White matter tractography clustering and more...

Free water modeling of peritumoral edema using multi-fiber tractography: Application to tracking the arcuate fasciculus for neurosurgical planning

White matter association tracts underlying language and theory of mind: An investigation of 809 brains from the Human Connectome Project

Superficial White Matter Analysis: An Efficient Point-cloud-based Deep Learning Framework with Supervised Contrastive Learning for Consistent Tractography Parcellation across Populations and dMRI Acquisitions

SupWMA: Consistent and Efficient Tractography Parcellation of Superficial White Matter with Deep Learning

Deep fiber clustering: Anatomically informed fiber clustering with self-supervised deep learning for fast and effective tractography parcellation

Model and predict age and sex in healthy subjects using brain white matter features: A deep learning approach

Alignment of Tractograms As Graph Matching

Harmonized diffusion MRI data and white matter measures from the Adolescent Brain Cognitive Development Study

The organization of frontostriatal brain wiring in non-affective early psychosis compared with healthy subjects using a novel diffusion imaging fiber cluster analysis

Automatic oculomotor nerve identification based on data‐driven fiber clustering


My experimental tools on top of htslib. NOT OFFICIAL!!!

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

Grey wolf genomic history reveals a dual ancestry of dogs

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

A single introduction of wild rabbits triggered the biological invasion of Australia

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

Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids

Archives of human-dog relationships: Genetic and stable isotope analysis of Arctic fur clothing

Limited historical admixture between European wildcats and domestic cats

Yersinia pestis genomes reveal plague in Britain 4,000 years ago


Astronomy & Astrophysics Software Pacakge

The Large Array Survey Telescope—System Overview and Performances

The Large Array Survey Telescope—Science Goals

The Large Array Survey Telescope—Pipeline. I. Basic Image Reduction and Visit Coaddition

UV to near-IR observations of the DART-Dimorphos collision


Implementation of the FV3GFS / SHiELD atmospheric model in Python


Interactive assembly and analysis of RAD-seq data sets

ipyrad: Interactive assembly and analysis of RADseq datasets

Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra

Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci

Adaptation to hummingbird pollination is associated with reduced diversification in Penstemon

Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage.

Reconciling species diversity in a tropical plant clade (Canarium, Burseraceae)

Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae)

Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum)

Genomics-Based Phylogenetic and Population Genetic Analysis of Global Samples Confirms Halophila johnsonii Eiseman as Halophila ovalis (R.Br.) Hook.f.

DiscoSnp-RAD: de novo detection of small variants for population genomics


Python library for real space quantum Monte Carlo

Recent developments in the PySCF program package

Excited states in variational Monte Carlo using a penalty method

A light weight regularization for wave function parameter gradients in quantum Monte Carlo

ipie: A Python-based Auxiliary-Field Quantum Monte Carlo Program with Flexibility and Efficiency on CPUs and GPUs

Bootstrap Embedding on a Quantum Computer

Quantification of electron correlation for approximate quantum calculations


Cartesian k-means for approximate nearest neghbor search, codebook learning, etc.

Cartesian K-Means

Stacked Quantizers for Compositional Vector Compression

Scalable Image Retrieval by Sparse Product Quantization


Implementation of the CheXNet network (PyTorch)

CheXNet: Radiologist-Level Pneumonia Detection on Chest X-Rays with Deep Learning

Learning to Transfer Learn: Reinforcement Learning-Based Selection for Adaptive Transfer Learning

Knowledge-Guided Data-Centric AI in Healthcare: Progress, Shortcomings, and Future Directions

Machine Learning for Exam Triage


Implementation of our papers Joint entity recognition and relation extraction as a multi-head selection problem (Expert Syst. Appl, 2018) and Adversarial training for multi-context joint entity and relation extraction (EMNLP, 2018).

Neural Metric Learning for Fast End-to-End Relation Extraction

Putting Them under Microscope: A Fine-Grained Approach for Detecting Redundant Test Cases in Natural Language


UNION: An Unreferenced Metric for Evaluating Open-ended Story Generation

COMPASS: a Creative Support System that Alerts Novelists to the Unnoticed Missing Contents

Event Causality Is Key to Computational Story Understanding


a bert for retrieval and generation

ChatGPT-EDSS: Empathetic Dialogue Speech Synthesis Trained from ChatGPT-derived Context Word Embeddings

UniASM: Binary Code Similarity Detection without Fine-tuning

SpeechCraft: A Fine-grained Expressive Speech Dataset with Natural Language Description

MSMix: An Interpolation-Based Text Data Augmentation Method Manifold Swap Mixup

A Chinese Machine Reading Comprehension Dataset Automatic Generated Based on Knowledge Graph

The Short Text Matching Model Enhanced with Knowledge via Contrastive Learning


Hierarchy-Aware Global Model for Hierarchical Text Classification

Meeting of the Association for Computational Linguistics

Hierarchical Interdisciplinary Topic Detection Model for Research Proposal Classification

Exploring Label Hierarchy in a Generative Way for Hierarchical Text Classification

International Conference on Computational Linguistics

Interdisciplinary Fairness in Imbalanced Research Proposal Topic Inference: A Hierarchical Transformer-based Method with Selective Interpolation

A Multi-Dimensional, Cross-Domain and Hierarchy-Aware Neural Architecture for ISO-Standard Dialogue Act Tagging


Trex: Learning Execution Semantics from Micro-Traces for Binary Similarity

Learning Approximate Execution Semantics From Traces for Binary Function Similarity

IEEE Transactions on Software Engineering


Nonparametric Causal Effects Based on Incremental Propensity Score Interventions

Causal mediation analysis for stochastic interventions

Journal of the Royal Statistical Society Series B: Statistical Methodology

Semiparametric counterfactual density estimation

GCF: Generalized Causal Forest for Heterogeneous Treatment Effect Estimation in Online Marketplace

Incremental causal effects: an introduction and review

Covariate balancing for causal inference on categorical and continuous treatments


categorical variational autoencoder using the Gumbel-Softmax estimator

Categorical Reparameterization with Gumbel-Softmax

ARSM: Augment-REINFORCE-Swap-Merge Estimator for Gradient Backpropagation Through Categorical Variables

Reliable Categorical Variational Inference with Mixture of Discrete Normalizing Flows


This repository contains scripts, data and jupyter notebooks used to produce the evaluation results in the BioPhi 2021 publication

Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires

Thera-SAbDab: the Therapeutic Structural Antibody Database

BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning

Humanization of antibodies using a machine learning approach on large-scale repertoire data

Humanization of Antibodies using a Statistical Inference Approach


VICReg official code base

VICReg: Variance-Invariance-Covariance Regularization for Self-Supervised Learning

The Hidden Uniform Cluster Prior in Self-Supervised Learning

Blockwise Self-Supervised Learning at Scale

A Survey on Self-Supervised Representation Learning

LiDAR: Sensing Linear Probing Performance in Joint Embedding SSL Architectures

Self-supervised learning for skin cancer diagnosis with limited training data

Self-supervised learning with rotation-invariant kernels

LDReg: Local Dimensionality Regularized Self-Supervised Learning

InfoNCE: Identifying the Gap Between Theory and Practice


adds sample names and read-group (RG) tags to BAM alignments

Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm

Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils

Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L.

Diversity of Neofusicoccum parvum for the Production of the Phytotoxic Metabolites (-)-Terremutin and (R)-Mellein

Genome editing excisase origins illuminated by somatic genome of Blepharisma

Origins of genome-editing excisases as illuminated by the somatic genome of the ciliate Blepharisma


Automatically exported from code.google.com/p/berkeleyparser

A Top-Down Neural Architecture towards Text-Level Parsing of Discourse Rhetorical Structure

Chinese Zero Pronoun Resolution with Deep Memory Network

Empirical Methods in Natural Language Processing

Building a comprehensive syntactic and semantic corpus of Chinese clinical texts

SCTB: A Chinese Treebank in Scientific Domain

Language Independent Dependency to Constituent Tree Conversion

From generic partition refinement to weighted tree automata minimization

Automatic Topological Field Identification in (Historical) German Texts

Supervised Syntax-based Alignment between English Sentences and Abstract Meaning Representation Graphs

Cross-language Projection of Dependency Trees with Constrained Partial Parsing for Tree-to-Tree Machine Translation

Proceedings of the First Conference on Machine Translation: Volume 1,
          Research Papers

DynamicPower at SemEval-2016 Task 8: Processing syntactic parse trees with a Dynamic Semantics core

North American Chapter of the Association for Computational Linguistics


Seeking information like heteroplasmy, structure variants, etc. on  Mitochondrial genome from next generation sequencing

mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

“Mitochondrial Toolbox” – A Review of Online Resources to Explore Mitochondrial Genomics


[ICCV 2023] BlendFace: Re-designing Identity Encoders for Face-Swapping https://arxiv.org/abs/2307.10854

Transcending Forgery Specificity with Latent Space Augmentation for Generalizable Deepfake Detection

DF40: Toward Next-Generation Deepfake Detection


Creative Commons Attribution Share Alike 4.0 International

StereoSet: Measuring stereotypical bias in pretrained language models

Measuring Fairness with Biased Rulers: A Comparative Study on Bias Metrics for Pre-trained Language Models

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

Measuring Fairness with Biased Rulers: A Survey on Quantifying Biases in Pretrained Language Models

Tackling Bias in Pre-trained Language Models: Current Trends and Under-represented Societies

Assessing gender bias in medical and scientific masked language models with StereoSet

An Efficient Multilingual Language Model Compression through Vocabulary Trimming

Robust Evaluation Measures for Evaluating Social Biases in Masked Language Models

How Different Is Stereotypical Bias Across Languages?


ZOO: Zeroth Order Optimization based Black-box Attacks to Deep Neural
  Networks without Training Substitute Models

Proceedings of the 10th ACM Workshop on Artificial Intelligence and Security

AutoZOOM: Autoencoder-based Zeroth Order Optimization Method for Attacking Black-box Neural Networks

GenAttack: Practical Black-box Attacks with Gradient-Free Optimization

Impact of Low-bitwidth Quantization on the Adversarial Robustness for Embedded Neural Networks

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

Exact and Consistent Interpretation of Piecewise Linear Models Hidden behind APIs: A Closed Form Solution


Towards Automatic Concept-based Explanations

Implementing local-explainability in Gradient Boosting Trees: Feature Contribution

A Framework to Learn with Interpretation

Computer Vision Analysis of Specimen Mammography to Predict Margin Status

medRxiv : the preprint server for health sciences


GraphParser is a semantic parser which can convert natural language sentences to logical forms and graphs.

