The Effect of Multi-step Methods on Overestimation in Deep Reinforcement Learning

Optimistic Linear Support and Successor Features as a Basis for Optimal Policy Transfer

Steady State Analysis of Episodic Reinforcement Learning

Risk-Aware Transfer in Reinforcement Learning using Successor Features

What Went Wrong? Closing the Sim-to-Real Gap via Differentiable Causal Discovery

EvoTorch: Scalable Evolutionary Computation in Python

GUARD: A Safe Reinforcement Learning Benchmark


just annotate it, dammit!

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis

Streamlining data-intensive biology with workflow systems

Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury

Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent, Peromyscus eremicus

Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size

The Relationship Between Microbiomes and Selective Regimes in the Sponge Genus Ircinia

Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa

RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification

Characterizing the Adult and Larval Transcriptome of the Multicolored Asian Lady Beetle, Harmonia axyridis


This is an official implementation for "Swin Transformer: Hierarchical Vision Transformer using Shifted Windows".

Swin Transformer V2: Scaling Up Capacity and Resolution

Local Relation Networks for Image Recognition

Focal Self-attention for Local-Global Interactions in Vision Transformers

HTS-AT: A Hierarchical Token-Semantic Audio Transformer for Sound Classification and Detection

Efficient Self-supervised Vision Transformers for Representation Learning

Self-Supervised Learning with Swin Transformers

Efficient Training of Visual Transformers with Small Datasets

Tutel: Adaptive Mixture-of-Experts at Scale

Vision Transformers with Patch Diversification


Software that can generate photos from paintings,  turn horses into zebras,  perform style transfer, and more.

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

Image Synthesis with Adversarial Networks: a Comprehensive Survey and Case Studies

Harmonic Unpaired Image-to-image Translation

Imperfect ImaGANation: Implications of GANs Exacerbating Biases on Facial Data Augmentation and Snapchat Selfie Lenses

Cycle-Consistent Counterfactuals by Latent Transformations

Virtualization of tissue staining in digital pathology using an unsupervised deep learning approach

Ten Years of Generative Adversarial Nets (GANs): A survey of the state-of-the-art

AR-NeRF: Unsupervised Learning of Depth and Defocus Effects from Natural Images with Aperture Rendering Neural Radiance Fields

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

Investigating the Performance of Generative Adversarial Networks for Prostate Tissue Detection and Segmentation


Software package for neuron reconstruction and visualization

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

The comprehensive connectome of a neural substrate for ‘ON’ motion detection in Drosophila

VAST (Volume Annotation and Segmentation Tool): Efficient Manual and Semi-Automatic Labeling of Large 3D Image Stacks

Comparisons between the ON- and OFF-edge motion pathways in the Drosophila brain

Simple integration of fast excitation and offset, delayed inhibition computes directional selectivity in Drosophila

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

Automatic Neuron Type Identification by Neurite Localization in the Drosophila Medulla

Hierarchical architecture of dopaminergic circuits enables second-order conditioning in Drosophila

Large-Scale Electron Microscopy Image Segmentation in Spark

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


Tools for visualizing spectrosopic light curves, with flux as a function of wavelength and time.

Early Release Science of the exoplanet WASP-39b with JWST NIRISS

Early Release Science of the exoplanet WASP-39b with JWST NIRCam

Quantifying the Transit Light Source Effect: Measurements of Spot Temperature and Coverage on the Photosphere of AU Microscopii with High-resolution Spectroscopy and Multicolor Photometry


Pythonic stellar model grid access; easy MCMC fitting of stellar properties

A resonant chain of four transiting, sub-Neptune planets

The California-Kepler Survey. II. Precise Physical Properties of 2025 Kepler Planets and Their Host Stars

Stellar and planetary properties of K2 campaign 1 candidates and validation of 17 planets, including a planet receiving Earth-like insolation

Inferring the age of the universe with globular clusters

Journal of Cosmology and Astroparticle Physics

Absence of a Metallicity Effect for Ultra-short-period Planets

Spectroscopic Parameters and atmosphEric ChemIstriEs of Stars (SPECIES) - I. Code description and dwarf stars catalogue

KEPLER-108: A MUTUALLY INCLINED GIANT PLANET SYSTEM

An exomoon survey of 70 cool giant exoplanets and the new candidate Kepler-1708 b-i

An Ultra Metal-poor Star Near the Hydrogen-burning Limit

A Noninteracting Galactic Black Hole Candidate in a Binary System with a Main-sequence Star


Pipeline for reducing JWST high-contrast imaging data. Published in Kammerer et al. 2022 and Carter et al. 2022.

