Code for the paper: GCDT: A Global Context Enhanced Deep Transition Architecture for Sequence Labeling

Handling Rare Entities for Neural Sequence Labeling

Meeting of the Association for Computational Linguistics

Segmenting Natural Language Sentences via Lexical Unit Analysis

Neural Sequence Segmentation as Determining the Leftmost Segments


PyTorch implementation of the Offline Reinforcement Learning algorithm CQL. Includes the versions DQN-CQL and SAC-CQL for discrete and continuous action spaces.

Conservative Q-Learning for Offline Reinforcement Learning

Hybrid RL: Using Both Offline and Online Data Can Make RL Efficient

Monte Carlo Augmented Actor-Critic for Sparse Reward Deep Reinforcement Learning from Suboptimal Demonstrations

ELA: Exploited Level Augmentation for Offline Learning in Zero-Sum Games


Data and code related to the paper "Probabilistic matrix factorization for automated machine learning", NIPS, 2018.

Automated Machine Learning: State-of-The-Art and Open Challenges

Probabilistic Matrix Factorization for Automated Machine Learning

Deep Pipeline Embeddings for AutoML


Code for MC Dropout and Model Ensembling Uncertainty Estimate experiments

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

Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles

What Uncertainties Do We Need in Bayesian Deep Learning for Computer Vision?


UNC-Chapel Hill Bioinformatics Utilities

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

Carolina Digital Repository (University of North Carolina at Chapel Hill)

Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors

Unifying cancer and normal RNA sequencing data from different sources

Mitochondrial respiratory gene expression is suppressed in many cancers

Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer

Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

Alterations in Wnt- and/or STAT3 signaling pathways and the immune microenvironment during metastatic progression

Enabling cross-study analysis of RNA-Sequencing data


qecsim is a Python 3 package for simulating quantum error correction using stabilizer codes.

Sparse Blossom: correcting a million errors per core second with minimum-weight matching

Data-driven decoding of quantum error correcting codes using graph neural networks

Optimization Tools for Distance-Preserving Flag Fault-Tolerant Error Correction

Decoding algorithms for surface codes

Entanglement Routing using Quantum Error Correction for Distillation


[ICML 2019] TensorFlow Code for Self-Supervised Exploration via Disagreement

See, Hear, Explore: Curiosity via Audio-Visual Association

Implicit Generative Modeling for Efficient Exploration

Touch-based Curiosity for Sparse-Reward Tasks


A collection of drug discovery, classification and representation learning papers with deep learning.

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

Applications of machine learning in drug discovery and development

Deep Neural Nets as a Method for Quantitative Structure-Activity Relationships

Journal of chemical information and modeling

Pushing the Boundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism

druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico

Deep-Learning-Based Drug-Target Interaction Prediction.

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

Predicting drug-target interaction using a novel graph neural network with 3D structure-embedded graph representation

Boosting Docking-Based Virtual Screening with Deep Learning

CGBVS‐DNN: Prediction of Compound‐protein Interactions Based on Deep Learning


Repository providing a wide range of self-supervised pretrained models for computer vision tasks.

A Simple Framework for Contrastive Learning of Visual Representations

Improved Baselines with Momentum Contrastive Learning

Self-Supervised Pretraining Improves Self-Supervised Pretraining


The code of multi-attention deepfake detection

Multi-attentional Deepfake Detection

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

Block shuffling learning for Deepfake Detection


DocNLI: A Large-scale Dataset for Document-level Natural Language Inference

WiCE: Real-World Entailment for Claims in Wikipedia

Post-Hoc Answer Attribution for Grounded and Trustworthy Long Document Comprehension: Task, Insights, and Challenges


[ICML 2021] Break-It-Fix-It: Unsupervised Learning for Program Repair

A Survey of Learning-based Automated Program Repair

A Survey on Automated Program Repair Techniques

A Chain of AI-based Solutions for Resolving FQNs and Fixing Syntax Errors in Partial Code


Repo for paper "Inverse deep learning methods and benchmarks for artificial electromagnetic material design"

Nanophotonic particle simulation and inverse design using artificial neural networks

Smart inverse design of graphene-based photonic metamaterials by an adaptive artificial neural network


Calibration of Convolutional Neural Networks

Intra Order-preserving Functions for Calibration of Multi-Class Neural Networks

Better Uncertainty Calibration via Proper Scores for Classification and Beyond

Introspective Learning : A Two-Stage Approach for Inference in Neural Networks

Post-hoc Calibration of Neural Networks by g-Layers

The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera

Scaling of Class-wise Training Losses for Post-hoc Calibration


SIGIR'21: Optimizing DR with hard negatives and achieving SOTA first-stage retrieval performance on TREC DL Track.

Optimizing Dense Retrieval Model Training with Hard Negatives

Jointly Optimizing Query Encoder and Product Quantization to Improve Retrieval Performance

Learning Discrete Representations via Constrained Clustering for Effective and Efficient Dense Retrieval

Learning To Retrieve: How to Train a Dense Retrieval Model Effectively and Efficiently

Hard Negatives or False Negatives: Correcting Pooling Bias in Training Neural Ranking Models

Information Retrieval with Entity Linking


TensorFlow implementation of TabTransformer

Revisiting Deep Learning Models for Tabular Data

TabTransformer: Tabular Data Modeling Using Contextual Embeddings

On Embeddings for Numerical Features in Tabular Deep Learning


A Go-based tracking of cosmic velocity fields through the use of tetrahedra

Universal at Last? The Splashback Mass Function of Dark Matter Halos

Flybys, Orbits, Splashback: Subhalos and the Importance of the Halo Boundary

The Splashback Radius of Halos from Particle Dynamics. III. Halo Catalogs, Merger Trees, and Host–Subhalo Relations

The Astrophysical Journal Supplement Series

Buzzard to Cardinal: Improved Mock Catalogs for Large Galaxy Surveys


Variational Denoising Network: Toward Blind Noise Modeling and Removal (NeurIPS, 2019) (Pytorch)

Deep Variational Network Toward Blind Image Restoration

Overparametrization of HyperNetworks at Fixed FLOP-Count Enables Fast Neural Image Enhancement


Utilities to perform Uncertainty Quantification on Keras Models

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

Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles

DropConnect Is Effective in Modeling Uncertainty of Bayesian Deep Networks

Deep Sub-Ensembles for Fast Uncertainty Estimation in Image Classification

Design Patterns for Machine Learning Based Systems with Human-in-the-Loop

Exploring the Limits of Epistemic Uncertainty Quantification in Low-Shot Settings


Multimodal Semi-Supervised Learning for Text Recognition (SemiMTR)

Sequence-to-Sequence Contrastive Learning for Text Recognition

CLIPTER: Looking at the Bigger Picture in Scene Text Recognition


One hundred challenge problems for logical formalizations of commonsense psychology

Recent Advances in Natural Language Inference: A Survey of Benchmarks, Resources, and Approaches

Commonsense Reasoning for Natural Language Understanding: A Survey of Benchmarks, Resources, and Approaches

Improving Fluency in Narrative Text Generation With Grammatical Transformations and Probabilistic Parsing

International Conference on Natural Language Generation

Extending Automated Deduction for Commonsense Reasoning


Equivariant Imaging (EI), ICCV'2021 Oral

Equivariant Imaging: Learning Beyond the Range Space

Sensing Theorems for Unsupervised Learning in Linear Inverse Problems

Invertible Diffusion Models for Compressed Sensing


AIGER And-Inverter-Graph Library

Shield Synthesis for LTL Modulo Theories

The Lattice-Theoretic Essence of Property Directed Reachability Analysis

An Automated Testing and Debugging Toolkit for Gate-Level Logic Synthesis Applications


PsiQuaSP -- Permutation symmetry for identical Quantum Systems Package

Open quantum systems with local and collective incoherent processes: Efficient numerical simulations using permutational invariance

Superradiant to subradiant phase transition in the open system Dicke model: dark state cascades

PsiQuaSP–A library for efficient computation of symmetric open quantum systems


Code for watermarking language models

Robust Distortion-free Watermarks for Language Models

DiPmark: A Stealthy, Efficient and Resilient Watermark for Large Language Models

REMARK-LLM: A Robust and Efficient Watermarking Framework for Generative Large Language Models

Distortion-free Watermarks are not Truly Distortion-free under Watermark
  Key Collisions


:earth_africa: :pencil: Modelling and forecasting deforestation in the tropics


Deep-learning Transfer Learning models of NTUA-SLP team submitted at the IEST of WASSA 2018 at EMNLP 2018.