Transforming Dependency Structures to Logical Forms for Semantic Parsing

Transactions of the Association for Computational Linguistics

Evaluating Induced CCG Parsers on Grounded Semantic Parsing


Unified Structure Generation for Universal Information Extraction

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

Large Language Model Is Not a Good Few-shot Information Extractor, but a Good Reranker for Hard Samples!

A Survey on Arabic Named Entity Recognition: Past, Recent Advances, and Future Trends

ChatLog: Carefully Evaluating the Evolution of ChatGPT Across Time

Few-shot Event Detection: An Empirical Study and a Unified View

ChatUIE: Exploring Chat-based Unified Information Extraction using Large
  Language Models


Code for our EACL-2021 paper "Generating Syntactically Controlled Paraphrases without Using Annotated Parallel Pairs".

Unsupervised Syntactically Controlled Paraphrase Generation with Abstract Meaning Representations

ParaAMR: A Large-Scale Syntactically Diverse Paraphrase Dataset by AMR Back-Translation

Exploiting Inductive Bias in Transformers for Unsupervised Disentanglement of Syntax and Semantics with VAEs


pre-process illumina reads

Trimmomatic: a flexible trimmer for Illumina sequence data

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

Earth history and the passerine superradiation

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes

Hidden histories of gene flow in highland birds revealed with genomic markers

Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest


Self-Supervised Learning for OOD Detection (NeurIPS 2019)

Using Self-Supervised Learning Can Improve Model Robustness and Uncertainty

AdvFlow: Inconspicuous Black-box Adversarial Attacks using Normalizing Flows

OODformer: Out-Of-Distribution Detection Transformer

Model-Agnostic Meta-Attack: Towards Reliable Evaluation of Adversarial Robustness


Code for paper EDDI: Efficient Dynamic Discovery of High-Value Information with Partial VAE

Simultaneous Missing Value Imputation and Structure Learning with Groups

VICause: Simultaneous Missing Value Imputation and Causal Discovery with Groups.

Generator Assisted Mixture of Experts For Feature Acquisition in Batch


Generating and Imputing Tabular Data via Diffusion and Flow XGBoost Models

Your Diffusion Model is Secretly a Zero-Shot Classifier

Intriguing properties of generative classifiers

Generating and Imputing Tabular Data via Diffusion and Flow-based Gradient-Boosted Trees


THELI is a data processing pipeline for astronomical images

Photometric Observations of the Binary Near-Earth Asteroid (65803) Didymos in 2015–2021 Prior to DART Impact

A Significant Excess in Major Merger Rate for AGNs with the Highest Eddington Ratios at z < 0.2

The Close AGN Reference Survey (CARS)

Chasing Tails: Active Asteroid, Centaur, and Quasi-Hilda Discovery with Astroinformatics and Citizen Science


Code for ACL 2022 paper "CONTaiNER: Few-Shot Named Entity Recognition via Contrastive Learning"

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

Type-Aware Decomposed Framework for Few-Shot Named Entity Recognition

Language Model Pre-Training with Sparse Latent Typing


Miscellaneous science/astronomy tools.

The Electromagnetic Counterpart of the Binary Neutron Star Merger LIGO/Virgo GW170817. VI. Radio Constraints on a Relativistic Jet and Predictions for Late-time Emission from the Kilonova Ejecta

DISCOVERY OF AN OUTFLOW FROM RADIO OBSERVATIONS OF THE TIDAL DISRUPTION EVENT ASASSN-14li

Nine-hour X-ray quasi-periodic eruptions from a low-mass black hole galactic nucleus

PS16dtm: A Tidal Disruption Event in a Narrow-line Seyfert 1 Galaxy

Fifteen years of XMM-Newton and Chandra monitoring of Sgr A★: evidence for a recent increase in the bright flaring rate

Monthly Notices of the Royal Astronomical Society

Radio Monitoring of the Tidal Disruption Event Swift J164449.3+573451. III. Late-time Jet Energetics and a Deviation from Equipartition

A Reverse Shock and Unusual Radio Properties in GRB 160625B

EVIDENCE FOR A CO DESORPTION FRONT IN THE OUTER AS 209 DISK

Radio Observations of an Ordinary Outflow from the Tidal Disruption Event AT2019dsg

A Radio Source Coincident with the Superluminous Supernova PTF10hgi: Evidence for a Central Engine and an Analog of the Repeating FRB 121102?


Meta-Learning with Differentiable Convex Optimization (CVPR 2019 Oral)

Few-Shot Learning via Embedding Adaptation with Set-to-Set Functions

Cross-Domain Few-Shot Classification via Learned Feature-Wise Transformation

Fine-Grained Few-Shot Classification with Feature Map Reconstruction Networks.

TAFSSL: Task-Adaptive Feature Sub-Space Learning for few-shot classification

Bridging Multi-Task Learning and Meta-Learning: Towards Efficient Training and Effective Adaptation

Cross-Domain Cross-Set Few-Shot Learning via Learning Compact and Aligned Representations

Learning an Explicit Hyperparameter Prediction Function Conditioned on Tasks

StarNet: towards weakly supervised few-shot detection and explainable few-shot classification


ImageNet-R(endition) and DeepAugment (ICCV 2021)

The Many Faces of Robustness: A Critical Analysis of Out-of-Distribution Generalization

Measuring Robustness to Natural Distribution Shifts in Image Classification

Improving robustness against common corruptions by covariate shift adaptation

Masked Siamese Networks for Label-Efficient Learning

Test-Time Adaptation to Distribution Shift by Confidence Maximization and Input Transformation

Dream the Impossible: Outlier Imagination with Diffusion Models

If your data distribution shifts, use self-learning

On the Strong Correlation Between Model Invariance and Generalization

Confidence and Dispersity Speak: Characterising Prediction Matrix for Unsupervised Accuracy Estimation

The Entropy Enigma: Success and Failure of Entropy Minimization


Auto-optimizing a neural net (and its architecture) on the CIFAR-100 dataset. Could be easily transferred to another dataset or another classification task. Monitoring with TensorBoard. Other visualizations available.

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

Striving for Simplicity: The All Convolutional Net

LARNN: Linear Attention Recurrent Neural Network


Subgraph Based Learning of Contextual Embedding

Graph Self-Supervised Learning: A Survey

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

Self-Supervised Learning on Graphs: Contrastive, Generative, or Predictive

Self-Supervised Learning of Contextual Embeddings for Link Prediction in Heterogeneous Networks

SMiLE: Schema-augmented Multi-level Contrastive Learning for Knowledge Graph Link Prediction


A Matlab package for Bayes Factor statistical analysis

Stimulus-induced gamma rhythms are weaker in human elderly with mild cognitive impairment and Alzheimer’s disease

Neural basis of somatosensory target detection independent of uncertainty, relevance, and reports

Resolution of impaired multisensory processing in autism and the cost of switching sensory modality

Anterior cingulate and medial prefrontal cortex oscillations underlie learning alterations in trait anxiety in humans

Interhemispheric symmetry of µ-rhythm phase-dependency of corticospinal excitability

Concurrent visual working memory bias in sequential integration of approximate number

Impaired perception of temporal contiguity between action and effect is associated with disorders of agency in schizophrenia

Inhibitory temporo-parietal effective connectivity is associated with explicit memory performance in older adults

Action sequence learning, habits, and automaticity in obsessive-compulsive disorder

Unreliable feedback deteriorates information processing in primary visual cortex


This is outdated -- New version: https://github.com/boyangumn/DCN-New

Towards K-means-friendly Spaces: Simultaneous Deep Learning and Clustering

Temporal Phenotyping using Deep Predictive Clustering of Disease Progression

Hierarchically Clustered Representation Learning

A Transfer Learning based Feature-Weak-Relevant Method for Image Clustering


Official Implementation of "A Hierarchical Network for Abstractive Meeting Summarization with Cross-Domain Pretraining""

Dialogue Discourse-Aware Graph Model and Data Augmentation for Meeting Summarization

An Exploratory Study on Long Dialogue Summarization: What Works and What's Next

TANet: Thread-Aware Pretraining for Abstractive Conversational Summarization

ORCHID: A Chinese Debate Corpus for Target-Independent Stance Detection and Argumentative Dialogue Summarization

Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing


Toolbox with R scripts

The concurrence of DNA methylation and demethylation is associated with transcription regulation

Downregulation of ST3GAL5 is associated with muscle invasion, high grade and a poor prognosis in patients with bladder cancer

Sexually dimorphic activation of innate antitumor immunity prevents adrenocortical carcinoma development

SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry

Inhibition of casein kinase 2 sensitizes mantle cell lymphoma to venetoclax through MCL-1 downregulation

The bromodomain protein TRIM28 controls the balance between growth and invasiveness in melanoma


Very Deep Convolutional Networks for Large-Scale Image Recognition

Deep Captioning with Multimodal Recurrent Neural Networks (m-RNN)

Exploring Nearest Neighbor Approaches for Image Captioning

Survey of Visual-Semantic Embedding Methods for Zero-Shot Image Retrieval


RECOD Titans participation at the ISBI 2017 challenge - Part 3

Knowledge Transfer for Melanoma Screening with Deep Learning

International Symposium on Biomedical Imaging

RECOD Titans at ISIC Challenge 2017

On Interpretability of Deep Learning based Skin Lesion Classifiers using Concept Activation Vectors

Towards Automated Melanoma Screening: Proper Computer Vision & Reliable Results.

Data, Depth, and Design: Learning Reliable Models for Melanoma Screening


This repository is for the paper "A Hybrid Approach to Automatic Corpus Generation for Chinese Spelling Check"

SpellGCN: Incorporating Phonological and Visual Similarities into Language Models for Chinese Spelling Check

Dynamic Connected Networks for Chinese Spelling Check

MultiCoNER v2: a Large Multilingual dataset for Fine-grained and Noisy Named Entity Recognition

Mask the Correct Tokens: An Embarrassingly Simple Approach for Error Correction

An Error-Guided Correction Model for Chinese Spelling Error Correction

A Chinese Spelling Check Framework Based on Reverse Contrastive Learning

UMRSpell: Unifying the Detection and Correction Parts of Pre-trained Models towards Chinese Missing, Redundant, and Spelling Correction

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


Implementation of "Embedding Watermarks into Deep Neural Networks," in Proc. of ICMR'17.