The JWST Early Release Science Program for Direct Observations of Exoplanetary Systems I: High-contrast Imaging of the Exoplanet HIP 65426 b from 2 to 16 μm

Performance of near-infrared high-contrast imaging methods with JWST from commissioning

JWST-TST High Contrast: Asymmetries, Dust Populations, and Hints of a Collision in the β Pictoris Disk with NIRCam and MIRI

JWST-TST High Contrast: Achieving direct spectroscopy of faint substellar companions next to bright stars with the NIRSpec IFU


Collection of hyperparameter optimization benchmark problems

SMAC3: A Versatile Bayesian Optimization Package for Hyperparameter Optimization

BoTorch: A Framework for Efficient Monte-Carlo Bayesian Optimization

HPOBench: A Collection of Reproducible Multi-Fidelity Benchmark Problems for HPO

Fast Hyperparameter Tuning using Bayesian Optimization with Directional Derivatives

Reinforced Few-Shot Acquisition Function Learning for Bayesian Optimization

EXPObench: Benchmarking Surrogate-based Optimisation Algorithms on Expensive Black-box Functions

Searching in the Forest for Local Bayesian Optimization


Latex code for making neural networks diagrams

On Circuit-Based Hybrid Quantum Neural Networks for Remote Sensing Imagery Classification

CNN-Based Tree Species Classification Using High Resolution RGB Image Data from Automated UAV Observations

Robotic Table Tennis with Model-Free Reinforcement Learning

Prediction of wall-bounded turbulence from wall quantities using convolutional neural networks

Radial Basis Function Networks for Convolutional Neural Networks to Learn Similarity Distance Metric and Improve Interpretability

FN-OCT: Disease Detection Algorithm for Retinal Optical Coherence Tomography Based on a Fusion Network

deepBlink: threshold-independent detection and localization of diffraction-limited spots

Dispersal inference from population genetic variation using a convolutional neural network

Deep Complex Networks for Protocol-Agnostic Radio Frequency Device Fingerprinting in the Wild

Learning to Play the Chess Variant Crazyhouse Above World Champion Level With Deep Neural Networks and Human Data


ChatGLM2-6B: An Open Bilingual Chat LLM | 开源双语对话语言模型

Chain-of-Thought Prompting Elicits Reasoning in Large Language Models

GLM: General Language Model Pretraining with Autoregressive Blank Infilling

GLM-130B: An Open Bilingual Pre-trained Model

Instruction Tuning for Large Language Models: A Survey

Zero-Shot Information Extraction via Chatting with ChatGPT

TrustLLM: Trustworthiness in Large Language Models

L-Eval: Instituting Standardized Evaluation for Long Context Language Models

RoleLLM: Benchmarking, Eliciting, and Enhancing Role-Playing Abilities of Large Language Models

MetaTool Benchmark for Large Language Models: Deciding Whether to Use Tools and Which to Use

SuperCLUE: A Comprehensive Chinese Large Language Model Benchmark


Submanifold sparse convolutional networks

SECOND: Sparsely Embedded Convolutional Detection

3D Semantic Segmentation with Submanifold Sparse Convolutional Networks

Fractional Max-Pooling

Spatially-sparse convolutional neural networks

Sparse 3D convolutional neural networks

Multi-view PointNet for 3D Scene Understanding

MASC: Multi-scale Affinity with Sparse Convolution for 3D Instance Segmentation

Large-Scale 3D Shape Reconstruction and Segmentation from ShapeNet Core55

Point Transformer V3: Simpler, Faster, Stronger


:zap: :aquarius: Rapid prokaryotic genome annotation

MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Cooperative Recognition of Internationally Disseminated Ceftriaxone-Resistant Neisseriagonorrhoeae Strain

Rapid evolution of bacterial mutualism in the plant rhizosphere

INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance

Synergy and oxygen adaptation for development of next-generation probiotics

Brasilianoids A–F, New Meroterpenoids From the Sponge-Associated Fungus Penicillium brasilianum

Beneficial Chromosomal Integration of the Genes for CTX-M Extended-Spectrum β-Lactamase in Klebsiella pneumoniae for Stable Propagation

Prospective study on human fecal carriage of Enterobacteriaceae possessing mcr-1 and mcr-2 genes in a regional hospital in Hong Kong