Universal Language Model Fine-tuning for Text Classification

Regularizing and Optimizing LSTM Language Models

Using millions of emoji occurrences to learn any-domain representations for detecting sentiment, emotion and sarcasm

Empirical Methods in Natural Language Processing

NTUA-SLP at IEST 2018: Ensemble of Neural Transfer Methods for Implicit Emotion Classification


Official code for Modeling the Background for Incremental Learning in Semantic Segmentation https://arxiv.org/abs/2002.00718

PLOP: Learning without Forgetting for Continual Semantic Segmentation

Learning Incrementally to Segment Multiple Organs in a CT Image

Modeling the Background for Incremental and Weakly-Supervised Semantic Segmentation

IEEE transactions on pattern analysis and machine intelligence

Causes of Catastrophic Forgetting in Class-Incremental Semantic Segmentation


Deep Adaptive Design: Amortizing Sequential Bayesian Experimental Design

Variational Sequential Optimal Experimental Design using Reinforcement Learning


L1000 peak deconvolution based on Bayesian analysis

A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing

A Bayesian approach to accurate and robust signature detection on LINCS L1000 data

Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing

Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer’s disease drug repurposing

Hierarchical multi-omics data integration and modeling predict cell-specific chemical proteomics and drug responses

Model-Free Error Assessment for Breadth-First Studies, with Applications to Cell-Perturbation Experiments


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


A collection of optimization algorithms for maximizing unconstrained submodular set functions.

Interpretable Decision Sets: A Joint Framework for Description and Prediction

A Tight Linear Time (1/2)-Approximation for Unconstrained Submodular Maximization

Submodular Functions Maximization Problems

Handbook of Approximation Algorithms and Metaheuristics, Second Edition


Code for "ATTA: Anomaly-aware Test-Time Adaptation for Out-of-Distribution Detection in Segmentation"

Scaling Out-of-Distribution Detection for Real-World Settings

Pixel-wise Energy-biased Abstention Learning for Anomaly Segmentation on Complex Urban Driving Scenes


Collection of various scripts

De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

Hopping or Jumping on the Cliffs: The Unusual Phylogeographical and Demographic Structure of an Extremely Narrow Endemic Mediterranean Plant

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb?


Code for the paper "Better Diffusion Models Further Improve Adversarial Training" (ICML 2023)

Fixing Data Augmentation to Improve Adversarial Robustness

Toward Understanding Generative Data Augmentation


CLI tool to annotate genes with KOfam

Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs.

Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome

Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications

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

Comparison of the Nutritional Properties and Transcriptome Profiling Between the Two Different Harvesting Periods of Auricularia polytricha


Official implementation of "When Machine Unlearning Jeopardizes Privacy" (ACM CCS 2021)

Conference on Computer and Communications Security

A Survey of Machine Unlearning

Accident Risk Prediction based on Heterogeneous Sparse Data: New Dataset and Insights

Advances in Geographic Information Systems

Graph Unlearning

How to Combine Membership-Inference Attacks on Multiple Updated Models


Tensorflow2 implementation of CircleLoss. Support class-level, sparse class-level, pair-wise labels

Additive Margin Softmax for Face Verification

Circle Loss: A Unified Perspective of Pair Similarity Optimization

Proxy Anchor Loss for Deep Metric Learning


Joint Transmit Beamforming and Phase Shifts Design with Deep Reinforcement Learning

Continuous control with deep reinforcement learning

Reconfigurable Intelligent Surface Assisted Multiuser MISO Systems Exploiting Deep Reinforcement Learning

Deep Reinforcement Learning Based Joint Downlink Beamforming and RIS Configuration in RIS-aided MU-MISO Systems Under Hardware Impairments and Imperfect CSI


This blog post visualize vector norms of FastText embedding and evaluates use of FastText word vector norm multiplied with number of word n-grams for detecting non-english OOV words.

Enriching Word Vectors with Subword Information

Measuring Word Significance using Distributed Representations of Words

Don't Settle for Average, Go for the Max: Fuzzy Sets and Max-Pooled Word Vectors


Graph matching and clustering by comparing heat kernels via optimal transport.

Generalized Spectral Clustering via Gromov-Wasserstein Learning

A Convergent Single-Loop Algorithm for Relaxation of Gromov-Wasserstein in Graph Data


An opensource TAR framework for experiments and applications

On Minimizing Cost in Legal Document Review Workflows

Proceedings of the 21st ACM Symposium on Document Engineering

TARexp: A Python Framework for Technology-Assisted Review Experiments

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


Preference Completion: Large-scale Collaborative Ranking from Pairwise Comparisons

Advances in Collaborative Filtering and Ranking

A Harmonic Extension Approach for Collaborative Ranking


Training wheels, side rails, and helicopter parent for your Deep Learning projects in PyTorch

UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

Universal Language Model Fine-tuning for Text Classification

A System for Massively Parallel Hyperparameter Tuning

Continual spatio-temporal graph convolutional networks


This page is a companion for our paper on overfitting and underfitting of community detection methods on real networks, written by Amir Ghasemian, Homa Hosseinmardi, and Aaron Clauset. (arXiv:1802.10582)

Evaluating Overfit and Underfit in Models of Network Community Structure

IEEE Transactions on Knowledge and Data Engineering

Stacking models for nearly optimal link prediction in complex networks

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

Community structure: A comparative evaluation of community detection methods


Simulation tools for plasma chemistry

On the quasi-stationary approach to solve the electron Boltzmann equation in pulsed plasmas

The 2021 release of the Quantemol database (QDB) of plasma chemistries and reactions

Comparison between 1D radial and 0D global models for low-pressure oxygen DC glow discharges

Charged-particle transport models for global models

Particle Propagation and Electron Transport in Gases


NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean

The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis

Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments

Light Intensity Modulates the Functional Composition of Leaf Metabolite Groups and Phyllosphere Prokaryotic Community in Garden Lettuce (Lactuca sativa L.) Plants at the Vegetative Stage

International journal of molecular sciences

Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean

Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland


A 3'-end adapter contaminant trimmer

AdapterRemoval v2: rapid adapter trimming, identification, and read merging

Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver

Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts

The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy

Zenodo (CERN European Organization for Nuclear Research)

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

Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum

Sequencing the transcriptome of milk production: milk trumps mammary tissue

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

Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

Synthetic and Evolutionary Construction of a Chlorate-Reducing Shewanella oneidensis MR-1


Parallel (asynchronous) sparse coding implementation for obtaining sparse overcomplete word vectors

Sparse Overcomplete Word Vector Representations

A Generative Word Embedding Model and its Low Rank Positive Semidefinite Solution

PSDVec: a Toolbox for Incremental and Scalable Word Embedding

Neural-based Noise Filtering from Word Embeddings

Sparse Lifting of Dense Vectors: Unifying Word and Sentence Representations


An R package for creating mirrored Manhattan plots

Investigation of Autosomal Genetic Sex Differences in Parkinson's Disease

A unified framework identifies new links between plasma lipids and diseases from electronic medical records across large-scale cohorts

GALCvariants affect galactosylceramidase enzymatic activity and risk of Parkinson's disease

Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults

Medical data and machine learning improve power of stroke genome-wide association studies


WHAT-IF (Water, Hydropower, Agriculture Tool for Investment and Financing) decision support tool

WHAT-IF: an open-source decision support tool for water infrastructure investment planning within the water–energy–food–climate nexus

Nexus vs. Silo Investment Planning Under Uncertainty


Supervised Predictive Medical Image Registration Model

DeepFLASH: An Efficient Network for Learning-based Medical Image Registration

Fourier-Net: Fast Image Registration with Band-limited Deformation

Fourier-Net+: Leveraging Band-Limited Representation for Efficient 3D Medical Image Registration


Imputation of single cell RNA-sequencing data with autoencoder

Imputation of single-cell gene expression with an autoencoder neural network

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

基因组蛋白质组与生物信息学报

Imputation Methods for scRNA Sequencing Data

An Overview of Algorithms and Associated Applications for Single Cell RNA-Seq Data Imputation


NLP pipelines for Tagalog using spaCy

Developing a Named Entity Recognition Dataset for Tagalog


Code for the CoNLL 2019 paper "Compositional Generalization in Image Captioning" by Mitja Nikolaus, Mostafa Abdou, Matthew Lamm, Rahul Aralikatte and Desmond Elliott

Show, Attend and Tell: Neural Image Caption Generation with Visual Attention

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

VSE++: Improving Visual-Semantic Embeddings with Hard Negatives

Conference on Computational Natural Language Learning


Unsupervised Domain Adaptation Augmented by Mutually Boosted Attention for Semantic Segmentation of VHR Remote Sensing Images

IEEE Transactions on Geoscience and Remote Sensing

SAM-Assisted Remote Sensing Imagery Semantic Segmentation with Object and Boundary Constraints

Frequency Decomposition-Driven Unsupervised Domain Adaptation for Remote
  Sensing Image Semantic Segmentation

RS3Mamba: Visual State Space Model for Remote Sensing Images Semantic
  Segmentation


Calculate perplexity on a text with pre-trained language models. Support MLM (eg. DeBERTa), recurrent LM (eg. GPT3), and encoder-decoder LM (eg. Flan-T5).