PROCEEDINGS OF THE 2017 ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA RETRIEVAL (ICMR'17)

Digital watermarking for deep neural networks

International Journal of Multimedia Information Retrieval

Performance Comparison of Contemporary DNN Watermarking Techniques

Deep Intellectual Property Protection: A Survey

Cracking White-box DNN Watermarks via Invariant Neuron Transforms


Conformalized Quantile Regression

Conformalized Quantile Regression

Nested conformal prediction and quantile out-of-bag ensemble methods

With Malice Towards None: Assessing Uncertainty via Equalized Coverage

Achieving Equalized Odds by Resampling Sensitive Attributes

Estimating Uncertainty Intervals from Collaborating Networks

Distribution-Free Finite-Sample Guarantees and Split Conformal Prediction


Official code for our ECCV'22 paper "A Fast Knowledge Distillation Framework for Visual Recognition"

EfficientNetV2: Smaller Models and Faster Training

FBNet: Hardware-Aware Efficient ConvNet Design via Differentiable Neural Architecture Search


Official PyTorch Implementation of SAGPool - ICML 2019

Self-Attention Graph Pooling

State of the Art and Potentialities of Graph-level Learning

Learning to Pool in Graph Neural Networks for Extrapolation


⛷ LLaMA-MoE: Building Mixture-of-Experts from LLaMA with Continual Pre-training (EMNLP 2024)

OpenMoE: An Early Effort on Open Mixture-of-Experts Language Models

Knowledge Graphs Meet Multi-Modal Learning: A Comprehensive Survey

A Survey on Mixture of Experts

Demystifying the Compression of Mixture-of-Experts Through a Unified
  Framework


Mid-Level Visual Representations Improve Generalization and Sample Efficiency for Learning Visuomotor Policies

Deep Residual Learning for Image Recognition

Learning to Navigate Using Mid-Level Visual Priors


❄ Visual Prompt Tuning [ECCV 2022] https://arxiv.org/abs/2203.12119

Visual Prompt Tuning

Visual Query Tuning: Towards Effective Usage of Intermediate Representations for Parameter and Memory Efficient Transfer Learning

Learning Expressive Prompting With Residuals for Vision Transformers

Dynamic Prompting: A Unified Framework for Prompt Tuning

Distribution-Aware Prompt Tuning for Vision-Language Models

Distilling from Similar Tasks for Transfer Learning on a Budget


[ECCV 2020] PyTorch code for XML on TVRetrieval dataset - TVR: A Large-Scale Dataset for Video-Subtitle Moment Retrieval

Learning a Text-Video Embedding from Incomplete and Heterogeneous Data

ExCL: Extractive Clip Localization Using Natural Language Descriptions

AssistSR: Task-oriented Video Segment Retrieval for Personal AI Assistant

Video Moment Retrieval with Text Query Considering Many-to-Many Correspondence Using Potentially Relevant Pair

AssistSR: Affordance-centric Question-driven Video Segment Retrieval

Finding Moments in Video Collections Using Natural Language


Why do tree-based models still outperform deep learning on typical tabular data?

Why do tree-based models still outperform deep learning on tabular data?

Mechanism of feature learning in deep fully connected networks and kernel machines that recursively learn features

Trompt: Towards a Better Deep Neural Network for Tabular Data

BiSHop: Bi-Directional Cellular Learning for Tabular Data with
  Generalized Sparse Modern Hopfield Model


2nd solution of ICDAR 2021 Competition on Scientific Literature Parsing, Task B.

Shape Robust Text Detection with Progressive Scale Expansion Network

Image-based table recognition: data, model, and evaluation

MASTER: Multi-aspect non-local network for scene text recognition

PingAn-VCGroup's Solution for ICDAR 2021 Competition on Scientific Literature Parsing Task B: Table Recognition to HTML

Improving Table Structure Recognition with Visual-Alignment Sequential Coordinate Modeling


Codes for "CSDI: Conditional Score-based Diffusion Models for Probabilistic Time Series Imputation"

Diffusion models for missing value imputation in tabular data

Non-autoregressive Conditional Diffusion Models for Time Series Prediction

Predict, Refine, Synthesize: Self-Guiding Diffusion Models for Probabilistic Time Series Forecasting

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

Diffusion-TS: Interpretable Diffusion for General Time Series Generation

Improving Diffusion Models for ECG Imputation with an Augmented Template Prior


From Simulated Mixtures to Simulated Conversations as Training Data for End-to-End Neural Diarization

Multi-Speaker and Wide-Band Simulated Conversations as Training Data for End-to-End Neural Diarization

Neural Diarization with Non-autoregressive Intermediate Attractors

DiaCorrect: Error Correction Back-end For Speaker Diarization

DiaPer: End-to-End Neural Diarization with Perceiver-Based Attractors

Target Speech Diarization with Multimodal Prompts

Do End-to-End Neural Diarization Attractors Need to Encode Speaker
  Characteristic Information?


Malware Mutation Using Reinforcement Learning and Generative Adversarial Networks

Generating Adversarial Malware Examples for Black-Box Attacks Based on GAN

Creating Valid Adversarial Examples of Malware


Tools for fast and flexible genome assembly scaffolding and improvement

RaGOO: fast and accurate reference-guided scaffolding of draft genomes

Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing

The Genome Assembly and Annotation of the Apollo Butterfly Parnassius apollo, a Flagship Species for Conservation Biology

Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases

Biosynthesis of mushroom-derived type II ganoderic acids by engineered yeast

CAMSA: a tool for comparative analysis and merging of scaffold assemblies

A beginner’s guide to assembling a draft genome and analyzing structural variants with long-read sequencing technologies

Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication

Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus

Draft Genome Sequence of "Candidatus Nardonella dryophthoridicola" Strain NARMHE1, Endosymbiont of Metamasius hemipterus (Coleoptera, Curculionidae, Dryophthorinae).


iSTFTNet : Fast and Lightweight Mel-spectrogram Vocoder Incorporating Inverse Short-time Fourier Transform

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

Vocos: Closing the gap between time-domain and Fourier-based neural vocoders for high-quality audio synthesis

APNet: An All-Frame-Level Neural Vocoder Incorporating Direct Prediction of Amplitude and Phase Spectra

HiFTNet: A Fast High-Quality Neural Vocoder with Harmonic-plus-Noise Filter and Inverse Short Time Fourier Transform

APNet2: High-quality and High-efficiency Neural Vocoder with Direct Prediction of Amplitude and Phase Spectra


Density estimation using Gaussian mixtures in the presence of noisy, heterogeneous and incomplete data

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

EXPLORING ANTICORRELATIONS AND LIGHT ELEMENT VARIATIONS IN NORTHERN GLOBULAR CLUSTERS OBSERVED BY THE APOGEE SURVEY

Characterization and photometric performance of the Hyper Suprime-Cam Software Pipeline

Publications of the Astronomical Society of Japan

Evidence for a Vast Prograde Stellar Stream in the Solar Vicinity

CLEAR EVIDENCE FOR THE PRESENCE OF SECOND-GENERATION ASYMPTOTIC GIANT BRANCH STARS IN METAL-POOR GALACTIC GLOBULAR CLUSTERS

EmpiriciSN: Re-sampling Observed Supernova/Host Galaxy Populations Using an XD Gaussian Mixture Model

Addressing Systematics in the Traceback Age of the β Pictoris Moving Group

Mixture Models in Astronomy

Tracing the Origin of Moving Groups. III. Detecting Moving Groups in LAMOST DR7

Young open cluster IC 4996 and its vicinity: multicolor photometry and Gaia DR2 astrometry


Pre-trained Language Models in Biomedical Domain: A Systematic Survey

MSˆ2: Multi-Document Summarization of Medical Studies

Discriminative Marginalized Probabilistic Neural Method for Multi-Document Summarization of Medical Literature

Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)

A Survey for Biomedical Text Summarization: From Pre-trained to Large Language Models


Dataset and starting code for visual entailment dataset

CLEVR: A Diagnostic Dataset for Compositional Language and Elementary Visual Reasoning

UNITER: UNiversal Image-TExt Representation Learning

Making the V in VQA Matter: Elevating the Role of Image Understanding in Visual Question Answering

UniT: Multimodal Multitask Learning with a Unified Transformer

Visual Entailment: A Novel Task for Fine-Grained Image Understanding

Trends in Integration of Vision and Language Research: A Survey of Tasks, Datasets, and Methods

Visual Entailment Task for Visually-Grounded Language Learning

What You See is What You Read? Improving Text-Image Alignment Evaluation

e-SNLI-VE: Corrected Visual-Textual Entailment with Natural Language Explanations

AlignVE: Visual Entailment Recognition Based on Alignment Relations


SGPT: GPT Sentence Embeddings for Semantic Search

Generative Representational Instruction Tuning

Neural Embeddings for Text

Coupling Symbolic Reasoning with Language Modeling for Efficient Longitudinal Understanding of Unstructured Electronic Medical Records


DRUGZ software

CRISPR-Cas9 screen identifies oxidative phosphorylation as essential for cancer cell survival at low extracellular pH

Genome-scale chemogenomic CRISPR screens in human cells using the TKOv3 library

Identifying chemogenetic interactions from CRISPR knockout screens with drugZ

RAD54L2-mediated DNA damage avoidance pathway specifically preserves genome integrity in response to topoisomerase 2 poisons

DePARylation is critical for S phase progression and cell survival


De-Novo Repeat Discovery Tool

RepeatModeler2 for automated genomic discovery of transposable element families

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

Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus

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

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzuspersicae

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

Repetitive DNA sequence detection and its role in the human genome

Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila

Genetics of nodulation in Aeschynomene evenia uncovers new mechanisms of the rhizobium-legume symbiosis

Genomic and Metabolomic Analyses of the Medicinal Fungus Inonotus hispidus for Its Metabolite’s Biosynthesis and Medicinal Application


Shopping Queries Dataset: A Large-Scale ESCI Benchmark for Improving Product Search

eCeLLM: Generalizing Large Language Models for E-commerce from
  Large-scale, High-quality Instruction Data

Improving Retrieval in Theme-specific Applications using a Corpus Topical Taxonomy


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

HoHoNet: 360 Indoor Holistic Understanding with Latent Horizontal Features

Monocular spherical depth estimation with explicitly connected weak layout cues

Zenodo (CERN European Organization for Nuclear Research)

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


An Evaluation of Change Point Detection Algorithms

Doubly Robust Bayesian Inference for Non-Stationary Streaming Data with β-Divergences

Spatio-temporal Bayesian On-line Changepoint Detection with Model Selection

On Matched Filtering for Statistical Change Point Detection

Monitoring Deforestation Using Multivariate Bayesian Online Changepoint Detection with Outliers

MECATS: Mixture-of-Experts for Quantile Forecasts of Aggregated Time Series


Virtual adversarial training with Tensorflow

Virtual Adversarial Training: A Regularization Method for Supervised and Semi-Supervised Learning

Semi-Supervised Sequence Modeling with Cross-View Training

Semi-Supervised Learning by Augmented Distribution Alignment

Enhancing MR Image Segmentation with Realistic Adversarial Data Augmentation

MetaTS: Meta Teacher-Student Network for Multilingual Sequence Labeling with Minimal Supervision

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


Variational Autoencoder and Conditional Variational Autoencoder on MNIST in PyTorch

Stochastic Gradient VB and the Variational Auto-Encoder

Homogeneous Linear Inequality Constraints for Neural Network Activations

Evidential Sparsification of Multimodal Latent Spaces in Conditional Variational Autoencoders

Efficient Planning with Latent Diffusion

Residual-Recursion Autoencoder for Shape Illustration Images


Codebase for CVPR2020 A Local-to-Global Approach to Multi-modal Movie Scene Segmentation

Scene Consistency Representation Learning for Video Scene Segmentation

Boundary-aware Self-supervised Learning for Video Scene Segmentation


Pytorch port of Google Research's VGGish model used for extracting audio features.