The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study

The Journal of antimicrobial chemotherapy

Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation


Image-to-image translation with conditional adversarial nets

Image-to-Image Translation with Conditional Adversarial Networks

Shift-Net: Image Inpainting via Deep Feature Rearrangement

UV-GAN: Adversarial Facial UV Map Completion for Pose-invariant Face Recognition

Random sampling for fast face sketch synthesis

Radar-on-Lidar: metric radar localization on prior lidar maps

Scene Compliant Trajectory Forecast With Agent-Centric Spatio-Temporal Grids

River segmentation for flood monitoring

Zenodo (CERN European Organization for Nuclear Research)

SUSAN: Segment Unannotated image Structure using Adversarial Network

CSGAN: Cyclic-Synthesized Generative Adversarial Networks for Image-to-Image Transformation

SANTIS: Sampling-Augmented Neural neTwork with Incoherent Structure for MR image reconstruction


A random forest

High-Dimensional Materials and Process Optimization Using Data-Driven Experimental Design with Well-Calibrated Uncertainty Estimates

Integrating materials and manufacturing innovation

Overcoming data scarcity with transfer learning

The Materials Simulation Toolkit for Machine learning (MAST-ML): An automated open source toolkit to accelerate data-driven materials research

Uncertainty-Aware Mixed-Variable Machine Learning for Materials Design

By how much can closed-loop frameworks accelerate computational materials discovery?

Multivariate prediction intervals for bagged models


bioBakery tools for meta'omic profiling

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche

Bioinformatic approaches for studying the microbiome of fermented food

Studying the Association between Antibiotic Resistance Genes and Insertion Sequences in Metagenomes: Challenges and Pitfalls

Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut

Frontiers in cellular and infection microbiology

LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data

G. lucidum triterpenes restores intestinal flora balance in non-hepatitis B virus-related hepatocellular carcinoma: evidence of 16S rRNA sequencing and network pharmacology analysis

Plasma metagenomics reveals regional variations of emerging and re-emerging pathogens in Chinese blood donors with an emphasis on human parvovirus B19

Environmental sources along natural cave ripening shape the microbiome and metabolome of artisanal blue-veined cheeses


Library for unit extraction - fork of quantulum for python3

ACES: Translation Accuracy Challenge Sets for Evaluating Machine Translation Metrics

Measurement Extraction with Natural Language Processing: A Review

Findings of the Association for Computational Linguistics: EMNLP 2022

CQE: A Comprehensive Quantity Extractor


Clustering cONtigs with COverage and ComposiTion

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

Computational and structural biotechnology journal

CONCOCT: Clustering cONtigs on COverage and ComposiTion

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

Machine learning for metagenomics: methods and tools

Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses

RepBin: Constraint-based Graph Representation Learning for Metagenomic Binning

IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses


ELF: a platform for game research with AlphaGoZero/AlphaZero reimplementation

Deep Reinforcement Learning

Playing the lottery with rewards and multiple languages: lottery tickets in RL and NLP

ELF OpenGo: An Analysis and Open Reimplementation of AlphaZero

Practical Massively Parallel Monte-Carlo Tree Search Applied to Molecular Design

Artificial Intelligence for Games

Deep Pepper: Expert Iteration based Chess agent in the Reinforcement Learning Setting

Practical Large-Scale Distributed Parallel Monte-Carlo Tree Search Applied to Molecular Design.


Official public repository for the XCP Engine. This tool is deprecated in favor of XCP-D and ASLPrep.

Childhood trauma history is linked to abnormal brain connectivity in major depression

Functional Alignment with Anatomical Networks is Associated with Cognitive Flexibility

Associations between Neighborhood SES and Functional Brain Network Development

Daily Morning Blue Light Therapy for Post-mTBI Sleep Disruption: Effects on Brain Structure and Function

Exploration of the relationships between clinical traits and functional connectivity based on surface morphology abnormalities in bulimia nervosa


Sionna: An Open-Source Library for Next-Generation Physical Layer Research

Deep Learning Methods for Improved Decoding of Linear Codes

IEEE Journal on Selected Topics in Signal Processing

Learning to Decode Linear Codes Using Deep Learning

Improved Nonlinear Transform Source-Channel Coding to Catalyze Semantic Communications


Separate repository for svSolver

Automated generation of 0D and 1D reduced-order models of patient-specific blood flow

