Multilingual AMR Parsing with Noisy Knowledge Distillation

Retrofitting Multilingual Sentence Embeddings with Abstract Meaning Representation

Multilingual Abstract Meaning Representation for Celtic Languages


PyTorch implementation of two variants of the Harlow visual fixation task (PsychLab and 1D version). Reproduces the results found in two papers. Check the ReadMe for more details!

Asynchronous Methods for Deep Reinforcement Learning

Learning to reinforcement learn

Go with the Flow: Adaptive Control for Neural ODEs


Deep direct likelihood knockoffs

Deep Direct Likelihood Knockoffs

Normalizing Flows for Knockoff-free Controlled Feature Selection


Rationalizing Neural Predictions

Invariant Rationalization

Rethinking Cooperative Rationalization: Introspective Extraction and Complement Control


KCWI data reduction pipeline. Developers: Don Neill, Matt Matuszewski, Chris Martin (Caltech)

Circumgalactic Mg ii Emission from an Isotropic Starburst Galaxy Outflow Mapped by KCWI

Optically thin spatially resolved Mg II emission maps the escape of ionizing photons

Monthly notices of the Royal Astronomical Society

Extreme chemical abundance ratio suggesting an exotic origin for an ultradiffuse galaxy

Spatially Resolved Stellar Kinematics of the Ultra-diffuse Galaxy Dragonfly 44. II. Constraints on Fuzzy Dark Matter

Integral Field Spectroscopy of Fast Outflows in Dwarf Galaxies with AGNs

The KBSS-KCWI survey: the connection between extended Ly alpha haloes and galaxy azimuthal angle at z similar to 2-3

Monthly Notices of the Royal Astronomical Society

The CGM at Cosmic Noon with KCWI: Outflows from a Star-forming Galaxy at z = 2.071

Revisiting the gas kinematics in SSA22 Lyman-α Blob 1 with radiative transfer modelling in a multiphase, clumpy medium

Imaging Spectroscopy of Ionized Gaseous Nebulae around Optically Faint AGNs at Redshift z ∼ 2

A Complex Multiphase DLA Associated with a Compact Group at z=2.431
  Traces Accretion, Outflows, and Tidal Streams


Code for "CharManteau: Character Embedding Models For Portmanteau Creation. EMNLP 2017. Varun Gangal*, Harsh Jhamtani*, Graham Neubig, Eduard Hovy, Eric Nyberg"

Simple Models for Word Formation in Slang

North American Chapter of the Association for Computational Linguistics

Simple Models for Word Formation in English Slang


StePar is an automatic code used to infer stellar atmospheric parameters using the EW method.

ESPRESSO high-resolution transmission spectroscopy of WASP-76 b

The atmosphere of HD 209458b seen with ESPRESSO

SteParSyn: A Bayesian code to infer stellar atmospheric parameters using spectral synthesis

Stellar atmospheric parameters of FGK-type stars from high-resolution optical and near-infrared CARMENES spectra

Photometric Calibrations of M-dwarf Metallicity with Markov Chain Monte
  Carlo and Bayesian Inference


Searching a Compact Architecture for Robust Multi-Exposure Image Fusion （IEEE TCSVT 24）

PAIF: Perception-Aware Infrared-Visible Image Fusion for Attack-Tolerant Semantic Segmentation

Embracing Compact and Robust Architectures for Multi-Exposure Image
  Fusion


The CARMENES search for exoplanets around M dwarfs. Radial velocities and activity indicators from cross-correlation functions with weighted binary masks.

The CARMENES search for exoplanets around M dwarfs. Guaranteed time
  observations Data Release 1 (2016-2020)

HD 191939 revisited: New and refined planet mass determinations, and a new planet in the habitable zone

Precise mass determination for the keystone sub-Neptune planet transiting the mid-type M dwarf G 9-40

Two super-Earths at the edge of the habitable zone of the nearby M dwarf
  TOI-2095


Dual Attentive Sequential Learning for Cross-Domain Click-Through Rate Prediction

Mixed Attention Network for Cross-domain Sequential Recommendation

Rethinking Cross-Domain Sequential Recommendation under Open-World
  Assumptions

Towards Open-world Cross-Domain Sequential Recommendation: A
  Model-Agnostic Contrastive Denoising Approach


Group Sparsity: The Hinge Between Filter Pruning and Decomposition for Network Compression

DHP: Differentiable Meta Pruning via HyperNetworks

Learning Filter Basis for Convolutional Neural Network Compression

The Heterogeneity Hypothesis: Finding Layer-Wise Differentiated Network Architectures


NeurIPS 2020 Spotlight Paper

DAGs with No Fears: A Closer Look at Continuous Optimization for Learning Bayesian Networks

On the Convergence of Continuous Constrained Optimization for Structure Learning

Optimizing NOTEARS Objectives via Topological Swaps


Sequence Tagging for Biomedical Extractive Question Answering (Bioinformatics'2020)

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

Sequence tagging for biomedical extractive question answering

ConditionalQA: A Complex Reading Comprehension Dataset with Conditional Answers

LIQUID: A Framework for List Question Answering Dataset Generation


Rich Feature Construction for the Optimization-Generalization Dilemma

Understanding and Improving Feature Learning for Out-of-Distribution
  Generalization

Learning useful representations for shifting tasks and distributions


Graph Self-Supervised Learning: A Survey

Self-supervised Heterogeneous Graph Neural Network with Co-contrastive Learning

Leveraging Meta-path Contexts for Classification in Heterogeneous Information Networks

Hierarchical Contrastive Learning Enhanced Heterogeneous Graph Neural Network


Skew Gaussian Processes by Alessio Benavoli, Dario Azzimonti and Dario Piga

Skew Gaussian Processes for Classification

Preferential Bayesian optimisation with Skew Gaussian Processes

A unified framework for closed-form nonparametric regression, classification, preference and mixed problems with Skew Gaussian Processes

Bayesian Optimisation for Sequential Experimental Design with Applications in Additive Manufacturing

Towards Practical Preferential Bayesian Optimization with Skew Gaussian
  Processes


MindSpore implementations of deep reinforcement learning algorithms and environments

Proximal Policy Optimization Algorithms

Continuous control with deep reinforcement learning

Playing Atari with Deep Reinforcement Learning

Deep Reinforcement Learning with Double Q-learning

Addressing Function Approximation Error in Actor-Critic Methods

Dueling Network Architectures for Deep Reinforcement Learning

Prioritized Experience Replay

Hindsight Experience Replay

Soft Actor-Critic Algorithms and Applications

Hierarchical Deep Reinforcement Learning: Integrating Temporal Abstraction and Intrinsic Motivation


All code related to the paper: "A Copula Statistic for Measuring Nonlinear Multivariate Dependence"

Copula index for detecting dependence and monotonicity between stochastic signals

A Copula Statistic for Measuring Nonlinear Dependence with Application to Feature Selection in Machine Learning

International journal of advanced computer science and applications/International journal of advanced computer science & applications


Object Detection

YOLO9000: Better, Faster, Stronger

Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour

FoveaBox: Beyond Anchor-based Object Detector

iffDetector: Inference-aware Feature Filtering for Object Detection


Modular framework for property inference attacks on deep neural networks

Leakage of Dataset Properties in Multi-Party Machine Learning

Distribution Inference Risks: Identifying and Mitigating Sources of Leakage

Formalizing Distribution Inference Risks


This repository contains an implementation of the Batch-BKB algorithm as described in the ICML 2020 paper "Near-linear time Gaussian process optimization with adaptive batching and resparsification" by Calandriello Daniele, Luigi Carratino, Alessandro Lazaric, Michal Valko and Lorenzo Rosasco

Gaussian Process Optimization with Adaptive Sketching: Scalable and No Regret

Near-linear Time Gaussian Process Optimization with Adaptive Batching and Resparsification

Scaling Gaussian Process Optimization by Evaluating a Few Unique
  Candidates Multiple Times


White-box Fairness Testing through Adversarial Sampling

Fairness Testing: A Comprehensive Survey and Analysis of Trends

NeuronFair: Interpretable White-Box Fairness Testing through Biased Neuron Identification

Search-based fairness testing for regression-based machine learning systems

Automatic Fairness Testing of Neural Classifiers Through Adversarial Sampling

Explanation-Guided Fairness Testing through Genetic Algorithm

Proceedings of the 44th International Conference on Software Engineering


My solution to Kaggle challenge "IEEE Camera Model Identification" [top 3%]

Distilling the Knowledge in a Neural Network

mixup: Beyond Empirical Risk Minimization

Cyclical Learning Rates for Training Neural Networks

Snapshot Ensembles: Train 1, get M for free


DimeNet and DimeNet++ models, as proposed in "Directional Message Passing for Molecular Graphs" (ICLR 2020) and "Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules" (NeurIPS-W 2020)

Equivariant message passing for the prediction of tensorial properties and molecular spectra

Recent advances and applications of deep learning methods in materials science

SpookyNet: Learning force fields with electronic degrees of freedom and nonlocal effects

3D Infomax improves GNNs for Molecular Property Prediction

Graph-based Molecular Representation Learning


Do We Really Need to Access the Source Data? Source Hypothesis Transfer for Unsupervised Domain Adaptation

Improving robustness against common corruptions by covariate shift adaptation

Test-Time Adaptation via Self-Training with Nearest Neighbor Information

Optimization-Free Test-Time Adaptation for Cross-Person Activity Recognition


abawaca is a binning program for metagenomics

Recovering complete and draft population genomes from metagenome datasets

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

Depth-related variability in viral communities in highly stratified sulfidic mine tailings

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil

Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert

Genome-resolved metagenomics using environmental and clinical samples

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

Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats


visual question answering prompting recipes for large vision-language models

BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image
  Encoders and Large Language Models

Kosmos-2: Grounding Multimodal Large Language Models to the World

COSMic: A Coherence-Aware Generation Metric for Image Descriptions

Investigating Prompting Techniques for Zero- and Few-Shot Visual
  Question Answering


Official code implementation for "Neural Image Compression: Generalization, Robustness, and Spectral Biases" (NeurIPS 2023).

Variational image compression with a scale hyperprior

To prune, or not to prune: exploring the efficacy of pruning for model compression

ELIC: Efficient Learned Image Compression with Unevenly Grouped Space-Channel Contextual Adaptive Coding


ToyADMOS2: Another dataset of miniature-machine operating sounds for anomalous sound detection under domain shift conditions

ToyADMOS: A Dataset of Miniature-Machine Operating Sounds for Anomalous Sound Detection

ToyADMOS2 dataset: Another dataset of miniature-machine operating sounds for anomalous sound detection under domain shift conditions

MIMII DUE: Sound Dataset for Malfunctioning Industrial Machine Investigation and Inspection with Domain Shifts due to Changes in Operational and Environmental Conditions


Package for computing the Atos Q-score.