CNN Architectures for Large-Scale Audio Classification

FakeSV: A Multimodal Benchmark with Rich Social Context for Fake News Detection on Short Video Platforms

Continuous Emotion Recognition using Visual-audio-linguistic Information: A Technical Report for ABAW3

Multimodal Continuous Emotion Recognition: A Technical Report for ABAW5

Low-Resource Music Genre Classification with Cross-Modal Neural Model Reprogramming

A Hybrid Neuro-Symbolic Approach for Complex Event Processing

Recursive Joint Cross-Modal Attention for Multimodal Fusion in Dimensional Emotion Recognition

Using DeepProbLog to perform Complex Event Processing on an Audio Stream

Rank-based loss for learning hierarchical representations

Audio Embeddings as Teachers for Music Classification


SOLECTRUS is a smart photovoltaic dashboard that shows your energy production and usage. It also calculates costs and savings, helping you get the most out of your solar system.


Prepare Sailfish and Salmon output for downstream analysis

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia

Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR

Differential regulation of cranial and cardiac neural crest by serum response factor and its cofactors


Neural network visualization toolkit for tf.keras

Determining the Dark Matter distribution in galaxies with Deep Learning

Accurate staging of chick embryonic tissues via deep learning

Gastrointestinal Disease Classification through Explainable and Cost-Sensitive Deep Neural Networks with Supervised Contrastive Learning


R package for spatial analysis and modelling of ecological systems

Siberian taiga and tundra fire regimes from 2001–2020

Satellite Tracking Reveals Nesting Patterns, Site Fidelity, and Potential Impacts of Warming on Major Green Turtle Rookeries in the Red Sea

Geographic patterns of genomic diversity and structure in the C-4 grass Panicum hallii across its natural distribution

An Orchid in Retrograde: Climate-Driven Range Shift Patterns of Ophrys helenae in Greece

Identification of the Optimal Season and Spectral Regions for Shrub Cover Estimation in Grasslands

Subtidal Natural Hard Substrate Quantitative Habitat Mapping: Interlinking Underwater Acoustics and Optical Imagery with Machine Learning

Potential distribution of invasive boxwood blight pathogen (Calonectria pseudonaviculata) as predicted by process-based and correlative models

Distribution of Charophyte Oospores in the Curonian Lagoon and their Relationship to Environmental Forcing

Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds

Behavioral responses of Canada geese to winter harassment in the context of human‐wildlife conflicts


log anomaly detection via BERT

LogBERT: Log Anomaly Detection via BERT

LogGPT: Log Anomaly Detection via GPT

RAPID: Training-free Retrieval-based Log Anomaly Detection with PLM considering Token-level information


Genomic interval machine learning

Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings

Methods for constructing and evaluating consensus genomic interval sets

Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets

Methods for evaluating unsupervised vector representations of genomic regions


Python bindings around Google Chromium's embedded compact language detection library (CLD2)

OpusTools and Parallel Corpus Diagnostics

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

European Language Resource Coordination: Collecting Language Resources for Public Sector Multilingual Information Management

PROCEEDINGS OF THE ELEVENTH INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION (LREC 2018)

Softmax Bottleneck Makes Language Models Unable to Represent Multi-mode Word Distributions

Tweeting your Destiny: Profiling Users in the Twitter Landscape around an Online Game

NRC Parallel Corpus Filtering System for WMT 2019

Proceedings of the Fourth Conference on Machine Translation (Volume 3: Shared Task Papers, Day 2)

The University of Helsinki submissions to the WMT19 news translation task

Measuring sentence parallelism using Mahalanobis distances: The NRC unsupervised submissions to the WMT18 Parallel Corpus Filtering shared task

Proceedings of the Third Conference on Machine Translation: Shared Task Papers

The University of Helsinki Submission to the WMT19 Parallel Corpus Filtering Task

Democratizing neural machine translation with OPUS-MT

Improving Parallel Data Identification using Iteratively Refined Sentence Alignments and Bilingual Mappings of Pre-trained Language Models

Empirical Methods in Natural Language Processing


Learning Model Predictive Controllers with Real-Time Attention for Real-World Navigation

CALIPSO: A Differentiable Solver for Trajectory Optimization with Conic and Complementarity Constraints

Agile Catching with Whole-Body MPC and Blackbox Policy Learning

Transductive Active Learning: Theory and Applications

The Power of Learned Locally Linear Models for Nonlinear Policy Optimization


A library with extensible implementations of DPO, KTO, PPO, ORPO, and other human-aware loss functions (HALOs).

KTO: Model Alignment as Prospect Theoretic Optimization

Large Language Models: A Survey

A Long Way to Go: Investigating Length Correlations in RLHF

Preference Fine-Tuning of LLMs Should Leverage Suboptimal, On-Policy Data

Towards Analyzing and Understanding the Limitations of DPO: A
  Theoretical Perspective

RaFe: Ranking Feedback Improves Query Rewriting for RAG

How Far Are We From AGI

PolygloToxicityPrompts: Multilingual Evaluation of Neural Toxic
  Degeneration in Large Language Models

NeMo-Aligner: Scalable Toolkit for Efficient Model Alignment

PAL: Pluralistic Alignment Framework for Learning from Heterogeneous Preferences


A high-fidelity E. coli RNA-seq compendium

The Escherichia coli transcriptome mostly consists of independently regulated modules

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response

Independent component analysis recovers consistent regulatory signals from disparate datasets

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

Matrix factorization recovers consistent regulatory signals from disparate datasets


Quantitative Information Flow library for python and C++.

Information Leakage Games: Exploring Information as a Utility Function

Flexible and scalable privacy assessment for very large datasets, with an application to official governmental microdata

A Novel Analysis of Utility in Privacy Pipelines, Using Kronecker Products and Quantitative Information Flow


R package for detecting doublets in single-cell RNA sequencing data

Single cell transcriptional signatures of the human placenta in term and preterm parturition

Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs

HypoMap—a unified single-cell gene expression atlas of the murine hypothalamus

Cardiac cell type–specific gene regulatory programs and disease risk association

Single-cell RNA sequencing reveals time- and sex-specific responses of mouse spinal cord microglia to peripheral nerve injury and links ApoE to chronic pain

Resolving the graft ischemia-reperfusion injury during liver transplantation at the single cell resolution

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

Single-cell profiling reveals pathogenic role and differentiation trajectory of granzyme K+CD8+ T cells in primary Sjögren’s syndrome

Sex differences in coronary artery disease and diabetes revealed by scRNA-Seq and CITE-Seq of human CD4+ T cells

A novel molecular classification method for osteosarcoma based on tumor cell differentiation trajectories


DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models

DockQ: A Quality Measure for Protein-Protein Docking Models

Learning Harmonic Molecular Representations on Riemannian Manifold

Improved cluster ranking in protein–protein docking using a regression approach

Computational and structural biotechnology journal

DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment

Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction

Structural assembly of the bacterial essential interactome


Multi-lingual & multi-domain (specialisation for biomedical data) translation model

A Multilingual Neural Machine Translation Model for Biomedical Data

Naver Labs Europe’s Participation in the Robustness, Chat, and Biomedical Tasks at WMT 2020

Do Multilingual Neural Machine Translation Models Contain Language Pair Specific Attention Heads?


Two-temperature General Relativistic Radiation Magnetohydrodynamics

Pair Drizzle around Sub-Eddington Supermassive Black Holes

Radiation GRMHD Simulations of the Hard State of Black Hole X-Ray Binaries and the Collapse of a Hot Accretion Flow

Radiation GRMHD simulations of M87: funnel properties and prospects for gap acceleration

Monthly notices of the Royal Astronomical Society


software to detect doublets

Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning

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

基因组蛋白质组与生物信息学报

Protocol for Executing and Benchmarking Eight Computational Doublet-Detection Methods in Single-Cell RNA Sequencing Data Analysis

Solo: doublet identification via semi-supervised deep learning

Vaeda computationally annotates doublets in single-cell RNA sequencing data


ClusterJob: An automated system for painless and reproducible massive computational experiments

Prevalence of neural collapse during the terminal phase of deep learning training

The Full Spectrum of Deepnet Hessians at Scale: Dynamics with SGD Training and Sample Size

Traces of Class/Cross-Class Structure Pervade Deep Learning Spectra


Planck 2018 results. VIII. Gravitational lensing

Maximum a posteriori CMB lensing reconstruction

Planck intermediate results. LIII. Detection of velocity dispersion from the kinetic Sunyaev-Zeldovich effect

Quadratic estimators for CMB weak lensing

Internal Delensing of Cosmic Microwave Background Polarization B-Modes with the POLARBEAR Experiment.

Optimal filtering for CMB lensing reconstruction

Impact of thermal Sunyaev–Zeldovich effect on cross-correlations between Planck cosmic microwave background lensing and SDSS galaxy density fields

CMB delensing with neural network based lensing reconstruction in the presence of primordial tensor perturbations

Cluster profiles from beyond-the-QE CMB lensing mass maps


Astrocats module for the Open Supernova Catalog (OSC). Please use the issue tracker on this repo for all OSC issues.