A note on the accuracy of the generalized‐ α scheme for the incompressible Navier‐Stokes equations

International Journal for Numerical Methods in Engineering

A reduced unified continuum formulation for vascular fluid–structure interaction

svMorph: Interactive geometry-editing tools for virtual patient-specific vascular anatomies

Rapid model-guided design of organ-scale synthetic vasculature for biomanufacturing

Bayesian Windkessel calibration using optimized 0D surrogate models


A minimal PyTorch re-implementation of the OpenAI GPT (Generative Pretrained Transformer) training

Attention Is All You Need

Decision Transformer: Reinforcement Learning via Sequence Modeling

Offline Reinforcement Learning as One Big Sequence Modeling Problem

Bailando: 3D Dance Generation by Actor-Critic GPT with Choreographic Memory

Transformers are Sample-Efficient World Models

Inductive Biases and Variable Creation in Self-Attention Mechanisms

Towards Revealing the Mystery behind Chain of Thought: A Theoretical Perspective

Broken Neural Scaling Laws

Q-learning Decision Transformer: Leveraging Dynamic Programming for Conditional Sequence Modelling in Offline RL

A smile is all you need: Predicting limiting activity coefficients from SMILES with natural language processing


A library for preparing data for machine translation research (monolingual preprocessing, bitext mining, etc.) built by the FAIR NLLB team.

Sequence-Level Knowledge Distillation

No Language Left Behind: Scaling Human-Centered Machine Translation

Seamless: Multilingual Expressive and Streaming Speech Translation

Detecting and Mitigating Hallucinations in Machine Translation: Model Internal Workings Alone Do Well, Sentence Similarity Even Better

SeamlessM4T: Massively Multilingual & Multimodal Machine Translation

HalOmi: A Manually Annotated Benchmark for Multilingual Hallucination and Omission Detection in Machine Translation

Toxicity in Multilingual Machine Translation at Scale

BLASER: A Text-Free Speech-to-Speech Translation Evaluation Metric

Making Flow-Matching-Based Zero-Shot Text-to-Speech Laugh as You Like

ReSeTOX: Re-learning attention weights for toxicity mitigation in machine translation


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

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

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

DNAModAnnot: a R toolbox for DNA modification filtering and annotation

Adenine methylation is very scarce in the drosophila genome and not erased by the Ten Eleven Translocation dioxygenase


Computer generated building footprints for the United States

Deep Learning-Based Generation of Building Stock Data from Remote Sensing for Urban Heat Demand Modeling

ISPRS International Journal of Geo-Information

Understanding the mesoscopic scaling patterns within cities

Assessing Property Level Economic Impacts of Climate in the US, New Insights and Evidence from a Comprehensive Flood Risk Assessment Tool

Automatic Building Outline Extraction from ALS Point Clouds by Ordered Points Aided Hough Transform

Tools for mapping multi-scale settlement patterns of building footprints: An introduction to the R package foot

Simulating historical flood events at the continental scale: observational validation of a large-scale hydrodynamic model

Natural hazards and earth system sciences

Fine-grained, spatiotemporal datasets measuring 200 years of land development in the United States

Open Data and Deep Semantic Segmentation for Automated Extraction of Building Footprints

Road Network Evolution in the Urban and Rural United States Since 1900

IS-COUNT: Large-scale Object Counting from Satellite Images with Covariate-based Importance Sampling


rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

RNA 3D structure prediction guided by independent folding of homologous sequences

Ribonanza: deep learning of RNA structure through dual crowdsourcing

bioRxiv : the preprint server for biology


Optimal Retrieval of Aerosol and Cloud

Remote Sensing of Droplet Number Concentration in Warm Clouds: A Review of the Current State of Knowledge and Perspectives

Reviews of geophysics (Washington, D.C. : 1985)

Cloud_cci Advanced Very High Resolution Radiometer post meridiem (AVHRR-PM) dataset version 3: 35-year climatology of global cloud and radiation properties

The Community Cloud retrieval for CLimate (CC4CL) – Part 2: The optimal estimation approach

Cloud_cci ATSR-2 and AATSR dataset version 3: a 17-yearclimatology of global cloud and radiation properties

Authors' response to Referee #2


InternEvo is an open-sourced lightweight training framework aims to support model pre-training without the need for extensive dependencies.