Language Models are Few-Shot Learners

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

Scope is all you need: Transforming LLMs for HPC Code


An artificial neural network framework for emotion expression recognition which self-regulates the interplay between generalized and personalized emotion perception

The FaceChannel: A Light-weight Deep Neural Network for Facial Expression Recognition

IEEE International Conference on Automatic Face & Gesture Recognition

A Deep Neural Model Of Emotion Appraisal

The FaceChannelS: Strike of the Sequences for the AffWild 2 Challenge


A Universal Music Translation Network Implementation

Domain-Adversarial Training of Neural Networks

WaveNet: A Generative Model for Raw Audio

A Universal Music Translation Network


Miscellaneous functions for analysis of species association and niche overlap

Diet drives the gut microbiome composition and assembly processes in winter migratory birds in the Poyang Lake wetland, China

From the Sunlit to the Aphotic Zone: Assembly Mechanisms and Co-Occurrence Patterns of Protistan-Bacterial Microbiotas in the Western Pacific Ocean

Protistan-Bacterial Microbiota Exhibit Stronger Species Sorting and Greater Network Connectivity Offshore than Nearshore across a Coast-to-Basin Continuum

Herbivore camping reshapes the taxonomy, function and network of pasture soil microbial communities

A phylogenetic approach identifies patterns of beta diversity and floristic subregions of the Qinghai-Tibet Plateau

Establishment of an invasive snail Melanoides tuberculata (Müller, 1774) in a Sahelian urban reservoir in Ouagadougou, Burkina Faso


Conducting and Visualizing Specification Curve Analyses

Neural indicators of food cue reactivity, regulation, and valuation and their associations with body composition and daily eating behavior

Social Cognitive and Affective Neuroscience

Mindsets of conspiracy: A typology of affinities towards conspiracy myths in digital environments

Convergence: The International Journal of Research into New Media Technologies

Beyond Screen Time: Exploring the Associations between Types of Smartphone Use Content and Adolescents’ Social Relationships

International journal of environmental research and public health

Investigating Associations Between Screen Time and Symptomatology in Individuals With Serious Mental Illness: Longitudinal Observational Study

Be Yourself and Behave Appropriately: Exploring Associations Between Incongruent Personality States and Positive Affect, Tiredness, and Cognitive Performance


Transcriptomic tools to classify bladder tumours according to six published molecular classifications : Baylor, UNC, MDA, Lund, CIT-Curie, TCGA

A Consensus Molecular Classification of Muscle-invasive Bladder Cancer

NKG2A and PD-L1 expression panel predicts clinical benefits from adjuvant chemotherapy and PD-L1 blockade in muscle-invasive bladder cancer

Synergistic induction of tertiary lymphoid structures by chemoimmunotherapy in bladder cancer

Development of a Molecular-Subtype-Associated Immune Prognostic Signature That Can Be Recognized by MRI Radiomics Features in Bladder Cancer

Integrative tumour mutation burden with CD39 and PD-L1 for the prediction of response to PD-L1 blockade and adjuvant chemotherapy in muscle-invasive bladder cancer patients

Predictive molecular biomarkers for determining neoadjuvant chemosensitivity in muscle invasive bladder cancer

Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping


Imbalanced learning tool for imbalanced recognition and segmentation

Improving Calibration for Long-Tailed Recognition

Parametric Contrastive Learning

Vision GNN: An Image is Worth Graph of Nodes

ResLT: Residual Learning for Long-tailed Recognition

Generalized Parametric Contrastive Learning

Understanding Imbalanced Semantic Segmentation Through Neural Collapse

Region Rebalance for Long-Tailed Semantic Segmentation

Rebalanced Siamese Contrastive Mining for Long-Tailed Recognition


SNARE Dataset with MATCH and LaGOR models

Language Grounding with 3D Objects

Voxel-informed Language Grounding


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

Вестник компьютерных и информационных технологий

Learning Incompressible Fluid Dynamics from Scratch -- Towards Fast, Differentiable Fluid Models that Generalize

Spline-PINN: Approaching PDEs without Data using Fast, Physics-Informed Hermite-Spline CNNs

Teaching the incompressible Navier–Stokes equations to fast neural surrogate models in three dimensions


ACL 2021: Question Answering over Temporal Knowledge Graphs

Tensor Decompositions for temporal knowledge base completion

Question Answering Over Temporal Knowledge Graphs

ForecastTKGQuestions: A Benchmark for Temporal Question Answering and Forecasting over Temporal Knowledge Graphs


Source codes for X-STILT(NOx) [Wu et al., 2018, 2023] based on STILT-R version 2 [Fasoli et al., 2018] and STILT [Lin et al., 2003].

Space-based quantification of per capita CO2 emissions from cities

A Lagrangian Approach Towards Extracting Signals of Urban CO2
Emissions from Satellite Observations of Atmospheric Column CO2
(XCO2): X-Stochastic Time-Inverted Lagrangian Transport model ("X-STILT v1.1")

Towards sector-based attribution using intra-city variations in satellite-based emission ratios between CO2 and CO


Text-to-SQL Generation for Question Answering on Electronic Medical Records

Knowledge Graph-based Question Answering with Electronic Health Records

EHRAgent: Code Empowers Large Language Models for Complex Tabular Reasoning on Electronic Health Records

Question Answering for Complex Electronic Health Records Database using Unified Encoder-Decoder Architecture

Integrating question answering and text-to-SQL in Portuguese

Uncertainty-Aware Text-to-Program for Question Answering on Structured Electronic Health Records


LIBS2ML: A Library for Scalable Second Order Machine Learning Algorithms

ON THE USE OF STOCHASTIC HESSIAN INFORMATION IN OPTIMIZATION METHODS FOR MACHINE LEARNING

Stochastic trust region inexact Newton method for large-scale machine learning

International Journal of Machine Learning and Cybernetics


Densely Connected Graph Convolutional Networks for Graph-to-Sequence Learning (authors' MXNet implementation for the TACL19 paper)

Graph-to-Sequence Learning using Gated Graph Neural Networks

Neural AMR: Sequence-to-Sequence Models for Parsing and Generation


Code for "On Feature Collapse and Deep Kernel Learning for Single Forward Pass Uncertainty".

Simple and Principled Uncertainty Estimation with Deterministic Deep Learning via Distance Awareness

On the Practicality of Deterministic Epistemic Uncertainty

Training, Architecture, and Prior for Deterministic Uncertainty Methods

Beyond AUROC & co. for evaluating out-of-distribution detection performance


End-to-End Speech Recognition Using Tensorflow

Attention-Based Models for Speech Recognition

State-of-the-art Speech Recognition With Sequence-to-Sequence Models

Listen, Attend and Spell

On the Choice of Modeling Unit for Sequence-to-Sequence Speech Recognition

Attention-based sequence-to-sequence model for speech recognition: development of state-of-the-art system on LibriSpeech and its application to non-native English


Multi-CCD data-driven PSF modelling

Multi-CCD modelling of the point spread function

HAL (Le Centre pour la Communication Scientifique Directe)

Rethinking data-driven point spread function modeling with a differentiable optical model

Point spread function modelling for astronomical telescopes: a review focused on weak gravitational lensing studies

Frontiers in Astronomy and Space Sciences


[CVPR 2023 Highlight] Video-Text as Game Players: Hierarchical Banzhaf Interaction for Cross-Modal Representation Learning

Expectation-Maximization Contrastive Learning for Compact Video-and-Language Representations

DiffusionRet: Generative Text-Video Retrieval with Diffusion Model

Text-Video Retrieval with Disentangled Conceptualization and Set-to-Set Alignment


Official PyTorch implementation of "Railroad is not a Train: Saliency as Pseudo-pixel Supervision for Weakly Supervised Semantic Segmentation", CVPR2021

DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs

Wider or Deeper: Revisiting the ResNet Model for Visual Recognition

Pyramid Feature Attention Network for Saliency detection


The Codebase for Causal Distillation for Language Models (NAACL '22)

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

Inducing Causal Structure for Interpretable Neural Networks

ReaSCAN: Compositional Reasoning in Language Grounding

Causal Distillation for Language Models


Tools for processing treebank trees

Unlexicalized Transition-based Discontinuous Constituency Parsing

Neural Discontinuous Constituency Parsing

Empirical Methods in Natural Language Processing

Span-Based LCFRS-2 Parsing

International Workshop/Conference on Parsing Technologies

discoursegraphs: A graph-based merging tool and converter for multilayer annotated corpora

Nordic Conference of Computational Linguistics

Parsing German: How Much Morphology Do We Need?