An Open Catalog for Supernova Data

Oxygen and calcium nebular emission line relationships in core-collapse supernovae and Ca-rich transients

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

Collapsars as Sites of r-process Nucleosynthesis: Systematic Photometric Near-infrared Follow-up of Type Ic-BL Supernovae

Intermediate-luminosity Type IIP SN 2021gmj: a low-energy explosion with signatures of circumstellar material

Thermonuclear explosions as Type II supernovae


nGraph-HE: Deep learning with Homomorphic Encryption (HE) through Intel nGraph

Homomorphic Encryption for Machine Learning in Medicine and Bioinformatics

CaPC Learning: Confidential and Private Collaborative Learning

Is Homomorphic Encryption-Based Deep Learning Secure Enough?


Multiscale Solar Water Heating

Multiscale Solar Water Heating


A repository with several curated datasets of counter-narratives to fight online hate speech.

CONAN - COunter NArratives through Nichesourcing: a Multilingual Dataset of Responses to Fight Online Hate Speech

Meeting of the Association for Computational Linguistics

Human-in-the-Loop for Data Collection: a Multi-Target Counter Narrative Dataset to Fight Online Hate Speech

Towards Knowledge-Grounded Counter Narrative Generation for Hate Speech

Human-Machine Collaboration Approaches to Build a Dialogue Dataset for Hate Speech Countering

A Multi-Aspect Framework for Counter Narrative Evaluation using Large Language Models


Workflow Description Language (WDL) scripts for common vg workflows

Benchmarking challenging small variants with linked and long reads

Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit

A complete pedigree-based graph workflow for rare candidate variant analysis

Personalized Pangenome References

bioRxiv : the preprint server for biology


Official PyTorch implementation of LF-Font (Few-shot Font Generation with Localized Style Representations and Factorization) AAAI 2021

Few-shot Compositional Font Generation with Dual Memory

Multiple Heads are Better than One: Few-shot Font Generation with Multiple Localized Experts

Few-shot Font Generation with Weakly Supervised Localized Representations


Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

Single cell analysis in head and neck cancer reveals potential immune evasion mechanisms during early metastasis

Selective Vulnerability of Layer 5a Corticostriatal Neurons in Huntington’s Disease

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

Single-nucleus chromatin accessibility and RNA sequencing reveal impaired brain development in prenatally e-cigarette exposed neonatal rats

Zeb2 regulates differentiation of long-lived effector of invariant natural killer T cells


Code, Models and Datasets for OpenViDial Dataset

OpenViDial: A Large-Scale, Open-Domain Dialogue Dataset with Visual Contexts

OpenViDial 2.0: A Larger-Scale, Open-Domain Dialogue Generation Dataset with Visual Contexts

Modeling Text-visual Mutual Dependency for Multi-modal Dialog Generation

Enabling Harmonious Human-Machine Interaction with Visual-Context Augmented Dialogue System: A Review


McLuster - a tool to make a star cluster

Formation of massive black holes in galactic nuclei: runaway tidal encounters

Monthly Notices of the Royal Astronomical Society

TIDAL STREAM MORPHOLOGY AS AN INDICATOR OF DARK MATTER HALO GEOMETRY: THE CASE OF PALOMAR 5

Direct N-body simulations of globular clusters – II. Palomar 4

Complete ejection of OB stars from very young star clusters and the formation of multiple populations

Exploding Satellites - The Tidal Debris of the Ultra-Faint Dwarf Galaxy Hercules

Direct N-body simulations of globular clusters – III. Palomar 4 on an eccentric orbit

The effect of primordial mass segregation on the size scale of globular clusters

A Monte Carlo study of early gas expulsion and evolution of star clusters: new simulations with the MOCCA code in the amuse framework

MOCCA: Dynamics and evolution of binary stars of multiple stellar populations in tidally filling and underfilling globular star clusters


BIOMASS Product Algorithm Laboratory


Solving LPs with convergent message passing

A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching

A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems

A Novel Convex Relaxation for Non-binary Discrete Tomography

Scale Space and Variational Methods in Computer Vision


Machine Learning - accelerated Bayesian inference

A Measurement of the CMB Temperature Power Spectrum and Constraints on Cosmology from the SPT-3G 2018 TT/TE/EE Data Set

The future of cosmological likelihood-based inference: accelerated high-dimensional parameter estimation and model comparison

12 × 2 pt combined probes: pipeline, neutrino mass, and data compression

Journal of Cosmology and Astroparticle Physics

Detection of the CMB lensing -- galaxy bispectrum

class_sz I: Overview


Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

The Cymbidium genome reveals the evolution of unique morphological traits

Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor

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

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

Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

Independent Whole-Genome Duplications Define the Architecture of the Genomes of the Devastating West African Cacao Black Pod Pathogen Phytophthora megakarya and Its Close Relative Phytophthora palmivora

Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice

Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery

Comparative Genomic Analysis and Metabolic Potential Profiling of a Novel Culinary-Medicinal Mushroom, Hericium rajendrae (Basidiomycota)

Thirteen Dipterocarpoideae genomes provide insights into their evolution and borneol biosynthesis


Planck 2018 lensing pipeline

CMB lensing from Planck PR4 maps

Quadratic estimators for CMB weak lensing

An estimator for the lensing potential from galaxy number counts

Lensing power spectrum of the cosmic microwave background with deep polarization experiments

Foreground separation and constraints on primordial gravitational waves with the PICO space mission

CMB lensing reconstruction biases from masking extragalactic sources

Forecasts of CMB lensing reconstruction of AliCPT-1 from the foreground cleaned polarization data

Real-world CMB lensing quadratic estimator power spectrum response

Planck integrated Sachs-Wolfe-lensing likelihood and the CMB temperature

Impact of thermal Sunyaev–Zeldovich effect on cross-correlations between Planck cosmic microwave background lensing and SDSS galaxy density fields


Library for computing persistent homology

Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks

Topological Descriptors Help Predict Guest Adsorption in Nanoporous Materials

Generalized Penalty for Circular Coordinate Representation

Persistent homology advances interpretable machine learning for nanoporous materials.

Algebraic and Geometric Models for Space Networking

Topological data analysis enhanced prediction of hydrogen storage in metal–organic frameworks (MOFs)

Machine learning assisted high-throughput screening of zeolites for the selective adsorption of xylene isomers


LOWTRAN atmospheric absorption extinction, scatter and irradiance model--in Python and Matlab


GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

Whole-Genome Sequencing Analysis of Salmonella Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010–2017

Prevalence and distribution of multilocus sequence types of Staphylococcus aureus isolated from bulk tank milk and cows with mastitis in Pennsylvania

Genomic Background and Phylogeny of cfiA-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA

Atypical Serogroup IVb-v1 of Listeria monocytogenes Assigned to New ST2801, Widely Spread and Persistent in the Environment of a Pork-Meat Producing Plant of Central Italy

Listeria monocytogenes in ready to eat meat products from Zambia: phenotypical and genomic characterization of isolates

Retrospective Investigation of the Whole Genome of the Hypovirulent Listeria monocytogenes Strain of ST201, CC69, Lineage III, Isolated from a Piglet with Fatal Neurolisteriosis

Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences

International journal of molecular sciences


PySM: Software for simulating the Galactic microwave sky

CMB-S4 Science Case, Reference Design, and Project Plan

CMB-S4: Forecasting Constraints on Primordial Gravitational Waves

The Python Sky Model: software for simulating the Galactic microwave sky

The large scale polarization explorer (LSPE) for CMB measurements: performance forecast

Internal Delensing of Cosmic Microwave Background Polarization B-Modes with the POLARBEAR Experiment.

A Projected Estimate of the Reionization Optical Depth Using the CLASS Experiment’s Sample Variance Limited E-mode Measurement

Impact of polarized galactic foreground emission on CMB lensing reconstruction and delensing of B-modes

Foreground model recognition through Neural Networks for CMB B-mode observations

Requirements for future CMB satellite missions: photometric and band-pass response calibration

Removal of Galactic foregrounds for the Simons Observatory primordial gravitational wave search


hyperSpec: Tools for Spectroscopy (R package)

Metabolite Quantification by Fourier Transform Infrared Spectroscopy in Diatoms: Proof of Concept on Phaeodactylum tricornutum

Label-free Surface Enhanced Raman Scattering (SERS) on Centrifugal Silver Plasmonic Paper (CSPP): A Novel Methodology for Unprocessed Biofluids Sampling and Analysis

Raman Spectroscopic Differentiation of Streptococcus pneumoniae From Other Streptococci Using Laboratory Strains and Clinical Isolates

Frontiers in cellular and infection microbiology


3D Monte Carlo radiative transfer code for supernovae/kilonovae

Modelling the ionization state of Type Ia supernovae in the nebular phase

Self-consistent 3D Radiative Transfer for Kilonovae: Directional Spectra from Merger Simulations


Fast C code for sampling Polya-gamma random variates. Builds on Jesse Windle's BayesLogit library.

Recurrent switching linear dynamical systems

Bayesian Few-Shot Classification with One-vs-Each Pólya-Gamma Augmented Gaussian Processes

Bayesian latent structure discovery from multi-neuron recordings

Mixed Hamiltonian Monte Carlo for Mixed Discrete and Continuous Variables

Efficient Bayesian Inference for a Gaussian Process Density Model

A mathematical model of local and global attention in natural scene viewing

Variational Bayesian Inference for Nonlinear Hawkes Process with Gaussian Process Self-Effects

Nonlinear Hawkes Process with Gaussian Process Self Effects

A Mathematical Model of Exploration and Exploitation in Natural Scene Viewing


Decombinator v5: fast, error-correcting analysis of TCR repertoires

Feature selection using a one dimensional naïve Bayes’ classifier increases the accuracy of support vector machine classification of CDR3 repertoires

Persistent T Cell Repertoire Perturbation and T Cell Activation in HIV After Long Term Treatment

Decombinator V4: an improved AIRR compliant-software package for T-cell receptor sequence annotation?

The clonal structure and dynamics of the human T cell response to an organic chemical hapten

Plasticity of the Immune System in Children Following Treatment Interruption in HIV-1 Infection

FUME-TCRseq Enables Sensitive and Accurate Sequencing of the T-cell Receptor from Limited Input of Degraded RNA


Tissue-specific variant effect predictions on splicing

Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing

Modular modeling improves the predictions of genetic variant effects on splicing

Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay

A Missense Mutation rs781536408 (c.2395G>A) of TYK2 Affects Splicing and Causes Skipping of Exon18 in vivo


Penglai Enclave is an open-sourced, secure and scalable TEE system for RISC-V.