InternLM-Math: Open Math Large Language Models Toward Verifiable
  Reasoning

Characterization of Large Language Model Development in the Datacenter

InternEvo: Efficient Long-sequence Large Language Model Training via Hybrid Parallelism and Redundant Sharding

AMSP: Reducing Communication Overhead of ZeRO for Efficient LLM Training

LoongTrain: Efficient Training of Long-Sequence LLMs with Head-Context
  Parallelism


Grizli:  The "Grism redshift and line" analysis software

The Emergence of a Lanthanide-rich Kilonova Following the Merger of Two Neutron Stars

A population of red candidate massive galaxies ~600 Myr after the Big Bang

The evolution of the galaxy UV luminosity function at redshifts z ~ 8-15 from deep JWST and ground-based near-infrared imaging

Two Remarkably Luminous Galaxy Candidates at z ≈ 10–12 Revealed by JWST

The GLASS-JWST Early Release Science Program. I. Survey Design and Release Plans

Revealing Galaxy Candidates out to z ∼ 16 with JWST Observations of the Lensing Cluster SMACS0723

COSMOS-DASH: The Evolution of the Galaxy Size-Mass Relation since z similar to 3 from New Wide-field WFC3 Imaging Combined with CANDELS/3D-HST

The ALPINE–ALMA [C ii] Survey: Multiwavelength Ancillary Data and Basic Physical Measurements

The Astrophysical Journal Supplement Series

CEERS Epoch 1 NIRCam Imaging: Reduction Methods and Simulations Enabling Early JWST Science Results

First look with JWST spectroscopy: z ∼ 8 galaxies resemble local analogues


An extensible framework for program autotuning

HEBO Pushing The Limits of Sample-Efficient Hyperparameter Optimisation

Compiler Autotuning through Multiple-phase Learning

Search for Optimal Systolic Arrays: A Comprehensive Automated Exploration Framework and Lessons Learned


Super-scale your images and run experiments with Residual Dense and Adversarial Networks.

Photo-Realistic Single Image Super-Resolution Using a Generative Adversarial Network

Residual Dense Network for Image Super-Resolution

ESRGAN: Enhanced Super-Resolution Generative Adversarial Networks

Diabetic foot ulcers monitoring by employing super resolution and noise reduction deep learning techniques

Chameleons on Cloudlets: Elastic Edge Computing Through Microservice Variants


Canvas - Copy number variant (CNV) calling from DNA sequencing data

Canvas: versatile and scalable detection of copy number variants

Canvas SPW: calling de novo copy number variants in pedigrees

The molecular landscape of well differentiated retroperitoneal liposarcoma


Climate downscaling using CMIP6 data

Downscaling and bias-correction contribute considerable uncertainty to local climate projections in CMIP6

Climate risks to carbon sequestration in US forests


Ruby on Rails

Understanding Review Expertise of Developers: A Reviewer Recommendation Approach Based on Latent Dirichlet Allocation

Will you come back to contribute? Investigating the inactivity of OSS core developers in GitHub

New Directions in Cloud Programming

Automatic Identification of Similar Pull-Requests in GitHub's Repositories Using Machine Learning

Backports: Change Types, Challenges and Strategies

Proceedings of the 30th IEEE/ACM International Conference on Program Comprehension

Finding Regressions in Projects under Version Control Systems

GHTraffic: A Dataset for Reproducible Research in Service-Oriented Computing

License Incompatibilities in Software Ecosystems

Beyond Agile: Studying The Participatory Process in Software Development


Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

Novel modes of RNA editing in mitochondria

Regulation of S100A8 Stability by RNF5 in Intestinal Epithelial Cells Determines Intestinal Inflammation and Severity of Colitis

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

Src promotes castration-recurrent prostate cancer through androgen receptor-dependent canonical and non-canonical transcriptional signatures

Low expression of long noncoding RNA CDKN2B-AS1 in patients with idiopathic pulmonary fibrosis predicts lung cancer by regulating the p53-signaling pathway

Comparative population genomics dissects the genetic basis of seven domestication traits in jujube

Improving drug discovery using image-based multiparametric analysis of the epigenetic landscape

Identifying deer antler uhrf1 proliferation and s100a10 mineralization genes using comparative RNA-seq

Long Noncoding RNA MIR4435-2HG Suppresses Colorectal Cancer Initiation and Progression By Reprogramming Neutrophils.


Full public release of large scale and linear scaling DFT code CONQUEST

Polar morphologies from first principles: PbTiO_3 films on SrTiO_3 substrates and the p(2 ×Λ) surface reconstruction

The pseudoatomic orbital basis: electronic accuracy and soft-mode distortions in ABO_3 perovskites.