Discosuite - A parser test suite for German discontinuous structures

Genres, Parsers, and BERT: The Interaction Between Parsers and BERT Models in Cross-Genre Constituency Parsing in English and Swedish


This is the official repository for Retrieval Augmented Visual Question Answering

Retrieval Augmented Visual Question Answering with Outside Knowledge

Fine-grained Late-interaction Multi-modal Retrieval for Retrieval Augmented Visual Question Answering

PreFLMR: Scaling Up Fine-Grained Late-Interaction Multi-modal Retrievers

FVQA 2.0: Introducing Adversarial Samples into Fact-based Visual Question Answering


JetSeT a framework for self-consistent modeling and fitting of  astrophysical relativistic jets

Multiwavelength study of the quiescent states of six brightest flat-spectrum radio quasars detected by Fermi-LAT

Monthly Notices of the Royal Astronomical Society

Multi-messenger characterization of Mrk501 during historically low X-ray and gamma-ray activity

The Astrophysical Journal Supplement Series

Radio-γ-ray response in blazars as a signature of adiabatic blob expansion

Broadband modelling of Orphan gamma ray flares

Temporal and spectral study of PKS B1222 + 216 flares in 2014

Monthly notices of the Royal Astronomical Society

A model-driven search for extreme BL Lacs among LAT BCU

Proceedings of 37th International Cosmic Ray Conference — PoS(ICRC2021)


Creative Commons Attribution Share Alike 4.0 International

The FLORES+ Machine Translation Benchmark

IndicTrans2: Towards High-Quality and Accessible Machine Translation Models for all 22 Scheduled Indian Languages

Machine Translation for Nko: Tools, Corpora and Baseline Results

Pushing the Limits of Zero-shot End-to-End Speech Translation

Curated Datasets and Neural Models for Machine Translation of Informal Registers between Mayan and Spanish Vernaculars


Official implementation of MCVD: Masked Conditional Video Diffusion for Prediction, Generation, and Interpolation (https://arxiv.org/abs/2205.09853)

Pseudo Numerical Methods for Diffusion Models on Manifolds

Non Gaussian Denoising Diffusion Models

LDMVFI: Video Frame Interpolation with Latent Diffusion Models

Physion++: Evaluating Physical Scene Understanding that Requires Online Inference of Different Physical Properties

A Control-Centric Benchmark for Video Prediction


Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis

Origin and adaptation to high altitude of Tibetan semi-wild wheat

Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil

Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments

Genomic insights into the evolution of Echinochloa species as weed and orphan crop

Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research

The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability

Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs

Population history provides foundational knowledge for utilizing and developing native plant restoration materials


Multidocument Summarization for Literature Review Shared Task 2022

BERTScore: Evaluating Text Generation with BERT

MSˆ2: Multi-Document Summarization of Medical Studies

Generating (Factual?) Narrative Summaries of RCTs: Experiments with Neural Multi-Document Summarization

Automated Metrics for Medical Multi-Document Summarization Disagree with Human Evaluations

Artificial Intelligence for Literature Reviews: Opportunities and
  Challenges

Overview of MSLR2022: A Shared Task on Multi-document Summarization for Literature Reviews

LED down the rabbit hole: exploring the potential of global attention for biomedical multi-document summarisation

An Extractive-Abstractive Approach for Multi-document Summarization of Scientific Articles for Literature Review


Statistical method for measuring modified GW propagation and Hubble parameter with dark sirens and galaxy catalogues

Cosmology with the Laser Interferometer Space Antenna

Cosmology with LIGO/Virgo dark sirens: Hubble parameter and modified gravitational wave propagation

ICAROGW: A python package for inference of astrophysical population properties of noisy, heterogeneous, and incomplete observations


These Python notebooks reproduce some figures in the following preprint using the libraries pyMOU and NetDynFlow: https://www.biorxiv.org/content/10.1101/531830v2

Functional connectivity in resting-state fMRI: Is linear correlation sufficient?

Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome

Effective connectivity inferred from fMRI transition dynamics during movie viewing points to a balanced reconfiguration of cortical interactions

Model-based whole-brain effective connectivity to study distributed cognition in health and disease

Extracting orthogonal subject- and condition-specific signatures from fMRI data using whole-brain effective connectivity


Code for our ACL 2021 paper - ConSERT: A Contrastive Framework for Self-Supervised Sentence Representation Transfer

Differentiable Data Augmentation for Contrastive Sentence Representation Learning

Unsupervised Sentence Representation Learning with Frequency-induced Adversarial Tuning and Incomplete Sentence Filtering

A Low-Cost, Controllable and Interpretable Task-Oriented Chatbot: With Real-World After-Sale Services as Example


Pytorch implementation of the paper Deep learning for extreme multi-label text classification

A Survey on Text Classification: From Shallow to Deep Learning

Extreme Classification via Adversarial Softmax Approximation

Large-scale Stochastic Optimization of NDCG Surrogates for Deep Learning with Provable Convergence

A Survey on Extreme Multi-label Learning


Universal Physical Camouflage Attacks on Object Detectors

ACTIVE: Towards Highly Transferable 3D Physical Camouflage for Universal and Robust Vehicle Evasion

Physical Adversarial Attacks for Camera-Based Smart Systems: Current Trends, Categorization, Applications, Research Challenges, and Future Outlook


DFOIL: Introgression Testing for Five Taxa

The rice paradox: Multiple origins but single domestication in Asian rice

Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus

Genetic homogenization of the nuclear ITS loci across two morphologically distinct gentians in their overlapping distributions in the Qinghai-Tibet Plateau

Selection and gene flow define polygenic barriers between incipient butterfly species

Speciation in sympatry with ongoing secondary gene flow and an olfactory trigger in a radiation of Cameroon cichlids


Code for the Neural Processes website and replication of 4 papers on NPs. Pytorch implementation.

Meta-Learning Stationary Stochastic Process Prediction with Convolutional Neural Processes

Conditional Image Generation by Conditioning Variational Auto-Encoders

Learning Objective-Specific Active Learning Strategies with Attentive Neural Processes


Convolutional Recurrent Neural Networks for Music Classification

Automatic tagging using deep convolutional neural networks

Semi-supervised Music Tagging Transformer


DCEKit (Data Chemical Engineering toolKit)

Cross‐validated permutation feature importance considering correlation between features

Interpretation of Machine Learning Models for Data Sets with Many Features Using Feature Importance

Molecular Descriptors, Structure Generation, and Inverse QSAR/QSPR Based on SELFIES

Genetic Algorithm-Based Partial Least-Squares with Only the First Component for Model Interpretation

Development of Prediction Models for the Self-Accelerating Decomposition Temperature of Organic Peroxides

Support vector regression that takes into consideration the importance of explanatory variables

True Gaussian mixture regression and genetic algorithm-based optimization with constraints for direct inverse analysis

Science and Technology of Advanced Materials: Methods

Predictive Modeling of HMG-CoA Reductase Inhibitory Activity and Design of New HMG-CoA Reductase Inhibitors


R Package for Single-Cell Dataset Processing and Visualization

Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted murine heart

Expression and regulatory characteristics of peripheral blood immune cells in primary Sjögren’s syndrome patients using single-cell transcriptomic

Single-cell evaluation reveals shifts in the tumor-immune niches that shape and maintain aggressive lesions in the breast

An integrative analysis of single-cell and bulk transcriptome and bidirectional mendelian randomization analysis identified C1Q as a novel stimulated risk gene for Atherosclerosis

Exploring the Role of Neutrophil-Related Genes in Osteosarcoma via an Integrative Analysis of Single-Cell and Bulk Transcriptome


An R Package for Importing Data from Our World in Data


Code for "Typilus: Neural Type Hints" PLDI 2020

Typilus: neural type hints

Programming Language Design and Implementation

Type4Py: Practical Deep Similarity Learning-Based Type Inference for Python

Proceedings of the 44th International Conference on Software Engineering

HiTyper: A Hybrid Static Type Inference Framework with Neural Prediction.