Quantum Volume in Practice: What Users Can Expect From NISQ Devices

IEEE transactions on quantum engineering

Benchmarking Simulated and Physical Quantum Processing Units Using Quantum and Hybrid Algorithms

Neutral atom quantum computing hardware: performance and end-user perspective

Application-Oriented Benchmarking of Quantum Generative Learning Using QUARK


Intelligent Health Care: Applications of Deep Learning in Computational Medicine

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

Computational and structural biotechnology journal

EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model


Collaborative Translational Metric Learning (ICDM 2018)

Symmetric Metric Learning with Adaptive Margin for Recommendation

THIRTY-FOURTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, THE THIRTY-SECOND INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE AND THE TENTH AAAI SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE

Multi-Facet Recommender Networks with Spherical Optimization


DenseCL + regionCL-D

Momentum Contrast for Unsupervised Visual Representation Learning

Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour

Improved Baselines with Momentum Contrastive Learning

Dense Contrastive Learning for Self-Supervised Visual Pre-Training

RegionCL: Can Simple Region Swapping Contribute to Contrastive Learning?


A bundle of analytics tools for fisheries scientists


Official implementation of FOP method as described in "Fusion and Orthogonal Projection for Improved Face-Voice Association"

Utterance-level Aggregation For Speaker Recognition In The Wild

Learning Branched Fusion and Orthogonal Projection for Face-Voice
  Association


LOW-RESOURCE NEURAL MACHINE TRANSLATION: A BENCHMARK  FOR FIVE AFRICAN LANGUAGES

Improving Neural Machine Translation Models with Monolingual Data

Transfer Learning in Multilingual Neural Machine Translation with Dynamic Vocabulary

Low Resource Neural Machine Translation: A Benchmark for Five African Languages

Natural Language Processing in Ethiopian Languages: Current State, Challenges, and Opportunities


Code for paper: AdvKnn: Adversarial Attacks On K-Nearest Neighbor Classifiers With Approximate Gradients

Deep k-Nearest Neighbors: Towards Confident, Interpretable and Robust Deep Learning

On the Robustness of Deep K-Nearest Neighbors


A model for unsupervised morphological analysis that integrates orthographic and semantic views of words.

An Unsupervised Method for Uncovering Morphological Chains

MorphAGram, Evaluation and Framework for Unsupervised Morphological Segmentation

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

From Segmentation to Analyses: a Probabilistic Model for Unsupervised Morphology Induction

Conference of the European Chapter of the Association for Computational Linguistics


Pytorch code for ICRA'22 paper: "Single-Shot Multi-Object 3D Shape Reconstruction and Categorical 6D Pose and Size Estimation"

Normalized Object Coordinate Space for Category-Level 6D Object Pose and Size Estimation

CenterSnap: Single-Shot Multi-Object 3D Shape Reconstruction and Categorical 6D Pose and Size Estimation

ShAPO: Implicit Representations for Multi-Object Shape, Appearance, and
  Pose Optimization

CenterGrasp: Object-Aware Implicit Representation Learning for
  Simultaneous Shape Reconstruction and 6-DoF Grasp Estimation


Personalized Federated Learning under Mixture of Distributions

Federated Optimization in Heterogeneous Networks

Adaptive Personalized Federated Learning


Indonesian part-of-speech (POS) tagging

Toward a Standardized and More Accurate Indonesian Part-of-Speech Tagging

No Budget? Don't Flex! Cost Consideration when Planning to Adopt NLP for Your Business.

Which Student is Best? A Comprehensive Knowledge Distillation Exam for
  Task-Specific BERT Models


Recursive Diffeomorphism-Based Regression for Shape Functions

Multiresolution mode decomposition for adaptive time series analysis

A Fast Algorithm for Multiresolution Mode Decomposition


[AAAI 2022] Detecting Human-Object Interactions with Object-Guided Cross-Modal Calibrated Semantics.

RLIP: Relational Language-Image Pre-training for Human-Object
  Interaction Detection

RLIPv2: Fast Scaling of Relational Language-Image Pre-training


A generalized score-based method for Causal Discovery

Learning Sparse Nonparametric DAGs

A polynomial-time algorithm for learning nonparametric causal graphs

Causal Adversarial Network for Learning Conditional and Interventional Distributions

A Hybrid Causal Structure Learning Algorithm for Mixed-Type Data

THIRTY-SIXTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE / THIRTY-FOURTH CONFERENCE ON INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE / TWELVETH SYMPOSIUM ON EDUCATIONAL ADVANCES IN ARTIFICIAL INTELLIGENCE

Reframed GES with a Neural Conditional Dependence Measure


Testing and Estimation of structural breaks in Stata

Structural Breaks in Interactive Effects Panels and the Stock Market Reaction to COVID-19

Testing and Estimating Structural Breaks in Time Series and Panel Data
  in Stata


This is a PyTorch reimplementation of Influence Functions from the ICML2017 best paper: Understanding Black-box Predictions via Influence Functions by Pang Wei Koh and Percy Liang.

Understanding Rare Spurious Correlations in Neural Networks


The Python PSDD Package

Three Modern Roles for Logic in AI

Symposium on Principles of Database Systems

Tractable Inference in Credal Sentential Decision Diagrams

Tractable Boolean and Arithmetic Circuits

Leveraging Unlabeled Data for Entity-Relation Extraction through
  Probabilistic Constraint Satisfaction


FIRECAM: Fire Inventories - Regional Evaluation, Comparison, and Metrics

The Fire INventory from NCAR (FINN): a high resolution global model to estimate the emissions from open burning

Global fire emissions estimates during 1997–2016

Biomass burning emissions estimated with a global fire assimilation system based on observed fire radiative power

Global top-down smoke aerosol emissions estimation using satellite fire radiative power measurements

Diagnosing spatial biases and uncertainties in global fire emissions inventories: Indonesia as regional case study


Cost-efficient genome-wide gene expression profiling

Evolutionary Consequences of DNA Methylation in a Basal Metazoan

Functional genomic analysis of corals from natural CO2-seeps reveals core molecular responses involved in acclimatization to ocean acidification

Genetic patterns in Montipora capitata across an environmental mosaic in Kaneohe Bay

Resilience of Atlantic Slippersnail Crepidula fornicata Larvae in the Face of Severe Coastal Acidification

Magnitude and Predictability of pH Fluctuations Shape Plastic Responses to Ocean Acidification

Decoupling behavioral and transcriptional responses to color in an eyeless cnidarian

The role of gene expression and symbiosis in reef-building coral acquired heat tolerance

Blood and brain gene expression signatures of chronic intermittent ethanol consumption in mice

The Marine Gastropod Crepidula fornicata Remains Resilient to Ocean Acidification Across Two Life History Stages

Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)


A reimplementation of LastPyMile: A Python-based library to Identify the differences between build artifacts of PyPI packages and the respective source code repository

Backstabber's Knife Collection: A Review of Open Source Software Supply
  Chain Attacks

Towards Using Source Code Repositories to Identify Software Supply Chain Attacks

Conference on Computer and Communications Security

LastPyMile: identifying the discrepancy between sources and packages

PROCEEDINGS OF THE 29TH ACM JOINT MEETING ON EUROPEAN SOFTWARE ENGINEERING CONFERENCE AND SYMPOSIUM ON THE FOUNDATIONS OF SOFTWARE ENGINEERING (ESEC/FSE '21)


PyTorch Implementation of "Lossless Image Compression through Super-Resolution"

End-to-end lossless compression of high precision depth maps guided by pseudo-residual

GOLLIC: Learning Global Context beyond Patches for Lossless
  High-Resolution Image Compression


Github for the conference paper GLOD-Gaussian Likelihood OOD detector

A Baseline for Detecting Misclassified and Out-of-Distribution Examples in Neural Networks

Enhancing The Reliability of Out-of-distribution Image Detection in Neural Networks

Deep Anomaly Detection with Outlier Exposure

FOOD: Fast Out-Of-Distribution Detector

GLOD: Gaussian Likelihood Out of Distribution Detector.


Variational Auto-Encoder that generates synthetic gene expression data

Balancing Reconstruction Error and Kullback-Leibler Divergence in Variational Autoencoders

Integrated Multi-omics Analysis Using Variational Autoencoders: Application to Pan-cancer Classification

IEEE International Conference on Bioinformatics and Biomedicine

Correlated Variational Auto-Encoders

Variance Loss in Variational Autoencoders


SVsim: a tool that generates synthetic Structural Variant calls as benchmarks to test/evaluate SV calling pipelines.

LUMPY: A probabilistic framework for structural variant discovery

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis

Mutation-Simulator: fine-grained simulation of random mutations in any genome

FNBtools: A Software to Identify Homozygous Lesions in Deletion Mutant Populations

Short-range, orientation-reversing template-switching events occur at a high frequency in the human and yeast genomes


Automatic earthquake catalog building workflow: EQTransformer + Siamese EQTransformer + PickNet + REAL + HypoInverse

Earthquake transformer—an attentive deep-learning model for simultaneous earthquake detection and phase picking

Rapid Earthquake Association and Location

Deep Learning for Picking Seismic Arrival Times

Journal of geophysical research. Solid earth

Siamese Earthquake Transformer: A Pair‐Input Deep‐Learning Model for Earthquake Detection and Phase Picking on a Seismic Array

Building Precise Local Submarine Earthquake Catalogs via a Deep-Learning-Empowered Workflow and its Application to the Challenger Deep


CODEC is a document and entity ranking dataset that focuses on complex essay-style topics.

Approximate Nearest Neighbor Negative Contrastive Learning for Dense Text Retrieval

CODEC: Complex Document and Entity Collection


Learning diverse options through the Laplacian representation.

Eigenoption Discovery through the Deep Successor Representation

Towards Better Laplacian Representation in Reinforcement Learning with Generalized Graph Drawing

Deep Laplacian-based Options for Temporally-Extended Exploration


Co-expression network management based on WGCNA + k-means

An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks

Dystonia genes functionally converge in specific neurons and share neurobiology with psychiatric disorders

Integrated analyses of the methylome and transcriptome to unravel sex differences in the perirenal fat from suckling lambs

The chromatin modulating NSL complex regulates genes and pathways genetically linked to Parkinson’s disease


fastText + Bloom embeddings for compact, full-coverage vectors with spaCy

Enriching Word Vectors with Subword Information

Bag of Tricks for Efficient Text Classification

FastText.zip: Compressing text classification models

Multi hash embeddings in spaCy

Learning Word Embeddings for Ukrainian: A Comparative Study of FastText Hyperparameters

Proceedings of the Second Ukrainian Natural Language Processing Workshop (UNLP)


Adversarial Deep Network Embedding for Cross-network Node Classification

Domain Adaptive Graph Infomax via Conditional Adversarial Networks

IEEE transactions on network science and engineering

Semi-supervised Domain Adaptation on Graphs with Contrastive Learning
  and Minimax Entropy


An implementation of paper: Dynamic Network Embedding: An Extended Approach for Skip-gram based Network Embedding

GloDyNE: Global Topology Preserving Dynamic Network Embedding

IEEE transactions on knowledge and data engineering

Accelerating Dynamic Network Embedding with Billions of Parameter Updates to Milliseconds

Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining

Robust Dynamic Network Embedding via Ensembles


Calculate flow statistics from a given network capture file.