Origin of Ferroelectric Domain Wall Alignment with Surface Trenches in Ultrathin Films.


A library that incorporates state-of-the-art explainers for text-based machine learning models and visualizes the result with a built-in dashboard.

Explainable AI for Bioinformatics: Methods, Tools, and Applications


Resource-adaptive cluster scheduler for deep learning training.

An Empirical Model of Large-Batch Training

Pollux: Co-adaptive Cluster Scheduling for Goodput-Optimized Deep Learning

AdaScale SGD: A User-Friendly Algorithm for Distributed Training

Blox: A Modular Toolkit for Deep Learning Schedulers


FauxPilot - an open-source alternative to GitHub Copilot server

Is Your Code Generated by ChatGPT Really Correct? Rigorous Evaluation of Large Language Models for Code Generation

Programming Is Hard -- Or at Least It Used to Be: Educational Opportunities And Challenges of AI Code Generation

"It's Weird That it Knows What I Want": Usability and Interactions with Copilot for Novice Programmers

On the Design of AI-powered Code Assistants for Notebooks

A Survey of Neural Code Intelligence: Paradigms, Advances and Beyond


Public repository of the Cosmic Linear Anisotropy Solving System (master for the most recent version of the standard code; GW_CLASS to include Cosmic Gravitational Wave Background anisotropies; classnet branch for acceleration with neutral networks; ExoCLASS branch for exotic energy injection; class_matter branch for FFTlog)

MontePython 3: Boosted MCMC sampler and other features

Teleparallel Gravity: From Theory to Cosmology

Core Cosmology Library: Precision Cosmological Predictions for LSST

Nonlinear perturbation theory extension of the Boltzmann code CLASS

Cosmological viable models in f(T,B) gravity as solutions to the H_0
  tension

Exotic energy injection with ExoCLASS: application to the Higgs portal model and evaporating black holes

A deep learning approach to cosmological dark energy models

KiDS+GAMA: Constraints on Horndeski gravity from combined large-scale
  structure probes

Monthly Notices of the Royal Astronomical Society

Observational constraints on dark matter scattering with electrons

Lensing reconstruction in post-Born cosmic microwave background weak lensing


Get protein embeddings from protein sequences

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing

LambdaPP: Fast and accessible protein-specific phenotype predictions

PortPred: exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates


A Python parser for MediaWiki wikicode

Improving language models by retrieving from trillions of tokens

Wikipedia Citations: A comprehensive dataset of citations with identifiers extracted from English Wikipedia

WikiConv: A Corpus of the Complete Conversational History of a Large Online Collaborative Community

Vector Embedding of Wikipedia Concepts and Entities

Model Criticism for Long-Form Text Generation

TempEL: Linking Dynamically Evolving and Newly Emerging Entities

Graphemic Normalization of the Perso-Arabic Script

DaMuEL: A Large Multilingual Dataset for Entity Linking

Protection from Evil and Good: The Differential Effects of Page Protection on Wikipedia Article Quality

Language-Agnostic Modeling of Wikipedia Articles for Content Quality
  Assessment across Languages


DeepSeek Coder: Let the Code Write Itself

DeepSeek-Coder: When the Large Language Model Meets Programming -- The Rise of Code Intelligence

A Survey on Large Language Models for Software Engineering

Enhancing LLM-based Test Generation for Hard-to-Cover Branches via
  Program Analysis

ML-Bench: Evaluating Large Language Models and Agents for Machine Learning Tasks on Repository-Level Code

On Evaluating the Efficiency of Source Code Generated by LLMs

Automatic Programming: Large Language Models and Beyond


Python library containing wind analysis functions


Pretrained ConvNets for pytorch: NASNet, ResNeXt, ResNet, InceptionV4, InceptionResnetV2, Xception, DPN, etc.

Inception-v4, Inception-ResNet and the Impact of Residual Connections on Learning

Progressive Neural Architecture Search

Do ImageNet Classifiers Generalize to ImageNet?