Scalable Memory Protection in the PENGLAI Enclave

USENIX Symposium on Operating Systems Design and Implementation

SoK: A Systematic Review of TEE Usage for Developing Trusted Applications

Proceedings of the 18th International Conference on Availability, Reliability and Security


TrojanZoo provides a universal pytorch platform to conduct security researches (especially backdoor attacks/defenses) of image classification in deep learning.

BadNets: Identifying Vulnerabilities in the Machine Learning Model Supply Chain

Anti-Backdoor Learning: Training Clean Models on Poisoned Data

Backdoor Defense via Decoupling the Training Process

Model Agnostic Defence against Backdoor Attacks in Machine Learning

A Tale of Evil Twins: Adversarial Inputs versus Poisoned Models

Conference on Computer and Communications Security

AdvMind: Inferring Adversary Intent of Black-Box Attacks

TrojanZoo: Towards Unified, Holistic, and Practical Evaluation of Neural Backdoors

TROJANZOO: Everything you ever wanted to know about neural backdoors (but were afraid to ask).


Simple library/pipeline to generate and handle Hi-C data.

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

Zenodo (CERN European Organization for Nuclear Research)

Serpentine: a flexible 2D binning method for differential Hi-C analysis

koszullab/hicstuff: Use miniconda layer for docker and improved P(s) normalisation

Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes

Bacterial Membrane Vesicles as a Novel Strategy for Extrusion of Antimicrobial Bismuth Drug in Helicobacter pylori

Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection

Generation of gene-level resolution chromosome contact maps in bacteria and archaea

Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization.

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

Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL, a proximity ligation-based scaffolder


Object Centric Atari games

Unsupervised State Representation Learning in Atari

OCAtari: Object-Centric Atari 2600 Reinforcement Learning Environments

HackAtari: Atari Learning Environments for Robust and Continual
  Reinforcement Learning


A library for mining of path-based representations of code (and more)

code2vec: Learning Distributed Representations of Code

A General Path-Based Representation for Predicting Program Properties

Precise Learning of Source Code Contextual Semantics via Hierarchical Dependence Structure and Graph Attention Networks

Using Distributed Representation of Code for Bug Detection

Evaluation of Contrastive Learning with Various Code Representations for Code Clone Detection

Exploiting Token and Path-based Representations of Code for Identifying Security-Relevant Commits

A Comparison of Code Embeddings and Beyond

Old but Gold: Reconsidering the value of feedforward learners for software analytics


This is a fork of the Cooja network simulator from contiki-os/contiki

Energy-Efficient Message Bundling with Delay and Synchronization Constraints in Wireless Sensor Networks

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

DRiPLOF: An RPL Extension for Multi-Interface Wireless Sensor Networks in Interference-Prone Environments


Enrico helps you with your Fermi data analysis

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

Multiwaveband quasi-periodic oscillation in the blazar 3C 454.3

Enrico : a Python package to simplify Fermi-LAT analysis

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

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

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

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

X-ray and Gamma-ray Variability of NGC 1275


icclim: Python library for climate indices and climate indicators calculation.

Access to Analysis and Climate Indices Tools for Climate Researchers and End Users

icclim: Calculating Climate Indices and Indicators Made Easy


LAnguage Modelling Benchmarks

On the State of the Art of Evaluation in Neural Language Models

Mogrifier LSTM

Long Expressive Memory for Sequence Modeling

Pushing the bounds of dropout

iRNN: Integer-only Recurrent Neural Network

Training Integer-Only Deep Recurrent Neural Networks


Effective Long-Context Scaling of Foundation Models

Never Lost in the Middle: Improving Large Language Models via Attention Strengthening Question Answering


Official code repository of CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph

Generating 3D Molecules for Target Protein Binding

DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding

Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration


Use EMCEE to do MCMC analyses of spectra in XSPEC

A dynamic black hole corona in an active galaxy through X-ray reverberation mapping

Velocity width measurements of the coolest X-ray emitting material in the cores of clusters, groups and elliptical galaxies

The remarkable X-ray variability of IRAS 13224–3809 – I. The variability process

Light bending and X-ray echoes from behind a supermassive black hole

Testing General Relativity with NuSTAR Data of Galactic Black Holes

The nuclear environment of the NLS1 Mrk 335: Obscuration of the X-ray line emission by a variable outflow

Testing the accuracy of reflection-based supermassive black hole spin measurements in AGN

X-ray reflection from the inner disc of the AGN Ton S180

Multiwavelength study of the flaring activity of Sagittarius A in 2014 February−April

HAL (Le Centre pour la Communication Scientifique Directe)

NuSTAR monitoring of MAXI J1348-630: evidence of high density disc reflection


Pytorch Implementation for Graph Convolutional Neural Networks

Semi-Supervised Classification with Graph Convolutional Networks

Graph Attention Networks

Revisiting Semi-Supervised Learning with Graph Embeddings

Why Random Pruning Is All We Need to Start Sparse


Easily fine tune GPT-2 to fill in missing text

Enabling Language Models to Fill in the Blanks

Euphemistic Phrase Detection by Masked Language Model

Phrase-level Textual Adversarial Attack with Label Preservation

InFillmore: Frame-Guided Language Generation with Bidirectional Context


Automating Outlier Detection via Meta-Learning (Code, API, and Contribution Instructions)

MetaGL: Evaluation-Free Selection of Graph Learning Models via Meta-Learning

AutoOD: Automatic Outlier Detection

Proceedings of the ACM on Management of Data


MuTual: A Dataset for Multi-Turn Dialogue Reasoning

Representation Learning for Conversational Data using Discourse Mutual Information Maximization


Manipulating the inner representations of StyleGAN2

Network Bending: Expressive Manipulation of Deep Generative Models

Network Bending: Manipulating The Inner Representations of Deep Generative Models.

Network Bending: Expressive Manipulation of Generative Models in Multiple Domains


Multi Task RL Baselines

Multi-Task Reinforcement Learning with Context-based Representations

Learning Robust State Abstractions for Hidden-Parameter Block MDPs

Block Contextual MDPs for Continual Learning

PaCo: Parameter-Compositional Multi-Task Reinforcement Learning

Learning Action Translator for Meta Reinforcement Learning on Sparse-Reward Tasks

Contrastive Modules with Temporal Attention for Multi-Task Reinforcement Learning


The Ribosome Binding Site (RBS) Calculator can predict the translation initiation rate of a protein coding sequence in bacteria and design synthetic RBS sequences to rationally control the translation initiation rate. It is used to design synthetic biological systems.

Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

Metagenomic mining of regulatory elements enables programmable species-selective gene expression

OSTIR: open source translation initiation rate prediction


A collection of labeled car driving datasets

PhysGAN: Generating Physical-World-Resilient Adversarial Examples for Autonomous Driving

Real-time End-to-End Federated Learning: An Automotive Case Study

Continuous Conditional Generative Adversarial Networks: Novel Empirical Losses and Label Input Mechanisms

Distilling and Transferring Knowledge via cGAN-generated Samples for Image Classification and Regression

Road Context-aware Intrusion Detection System for Autonomous Cars

Label Encoding for Regression Networks

Improving Robustness of Learning-based Autonomous Steering Using Adversarial Images

Turning Waste into Wealth: Leveraging Low-Quality Samples for Enhancing Continuous Conditional Generative Adversarial Networks


named entity linking with latent relations

Improving Entity Linking by Modeling Latent Relations between Mentions

REL: An Entity Linker Standing on the Shoulders of Giants

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

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

Learning Dynamic Context Augmentation for Global Entity Linking

Improving Entity Linking by Introducing Knowledge Graph Structure Information


AttGAN PyTorch Arbitrary Facial Attribute Editing: Only Change What You Want

AttGAN: Facial Attribute Editing by Only Changing What You Want

Style Intervention: How to Achieve Spatial Disentanglement with Style-based Generators?

Informative Sample Mining Network for Multi-Domain Image-to-Image Translation

Semantic Image Attack for Visual Model Diagnosis


[ICLR 2021] Concept Learners for Few-Shot Learning

Concept Learners for Few-Shot Learning

Domain Adaptation under Open Set Label Shift

Concept Learners for Generalizable Few-Shot Learning.


Random quantum circuits for circuit sampling with superconducting qubits

Quantum supremacy using a programmable superconducting processor

Hyper-optimized tensor network contraction

Quantum Supremacy Is Both Closer and Farther than It Appears

General-Purpose Quantum Circuit Simulator with Projected Entangled-Pair States and the Quantum Supremacy Frontier.

Pareto-Efficient Quantum Circuit Simulation Using Tensor Contraction Deferral

Just Like the Real Thing: Fast Weak Simulation of Quantum Computation

Faster Schrödinger-style simulation of quantum circuits

Alibaba Cloud Quantum Development Platform: Large-Scale Classical Simulation of Quantum Circuits

Bit-Slicing the Hilbert Space: Scaling Up Accurate Quantum Circuit Simulation

Hybrid Schrödinger-Feynman Simulation of Quantum Circuits With Decision Diagrams


An overview of all nanopack tools

NanoPack: visualizing and processing long-read sequencing data

NanoPack2: population-scale evaluation of long-read sequencing data

Single-cell architecture and functional requirement of alternative splicing during hematopoietic stem cell formation

Application of third-generation sequencing in cancer research

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

The complete genome of Escherichia coli JM101 assembled with a combination of Nanopore and Illumina platforms


PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, programs abort or do not run at all, etc.). Problems with input data and general questions should be posted at https://groups.google.com/g/pamlsoftware?pli

Beginner's Guide on the Use of PAML to Detect Positive Selection

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event

Genomic insights into metabolic flux in hummingbirds

Genomic insights into metabolic flux in ruby-throated hummingbirds


third generation spectral wave model WAM Cycle 6

The Impact of a Reduced High‐Wind Charnock Parameter on Wave Growth With Application to the North Sea, the Norwegian Sea, and the Arctic Ocean

Unravelling the Relationship Between Microseisms and Spatial Distribution of Sea Wave Height by Statistical and Machine Learning Approaches

Wave boundary layer model in SWAN revisited

Modes of Operation and Forcing in Oil Spill Modeling: State-of-Art, Deficiencies and Challenges

Journal of Marine Science and Engineering


Estimate recombination rates from population genetic data

The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

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

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

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


Weather and climate graphics for science communication


CareGPT (关怀GPT)是一个医疗大语言模型，同时它集合了数十个公开可用的医疗微调数据集和开放可用的医疗大语言模型，包含LLM的训练、测评、部署等以促进医疗LLM快速发展。Medical LLM, Open Source Driven for a Healthy Future.