A Flexible SDN-Based Architecture for Identifying and Mitigating Low-Rate DDoS Attacks Using Machine Learning

Transport and Application Layer DDoS Attacks Detection to IoT Devices by Using Machine Learning and Deep Learning Models

On the Detection of Low-Rate Denial of Service Attacks at Transport and Application Layers

Toward the Protection of IoT Networks: Introducing the LATAM-DDoS-IoT Dataset


Calculate GC% and GC deviation for circular genomes

Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies

The expanded plant-like mitogenome of the invasive quagga mussel, Dreissena rostriformis

Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium

Diversity and Evolution of an Abundant ICEclc-Family of Integrative and Conjugative Elements inPseudomonas aeruginosa


some useful scripts for working with genomics and sequencing data

Unusual biology across a group comprising more than 15% of domain Bacteria

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation

Targeted Genome Editing of Bacteria Within Microbial Communities

910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens

Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut


A scikit-learn compatible Python package for GPU-accelerated computation of the signature kernel using CuPy.

Fast and scalable polynomial kernels via explicit feature maps

Signature moments to characterize laws of stochastic processes

Approximate Bayesian Computation with Path Signatures

Amortised Likelihood-free Inference for Expensive Time-series Simulators
  with Signatured Ratio Estimation

The Signature Kernel


Python package to compute interaction indices that extend the Shapley Value. AISTATS 2023.

FastSHAP: Real-Time Shapley Value Estimation

Faith-Shap: The Faithful Shapley Interaction Index

From Shapley Values to Generalized Additive Models and back


DAG-GNN: DAG Structure Learning with Graph Neural Networks

Learning Sparse Nonparametric DAGs

CausalVAE: Disentangled Representation Learning via Neural Structural Causal Models

Ordering-Based Causal Discovery with Reinforcement Learning

DAGs with No Curl: An Efficient DAG Structure Learning Approach

Learning Neural Causal Models with Active Interventions

Differentiable DAG Sampling

Benchmarking of Data-Driven Causality Discovery Approaches in the Interactions of Arctic Sea Ice and Atmosphere

Causal Adversarial Network for Learning Conditional and Interventional Distributions


Code for TEDVAE, a VAE-based treatment effect estimation algorithm.

A Unified Survey of Treatment Effect Heterogeneity Modelling and Uplift Modelling

Treatment effect estimation with disentangled latent factors

Targeted VAE: Variational and Targeted Learning for Causal Inference

Disentangled Representation for Causal Mediation Analysis

Causal Inference with Conditional Instruments using Deep Generative
  Models


MatBuilder: Mastering Sampling Uniformity Over Projections


The Exoplanet Population Observation Simulator. I. The Inner Edges of Planetary Systems

The Occurrence of Rocky Habitable-zone Planets around Solar-like Stars from Kepler Data

Exoplanet Statistics and Theoretical Implications

A Probabilistic Approach to Kepler Completeness and Reliability for Exoplanet Occurrence Rates

Occurrence and Architecture of Kepler Planetary Systems as Functions of Stellar Mass and Effective Temperature

A Joint Mass–Radius–Period Distribution of Exoplanets

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

A Closer Look at Exoplanet Occurrence Rates: Considering the Multiplicity of Stars without Detected Planets

Evaluating the Evidence for Water World Populations Using Mixture Models

The Demographics of Kepler's Earths and Super-Earths into the Habitable Zone


This is a sample implementation of "Billion-scale Network Embedding with Iterative Random Projection" (ICDM 2018).

Multiplex Heterogeneous Graph Convolutional Network

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

Subset Node Representation Learning over Large Dynamic Graphs

Accelerating Dynamic Network Embedding with Billions of Parameter Updates to Milliseconds


Optimised estimates of reproduction numbers over time, which extract more information from an incidence curve than many conventional approaches

Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves

Deciphering early-warning signals of SARS-CoV-2 elimination and resurgence from limited data at multiple scales

Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges


Implementation of AAAI2021 paper: Invariant Teacher and Equivariant Student for Unsupervised 3D Human Pose Estimation

3D human pose estimation in video with temporal convolutions and semi-supervised training

Semantic Graph Convolutional Networks for 3D Human Pose Regression

C3DPO: Canonical 3D Pose Networks for Non-Rigid Structure From Motion


WORLD: A Vocoder-Based High-Quality Speech Synthesis System for Real-Time Applications

IEICE transactions on information and systems

Unified Source-Filter GAN: Unified Source-filter Network Based On Factorization of Quasi-Periodic Parallel WaveGAN

Harmonic-Net: Fundamental Frequency and Speech Rate Controllable Fast Neural Vocoder

IEEE/ACM transactions on audio, speech, and language processing


This repository contains a Python implementation of the l1 periodogram as described in Hara, Boué, Laskar, Correia 2017, MNRAS, Vol. 464, Issue 1, p.1220-1246, with a few additions.

Six transiting planets and a chain of Laplace resonances in TOI-178

Investigating the architecture and internal structure of the TOI-561 system planets with CHEOPS, HARPS-N, and TESS

Monthly Notices of the Royal Astronomical Society

A continuous multiple hypothesis testing framework for optimal exoplanet
  detection


Unsupervised speech enhancement using DVAEs

MetricGAN-U: Unsupervised speech enhancement/ dereverberation based only
  on noisy/ reverberated speech

Unsupervised Speech Enhancement Using Dynamical Variational Autoencoders


Compressor for Nanopore Sequencing Reads

Portable nanopore-sequencing technology: Trends in development and applications

NanoSpring: reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach

Reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach


To be a next-generation DL-based phenotype prediction from genome mutations.

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome

Predicting the pathogenicity of protein coding mutations using Natural Language Processing

International Conference of the IEEE Engineering in Medicine and Biology Society


Clubmark: a Parallel Isolation Framework for Benchmarking and Profiling of Clustering (Community Detection) Algorithms Considering Overlaps (Covers)

Accuracy Evaluation of Overlapping and Multi-resolution Clustering Algorithms on Large Datasets

Clubmark: a Parallel Isolation Framework for Benchmarking and Profiling Clustering Algorithms on NUMA Architectures

DAOC: Stable Clustering of Large Networks


A list of academic papers related to Docker containers & Docker Hub

Too many images on DockerHub! How different are images for the same system?

A study of how Docker Compose is used to compose multi-component systems

An empirical study on self-admitted technical debt in Dockerfiles

Helping Your Docker Images to Spread Based on Explainable Models

MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2018, PT III

SemiTagRec: A Semi-supervised Learning Based Tag Recommendation Approach for Docker Repositories

Explaining Successful Docker Images Using Pattern Mining Analysis

Software Technologies: Applications and Foundations

Latest Image Recommendation Method for Automatic Base Image Update in Dockerfile


Repo with code for Ludii's built-in AIs.

Biasing MCTS with Features for General Games

Deep Learning for General Game Playing with Ludii and Polygames

Manipulating the Distributions of Experience used for Self-Play Learning in Expert Iteration


Module for modeling gravitational lensing systems in which the data are not images but interferometric visibilities.

ALMA IMAGING AND GRAVITATIONAL LENS MODELS OF SOUTH POLE TELESCOPE—SELECTED DUSTY, STAR-FORMING GALAXIES AT HIGH REDSHIFTS

Galaxy growth in a massive halo in the first billion years of cosmic history

PyAutoLens: Open-Source Strong Gravitational Lensing

ALMA [N ii] 205 μm Imaging Spectroscopy of the Lensed Submillimeter Galaxy ID 141 at Redshift 4.24

The ramp-up of interstellar medium enrichment at z > 4


Vision

Deeper Depth Prediction with Fully Convolutional Residual Networks

Benchmarking Single-Image Dehazing and Beyond

O-HAZE: a dehazing benchmark with real hazy and haze-free outdoor images

I-HAZE: a dehazing benchmark with real hazy and haze-free indoor images


CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

基因组蛋白质组与生物信息学报

Disease-Associated Circular RNAs: From Biology to Computational Identification

A CLEAR pipeline for direct comparison of circular and linear RNA expression

Computational approaches for circRNAs prediction and in silico characterization


R package

pRRophetic: An R Package for Prediction of Clinical Chemotherapeutic Response from Tumor Gene Expression Levels

M2-like tumor-associated macrophage-related biomarkers to construct a novel prognostic signature, reveal the immune landscape, and screen drugs in hepatocellular carcinoma

Identification and Validation of a Prognostic Prediction Model of m6A Regulator-Related LncRNAs in Hepatocellular Carcinoma

Identification and validation of a prognostic model of necroptosis-related lncRNAs in hepatocellular carcinoma

A Prognostic Autophagy-Related Gene Pair Signature and Small-Molecule Drugs for Hepatocellular Carcinoma

Identification of a Novel Gene Signature with DDR and EMT Difunctionalities for Predicting Prognosis, Immune Activity, and Drug Response in Breast Cancer

A novel recurrence-associated metabolic prognostic model for risk stratification and therapeutic response prediction in patients with stage I lung adenocarcinoma

Construction and Validation of a Novel Prognosis Model in Colon Cancer Based on Cuproptosis-Related Long Non-Coding RNAs

The Prognostic Value of a lncRNA Risk Model Consists of 9 m6A Regulator-Related lncRNAs in Hepatocellular Carcinoma (HCC)


PyTorch toolkit for streaming speech recognition, speech translation and simultaneous translation based on fairseq.

Transformers with convolutional context for ASR

Emformer: Efficient Memory Transformer Based Acoustic Model For Low Latency Streaming Speech Recognition

Monotonic Multihead Attention

CIF: Continuous Integrate-and-Fire for End-to-End Speech Recognition


INCOME: An Easy Repository for Training and Evaluation of Index Compression Methods in Dense Retrieval. Includes BPR and JPQ.