Measuring Robustness to Natural Distribution Shifts in Image Classification

Skip Connections Matter: On the Transferability of Adversarial Examples Generated with ResNets

UNIQ: Uniform Noise Injection for Non-Uniform Quantization of Neural Networks

MultiGrain: a unified image embedding for classes and instances

Subspace Attack: Exploiting Promising Subspaces for Query-Efficient Black-box Attacks

An Overview of Neural Network Compression

Consensus-Driven Propagation in Massive Unlabeled Data for Face Recognition


OWLTools

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium

ROBOT: A Tool for Automating Ontology Workflows

Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools

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

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems

A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs

Candidate regulators and target genes of drought stress in needles and roots of Norway spruce

How, What and Why to test an ontology

Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat

GOcats: A tool for categorizing Gene Ontology into subgraphs of user-defined concepts


Code for loralib, an implementation of "LoRA: Low-Rank Adaptation of Large Language Models"

Towards a Unified View of Parameter-Efficient Transfer Learning

AdaLoRA: Adaptive Budget Allocation for Parameter-Efficient Fine-Tuning

Scaling Down to Scale Up: A Guide to Parameter-Efficient Fine-Tuning

On the Effectiveness of Parameter-Efficient Fine-Tuning

Novelty Controlled Paraphrase Generation with Retrieval Augmented Conditional Prompt Tuning

FlexRound: Learnable Rounding based on Element-wise Division for Post-Training Quantization

Exploring the impact of low-rank adaptation on the performance, efficiency, and regularization of RLHF

Meta-Learning the Difference: Preparing Large Language Models for Efficient Adaptation

Memory Efficient Optimizers with 4-bit States


The next version of bwa-mem

Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems

SARS-CoV-2 Omicron spike mediated immune escape and tropism shift

Technology dictates algorithms: Recent developments in read alignment

Culture and identification of a “Deltamicron” SARS‐CoV‐2 in a three cases cluster in southern France

First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France

Accelerated Seeding for Genome Sequence Alignment with Enumerated Radix Trees

International Symposium on Computer Architecture

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

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

The discovery of a key prenyltransferase gene assisted by a chromosome-level Epimedium pubescens genome

First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco


PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.

PESTO: Parameter EStimation TOolbox

Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis

Integration based profile likelihood calculation for PDE constrained parameter estimation problems

COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modeling

pyPESTO: a modular and scalable tool for parameter estimation for dynamic models

Optimization and uncertainty analysis of ODE models using 2nd order adjoint sensitivity analysis

Modeling early treatment response in AML from cell-free tumor DNA

COVID-19 outbreak in Wuhan demonstrates the limitations of publicly available case numbers for epidemiological modelling.


Tools for processing 2P recordings

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

Negative feedback control of neuronal activity by microglia

Robustness of Spike Deconvolution for Neuronal Calcium Imaging

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

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

Community-based benchmarking improves spike inference from two-photon calcium imaging data

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

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

Arousal regulates frequency tuning in primary auditory cortex

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

Behaviorally relevant decision coding in primary somatosensory cortex neurons

Neural signatures of auditory hypersensitivity following acoustic trauma


JDet is an object detection benchmark based on Jittor. Mainly focus on aerial image object detection (oriented object detection).

MMRotate: A Rotated Object Detection Benchmark using PyTorch

Proceedings of the 30th ACM International Conference on Multimedia

The KFIoU Loss for Rotated Object Detection

H2RBox-v2: Incorporating Symmetry for Boosting Horizontal Box Supervised Oriented Object Detection

Theoretically Achieving Continuous Representation of Oriented Bounding
  Boxes


High-level library to help with training and evaluating neural networks in PyTorch flexibly and transparently.

Machine Learning in Python: Main developments and technology trends in data science, machine learning, and artificial intelligence

Learning explanations that are hard to vary

Machine Learning the Physical Nonlocal Exchange-Correlation Functional of Density-Functional Theory.

The journal of physical chemistry letters

Object Representations as Fixed Points: Training Iterative Refinement Algorithms with Implicit Differentiation

Hitachi at SemEval-2020 Task 8: Simple but Effective Modality Ensemble for Meme Emotion Recognition

International Workshop on Semantic Evaluation

Lost in Latent Space: Disentangled Models and the Challenge of Combinatorial Generalisation

GaMPEN: A Machine-learning Framework for Estimating Bayesian Posteriors of Galaxy Morphological Parameters

Is It Enough to Recommend Tasks to Newcomers? Understanding Mentoring on Good First Issues

VoicePrivacy 2022 System Description: Speaker Anonymization with Feature-matched F0 Trajectories

Morphological Parameters and Associated Uncertainties for 8 Million Galaxies in the Hyper Suprime-Cam Wide Survey