Detection-based astronomical image registration.

The Gravitational-wave Optical Transient Observer (GOTO): prototype performance and prospects for transient science

Studying the environment of AT 2018cow with MUSE

Transient-optimized real-bogus classification with Bayesian convolutional neural networks - sifting the GOTO candidate stream

Searching for Fermi GRB optical counterparts with the prototype Gravitational-wave Optical Transient Observer (GOTO)


R interface to the Greek National Data Bank for Hydrometeorological Information

hydroscoper: R interface to the Greek National Data Bank for Hydrological and Meteorological Information

ropensci/hydroscoper: hydroscoper 1.0.0


This repo contains evaluation code for the paper "MMMU: A Massive Multi-discipline Multimodal Understanding and Reasoning Benchmark for Expert AGI"

Vision-Flan: Scaling Human-Labeled Tasks in Visual Instruction Tuning

MuirBench: A Comprehensive Benchmark for Robust Multi-image
  Understanding


[NeurIPS 2023] DeepACO: Neural-enhanced Ant Systems for Combinatorial Optimization

RL4CO: an Extensive Reinforcement Learning for Combinatorial Optimization Benchmark

Ant Colony Sampling with GFlowNets for Combinatorial Optimization


Tools to analyze Dip-C (or other 3C/Hi-C) data

Lifelong restructuring of 3D genome architecture in cerebellar granule cells

Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice

Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization

RNA-mediated symmetry breaking enables singular olfactory receptor choice

Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice

Determining the 3D genome structure of a single mammalian cell with Dip-C


Functions for single cell data analysis

Trophoblast Cell Subtypes and Dysfunction in the Placenta of Individuals with Preeclampsia Revealed by Single-Cell RNA Sequencing

Diversity and heterogeneity in human breast cancer adipose tissue revealed at single-nucleus resolution

An advanced comprehensive muti-cell-type-specific model for predicting anti-PD-1 therapeutic effect in melanoma


Hanzi Converter for Traditional and Simplified Chinese

Beyond English-Centric Multilingual Machine Translation

m^4Adapter: Multilingual Multi-Domain Adaptation for Machine Translation with a Meta-Adapter

Character Mapping and Ad-hoc Adaptation: Edinburgh’s IWSLT 2020 Open Domain Translation System

Proceedings of the 17th International Conference on Spoken Language Translation

Hansel: A Chinese Few-Shot and Zero-Shot Entity Linking Benchmark

2kenize: Tying Subword Sequences for Chinese Script Conversion

Kakao Enterprise’s WMT21 Machine Translation Using Terminologies Task Submission

Papago’s Submissions to the WMT21 Triangular Translation Task

ISTIC’s Triangular Machine Translation System for WMT2021


PyTorch implementation of LeNet-5 with live visualization

No Subclass Left Behind: Fine-Grained Robustness in Coarse-Grained Classification Problems

Practices and Applications of Convolutional Neural Network-Based Computer Vision Systems in Animal Farming: A Review

Loss Surface Simplexes for Mode Connecting Volumes and Fast Ensembling

Fast Adaptation with Linearized Neural Networks

G2R Bound: A Generalization Bound for Supervised Learning from GAN-Synthetic Data


A wrapper class for the scikit-learn BaseEstimator class that implements both the astroML and Bovy et al. (2011) XDGMM methods.

The contribution of N-rich stars to the Galactic stellar halo using APOGEE red giants

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

The stellar halo of the Milky Way traced by blue horizontal-branch stars
  in the Subaru Hyper Suprime-Cam Survey

Galactic double neutron star total masses and Gaussian mixture model selection

Paving the Way for Euclid and JWST via Optimal Selection of High-z Quasars

The VVV open cluster project II. Near-infrared sequences of 37 open clusters on eight-dimensional parameter space


code for Graph Neural Networks for Link Prediction with Subgraph Sketching https://arxiv.org/abs/2209.15486

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

Revisiting Link Prediction: A Data Perspective

Simplifying Subgraph Representation Learning for Scalable Link Prediction


Audio-based AI classifiers show no evidence of improved COVID-19 screening over simple symptoms checkers

A large-scale and PCR-referenced vocal audio dataset for COVID-19

The UK COVID-19 Vocal Audio Dataset

Zenodo (CERN European Organization for Nuclear Research)


Mapping astronomical survey data on the sky, handsomely

Dark Energy Survey Year 1 results: Cosmological constraints from cosmic shear

Dark Energy Survey Year 1 results: curved-sky weak lensing mass map

Dark Energy Survey Year 1 results: the impact of galaxy neighbours on weak lensing cosmology with IM3SHAPE

On the relative bias of void tracers in the Dark Energy Survey

Improving weak lensing mass map reconstructions using Gaussian and sparsity priors: application to DES SV

The Dark Energy Survey Year 3 and eBOSS: constraining galaxy intrinsic alignments across luminosity and colour space

KaRMMa 2.0 -- Kappa Reconstruction for Mass Mapping

Dark Energy Survey Year 1 Results: Wide-field mass maps via forward fitting in harmonic space

Detection and removal of B-mode dust foregrounds with signatures of statistical anisotropy


Julia package that downloads satellite measurements and observational data


Image analysis for plasma physics

Laser-Produced Magnetic-Rayleigh-Taylor Unstable Plasma Slabs in a 20 T Magnetic Field

Laser-driven shock compression of “synthetic planetary mixtures” of water, ethanol, and ammonia

Characterizing equation of state and optical properties of dynamically pre-compressed materials

Laboratory radiative accretion shocks on GEKKO XII laser facility for POLAR project


Elegant implementations of offline safe RL algorithms in PyTorch

Constrained Decision Transformer for Offline Safe Reinforcement Learning

Datasets and Benchmarks for Offline Safe Reinforcement Learning

A Survey of Constraint Formulations in Safe Reinforcement Learning

Uncertainty-Aware Decision Transformer for Stochastic Driving Environments

Temporal Logic Specification-Conditioned Decision Transformer for
  Offline Safe Reinforcement Learning


Attentive Group Recommendation

ConsRec: Learning Consensus Behind Interactions for Group Recommendation

Deep Reinforcement Learning based Group Recommender System

DeepGroup: Representation Learning for Group Recommendation with Implicit Feedback


Create future EnergyPlus Weather files using CMIP6 data

Elastic buildings: Calibrated district-scale simulation of occupant-flexible campus operation for hybrid work optimization


A semi-analytical satellite galaxy and dark matter halo generator

SatGen: a semi-analytical satellite galaxy generator – I. The model and its application to Local-Group satellite statistics

The tidal evolution of dark matter substructure – II. The impact of artificial disruption on subhalo mass functions and radial profiles

SMBH seeds from dissipative dark matter

Journal of Cosmology and Astroparticle Physics

ELVES. IV. The Satellite Stellar-to-halo Mass Relation Beyond the Milky Way

SatGen -- II. Assessing the impact of a disc potential on subhalo populations

Core formation in high-z massive haloes: heating by post-compaction satellites and response to AGN outflows

Dynamics of stellar disc tilting from satellite mergers


Active Learning on a Budget - Opposite Strategies Suit High and Low Budgets

Active Learning on a Budget: Opposite Strategies Suit High and Low Budgets

Active Learning Through a Covering Lens

Exploring Active Learning in Meta-Learning: Enhancing Context Set Labeling


VMC: a Scalable, Open Source and Free Vulnerability Management Platform

Vulnerability Management Models Using a Common Vulnerability Scoring System

Efficient Algorithm for Providing Live Vulnerability Assessment in Corporate Network Environment


Combining SchNet and SHARC: The SchNarc Machine Learning Approach for Excited-State Dynamics

The journal of physical chemistry letters

Deep learning for UV absorption spectra with SchNarc: First steps toward transferability in chemical compound space

Physically inspired deep learning of molecular excitations and photoemission spectra

High-throughput property-driven generative design of functional organic molecules


Classifies galaxy morphology with Bayesian CNN

Galaxy Zoo DECaLS: Detailed Visual Morphology Measurements from Volunteers and Deep Learning for 314,000 Galaxies

Practical galaxy morphology tools from deep supervised representation learning

Galaxy Zoo DESI: Detailed morphology measurements for 8.7M galaxies in the DESI Legacy Imaging Surveys