Unsupervised Dense Information Retrieval with Contrastive Learning

Efficiently Teaching an Effective Dense Retriever with Balanced Topic Aware Sampling

GPL: Generative Pseudo Labeling for Unsupervised Domain Adaptation of Dense Retrieval

Injecting Domain Adaptation with Learning-to-hash for Effective and
  Efficient Zero-shot Dense Retrieval


CVPR2024: Dual Memory Networks: A Versatile Adaptation Approach for Vision-Language Models

Learning Transferable Visual Models From Natural Language Supervision

Learning to Prompt for Vision-Language Models

Conditional Prompt Learning for Vision-Language Models

Test-Time Prompt Tuning for Zero-Shot Generalization in Vision-Language
  Models


Original Inference Repository of the Paper: "Domain-Adaptive Self-Supervised Pre-training for Face & Body Detection in Drawings"

Cross-Domain Weakly-Supervised Object Detection through Progressive Domain Adaptation

Object Detection for Comics using Manga109 Annotations

ACFD: Asymmetric Cartoon Face Detector

Domain-Adaptive Self-Supervised Pre-Training for Face & Body Detection
  in Drawings


ScousePy

Molecular gas kinematics within the central 250 pc of the Milky Way

Monthly Notices of the RAS (0035-8711) - 'The Brick' is not a brick: A comprehensive study of the structure and dynamics of the Central Molecular Zone cloud G0.253+0.016

Monthly notices of the Royal Astronomical Society

ATOMS: ALMA Three-millimeter Observations of Massive Star-forming regions – XV. Steady accretion from global collapse to core feeding in massive hub-filament system SDC335

Decomposing magnetic fields in three dimensions over the central molecular zone

CMZoom III: Spectral line data release


Cleaned E2E NLG Challenge data + supporting scripts

Semantic Noise Matters for Neural Natural Language Generation

Neural Pipeline for Zero-Shot Data-to-Text Generation

Discourse-Aware Soft Prompting for Text Generation

How to Make Neural Natural Language Generation as Reliable as Templates in Task-Oriented Dialogue

PROCEEDINGS OF THE 2020 CONFERENCE ON EMPIRICAL METHODS IN NATURAL LANGUAGE PROCESSING (EMNLP)


#66DaysOfData challenge in Financial Machine Learning and NLP

Sequence to Sequence Learning with Neural Networks

A Neural Algorithm of Artistic Style

Unsupervised Pixel-Level Domain Adaptation with Generative Adversarial Networks

Quasi-Recurrent Neural Networks


A pipeline for isoseq

A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala x Culter alburnus

Unveiling the Complexity of Red Clover (Trifolium pratense L.) Transcriptome and Transcriptional Regulation of Isoflavonoid Biosynthesis Using Integrated Long- and Short-Read RNAseq

International journal of molecular sciences


Implements the Messenger environment and EMMA model.

Grounding Language to Entities and Dynamics for Generalization in Reinforcement Learning

Improving Policy Learning via Language Dynamics Distillation

Semantically Aligned Task Decomposition in Multi-Agent Reinforcement
  Learning


Repository for the CODAH dataset

Common Sense Beyond English: Evaluating and Improving Multilingual Language Models for Commonsense Reasoning

AQuA: An Adversarially Authored Question-Answer Dataset for Common Sense

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

Crystal: Introspective Reasoners Reinforced with Self-Feedback


Multivariate Gaussian distributions for Tensorflow.

Structured Uncertainty Prediction Networks

Training VAEs Under Structured Residuals

VAEs with structured image covariance applied to compressed sensing MRI


[MIDL 2022 Oral] Learning Morphological Feature Perturbations for Calibrated Semi Supervised Segmentation

Understanding the Effective Receptive Field in Deep Convolutional Neural Networks

Uncertainty-aware Self-ensembling Model for Semi-supervised 3D Left Atrium Segmentation

Semi-supervised semantic segmentation needs strong, varied perturbations

Learning Morphological Feature Perturbations for Calibrated
  Semi-Supervised Segmentation


Kippenhahn plotter for MESA

Seismic Signatures of the 12C(α, γ)16O Reaction Rate in White Dwarf Models with Overshooting

Zenodo (CERN European Organization for Nuclear Research)

Light axion emission and the formation of merging binary black holes


A principled framework to estimate annotation-stratified genetic covariance using GWAS summary statistics.

SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits

Insulinopathies of the brain? Genetic overlap between somatic insulin-related and neuropsychiatric disorders

Genome-Wide Pleiotropy Study Identifies Association of PDGFB with Age-Related Macular Degeneration and COVID-19 Infection Outcomes

Analysis of common genetic variation across targets of microRNAs dysregulated both in ASD and epilepsy reveals negative correlation


StyleSDF: High-Resolution 3D-Consistent Image and Geometry Generation

BallGAN: 3D-aware Image Synthesis with a Spherical Background

NARRATE: A Normal Assisted Free-View Portrait Stylizer

OrthoPlanes: A Novel Representation for Better 3D-Awareness of GANs


Tools for finding mobile element insertions from single-end datasets

A virome-wide clonal integration analysis platform for discovering cancer viral etiology

ITR-Seq, a next-generation sequencing assay, identifies genome-wide DNA editing sites in vivo following adeno-associated viral vector-mediated genome editing

Diverse and mobile: eccDNA-based identification of carrot low-copy-number LTR retrotransposons active in callus cultures.

The Plant journal : for cell and molecular biology

Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome

Genomics & informatics/Genomics & Informatics


A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cleaned" domain structure in CATH.

3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation

Вестник компьютерных и информационных технологий

3D Semantic Segmentation with Submanifold Sparse Convolutional Networks

EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation


Can Generative Pre-trained Transformers (GPT) Pass Assessments in Higher Education Programming Courses?

Sentence Embeddings and High-Speed Similarity Search for Fast Computer Assisted Annotation of Legal Documents

Discovering Explanatory Sentences in Legal Case Decisions Using Pre-trained Language Models

Data-Centric Machine Learning: Improving Model Performance and Understanding Through Dataset Analysis

International Conference on Legal Knowledge and Information Systems

Data-Centric Machine Learning in the Legal Domain


chia pet analysis software

Mango: a bias-correcting ChIA-PET analysis pipeline

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

Critical reviews in biochemistry and molecular biology

Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine


Pioneer Networks: Progressively Growing Generative Autoencoder

Semi-supervised image attribute editing using generative adversarial networks

A Plug-in Method for Representation Factorization in Connectionist Models

IEEE transactions on neural networks and learning systems


a parallel R package for detecting copy-number alterations from short sequencing reads

Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

The clonal evolution of metastatic colorectal cancer

Prognostic significance of esterase gene expression in multiple myeloma

Spontaneous aggressive ERα+ mammary tumor model is driven by Kras activation

Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient

Unraveling the chaotic genomic landscape of primary and metastatic canine appendicular osteosarcoma with current sequencing technologies and bioinformatic approaches.

S100 Calcium Binding Protein Family Members Associate With Poor Patient Outcome and Response to Proteasome Inhibition in Multiple Myeloma

Frontiers in cell and developmental biology


This repository is made for the paper: Masked Vision and Language Pre-training with Unimodal and Multimodal Contrastive Losses for Medical Visual Question Answering

Slake: A Semantically-Labeled Knowledge-Enhanced Dataset For Medical Visual Question Answering

PathVQA: 30000+ Questions for Medical Visual Question Answering

Self-Supervised Vision-Language Pretraining for Medial Visual Question Answering


X (weighted / probabilistic) Context-Free Grammars

Compound Probabilistic Context-Free Grammars for Grammar Induction

Unsupervised Recurrent Neural Network Grammars

Unsupervised Latent Tree Induction with Deep Inside-Outside Recursive Autoencoders

Visually Grounded Neural Syntax Acquisition

Meeting of the Association for Computational Linguistics

PCFGs Can Do Better: Inducing Probabilistic Context-Free Grammars with Many Symbols

An Empirical Study of Compound PCFGs


EfficientMORL (ICML'21)

Taming VAEs

Efficient Iterative Amortized Inference for Learning Symmetric and Disentangled Multi-Object Representations

Towards Improving the Generation Quality of Autoregressive Slot VAEs


Toward Deep Drum Source Separation

Learning to Groove with Inverse Sequence Transformations

Improving Perceptual Quality of Drum Transcription with the Expanded Groove MIDI Dataset.


testcode is a python module for testing for regression errors in numerical (principally scientific) software.

Advanced capabilities for materials modelling with Quantum ESPRESSO

Journal of physics. Condensed matter : an Institute of Physics journal

Wannier90 as a community code: new features and applications

HP – A code for the calculation of Hubbard parameters using density-functional perturbation theory


ENGINE: Energy-Based Inference Networks for Non-Autoregressive Machine Translation

Learning Approximate Inference Networks for Structured Prediction

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


序列模式挖掘相关研究

Top-k Self-Adaptive Contrast Sequential Pattern Mining

NetNMSP: Nonoverlapping maximal sequential pattern mining

Applied intelligence (Dordrecht, Netherlands)

OPP-Miner: Order-Preserving Sequential Pattern Mining for Time Series

OWSP-Miner: Self-adaptive One-off Weak-gap Strong Pattern Mining

ACM transactions on management information systems

ONP-Miner: One-off Negative Sequential Pattern Mining

MCoR-Miner: Maximal Co-Occurrence Nonoverlapping Sequential Rule Mining


The R tool associated with 3VmrMLM, a comprehensive GWAS method for identifying QTNs, QTN-by-environment interactions, and QTN-by-QTN interactions for quantitative traits.

Identification of QTNs, QTN-by-environment interactions, and their candidate genes for grain size traits in main crop and ratoon rice

Identification of QTNs, QTN-by-environment interactions and genes for yield-related traits in rice using 3VmrMLM

Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed

Identification of QTL, QTL-by-environment interactions, and their candidate genes for resistance HG Type 0 and HG Type 1.2.3.5.7 in soybean using 3VmrMLM


Implementation of the paper: Channel-wise Gated Res2Net: Towards Robust Detection of Synthetic Speech Attacks (INTERSPEECH 2021)

ASVspoof 2019: Future Horizons in Spoofed and Fake Audio Detection

Replay and Synthetic Speech Detection with Res2net Architecture


Generative adversarial networks integrating modules from FUNIT and SPADE for face-swapping.

Semantic Image Synthesis with Spatially-Adaptive Normalization

Few-Shot Unsupervised Image-to-Image Translation

The Creation and Detection of Deepfakes: A Survey

Adversarial Perturbations Fool Deepfake Detectors

FaceSigns: Semi-Fragile Neural Watermarks for Media Authentication and Countering Deepfakes

Psychophysical Evaluation of Human Performance in Detecting Digital Face Image Manipulations

Digital Face Manipulation in Biometric Systems

Handbook of Digital Face Manipulation and Detection

DF-Captcha: A Deepfake Captcha for Preventing Fake Calls


Hierarchical Text-Conditional Image Generation with CLIP Latents

Chatbots, ChatGPT, and Scholarly Manuscripts: WAME Recommendations on ChatGPT and Chatbots in Relation to Scholarly Publications

Open Access Macedonian Journal of Medical Sciences

The Gradient of Generative AI Release: Methods and Considerations

Evaluating the Social Impact of Generative AI Systems in Systems and
  Society

RePrompt: Automatic Prompt Editing to Refine AI-Generative Art Towards Precise Expressions

Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems

Towards best practices in AGI safety and governance: A survey of expert
  opinion

Sociotechnical Safety Evaluation of Generative AI Systems

FLIRT: Feedback Loop In-context Red Teaming

Typology of Risks of Generative Text-to-Image Models

Protecting Society from AI Misuse: When are Restrictions on Capabilities
  Warranted?


BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.

Introduction to Single-Cell DNA Methylation Profiling Methods

BS-Seeker3: ultrafast pipeline for bisulfite sequencing

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


The code is the implention of paper "Nonlocal Sparse Tensor Factorization for Semiblind Hyperspectral and Multispectral Image Fusion"

Tensor Decompositions for Hyperspectral Data Processing in Remote Sensing: A comprehensive review

Decoupled-and-Coupled Networks: Self-Supervised Hyperspectral Image Super-Resolution With Subpixel Fusion

BUSIFusion: Blind Unsupervised Single Image Fusion of Hyperspectral and RGB Images

IEEE transactions on computational imaging

Blind Fusion of Hyperspectral Multispectral Images Based on Matrix Factorization

Fast and Stable Hyperspectral Multispectral Image Fusion Technique Using Moore–Penrose Inverse Solver


Windowed Adaptive Trimming for fastq files using quality

Novel Roles for the Polyphenol Oxidase Enzyme in Secondary Metabolism and the Regulation of Cell Death in Walnut

Cumulus Cell Transcripts Transit to the Bovine Oocyte in Preparation for Maturation

Within patient microevolution of Mycobacterium tuberculosis correlates with heterogeneous responses to treatment

DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum

Sequencing the transcriptome of milk production: milk trumps mammary tissue

The Fumagillin Gene Cluster, an Example of Hundreds of Genes under veA Control in Aspergillus fumigatus

Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis

Genome-Wide Association and Genomic Prediction for Fry Color in Potato

(Per)Chlorate-Reducing Bacteria Can Utilize Aerobic and Anaerobic Pathways of Aromatic Degradation with (Per)Chlorate as an Electron Acceptor


Source code for "A Lightweight Recurrent Network for Sequence Modeling"

Quasi-Recurrent Neural Networks

Simple Recurrent Units for Highly Parallelizable Recurrence

Recurrent Additive Networks

Simplifying Neural Machine Translation with Addition-Subtraction Twin-Gated Recurrent Networks


Transient Search

A fast radio burst source at a complex magnetized site in a barred galaxy

Polarization properties of FRB 20201124A from detections with the Effelsberg 100-m radio telescope

FAST Observations of an Extremely Active Episode of FRB 20201124A. III. Polarimetry

A radio pulsar phase from SGR J1935+2154 provides clues to the magnetar FRB mechanism.

TRAPUM upper limits on pulsed radio emission for SMC X-ray pulsar J0058−7218

Monthly notices of the Royal Astronomical Society


An implementation of multimodal deep neural network, a new model for human breast cancer prognosis prediction.

The Application of Deep Learning in Cancer Prognosis Prediction

A Multimodal Deep Neural Network for Human Breast Cancer Prognosis Prediction by Integrating Multi-Dimensional Data

IEEE/ACM transactions on computational biology and bioinformatics

An Ensembled Framework for Human Breast Cancer Survivability Prediction Using Deep Learning


2.56%, 15.20%, 1.30% on CIFAR10, CIFAR100, and SVHN  https://arxiv.org/abs/1708.04552

Improved Regularization of Convolutional Neural Networks with Cutout

Unlabeled Data Improves Adversarial Robustness

An Empirical Study of Example Forgetting during Deep Neural Network Learning

General E(2)-Equivariant Steerable CNNs

Neural Attention Distillation: Erasing Backdoor Triggers from Deep
  Neural Networks

Avoiding Overfitting: A Survey on Regularization Methods for Convolutional Neural Networks

Relating Adversarially Robust Generalization to Flat Minima

Rethinking the Pruning Criteria for Convolutional Neural Network

Doubly Adaptive Scaled Algorithm for Machine Learning Using Second-Order Information

ASDL: A Unified Interface for Gradient Preconditioning in PyTorch


Torch code for our CVPR 2018 paper "Residual Dense Network for Image Super-Resolution" (Spotlight)

Residual Dense Network for Image Restoration

A Survey of Deep Learning for Scientific Discovery

edge-SR: Super-Resolution For The Masses

Back-Projection Pipeline

Multi-Grid Back-Projection Networks


M2DGR： a Multi-modal and Multi-scenario Dataset for Ground Robots(RA-L2021 & ICRA2022)

M2DGR: A Multi-Sensor and Multi-Scenario SLAM Dataset for Ground Robots


A collection of research papers, datasets and software on Deep Learning

Deep Learning with Domain Adaptation for Accelerated
  Projection-Reconstruction MR

A Deep Learning Reconstruction Framework for Differential Phase-Contrast Computed Tomography With Incomplete Data

Generative adversarial networks for specular highlight removal in endoscopic images

Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling

A curvature and density-based generative representation of shapes


A Survey and Benchmark for Automatic Surface Reconstruction from Point Clouds

Occupancy Networks: Learning 3D Reconstruction in Function Space

3D-R2N2: A Unified Approach for Single and Multi-view 3D Object Reconstruction

Convolutional Occupancy Networks

A Survey and Benchmark of Automatic Surface Reconstruction from Point Clouds


Disentangled Self-Supervision in Sequential Recommenders

Intent Contrastive Learning for Sequential Recommendation

Improving Micro-video Recommendation via Contrastive Multiple Interests

Generating Negative Samples for Sequential Recommendation

End-to-end Learnable Clustering for Intent Learning in Recommendation


Code and data for "CoditT5: Pretraining for Source Code and Natural Language Editing" in ASE 2022.

A Survey of Learning-based Automated Program Repair

A Survey on Large Language Models for Software Engineering


code for paper submission "Bonsai - Diverse and Shallow Trees for ExtremeMulti-label Classification"

AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification

Bonsai -- Diverse and Shallow Trees for Extreme Multi-label Classification

An Empirical Study on Large-Scale Multi-Label Text Classification Including Few and Zero-Shot Labels

Probabilistic Label Trees for Extreme Multi-label Classification

A Survey on Extreme Multi-label Learning


codes for the paper "Simulation-guided Beam Search for Neural Combinatorial Optimization"

Neural Combinatorial Optimization with Heavy Decoder: Toward Large Scale
  Generalization


Solution to Deepfake Detection Challenge

The DeepFake Detection Challenge (DFDC) Dataset

Multi-attentional Deepfake Detection

Towards Measuring Fairness in AI: the Casual Conversations Dataset

Analyzing Fairness in Deepfake Detection With Massively Annotated Databases

Assessment Framework for Deepfake Detection in Real-world Situations


We collected awesome medical image super-resolution (SR) methods and common benchmarks in this repository.

LRTV: MR Image Super-Resolution With Low-Rank and Total Variation Regularizations

Super-resolution in magnetic resonance imaging: A review

Concepts in magnetic resonance. Part A, Bridging education and research/Concepts in magnetic resonance. Part A, Bridging education and research.

MRI Super-Resolution With Ensemble Learning and Complementary Priors

Super-Resolution PET Imaging Using Convolutional Neural Networks

Lumbar Spine MRI Dataset


3D Extension of the Cellpose Algorithm by Stringer et al., 2021.

Cellpose: a generalist algorithm for cellular segmentation

Robust 3D Cell Segmentation: Extending the View of Cellpose


Deep Hashing expermiments

FaceNet: A Unified Embedding for Face Recognition and Clustering

In Defense of the Triplet Loss for Person Re-Identification

Deep metric learning using Triplet network

Deep Supervised Hashing with Triplet Labels


Low-variance, efficient and unbiased gradient estimation for optimizing models with binary latent variables.  (ICLR 2019)

ARM: Augment-REINFORCE-Merge Gradient for Stochastic Binary Networks

Direct Optimization through max for Discrete Variational Auto-Encoder

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


evaluation API for salicon : a counterpart of saliency prediction as https://github.com/tylin/coco-caption

Microsoft COCO Captions: Data Collection and Evaluation Server

A Dilated Inception Network for Visual Saliency Prediction

DIDEC: The Dutch Image Description and Eye-tracking Corpus

International Conference on Computational Linguistics

n-Reference Transfer Learning for Saliency Prediction


[ICML'21] Think Global and Act Local:  Bayesian Optimisation for Categorical and Mixed Search Spaces

Think Global and Act Local: Bayesian Optimisation over High-Dimensional Categorical and Mixed Search Spaces

Bayesian Optimization over Discrete and Mixed Spaces via Probabilistic
  Reparameterization

SOBER: Highly Parallel Bayesian Optimization and Bayesian Quadrature
  over Discrete and Mixed Spaces

Bayesian Optimization over High-Dimensional Combinatorial Spaces via
  Dictionary-based Embeddings

Adaptive Batch Sizes for Active Learning A Probabilistic Numerics Approach


This repository contains some of the latest data augmentation techniques and optimizers for image classification using pytorch and the CIFAR10 dataset

AutoAugment: Learning Augmentation Policies from Data

Improved Regularization of Convolutional Neural Networks with Cutout

Randaugment: Practical automated data augmentation with a reduced search space

AugMix: A Simple Data Processing Method to Improve Robustness and Uncertainty


Multi-label Image Recognition with Partial Labels (ESWA 2024, AAAI 2022)

Structured Semantic Transfer for Multi-Label Recognition with Partial Labels

Semantic-Aware Representation Blending for Multi-Label Image Recognition with Partial Labels

Heterogeneous Semantic Transfer for Multi-label Recognition with Partial
  Labels


MMD and Relative MMD test

A Test of Relative Similarity For Model Selection in Generative Models

A Non-Parametric Test to Detect Data-Copying in Generative Models

Fast Non-Parametric Tests of Relative Dependency and Similarity


Code accompanying the paper "Preserving Causal Constraints in Counterfactual Explanations for Machine Learning Classifiers"

Features of Explainability: How users understand counterfactual and
  causal explanations for categorical and continuous features in XAI

Prototype-based Counterfactual Explanation for Causal Classification.