How Abilities in Large Language Models are Affected by Supervised Fine-tuning Data Composition

Evaluating Hallucinations in Chinese Large Language Models

Large Language Models for Medicine: A Survey

Medical Dialogue: A Survey of Categories, Methods, Evaluation and
  Challenges


A framework for creating linguistic experiments

Cross-linguistic scope ambiguity: When two systems meet

In support of representational economy: Agreement in heritage Spanish

Glossa: a journal of general linguistics

Generalization of French and Portuguese plural alternations and initial syllable protection

Constraint cumulativity in phonotactics: evidence from artificial grammar learning studies

Weight and final vowels in the English stress system

Vowel unpredictability in Hijazi Arabic monosyllabic verbs


Compress conventional Vision-Language Pre-training data

Beyond neural scaling laws: beating power law scaling via data pruning

Dataset Distillation

Too Large; Data Reduction for Vision-Language Pre-Training


(ECCV 2020) Classes Matter: A Fine-grained Adversarial Approach to Cross-domain Semantic Segmentation

Graceful Degradation and Related Fields

Rethinking Unsupervised Domain Adaptation for Semantic Segmentation


[ECCV-2020 (spotlight)] Self-supervising Fine-grained Region Similarities for Large-scale Image Localization.  PyTorch open-source toolbox for image-based localization (place recognition).

NetVLAD: CNN Architecture for Weakly Supervised Place Recognition

Rethinking Visual Geo-localization for Large-Scale Applications

Stochastic Attraction-Repulsion Embedding for Large Scale Image Localization

StructVPR: Distill Structural Knowledge with Weighting Samples for Visual Place Recognition

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

CricaVPR: Cross-image Correlation-aware Representation Learning for
  Visual Place Recognition


NiftyMIC is a research-focused toolkit for motion correction and volumetric image reconstruction of 2D ultra-fast MRI.

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

NeSVoR: Implicit Neural Representation for Slice-to-Volume Reconstruction in MRI

An Automated Localization, Segmentation and Reconstruction Framework for Fetal Brain MRI

Medical Image Computing and Computer-Assisted Intervention

Retrospective motion correction in foetal MRI for clinical applications: existing methods, applications and integration into clinical practice

Motion correction and volumetric reconstruction for fetal functional magnetic resonance imaging data

Super‐resolution for upper abdominal MRI: Acquisition and post‐processing protocol optimization using brain MRI control data and expert reader validation

AFFIRM: Affinity Fusion-Based Framework for Iteratively Random Motion Correction of Multi-Slice Fetal Brain MRI

Fetal brain MRI atlases and datasets: A review

Reproducibility of Functional Connectivity Estimates in Motion Corrected Fetal fMRI

Smart Ultrasound Imaging and Perinatal, Preterm and Paediatric Image Analysis

Geometric Reliability of Super-Resolution Reconstructed Images from Clinical Fetal MRI in the Second Trimester


Diachronic Embedding for Temporal Knowledge Graph Completion

Representation Learning for Dynamic Graphs: A Survey

TimeTraveler: Reinforcement Learning for Temporal Knowledge Graph Forecasting

Temporal Knowledge Graph Forecasting with Neural ODE

xERTE: Explainable Reasoning on Temporal Knowledge Graphs for Forecasting Future Links

Few-Shot Inductive Learning on Temporal Knowledge Graphs using Concept-Aware Information

ECOLA: Enhancing Temporal Knowledge Embeddings with Contextualized Language Representations


SySeVR: A Framework for Using Deep Learning to Detect Software Vulnerabilities

IEEE Transactions on Dependable and Secure Computing

PreNNsem: A Heterogeneous Ensemble Learning Framework for Vulnerability Detection in Software

AdVulCode: Generating Adversarial Vulnerable Code against Deep Learning-Based Vulnerability Detectors


RNG-KBQA: Generation Augmented Iterative Ranking for Knowledge Base Question Answering

Do I have the Knowledge to Answer? Investigating Answerability of Knowledge Base Questions

How Proficient Are Large Language Models in Formal Languages? An In-Depth Insight for Knowledge Base Question Answering


pi-GAN: Periodic Implicit Generative Adversarial Networks for 3D-Aware Image Synthesis

StyleNeRF: A Style-based 3D-Aware Generator for High-resolution Image Synthesis

GET3D: A Generative Model of High Quality 3D Textured Shapes Learned from Images

3D-aware Image Synthesis via Learning Structural and Textural Representations

Generative Occupancy Fields for 3D Surface-Aware Image Synthesis

Multi-View Consistent Generative Adversarial Networks for 3D-aware Image Synthesis

Sem2NeRF: Converting Single-View Semantic Masks to Neural Radiance Fields

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

FIRe: Fast Inverse Rendering using Directional and Signed Distance Functions

Benchmarking and Analyzing 3D-aware Image Synthesis with a Modularized Codebase


Flexible Snow Model - a multi-physics energy balance model of accumulation and melt of snow on the ground and in forest canopies

Multi-physics ensemble snow modelling in the western Himalaya

Snow sensitivity to temperature and precipitation change during compound cold–hot and wet–dry seasons in the Pyrenees

Exploring the potential of thermal infrared remote sensing to improve a snowpack model through an observing system simulation experiment


Make river relative elevation models (REM) and REM visualizations from an input digital elevation model (DEM).


Neural Essay Assessor: An Automated Essay Scoring System Based on Deep Neural Networks

A Neural Approach to Automated Essay Scoring

Empirical Methods in Natural Language Processing

Neural Automated Essay Scoring and Coherence Modeling for Adversarially Crafted Input

A Trait-based Deep Learning Automated Essay Scoring System with Adaptive Feedback

International Journal of Advanced Computer Science and Applications

Fine-grained essay scoring of a complex writing task for native speakers

Workshop on Innovative Use of NLP for Building Educational Applications

Neural Multi-task Learning in Automated Assessment

Thank “Goodness”! A Way to Measure Style in Student Essays

NATURAL LANGUAGE PROCESSING TECHNIQUES FOR EDUCATIONAL APPLICATIONS


Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research

Explicit Strong Stability Preserving Multistage Two-Derivative Time-Stepping Schemes

Implicit and Implicit–Explicit Strong Stability Preserving Runge–Kutta Methods with High Linear Order

PROCEEDINGS OF THE INTERNATIONAL CONFERENCE ON NUMERICAL ANALYSIS AND APPLIED MATHEMATICS 2016 (ICNAAM-2016)

Optimized Explicit Runge--Kutta Schemes for the Spectral Difference Method Applied to Wave Propagation Problems

A purely hyperbolic discontinuous Galerkin approach for self-gravitating gas dynamics

A Strong Stability Preserving Analysis for Explicit Multistage Two-Derivative Time-Stepping Schemes Based on Taylor Series Conditions

Optimal Explicit Strong Stability Preserving Runge--Kutta Methods with High Linear Order and optimal Nonlinear Order

RK-Opt: A package for the design of numerical ODE solvers

NodePy: A package for the analysis of numerical ODE solvers


JAMP - Just Another Metabarcoding Pipeline

Validation of COI metabarcoding primers for terrestrial arthropods

Estimating intraspecific genetic diversity from community DNA metabarcoding data

Metabarcoding a diverse arthropod mock community

Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

Slippage of degenerate primers can cause variation in amplicon length

Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos

Improved freshwater macroinvertebrate detection from eDNA through minimized non-target amplification

Exploring the potential of metabarcoding to disentangle macroinvertebrate community dynamics in intermittent streams

Moray eels are more common on coral reefs subject to higher human pressure in the greater Caribbean

Pooling size sorted malaise trap fractions to maximise taxon recovery with metabarcoding


Neural generation model for Open Information Extraction

IMoJIE: Iterative Memory-Based Joint Open Information Extraction

DetIE: Multilingual Open Information Extraction Inspired by Object Detection

CompactIE: Compact Facts in Open Information Extraction

Syntactic Multi-view Learning for Open Information Extraction

IELM: An Open Information Extraction Benchmark for Pre-Trained Language Models

Open Information Extraction via Chunks


Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO

HGFDB: a collective database of helmeted guinea fowl genomics

Database : the journal of biological databases and curation

PanaxGDB: A Comprehensive Platform for Panax


Rapid Profiling and Deconvolution Tool for Metagenomes

Mash: fast genome and metagenome distance estimation using MinHash

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

miComplete: weighted quality evaluation of assembled microbial genomes

Mash Sketched Reference Dataset for Genome-Based Taxonomy and Comparative Genomics

Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes


Source codes for "Improved Few-Shot Visual Classification" (CVPR 2020), "Enhancing Few-Shot Image Classification with Unlabelled Examples" (WACV 2022), and "Beyond Simple Meta-Learning: Multi-Purpose Models for Multi-Domain, Active and Continual Few-Shot Learning" (SSRN Electronic Journal)

Meta-Dataset: A Dataset of Datasets for Learning to Learn from Few Examples

Improved Few-Shot Visual Classification

On the Importance of Distractors for Few-Shot Classification

Learning Instance and Task-Aware Dynamic Kernels for Few Shot Learning

Improving Few-Shot Visual Classification with Unlabelled Examples

On Label-Efficient Computer Vision: Building Fast and Effective Few-Shot Image Classifiers


Positive-instance driven dynamic programming for treewidth

Benchmarking treewidth as a practical component of tensor network simulations

Solving Vertex Cover in Polynomial Time on Hyperbolic Random Graphs

A Machine Learning Approach to Algorithm Selection for Exact Computation of Treewidth


ProphetNet: Predicting Future N-gram for Sequence-to-Sequence Pre-training

Adversarial Retriever-Ranker for dense text retrieval

Distill-VQ: Learning Retrieval Oriented Vector Quantization By Distilling Knowledge from Dense Embeddings

LED: Lexicon-Enlightened Dense Retriever for Large-Scale Retrieval

CodeRetriever: A Large Scale Contrastive Pre-Training Method for Code Search

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

Soft-Labeled Contrastive Pre-training for Function-level Code Representation

Generative Dense Retrieval: Memory Can Be a Burden

EmbedDistill: A Geometric Knowledge Distillation for Information Retrieval

CodeRetriever: Unimodal and Bimodal Contrastive Learning for Code Search


NAS-Bench-1Shot1: Benchmarking and Dissecting One-shot Neural Architecture Search

A Comprehensive Survey on Hardware-Aware Neural Architecture Search

Geometry-Aware Gradient Algorithms for Neural Architecture Search

ROME: Robustifying Memory-Efficient NAS via Topology Disentanglement and Gradients Accumulation

Zero-Cost Operation Scoring in Differentiable Architecture Search

ROME: Robustifying Memory-Efficient NAS via Topology Disentanglement and Gradient Accumulation


The source codes for Fine-grained Fact Verification with Kernel Graph Attention Network.