A Comparison of Deep Learning Architectures for Optical Galaxy Morphology Classification

Radio galaxy zoo EMU: Towards a semantic radio galaxy morphology taxonomy

Scaling Laws for Galaxy Images

Galaxy Zoo DESI: Detailed Morphology Classifications for 8.7M Galaxies in the DESI Legacy Imaging Surveys


Partially Observable Process Gym

Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling

Playing Atari with Deep Reinforcement Learning

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

On the Parameterization and Initialization of Diagonal State Space Models

POPGym: Benchmarking Partially Observable Reinforcement Learning


Official repository for Paper "Offline Goal-Conditioned Reinforcement Learning via f-Advantage Regression" (NeurIPS 2022)

From Play to Policy: Conditional Behavior Generation from Uncurated Robot Data

How Far I'll Go: Offline Goal-Conditioned Reinforcement Learning via f-Advantage Regression

Swapped goal-conditioned offline reinforcement learning

Learning to Reach Goals via Diffusion


Coronavirus (SARS-Cov-2) sequencing analysis

Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing

Whole‐genome sequencing of SARS‐CoV‐2: Comparison of target capture and amplicon single molecule real‐time sequencing protocols

SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing

VCFCons: a versatile VCF-based consensus sequence generator for small genomes


Thermochemical Equilibrium Abundances (TEA), a code to calculate gaseous molecular abundances under thermochemical equilibrium conditions

Equilibrium chemistry down to 100 K. Impact of silicates and phyllosilicates on the carbon to oxygen ratio

TEA: A CODE CALCULATING THERMOCHEMICAL EQUILIBRIUM ABUNDANCES

The Implications of 3D Thermal Structure on 1D Atmospheric Retrieval

The composition of hot Jupiter atmospheres assembled within chemically evolved protoplanetary discs

An Open-Source Bayesian Atmospheric Radiative Transfer (BART) Code: I. Design, Tests, and Application to Exoplanet HD 189733 b

An Open-source Bayesian Atmospheric Radiative Transfer (BART) Code. III. Initialization, Atmospheric Profile Generator, Post-processing Routines

Sulfur dioxide in the mid-infrared transmission spectrum of WASP-39b

Characterizing Exoplanet Atmospheres: From Light-curve Observations to Radiative-transfer Modeling

Observations, Thermochemical Calculations, and Modeling of Exoplanetary Atmospheres

Toward More Reliable Analytic Thermochemical-equilibrium Abundances


UTMOST (unified test for molecular signatures) is a method for cross-tissue gene expression imputation for transcriptome-wide association analyses.

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study

A tissue-specific collaborative mixed model for jointly analyzing multiple tissues in transcriptome-wide association studies

UTMOST, a single and cross-tissue TWAS (Transcriptome Wide Association Study), reveals new ASD (Autism Spectrum Disorder) associated genes

Cross-tissue transcriptome-wide association studies identify susceptibility genes shared between schizophrenia and inflammatory bowel disease

Innovative strategies for annotating the “relationSNP” between variants and molecular phenotypes

Biomarker and genomic analyses reveal molecular signatures of non-cardioembolic ischemic stroke

Influence of tissue context on gene prioritization for predicted transcriptome-wide association studies

Genetic determinants of IgG antibody response to COVID-19 vaccination

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


This small deep learning dataset was developed for research on biologically plausible error-backpropagation and deep learning in spiking neural networks.

Fast and energy-efficient neuromorphic deep learning with first-spike times

Event-based backpropagation can compute exact gradients for spiking neural networks

The Yin-Yang dataset

Learning efficient backprojections across cortical hierarchies in real time


Dust maps in the Milky Way

ON GALACTIC DENSITY MODELING IN THE PRESENCE OF DUST EXTINCTION

Weighing the stellar constituents of the galactic halo with APOGEE red giant stars

Faraday tomography of the local interstellar medium with LOFAR: Galactic foregrounds towards IC 342

Stellar chromospheric activity of 1674 FGK stars from the AMBRE-HARPS sample

Old, Metal-poor Extreme Velocity Stars in the Solar Neighborhood

A Gaia DR2 Mock Stellar Catalog

Publications of the Astronomical Society of the Pacific

The Splashback Radius of Planck SZ Clusters

A 'Quick Look' at All-Sky Galactic Archeology with TESS: 158,000 Oscillating Red Giants from the MIT Quick-Look Pipeline

The tale of the tail - disentangling the high transverse velocity stars in Gaia DR2

Prospects for Galactic and stellar astrophysics with asteroseismology of giant stars in the TESS continuous viewing zones and beyond


FedEval: A Holistic Evaluation Framework for Federated Learning

Practical Lossless Federated Singular Vector Decomposition over Billion-Scale Data

A Survey for Federated Learning Evaluations: Goals and Measures


Code to compute ionization field from density fields and source catalogue (CIFOG)

Astraeus I: the interplay between galaxy formation and reionization

The accuracy of seminumerical reionization models in comparison with radiative transfer simulations

The 21 cm bispectrum during reionization: a tracer of the ionization topology

The escape fraction of ionizing photons during the Epoch of Reionization: observability with the Square Kilometre Array

A short introduction to reionization physics


Rotation-Based Iterative Gaussianization algorithm.

Iterative Gaussianization: From ICA to Random Rotations

Information Theory Measures via Multidimensional Gaussianization

Information Theory in Density Destructors

Gaussianizing the Earth: Multidimensional Information Measures for Earth Data Analysis

Geostatistics in the Presence of Multivariate Complexities: Comparison of Multi-Gaussian Transforms


A robust way to calculate line-of-sight velocities.

Meridional flows in the disk around a young star

A Robust Method to Measure Centroids of Spectral Lines

Spiral Structure in the Gas Disk of TW Hya

The TW Hya Rosetta Stone Project. III. Resolving the Gaseous Thermal Profile of the Disk

Molecules with ALMA at Planet-forming Scales (MAPS). XVII. Determining the 2D Thermal Structure of the HD 163296 Disk

Mapping the 3D Kinematical Structure of the Gas Disk of HD 169142

Observability of the vertical shear instability in protoplanetary disk CO kinematics

Mapping the Complex Kinematic Substructure in the TW Hya Disk

bettermoments: A robust method to measure line centroids

Early Planet Formation in Embedded Disks (eDisk). III. A First High-resolution View of Submillimeter Continuum and Molecular Line Emission toward the Class 0 Protostar L1527 IRS


allesfitter is a convenient wrapper around the packages ellc (light curve and RV models), dynesty (static and dynamic nested sampling) emcee (Markov Chain Monte Carlo sampling) and celerite (Gaussian Process models).

Stellar Flares from the First TESS Data Release: Exploring a New Sample of M Dwarfs

Allesfitter: Flexible Star and Exoplanet Inference from Photometry and Radial Velocity

Complex Rotational Modulation of Rapidly Rotating M Stars Observed with TESS

The Aligned Orbit of the Eccentric Warm Jupiter K2-232b

TOI 694b and TIC 220568520b: Two Low-mass Companions near the Hydrogen-burning Mass Limit Orbiting Sun-like Stars

HD 191939: Three Sub-Neptunes Transiting a Sun-like Star Only 54 pc Away

Long-term stellar activity variations and their effect on radial-velocity measurements

NGTS-8b and NGTS-9b: two non-inflated hot-Jupiters

A sub-Neptune transiting the young field star HD 18599 at 40 pc


Canonical Correlation Analysis Zoo: A collection of Regularized, Deep Learning based, Kernel, and Probabilistic methods in a scikit-learn style framework

Deep Generalized Canonical Correlation Analysis

An iterative penalized least squares approach to sparse canonical correlation analysis

Deep Tensor CCA for Multi-view Learning

Tensor Canonical Correlation Analysis for Multi-view Dimension Reduction

Learning Representations without Compositional Assumptions


A repository for financial fraud detection

Credit Card Fraud Detection Using Convolutional Neural Networks

NEURAL INFORMATION PROCESSING, ICONIP 2016, PT III

Graph Neural Network for Fraud Detection via Spatial-Temporal Attention

IEEE Transactions on Knowledge and Data Engineering

Spatio-Temporal Attention-Based Neural Network for Credit Card Fraud Detection

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

Semi-supervised Credit Card Fraud Detection via Attribute-Driven Graph Representation

THIRTY-SEVENTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, VOL 37 NO 12


Single-cell data analysis

A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation

Efficient and scalable integration of single-cell data using domain-adversarial and variational approximation

Scbean: a python library for single-cell multi-omics data analysis


NRG Ljubljana is a numerical renormalization group implementation for solving quantum impurity problems in theoretical physics

Iron phthalocyanine on Au(111) is a "non-Landau" Fermi liquid

Topological quantum phase transition of nickelocene on Cu(100)

Josephson potentials for single impurity Anderson impurity in a junction between two superconductors


Python library for computing Finite-Amplitude Local Wave Activity Diagnostics from climate data.