Merge transcriptome assemblies

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome

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

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

Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa

De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression

Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae)

Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent, Ctenomys sociabilis

The Significance of Genotypic Diversity in Coral Competitive Interaction: A Transcriptomic Perspective


Convex Layerwise Adversarial Training (COLT)

Adversarial Training and Provable Defenses: Bridging the Gap

International Conference on Learning Representations

IBP Regularization for Verified Adversarial Robustness via
  Branch-and-Bound


Report processing and protein quantification for MS-based proteomics

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

A time-resolved proteomic and prognostic map of COVID-19

Pan-cancer proteomic map of 949 human cell lines

The proteomic landscape of genome-wide genetic perturbations

Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics

Deep proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of naïve mice

The bigger picture: global analysis of solubilization performance of classical detergents versus new synthetic polymers utilizing shotgun proteomics

Proteome Remodeling of the Eye Lens at 50 Years Identified With Data-Independent Acquisition


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

Learning to Embed Categorical Features without Embedding Tables for Recommendation

A Lightweight Blockchain Based Framework for Underwater IoT

Hash Adaptive Bloom Filter

copMEM: Finding maximal exact matches via sampling both genomes

MATE: Multi-Attribute Table Extraction


PyTorch and TensorFlow/Keras image models with automatic weight conversions and equal API/implementations - Vision Transformer (ViT), ResNetV2, EfficientNetV2, NeRF, SegFormer, MixTransformer, (planned...) DeepLabV3+, ConvNeXtV2, YOLO, etc.

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

NeRF: Representing Scenes as Neural Radiance Fields for View Synthesis

SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers

EfficientNetV2: Smaller Models and Faster Training


Efficient Robustness Verification for ReLU networks (this repository is outdated, don't use; checkout our new implementation at https://github.com/Verified-Intelligence/auto_LiRPA instead)

Towards Fast Computation of Certified Robustness for ReLU Networks

Efficient Neural Network Robustness Certification with General Activation Functions

Verification for Machine Learning, Autonomy, and Neural Networks Survey

RecurJac: An Efficient Recursive Algorithm for Bounding Jacobian Matrix of Neural Networks and Its Applications


The source code for SetExpan framework, published in ECML-PKDD 2017

SetExpan: Corpus-Based Set Expansion via Context Feature Selection and Rank Ensemble

Mining Entity Synonyms with Efficient Neural Set Generation


Create a pseudohaploid assembly from a partially resolved diploid assembly

Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.)

Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond

Genome assemblies for two Neotropical trees: Jacaranda copaia and Handroanthus guayacan

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


A repository with a data set including instances and results from literature for the Job Shop Scheduling Problem (JSSP). While the raw data is provided as text files, it is also compiled in an R package with an API around it.

Benchmarking in Optimization: Best Practice and Open Issues

An ant colony optimization algorithm for job shop scheduling problem

A Hybrid Bacterial Foraging Algorithm For Solving Job Shop Scheduling Problems

Boosting Binary Optimization via Binary Classification: A Case Study of
  Job Shop Scheduling

Solving the Job Shop Scheduling Problem with Ant Colony Optimization


Plug and Play Language Models: A Simple Approach to Controlled Text Generation

The BigScience ROOTS Corpus: A 1.6TB Composite Multilingual Dataset

SP-GPT2: Semantics Improvement in Vietnamese Poetry Generation


12-class joint frequency-phase modulated SSVEP dataset for estimating online BCI performance

Inter- and Intra-subject Template-Based Multivariate Synchronization Index Using an Adaptive Threshold for SSVEP-Based BCIs

Steady-State Visual Evoked Potential Classification Using Complex Valued Convolutional Neural Networks

Cross-Subject Transfer Method Based on Domain Generalization for Facilitating Calibration of SSVEP-Based BCIs

IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society


Grounding Representation Similarity with Statistical Testing

The Curse of Low Task Diversity: On the Failure of Transfer Learning to
  Outperform MAML and Their Empirical Equivalence


pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics

MS/MS Spectrum Prediction for Modified Peptides Using pDeep2 Trained by Transfer Learning

Hybrid Spectral Library Combining DIA-MS Data and a Targeted Virtual Library Substantially Deepens the Proteome Coverage


Data and code accompanying the paper "Reasoning about Goals, Steps, and Temporal Ordering with WikiHow"

PROCEEDINGS OF THE 2020 CONFERENCE ON EMPIRICAL METHODS IN NATURAL LANGUAGE PROCESSING (EMNLP)

Reasoning about Procedures with Natural Language Processing: A Tutorial

DiscrimLoss: A Universal Loss for Hard Samples and Incorrect Samples Discrimination

STGN: an Implicit Regularization Method for Learning with Noisy Labels in Natural Language Processing

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


This is all the code and data from the Pantheon analysis https://arxiv.org/abs/1710.00845

Early Dark Energy can Resolve the Hubble Tension

On the Hubble Constant Tension in the SNe Ia Pantheon Sample

Oscillating scalar fields and the Hubble tension: A resolution with novel signatures

Cosmic microwave background bounds on primordial black holes including dark matter halo accretion

Can late dark energy transitions raise the Hubble constant?

On the Evolution of the Hubble Constant with the SNe Ia Pantheon Sample and Baryon Acoustic Oscillations: A Feasibility Study for GRB-Cosmology in 2030

What can machine learning tell us about the background expansion of the Universe?

Null signal for the cosmic anisotropy in the Pantheon supernovae data

Is there really a Hubble tension?

Null test for interactions in the dark sector


Neural Network Enumeration Tool

Reluplex: An Efficient SMT Solver for Verifying Deep Neural Networks

Verification of Deep Convolutional Neural Networks Using ImageStars

The Second International Verification of Neural Networks Competition (VNN-COMP 2021): Summary and Results

Improved Geometric Path Enumeration for Verifying ReLU Neural Networks

A Review of Formal Methods applied to Machine Learning

The Third International Verification of Neural Networks Competition
  (VNN-COMP 2022): Summary and Results

ZoPE: A Fast Optimizer for ReLU Networks with Low-Dimensional Inputs


Code for the NeurIPS 2019 paper: "Learning Dynamics of Attention: Human Prior for Interpretable Machine Reasoning"

Neural Ordinary Differential Equations

GQA: A New Dataset for Real-World Visual Reasoning and Compositional Question Answering

Compositional Attention Networks for Machine Reasoning


Estimate the autocorrelation time of time-series data very quickly

emcee: The MCMC Hammer

Publications of the Astronomical Society of the Pacific

CosmoHammer: Cosmological parameter estimation with the MCMC Hammer

Comparison of sampling techniques for Bayesian parameter estimation

Monthly Notices of the Royal Astronomical Society

INFERRING THE GRAVITATIONAL POTENTIAL OF THE MILKY WAY WITH A FEW PRECISELY MEASURED STARS

K2-264: a transiting multiplanet system in the Praesepe open cluster

The First Day in the Life of a Magnetar: Evolution of the Inclination Angle, Magnetic Dipole Moment, and Braking Index of Millisecond Magnetars during Gamma-Ray Burst Afterglows

Spitzer Transit Follow-up of Planet Candidates from the K2 Mission

K2-288Bb: A Small Temperate Planet in a Low-mass Binary System Discovered by Citizen Scientists

A multi-scale sub-voxel perfusion model to estimate diffusive capillary wall conductivity in multiple sclerosis lesions from perfusion MRI data

Bayes Factors via Savage-Dickey Supermodels


TurnGPT: a Transformer-based Language Model for Predicting Turn-taking in Spoken Dialog

TransferTransfo: A Transfer Learning Approach for Neural Network Based Conversational Agents

Hello, It's GPT-2 -- How Can I Help You? Towards the Use of Pretrained Language Models for Task-Oriented Dialogue Systems

Do dialogue representations align with perception? An empirical study

Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics


NLP pipelines for Tagalog using spaCy


A collection of functions with emphasis on multivariate methods and handling of geographic datasets

Monarch butterfly population decline in North America: identifying the threatening processes

Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases Bacteroides fragilis Abundance Compared with an Isocaloric Snack in College Freshmen

Comparison of Cloud-Filling Algorithms for Marine Satellite Data

Exploratory Analysis of Urban Climate Using a Gap-Filled Landsat 8 Land Surface Temperature Data Set

ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients

Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet


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

Charting the Right Manifold: Manifold Mixup for Few-shot Learning

The Self-Optimal-Transport Feature Transform


A curated list of publically available human-robot interaction datasets

Timing in Multimodal Turn-Taking Interactions: Control and Analysis Using Timed Petri Nets

UE-HRI: a new dataset for the study of user engagement in spontaneous human-robot interactions

International Conference on Multimodal Interfaces

The PInSoRo dataset: Supporting the data-driven study of child-child and child-robot social dynamics

P2PSTORY: Dataset of Children as Storytellers and Listeners in Peer-to-Peer Interactions

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


Uncertainty-aware Self-ensembling Model for Semi-supervised 3D Left Atrium Segmentation

Shape-aware Semi-supervised 3D Semantic Segmentation for Medical Images

Medical Image Computing and Computer-Assisted Intervention

Semi-supervised Left Atrium Segmentation with Mutual Consistency Training

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

Translation Consistent Semi-supervised Segmentation for 3D Medical
  Images


Sliced Wasserstein Generator

Generative Modeling using the Sliced Wasserstein Distance

Orthogonal Estimation of Wasserstein Distances

Exploiting Chain Rule and Bayes' Theorem to Compare Probability Distributions


U-Net: Convolutional Networks for Biomedical Image Segmentation

Automatic Liver and Lesion Segmentation in CT Using Cascaded Fully Convolutional Neural Networks and 3D Conditional Random Fields

Automatic Liver and Tumor Segmentation of CT and MRI Volumes using
  Cascaded Fully Convolutional Neural Networks

SurvivalNet: Predicting patient survival from diffusion weighted
  magnetic resonance images using cascaded fully convolutional and 3D
  convolutional neural networks


Code for the paper "Training Binary Neural Networks with Bayesian Learning Rule

Training Binary Neural Networks using the Bayesian Learning Rule

AdaSTE: An Adaptive Straight-Through Estimator to Train Binary Neural Networks

Bias-Variance Tradeoffs in Single-Sample Binary Gradient Estimators


BNNs (XNOR, BNN and DoReFa) implementation for PyTorch 1.0+

XNOR-Net: ImageNet Classification Using Binary Convolutional Neural Networks

DoReFa-Net: Training Low Bitwidth Convolutional Neural Networks with Low Bitwidth Gradients

CoopNet: Cooperative Convolutional Neural Network for Low-Power MCUs

International Conference on Electronics, Circuits, and Systems

TentacleNet: A Pseudo-Ensemble Template for Accurate Binary Convolutional Neural Networks


Code for paper https://arxiv.org/abs/2102.13186

Towards a Unified Framework for Fair and Stable Graph Representation Learning

Improving Fairness in Graph Neural Networks via Mitigating Sensitive Attribute Leakage

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

Counterfactual Learning on Graphs: A Survey

Fairness and Explainability: Bridging the Gap Towards Fair Model
  Explanations

Graph Fairness Learning under Distribution Shifts


Data Programming by Demonstration (DPBD) for Document Classification

Snorkel: Rapid Training Data Creation with Weak Supervision

Data Programming: Creating Large Training Sets, Quickly

Ruler: Data Programming by Demonstration for Document Labeling

Data Programming by Demonstration: A Framework for Interactively Learning Labeling Functions


Accuracy 77%. Large batch deep learning optimizer LARS for ImageNet with PyTorch and ResNet, using Horovod for distribution. Optional accumulated gradient and NVIDIA DALI dataloader.