GEAR: Graph-based Evidence Aggregating and Reasoning for Fact Verification

Coreferential Reasoning Learning for Language Representation

BERT for Evidence Retrieval and Claim Verification

Which Linguist Invented the Lightbulb? Presupposition Verification for Question-Answering

How Robust are Fact Checking Systems on Colloquial Claims?

North American Chapter of the Association for Computational Linguistics

Natural Language Inference with Self-Attention for Veracity Assessment of Pandemic Claims

Adapting Open Domain Fact Extraction and Verification to COVID-FACT through In-Domain Language Modeling

Paragraph-based Transformer Pre-training for Multi-Sentence Inference

GLAF: Global-to-Local Aggregation and Fission Network for Semantic Level Fact Verification

International Conference on Computational Linguistics


Official implementation of BVAE-TTS

A Survey on Non-Autoregressive Generation for Neural Machine Translation and Beyond

Bidirectional Variational Inference for Non-Autoregressive Text-to-Speech

International Conference on Learning Representations

VARA-TTS: Non-Autoregressive Text-to-Speech Synthesis based on Very Deep VAE with Residual Attention


The CP solver Chuffed

Clingcon: The Next Generation

Optimal and Automated Deployment for Microservices

SUNNY-CP and the MiniZinc challenge

Theory and Practice of Logic Programming


DAGMM Tensorflow implementation

TranAD: Deep Transformer Networks for Anomaly Detection in Multivariate Time Series Data

Time Series Anomaly Detection for Cyber-physical Systems via Neural System Identification and Bayesian Filtering

Adaptive Model Pooling for Online Deep Anomaly Detection from a Complex Evolving Data Stream

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

A 3 : Activation Anomaly Analysis.

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

Coupled Attention Networks for Multivariate Time Series Anomaly Detection

Time-Series Anomaly Detection with Implicit Neural Representation

Correlation-aware Spatial-Temporal Graph Learning for Multivariate Time-series Anomaly Detection

DTAAD: Dual Tcn-Attention Networks for Anomaly Detection in Multivariate Time Series Data

Rare Life Event Detection via Mobile Sensing Using Multi-Task Learning


Repository for paper "SWAG: A Large-Scale Adversarial Dataset for Grounded Commonsense Inference"

Calibration of Pre-trained Transformers

Vera: A General-Purpose Plausibility Estimation Model for Commonsense Statements

Crystal: Introspective Reasoners Reinforced with Self-Feedback


TEASER: Fast and Certifiable Point Cloud Registration

Graduated Non-Convexity for Robust Spatial Perception: From Non-Minimal Solvers to Global Outlier Rejection

International Conference on Robotics and Automation

Certifiably Optimal Outlier-Robust Geometric Perception: Semidefinite Relaxations and Scalable Global Optimization

One Ring to Rule Them All: Certifiably Robust Geometric Perception with Outliers

Object Pose Estimation with Statistical Guarantees: Conformal Keypoint Detection and Geometric Uncertainty Propagation

Optimal and Robust Category-Level Perception: Object Pose and Shape Estimation From 2-D and 3-D Semantic Keypoints

Certifiable Outlier-Robust Geometric Perception: Exact Semidefinite Relaxations and Scalable Global Optimization.


Code for ACL 2020 paper: "Extractive Summarization as Text Matching"

Text Summarization with Oracle Expectation

Post-Editing Extractive Summaries by Definiteness Prediction

Findings of the Association for Computational Linguistics: EMNLP 2021


Fast + Non-Autoregressive Grammatical Error Correction using BERT. Code and Pre-trained models for paper "Parallel Iterative Edit Models for Local Sequence Transduction": www.aclweb.org/anthology/D19-1435.pdf (EMNLP-IJCNLP 2019)

Grammatical Error Correction in Low Error Density Domains: A New Benchmark and Analyses

Training for Grammatical Error Correction Without Human-Annotated L2 Learners’ Corpora


A new test set for ImageNet

Very Deep Convolutional Networks for Large-Scale Image Recognition

Do ImageNet Classifiers Generalize to ImageNet?

From ImageNet to Image Classification: Contextualizing Progress on Benchmarks

Identifying Statistical Bias in Dataset Replication

Model Similarity Mitigates Test Set Overuse

On the Strong Correlation Between Model Invariance and Generalization

Confidence and Dispersity Speak: Characterising Prediction Matrix for Unsupervised Accuracy Estimation

DMLR: Data-centric Machine Learning Research -- Past, Present and Future

The Entropy Enigma: Success and Failure of Entropy Minimization

Sequential Normalization: Embracing Smaller Sample Sizes for Normalization


Hyperparameter optimization with approximate gradient

Implicit differentiation of Lasso-type models for hyperparameter optimization

SHINE: SHaring the INverse Estimate from the forward pass for bi-level optimization and implicit models

Optimizing Large-Scale Hyperparameters via Automated Learning Algorithm

Bilevel Optimization for Machine Learning: Algorithm Design and Convergence Analysis


[NeurIPS'22 Spotlight] A Contrastive Framework for Neural Text Generation

Contrastive Search Is What You Need For Neural Text Generation

Click: Controllable Text Generation with Sequence Likelihood Contrastive Learning


SnapperDB: A database solution for routine sequencing analysis of bacterial isolates

Genomic approaches used to investigate an atypical outbreak of Salmonella Adjame

Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products


ParsBERT: Transformer-based Model for Persian Language Understanding

XL-WiC: A Multilingual Benchmark for Evaluating Semantic Contextualization

ParsiNLU: A Suite of Language Understanding Challenges for Persian

Exploiting BERT to Improve Aspect-Based Sentiment Analysis Performance on Persian Language


DrQ-v2: Improved Data-Augmented Reinforcement Learning

Mastering Visual Continuous Control: Improved Data-Augmented Reinforcement Learning

SURF: Semi-supervised Reward Learning with Data Augmentation for Feedback-efficient Preference-based Reinforcement Learning

VRL3: A Data-Driven Framework for Visual Deep Reinforcement Learning

Accelerating Reinforcement Learning with Value-Conditional State Entropy Exploration

Frustratingly Easy Regularization on Representation Can Boost Deep Reinforcement Learning

Pre-training Contextualized World Models with In-the-wild Videos for Reinforcement Learning

Off-Policy RL Algorithms Can be Sample-Efficient for Continuous Control via Sample Multiple Reuse

Diffusion Reward: Learning Rewards via Conditional Video Diffusion

Unsupervised Behavior Extraction via Random Intent Priors

Continuous Control with Coarse-to-fine Reinforcement Learning


[CVPR 2021]: The Spatially-Correlative Loss for Various Image Translation Tasks

Exploring Patch-wise Semantic Relation for Contrastive Learning in Image-to-Image Translation Tasks

Exploring Semantic Consistency in Unpaired Image Translation to Generate Data for Surgical Applications


Formal Concept Analysis with Python

A survey of ontology learning techniques and applications

Discrete Signal Processing on Meet/Join Lattices


Implementation of [Photo-Realistic Single Image Super-Resolution Using a Generative Adversarial Network arXiv:1609.04802v2]

Identity Mappings in Deep Residual Networks

Super-Resolution via Deep Learning


This library is an implementation of the algorithm described in Distributed Trajectory Estimation with Privacy and Communication Constraints: a Two-Stage Distributed Gauss-Seidel Approach.

Distributed Mapping with Privacy and Communication Constraints: Lightweight Algorithms and Object-based Models

BDPGO: Balanced Distributed Pose Graph Optimization Framework for Swarm Robotics

Asynchronous Distributed Smoothing and Mapping via On-Manifold Consensus ADMM


Subgraph Neural Networks (NeurIPS 2020)

Subgraph Neural Networks

State of the Art and Potentialities of Graph-level Learning

Position-Aware Subgraph Neural Networks with Data-Efficient Learning

Translating Subgraphs to Nodes Makes Simple GNNs Strong and Efficient for Subgraph Representation Learning

Models and Benchmarks for Representation Learning of Partially Observed Subgraphs


Unofficial Pytorch Implementation of WaveGrad2

Denoising Diffusion Probabilistic Models

WaveGrad: Estimating Gradients for Waveform Generation

Non-Attentive Tacotron: Robust and Controllable Neural TTS Synthesis Including Unsupervised Duration Modeling

WaveGrad 2: Iterative Refinement for Text-to-Speech Synthesis

DiffAR: Denoising Diffusion Autoregressive Model for Raw Speech Waveform Generation

Reinforcement Learning for Fine-tuning Text-to-speech Diffusion Models


Non-negative Positive-Unlabeled (nnPU) and unbiased Positive-Unlabeled (uPU) learning reproductive code on MNIST and CIFAR10

Positive-Unlabeled Learning with Non-Negative Risk Estimator

Generative Adversarial Positive-Unlabelled Learning

A Variational Approach for Learning from Positive and Unlabeled Data

Mixture Proportion Estimation and PU Learning: A Modern Approach

Generating Relevant Counter-Examples from a Positive Unlabeled Dataset for Image Classification

Positive-unlabeled classification under class-prior shift: a prior-invariant approach based on density ratio estimation

Learning Classifiers on Positive and Unlabeled Data with Policy Gradient


Fast Principal Component Analysis of Large-Scale Genome-Wide Data

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

Randomized algorithms for low-rank matrix approximation: Design, analysis, and applications

Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis

Genome-wide association study of cerebellar volume provides insights into heritable mechanisms underlying brain development and mental health

Brain-wide genome-wide colocalization study for integrating genetics, transcriptomics and brain morphometry in Alzheimer's disease

The Genetic Architectures of Functional and Structural Connectivity Properties within Cerebral Resting-State Networks

FlashPCA: fast sparse canonical correlation analysis of genomic data

Genome-wide association analysis identifies a susceptibility locus for sporadic vestibular schwannoma at 9p21