Atmospheric blocking as a traffic jam in the jet stream

Local Finite-Amplitude Wave Activity as a Diagnostic of Anomalous Weather Events


A survey of known lower bounds in arithmetic circuits.

On the complexity of partial derivatives

On Algebraic Branching Programs of Small Width

Succinct Hitting Sets and Barriers to Proving Algebraic Circuits Lower Bounds

An exponential lower bound for homogeneous depth-5 circuits over finite fields

Geometric complexity theory and matrix powering

Unbalancing Sets and An Almost Quadratic Lower Bound for Syntactically Multilinear Arithmetic Circuits

A Near-Optimal Depth-Hierarchy Theorem for Small-Depth Multilinear Circuits

The Chasm at Depth Four, and Tensor Rank : Old results, new insights

Ideals, determinants, and straightening: proving and using lower bounds for polynomial ideals

On geometric complexity theory: Multiplicity obstructions are stronger than occurrence obstructions


Energy System Description Language


An integrated high performance bioinformatics toolkit

Molecular identification of the wheat male fertility gene Ms1 and its prospects for hybrid breeding

Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy

Reproductive Stage Drought Tolerance in Wheat: Importance of Stomatal Conductance and Plant Growth Regulators

Genetic Identification and Transcriptome Analysis of Lintless and Fuzzless Traits in Gossypium arboreum L.

International journal of molecular sciences

Characterization and Genetic Mapping of Black Root Rot Resistance in Gossypium arboreum L.


Measuring the atmospheric neutrino oscillation parameters and constraining the 3+1 neutrino model with ten years of ANTARES data

Letter of interest for a neutrino beam from Protvino to KM3NeT/ORCA

Sensitivity to light sterile neutrino mixing parameters with KM3NeT/ORCA

Unveiling the outer core composition with neutrino oscillation tomography

Super-ORCA: Measuring the leptonic CP-phase with Atmospheric Neutrinos and Beam Neutrinos

Neutrino tagging: a new tool for accelerator based neutrino experiments

The ANTARES Collaboration: Contributions to ICRC 2017 Part III: Searches for dark matter and exotics, neutrino oscillations and detector calibration


Load fMRIprep confounds in python

Methods to detect, characterize, and remove motion artifact in resting state fMRI

fMRIPrep: a robust preprocessing pipeline for functional MRI

ICA-AROMA: A robust ICA-based strategy for removing motion artifacts from fMRI data

Benchmarking of participant-level confound regression strategies for the control of motion artifact in studies of functional connectivity

An evaluation of the efficacy, reliability, and sensitivity of motion correction strategies for resting-state functional MRI

Evaluation of denoising strategies for task‐based functional connectivity: Equalizing residual motion artifacts between rest and cognitively demanding tasks

Improved motion correction for functional MRI using an omnibus regression model

A reproducible benchmark of resting-state fMRI denoising strategies using fMRIPrep and Nilearn

Alignment of auditory artificial networks with massive individual fMRI brain data leads to generalizable improvements in brain encoding and downstream tasks


A belief propagation decoder for low density parity check (LDPC) codes

Toward Low-latency Iterative Decoding of QLDPC Codes Under Circuit-Level
  Noise

Analog information decoding of bosonic quantum LDPC codes

Decoding algorithms for surface codes


An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

Peptides: A Package for Data Mining of Antimicrobial Peptides

HeMoQuest: a webserver for qualitative prediction of transient heme binding to protein motifs

Genome-Wide Identification and Comparative Analysis for OPT Family Genes in Panax ginseng and Eleven Flowering Plants

Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins

Bottom-Up Design Approach for OBOC Peptide Libraries

TNKPVI, a Putative Bioaccessible Pharmacophore of Anti-Inflammatory Potato Patatin-Derived Decapeptide DIKTNKPVIF

Functional evolution of SARS-CoV-2 spike protein: Maintaining wide host spectrum and enhancing infectivity via surface charge of spike protein

Computational and structural biotechnology journal

Accelerating the Screening of Small Peptide Ligands by Combining Peptide-Protein Docking and Machine Learning

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


Algorithms for computations on random manifolds made easier

Pulling back information geometry

Laplacian Autoencoders for Learning Stochastic Representations

Neural Optimal Transport with Lagrangian Costs

Laplacian Segmentation Networks Improve Epistemic Uncertainty Quantification

Identifying latent distances with Finslerian geometry

Implicit Variational Inference for High-Dimensional Posteriors


Pipeline for Analysing Lesions after Stroke (PALS) is a scalable and user-friendly toolbox designed to facilitate standardised analysis and ensure quality in stroke research using T1-weighted MRIs

ENIGMA and Global Neuroscience: A Decade of Large-Scale Studies of the Brain in Health and Disease Across More Than 40 Countries

A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms

The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain-behavior relationships after stroke

A comparison of automated lesion segmentation approaches for chronic stroke T1-weighted MRI data

Pipeline for Analyzing Lesions After Stroke (PALS)

Management and Quality Control of Large Neuroimaging Datasets: Developments From the Barcelonaβeta Brain Research Center


Run the PACTA analysis on EQ & CB portfolios


A cloud platform for greenhouse gas (GHG) data analysis and collaboration.


Grid-based workflow management system for lattice field theory simulations

Using Gradient Flow to Renormalise Matrix Elements for Meson Mixing and Lifetimes

Inclusive semi-leptonic decays of charmed mesons with Möbius domain wall fermions

2+1 flavor fine lattice simulation at finite temperature with domain-wall fermions

BSM B - B̅ mixing on JLQCD and RBC/UKQCD N_f=2+1 DWF ensembles

K π scattering at physical pion mass using distillation


TTK data examples

Localized Topological Simplification of Scalar Data

Topological Analysis of Ensembles of Hydrodynamic Turbulent Flows An Experimental Study

A Progressive Approach to Scalar Field Topology

IEEE transactions on visualization and computer graphics

Parallel Computation of Piecewise Linear Morse-Smale Segmentations

Fast Approximation of Persistence Diagrams with Guarantees

Cinema Darkroom: A Deferred Rendering Framework for Large-Scale Datasets

TTK is Getting MPI-Ready


High performance radio data processing pipeline

A Synoptic VLBI Technique for Localizing Nonrepeating Fast Radio Bursts with CHIME/FRB

Localizing FRBs through VLBI with the Algonquin Radio Observatory 10 m Telescope

TONE: A CHIME/FRB Outrigger Pathfinder for localizations of Fast Radio Bursts using Very Long Baseline Interferometry


LayoutLM: Pre-training of Text and Layout for Document Image Understanding

Cutting the Error by Half: Investigation of Very Deep CNN and Advanced Training Strategies for Document Image Classification

International Conference on Document Analysis and Recognition

Document Image Classification with Intra-Domain Transfer Learning and Stacked Generalization of Deep Convolutional Neural Networks

Modular Multimodal Architecture for Document Classification


Computationally friendly hyper-parameter search with DP-SGD

TAN Without a Burn: Scaling Laws of DP-SGD

Differentially Private Image Classification by Learning Priors from Random Processes

DP-Mix: Mixup-based Data Augmentation for Differentially Private Learning


A novel Multimodal Large Language Model (MLLM) architecture, designed to structurally align visual and textual embeddings.

Ovis: Structural Embedding Alignment for Multimodal Large Language Model

Parrot: Multilingual Visual Instruction Tuning


collection of scripts and commands used by Ian Korf, Keith Bradnam, and Joe Fass in the analysis of Assemblathon 2 entries (assemblies)

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

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

Convergent molecular evolution among ash species resistant to the emerald ash borer

The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders

Genome survey and microsatellite motif identification of Pogonophryne albipinna

CRISPR/Cas9-Based Knock-Out of the PMR4 Gene Reduces Susceptibility to Late Blight in Two Tomato Cultivars

Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research


[ACL 20] TACRED Revisited: A Thorough Evaluation of the TACRED Relation Extraction Task

How to Unleash the Power of Large Language Models for Few-shot Relation Extraction?