Large Batch Training of Convolutional Networks

Large-Batch Training for LSTM and Beyond

NG+ : A Multi-Step Matrix-Product Natural Gradient Method for Deep
  Learning


JMIR AI'23: EEG dataset processing and EEG Self-supervised Learning

Self-supervised EEG Representation Learning for Automatic Sleep Staging

ManyDG: Many-domain Generalization for Healthcare Applications


Multi-directional Recurrent Neural Networks (MRNN) - IEEE TBME 2019

Estimating Missing Data in Temporal Data Streams Using Multi-Directional Recurrent Neural Networks

SAITS: Self-Attention-based Imputation for Time Series

Learning from Irregularly-Sampled Time Series: A Missing Data Perspective

A Survey on Principles, Models and Methods for Learning from Irregularly Sampled Time Series: From Discretization to Attention and Invariance.


A multi-planet Radial Velocity and Transit modelling software

pyaneti: a fast and powerful software suite for multiplanet radial velocity and transit fitting

Monthly notices of the Royal Astronomical Society

Two Intermediate-mass Transiting Brown Dwarfs from the TESS Mission

PYANETI - II. A multidimensional Gaussian process approach to analysing spectroscopic time-series

An 8 Mearth super-Earth in a 2.2 day orbit around the K5V star K2-216

One year of AU Mic with HARPS – I. Measuring the masses of the two transiting planets

Greening of the brown-dwarf desert EPIC 212036875b: a 51 M-J object in a 5-day orbit around an F7V star

K2-139 b: a low-mass warm Jupiter on a 29-d orbit transiting an active K0 V star

Detection and Doppler monitoring of K2-285 (EPIC 246471491), a system of four transiting planets smaller than Neptune

Planetary candidates transiting cool dwarf stars from campaigns 12 to 15 of K2

TOI-2196 b: Rare planet in the hot Neptune desert transiting a G-type star


Context-Based-Question-Answering

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

RoBERTa: A Robustly Optimized BERT Pretraining Approach

DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter

CamemBERT: a Tasty French Language Model

Meeting of the Association for Computational Linguistics


CANet: An Unsupervised Intrusion Detection System for High Dimensional CAN Bus Data

AI-Based Intrusion Detection Systems for In-Vehicle Networks: A Survey

CANShield: Deep-Learning-Based Intrusion Detection Framework for Controller Area Networks at the Signal Level

Detecting Message Modification Attacks on the CAN Bus with Temporal Convolutional Networks

Proceedings of the 7th International Conference on Vehicle Technology and Intelligent Transport Systems

Addressing the Lack of Comparability & Testing in CAN Intrusion
  Detection Research: A Comprehensive Guide to CAN IDS Data & Introduction of
  the ROAD Dataset


A benchmarking suite for maximum independent set solvers.

Combinatorial Optimization with Graph Convolutional Networks and Guided Tree Search

Learning What to Defer for Maximum Independent Sets

DIMES: A Differentiable Meta Solver for Combinatorial Optimization
  Problems

What's Wrong with Deep Learning in Tree Search for Combinatorial
  Optimization


The official repository for <Autoencoding Under Normalization Constraints> (Yoon, Noh and Park, ICML 2021).

Evaluating Out-of-Distribution Detectors Through Adversarial Generation
  of Outliers

Energy-Based Models for Anomaly Detection: A Manifold Diffusion Recovery
  Approach


Style Transfer from Non-Parallel Text by Cross-Alignment

Unsupervised Text Style Transfer using Language Models as Discriminators

Deep Learning for Text Style Transfer: A Survey

Fighting Offensive Language on Social Media with Unsupervised Text Style Transfer

Reinforced Rewards Framework for Text Style Transfer

Multi-type Disentanglement without Adversarial Training

DGSAN: Discrete Generative Self-Adversarial Network

Effective writing style imitation via combinatorial paraphrasing

Syntax Matters! Syntax-Controlled in Text Style Transfer

Enhance Long Text Understanding via Distilled Gist Detector from Abstractive Summarization


Graph Neural Network for Traffic Forecasting: A Survey

Transfer Learning with Graph Neural Networks for Short-Term Highway Traffic Forecasting

Spatio-Temporal Graph Neural Networks for Predictive Learning in Urban Computing: A Survey


CogNet: a large-scale, high-quality cognate database for 338 languages, 1.07M words, and 8.1 million cognates

CogNet: A Large-Scale Cognate Database

Zenodo (CERN European Organization for Nuclear Research)

MorphyNet: a Large Multilingual Database of Derivational and Inflectional Morphology

Special Interest Group on Computational Morphology and Phonology Workshop

A large and evolving cognate database


Transfer Learning for Improving Speech Emotion Classification Accuracy

Speech Emotion Recognition Using Multi-hop Attention Mechanism

International Conference on Acoustics, Speech, and Signal Processing

Attention-Augmented End-to-End Multi-Task Learning for Emotion Prediction from Speech


Multi-task deep learning framework for multi-omics data analysis

OmiEmbed: A Unified Multi-Task Deep Learning Framework for Multi-Omics Data

OmiTrans: Generative Adversarial Networks Based Omics-to-omics Translation Framework

SubOmiEmbed: Self-supervised Representation Learning of Multi-omics Data for Cancer Type Classification


BadNets: Identifying Vulnerabilities in the Machine Learning Model Supply Chain

An Empirical Cybersecurity Evaluation of GitHub Copilot's Code Contributions

Multimodal Chain-of-Thought Reasoning in Language Models

TenSEAL: A Library for Encrypted Tensor Operations Using Homomorphic
  Encryption

Neurotoxin: Durable Backdoors in Federated Learning

Single-Forward-Step Projective Splitting: Exploiting Cocoercivity


Adaptive Graph Convolutional Recurrent Network for Traffic Forecasting

Graph Neural Network for Traffic Forecasting: A Survey

Deciphering Spatio-Temporal Graph Forecasting: A Causal Lens and
  Treatment

Frequency-domain MLPs are More Effective Learners in Time Series
  Forecasting

Graph Neural Rough Differential Equations for Traffic Forecasting

Graph-Free Learning in Graph-Structured Data: A More Efficient and
  Accurate Spatiotemporal Learning Perspective

DG-Trans: Dual-level Graph Transformer for Spatiotemporal Incident
  Impact Prediction on Traffic Networks


Reproduction of OpenAI and DeepMind's "Deep Reinforcement Learning from Human Preferences"

Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning

Domain Randomization for Transferring Deep Neural Networks from Simulation to the Real World

Deep reinforcement learning from human preferences

Deep Exploration via Bootstrapped DQN


ABC–CDE: Toward Approximate Bayesian Computation With Complex High-Dimensional Data and Limited Simulations

Journal of computational and graphical statistics

Conditional density estimation tools in python and R with applications to photometric redshifts and likelihood-free cosmological inference

(f)RFCDE: Random Forests for Conditional Density Estimation and Functional Data


FOFE NER

A Local Detection Approach for Named Entity Recognition and Mention Detection

PROCEEDINGS OF THE 55TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS (ACL 2017), VOL 1

A FOFE-based Local Detection Approach for Named Entity Recognition and Mention Detection.

A Multi-task Learning Approach for Named Entity Recognition using Local Detection


A Deep Graph Neural Network Architecture for Modelling Spatio-temporal Dynamics in rs-fMRI Data

A deep graph neural network architecture for modelling spatio-temporal dynamics in resting-state functional MRI data

Towards a predictive spatio-temporal representation of brain data

A deep spatiotemporal graph learning architecture for brain connectivity analysis

International Conference of the IEEE Engineering in Medicine and Biology Society


A temporal ordering system for events and time expressions in written text.

Improving Temporal Relation Extraction with a Globally Acquired Statistical Resource

Contextualized Word Embeddings Enhanced Event Temporal Relation
  Extraction for Story Understanding

This before That: Causal Precedence in the Biomedical Domain

Neural Language Modeling for Contextualized Temporal Graph Generation

Inducing Temporal Relations from Time Anchor Annotation

North American Chapter of the Association for Computational Linguistics

Predicting Event Time by Classifying Sub-Level Temporal Relations Induced from a Unified Representation of Time Anchors

Multi-Scale Contrastive Knowledge Co-Distillation for Event Temporal Relation Extraction

Fusing Temporal Graphs into Transformers for Time-Sensitive Question Answering


Assembly by Reduced Complexity (ARC)

NOVOPlasty: de novo assembly of organelle genomes from whole genome data

Dietary breadth is positively correlated with venom complexity in cone snails

Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control

Venomix: A simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data

Characterization of the complete mitochondrial genome of the invasive tramp ant Cardiocondyla obscurior (Hymenoptera: Formicidae: Myrmicinae)

Complete Mitochondrial Genome Sequence of Bighorn Sheep

The complete mitochondrial genome of Ripeacma umbellata Wang, 2009 (Lepidoptera: Autostichidae)


Code for the paper "Putting a bug in ML: The moth olfactory network learns to read MNIST", by CB Delahunt and JN Kutz

Biological Mechanisms for Learning: A Computational Model of Olfactory Learning in the Manduca sexta Moth, with Applications to Neural Nets

Insect Cyborgs: Bio-mimetic Feature Generators Improve ML Accuracy on Limited Data

Insect cyborgs: Bio-mimetic feature generators improve machine learning accuracy on limited data


This is the official implementation of "Anomaly Detection with Deep Perceptual Autoencoders".

Deep Anomaly Detection Using Geometric Transformations

Anomaly Detection in Medical Imaging With Deep Perceptual Autoencoders

Towards Practical Unsupervised Anomaly Detection on Retinal Images

Perceptual Image Anomaly Detection


r:trån is a road space model transformer library for OpenDRIVE, CityGML and beyond

CITYGML AND THE STREETS OF NEW YORK -A PROPOSAL FOR DETAILED STREET SPACE MODELLING

ISPRS annals of the photogrammetry, remote sensing and spatial information sciences

Detailed Streetspace Modelling for Multiple Applications: Discussions on the Proposed CityGML 3.0 Transportation Model

ISPRS international journal of geo-information

Spatio-Semantic Road Space Modeling for Vehicle–Pedestrian Simulation to Test Automated Driving Systems

REQUIREMENT ANALYSIS OF 3D ROAD SPACE MODELS FOR AUTOMATED DRIVING


Regularly updated list of publicly available datasets with single-cell (scRNAseq) and T-cell/antibody immune repertoire (AIRR / RepSeq / immunosequencing) data of COVID-19 patients with SARS-CoV-2.

Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells

A molecular cell atlas of the human lung from single-cell RNA sequencing

SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells

Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing

B cell clonal expansion and convergent antibody responses to SARS-CoV-2

bioRxiv : the preprint server for biology

The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by single-cell RNA sequencing

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection

Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids

Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells


This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.

MGraphDTA: deep multiscale graph neural network for explainable drug–target binding affinity prediction

PADME: A Deep Learning-based Framework for Drug-Target Interaction Prediction


Source code for "A Globally Optimal Energy-Efficient Power Control Framework and its Efficient Implementation in Wireless Interference Networks" by Bho Matthiesen, Alessio Zappone, Karl-L. Besser, Eduard A. Jorswieck, and Merouane Debbah, accepted for publication in IEEE Transactions on Signal Processing.

A Globally Optimal Energy-Efficient Power Control Framework and Its Efficient Implementation in Wireless Interference Networks

Deep Learning for Optimal Energy-Efficient Power Control in Wireless Interference Networks.

Power Allocation for Wireless Federated Learning using Graph Neural
  Networks


Graph Transformer Architecture. Source code for "A Generalization of Transformer Networks to Graphs", DLG-AAAI'21.

Equivariant and Stable Positional Encoding for More Powerful Graph
  Neural Networks

Privacy-Enhancing Digital Contact Tracing with Machine Learning for Pandemic Response: A Comprehensive Review


MEDIQA-Chat Shared Tasks @ ACL-ClinicalNLP 2023

Overview of the MEDIQA-Chat 2023 Shared Tasks on the Summarization & Generation of Doctor-Patient Conversations

Proceedings of the 5th Clinical Natural Language Processing Workshop

ACI-BENCH: a Novel Ambient Clinical Intelligence Dataset for
  Benchmarking Automatic Visit Note Generation

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

NewAgeHealthWarriors at MEDIQA-Chat 2023 Task A: Summarizing Short Medical Conversation with Transformers


Learning Gender-Neutral Word Embeddings

Lipstick on a Pig: Debiasing Methods Cover up Systematic Gender Biases in Word Embeddings But do not Remove Them

Learning Gender-Neutral Word Embeddings

Equalizing Gender Bias in Neural Machine Translation with Word Embeddings Techniques

Gender-preserving Debiasing for Pre-trained Word Embeddings

Double-Hard Debias: Tailoring Word Embeddings for Gender Bias Mitigation

Gender Bias in Masked Language Models for Multiple Languages

Dictionary-based Debiasing of Pre-trained Word Embeddings

Automatically Identifying Gender Issues in Machine Translation using Perturbations

Conceptor Debiasing of Word Representations Evaluated on WEAT

A Causal Inference Method for Reducing Gender Bias in Word Embedding Relations


Realistic Lens Blur/Chromatic Aberration Filter

RGB Cameras Failures and Their Effects in Autonomous Driving Applications

Robust Traffic Sign Recognition Against Camera Failures

IEEE open journal of intelligent transportation systems


Code for Sanity-Checking Pruning Methods: Random Tickets can Win the Jackpot

The Lottery Ticket Hypothesis: Finding Sparse, Trainable Neural Networks

SNIP: Single-shot Network Pruning based on Connection Sensitivity

Picking Winning Tickets Before Training by Preserving Gradient Flow

A Survey on Deep Neural Network Pruning-Taxonomy, Comparison, Analysis,
  and Recommendations


MarginDistillation: distillation for margin-based softmax

Triplet Distillation for Deep Face Recognition

ShrinkTeaNet: Million-scale Lightweight Face Recognition via Shrinking Teacher-Student Networks.


This repository contains the code for our upcoming paper An Investigation of End-to-End Models for Robust Speech Recognition at ICASSP 2021.

A Noise-Robust Self-Supervised Pre-Training Model Based Speech Representation Learning for Automatic Speech Recognition

IEEE International Conference on Acoustics, Speech, and Signal Processing

Joint Training of Speech Enhancement and Self-supervised Model for
  Noise-robust ASR

Wav2code: Restore Clean Speech Representations via Codebook Lookup for
  Noise-Robust ASR

deHuBERT: Disentangling Noise in a Self-supervised Model for Robust
  Speech Recognition


This is the source code for Learning Deep Kernels for Non-Parametric Two-Sample Tests (ICML2020).

Two-sample Test with Kernel Projected Wasserstein Distance

E-Valuating Classifier Two-Sample Tests

A Learning Based Hypothesis Test for Harmful Covariate Shift

The Representation Jensen-Shannon Divergence

Detecting Adversarial Data by Probing Multiple Perturbations Using
  Expected Perturbation Score


DeepLab v3+ model in PyTorch. Support different backbones.

Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation

Post-Training Piecewise Linear Quantization for Deep Neural Networks

Knowledge Distillation via the Target-aware Transformer

ContexedNet: Context–Aware Ear Detection in Unconstrained Settings

Contour-Aware Equipotential Learning for Semantic Segmentation

Improving Predictive Performance and Calibration by Weight Fusion in
  Semantic Segmentation


Code for ICCV 2023 paper "Contrastive Pseudo Learning for Open-World DeepFake Attribution"

FaceForensics++: Learning to Detect Manipulated Facial Images

Celeb-DF: A Large-scale Challenging Dataset for DeepFake Forensics

On the Detection of Digital Face Manipulation

ForgeryNet: A Versatile Benchmark for Comprehensive Forgery Analysis


This repository contains code used in the EMNLP 2019 paper "Learning Dynamic Context Augmentation for Global Entity Linking".

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

Neural Fine-Grained Entity Type Classification with Hierarchy-Aware Loss

Improving Entity Linking by Modeling Latent Entity Type Information

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

Improving Few-Shot Domain Transfer for Named Entity Disambiguation with Pattern Exploitation

Findings of the Association for Computational Linguistics: EMNLP 2022


Code for 'Constrained Contrastive Distribution Learning for Unsupervised Anomaly Detection and Localisation in Medical Images'  [MICCAI 2021]

Weakly-supervised Video Anomaly Detection with Robust Temporal Feature Magnitude Learning

Self-supervised pseudo multi-class pre-training for unsupervised anomaly detection and segmentation in medical images


An unofficial Pytorch implementation of SNGAN, achieving IS of 8.21 and FID of 14.21 on CIFAR-10.

Content-Aware GAN Compression

Hierarchical Sliced Wasserstein Distance

Amortized Projection Optimization for Sliced Wasserstein Generative
  Models

Backpropagating through Fréchet Inception Distance

Overcoming Mode Collapse with Adaptive Multi Adversarial Training

Markovian Sliced Wasserstein Distances: Beyond Independent Projections


Connectivity between the World Wide Charging Protocol (WWCP) and the Open Charge Point Protocol (OCPP v1.6/v2.0.1/v2.1).


GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data

SpaGE: Spatial Gene Enhancement using scRNA-seq

SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment

A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

ActiveSVM selects minimal gene sets from gene expression data

Active feature selection discovers minimal gene sets for classifying cell types and disease states with single-cell mRNA-seq data

SpatialMap: Spatial Mapping of Unmeasured Gene Expression Profiles in Spatial Transcriptomic Data Using Generalized Linear Spatial Models


Plastid Genome Annotator

Complete plastome sequence of an endangered species, Calocedrus rupestris (Cupressaceae)

Comparative and Evolutionary Analyses on the Complete Plastomes of Five Kalanchoe Horticultural Plants

Characterization and phylogenetic analysis of the complete plastome of Alopecurus japonicus (Gramineae), an annual weed

Characterization of the complete chloroplast genome of Suaeda salsa (Amaranthaceae/Chenopodiaceae), an annual succulent halophyte

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

Complete chloroplast genome sequence of Oxytropis glabra (Leguminosae)

Characterization of the complete plastome of Alopecurus aequalis (Poaceae), a widespread weed

Characterization of the complete chloroplast genome of Salvia hispanica (Lamiaceae)

Chloroplast phylogenomics of Calocedrus (Cupressaceae)

The complete chloroplast genome of Foonchewia coriacea (Rubioideae: Rubiaceae): a monotypic species endemic to Guangdong, China


Quasi-Periodic Parallel WaveGAN Pytorch implementation

WORLD: A Vocoder-Based High-Quality Speech Synthesis System for Real-Time Applications

IEICE transactions on information and systems

Parallel Wavegan: A Fast Waveform Generation Model Based on Generative Adversarial Networks with Multi-Resolution Spectrogram

Quasi-Periodic Parallel WaveGAN: A Non-Autoregressive Raw Waveform Generative Model With Pitch-Dependent Dilated Convolution Neural Network

IEEE/ACM transactions on audio, speech, and language processing

Quasi-Periodic Parallel WaveGAN Vocoder: A Non-autoregressive Pitch-dependent Dilated Convolution Model for Parametric Speech Generation

Harmonic-Net: Fundamental Frequency and Speech Rate Controllable Fast Neural Vocoder


web documentation for Trinotate

Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay

Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process

Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae

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

Ultrafast functional profiling of RNA-seq data for nonmodel organisms

Microbiota Perturbation or Elimination Can Inhibit Normal Development and Elicit a Starvation-Like Response in an Omnivorous Model Invertebrate

A crustacean annotated transcriptome (CAT) database

Pearl Sac Gene Expression Profiles Associated With Pearl Attributes in the Silver-Lip Pearl Oyster, Pinctada maxima

A Combined Transcriptomics and Proteomics Approach Reveals the Differences in the Predatory and Defensive Venoms of the Molluscivorous Cone Snail Cylinder ammiralis (Caenogastropoda: Conidae)

Deinococcus radiodurans UWO298 Dependence on Background Radiation for Optimal Growth

Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection


ICD Coding from Clinical Text Using Multi-Filter Residual Convolutional Neural Network

A Label Attention Model for ICD Coding from Clinical Text

PROCEEDINGS OF THE TWENTY-NINTH INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE

Automated Medical Coding on MIMIC-III and MIMIC-IV: A Critical Review and Replicability Study

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

Automated clinical coding using off-the-shelf large language models


Official Pytorch Implementation of Paper "A Semantic Space is Worth 256 Language Descriptions: Make Stronger Segmentation Models with Descriptive Properties"

Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks

C-Pack: Packaged Resources To Advance General Chinese Embedding


Data and code for the IEEE S&P'22 paper SAILFISH: Vetting Smart Contract State-Inconsistency Bugs in Seconds

Turn the Rudder: A Beacon of Reentrancy Detection for Smart Contracts on Ethereum

EF↯CF: High Performance Smart Contract Fuzzing for Exploit Generation

DAppSCAN: Building Large-Scale Datasets for Smart Contract Weaknesses in
  DApp Projects