Generative Prompt Tuning for Relation Classification

Towards Realistic Low-resource Relation Extraction: A Benchmark with Empirical Baseline Study

Modeling Multi-Granularity Hierarchical Features for Relation Extraction

Retrieval-Augmented Generation-based Relation Extraction

Relation Extraction with Fine-Tuned Large Language Models in Retrieval Augmented Generation Frameworks


Adversarial Training of Denoising Diffusion Model Using Dual Discriminators for High-Fidelity Multi-Speaker TTS

FastSpeech 2: Fast and High-Quality End-to-End Text to Speech

Tackling the Generative Learning Trilemma with Denoising Diffusion GANs

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

DiffGAN-TTS: High-Fidelity and Efficient Text-to-Speech with Denoising Diffusion GANs


go-cfr implements several forms of Counter Factual Regret minimization in Golang

Deep Counterfactual Regret Minimization

Solving Imperfect-Information Games via Discounted Regret Minimization

Single Deep Counterfactual Regret Minimization


⇔  Calculate distance matrix from ChewBBACA cgMLST allele call tables

Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS

Using Genomics To Investigate an Outbreak of Vancomycin-Resistant Enterococcus faecium ST78 at a Large Tertiary Hospital in Queensland

Comparative Genomic Analyses of Escherichia coli from a Meat Processing Environment in Relation to Their Biofilm Formation and Persistence

Within-Host Genetic Variation in Neisseria gonorrhoeae over the Course of Infection

Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia

Frontiers in cellular and infection microbiology


[ECCV 2020] QAConv: Interpretable and Generalizable Person Re-Identification with Query-Adaptive Convolution and Temporal Lifting, and [CVPR 2022] GS: Graph Sampling Based Deep Metric Learning

Interpretable and Generalizable Person Re-identification with Query-Adaptive Convolution and Temporal Lifting

Graph Sampling Based Deep Metric Learning for Generalizable Person Re-Identification

TransMatcher: Deep Image Matching Through Transformers for Generalizable Person Re-identification

Cloning Outfits from Real-World Images to 3D Characters for Generalizable Person Re-Identification

Is Synthetic Dataset Reliable for Benchmarking Generalizable Person Re-Identification?

TAL: Two-stream Adaptive Learning for Generalizable Person Re-identification


Stochastic Video Generation with a Learned Prior

Physion: Evaluating Physical Prediction from Vision in Humans and Machines

Goal-Aware Prediction: Learning to Model What Matters

A General Method for Amortizing Variational Filtering

Noether Networks: Meta-Learning Useful Conserved Quantities

On the Choice of Perception Loss Function for Learned Video Compression

Video Reenactment as Inductive Bias for Content-Motion Disentanglement


Code for the Paper: Antonino Furnari and Giovanni Maria Farinella. What Would You Expect? Anticipating Egocentric Actions with Rolling-Unrolling LSTMs and Modality Attention. International Conference on Computer Vision, 2019.

Anticipative Video Transformer

Rolling-Unrolling LSTMs for Action Anticipation from First-Person Video

IEEE transactions on pattern analysis and machine intelligence

Deep Learning for Vision-based Prediction: A Survey

Towards Streaming Egocentric Action Anticipation

Streaming egocentric action anticipation: An evaluation scheme and approach


Sinhalese Language based Hate Speech Detection

Automated Hate Speech Detection and the Problem of Offensive Language

Hateful Symbols or Hateful People? Predictive Features for Hate Speech Detection on Twitter

North American Chapter of the Association for Computational Linguistics

Deep Learning for Hate Speech Detection in Tweets

WWW'17 COMPANION: PROCEEDINGS OF THE 26TH INTERNATIONAL CONFERENCE ON WORLD WIDE WEB

Are You a Racist or Am I Seeing Things? Annotator Influence on Hate Speech Detection on Twitter

Using Convolutional Neural Networks to Classify Hate-Speech

Meeting of the Association for Computational Linguistics


Emotion detection on multiparty dialogue.

Graph Based Network with Contextualized Representations of Turns in Dialogue

Is ChatGPT Equipped with Emotional Dialogue Capabilities?

EmotionX-KU: BERT-Max based Contextual Emotion Classifier

PT-CoDE: Pre-trained Context-Dependent Encoder for Utterance-level Emotion Recognition

A Dual-Stream Recurrence-Attention Network With Global-Local Awareness for Emotion Recognition in Textual Dialog


Weighted Principal Component Analysis (PCA) in Python

Learning and Tracking the 3D Body Shape of Freely Moving Infants from RGB-D sequences

A large sub-Neptune transiting the thick-disk M4V TOI-2406.

FIESTA II. Disentangling Stellar and Instrumental Variability from Exoplanetary Doppler Shifts in the Fourier Domain

Development of the SPECULOOS exoplanet search project

Ground-based and Airborne Telescopes VIII

: a data-driven approach to correct for systematics in RV data – Application to SPIRou data of the planet-hosting M dwarf GJ 251


Retrofitting Word Vectors to Semantic Lexicons

Improving Lexical Embeddings with Semantic Knowledge

PROCEEDINGS OF THE 52ND ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS, VOL 2

Learning Word Representations with Regularization from Prior Knowledge

Conference on Computational Natural Language Learning


A lightweight accelerated proximal-gradient package for matlab

RAPID: Rapidly Accelerated Proximal Gradient Algorithms for Convex Minimization

Generalized damped Newton algorithms in nonsmooth optimization via second-order subdifferentials

Information criteria for non-normalized models

Relaxed regularization for linear inverse problems


Resources for PVLDB 2023 submission

Semantics-aware Dataset Discovery from Data Lakes with Contextualized Column-based Representation Learning

Generative Benchmark Creation for Table Union Search


Research code for "Training Vision-Language Transformers from Captions Alone"

Masked Autoencoders Are Scalable Vision Learners

ViLT: Vision-and-Language Transformer Without Convolution or Region Supervision


Exposing DeepFake Videos By Detecting Face Warping Artifacts

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

A Novel Counterfeit Feature Extraction Technique for Exposing Face-Swap Images Based on Deep Learning and Error Level Analysis

DeepfakeBench: A Comprehensive Benchmark of Deepfake Detection

Exposing Face-Swap Images Based on Deep Learning and ELA Detection

The 5th International Electronic Conference on Entropy and Its Applications

How Generalizable are Deepfake Image Detectors? An Empirical Study


Code for the paper "The Impact of Positional Encoding on Length Generalization in Transformers", NeurIPS 2023

StarCoder: may the source be with you!

SantaCoder: don't reach for the stars!


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

Direct Diffusion Bridge using Data Consistency for Inverse Problems

DriftRec: Adapting diffusion models to blind JPEG restoration

Diffusion Bridge Implicit Models


Module to call Mycobacterium tuberculosis lineages

Transmission and Drug Resistance Genotype of Multidrug-Resistant or Rifampicin-Resistant Mycobacterium tuberculosis in Chongqing, China

Identification of region of difference and H37Rv-related deletion in Mycobacterium tuberculosis complex by structural variant detection and genome assembly

Endogenous relapse and exogenous reinfection in recurrent pulmonary tuberculosis: A retrospective study revealed by whole genome sequencing

Insight into the drug-resistant characteristics and genetic diversity of multidrug-resistant Mycobacterium tuberculosis in China

Afro-TB dataset as a large scale genomic data of Mycobacterium tuberuclosis in Africa


SMETANA: a tool to analyse interactions in microbial communities

Polarization of microbial communities between competitive and cooperative metabolism

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables


A new adversarial purification method that uses the forward and reverse processes of diffusion models to remove adversarial perturbations.

Diffusion Models for Adversarial Purification

Adversarial Example Does Good: Preventing Painting Imitation from Diffusion Models via Adversarial Examples

On the Limitations of Stochastic Pre-processing Defenses

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

Can Protective Perturbation Safeguard Personal Data from Being Exploited by Stable Diffusion?

Instruct2Attack: Language-Guided Semantic Adversarial Attacks

Unifying Gradients to Improve Real-World Robustness for Deep Networks

Classifier Guidance Enhances Diffusion-based Adversarial Purification by Preserving Predictive Information


Information Security Knowledge Graph  about NVD CAPEC CWE CPE ..

Cybersecurity knowledge graphs

A review of knowledge graph application scenarios in cyber security


Code for "Investigating and Simplifying Masking-based Saliency Methods for Model Interpretability" (https://arxiv.org/abs/2010.09750)

Generative Image Inpainting with Contextual Attention

Deep Fusion Network for Image Completion

Evaluation for Weakly Supervised Object Localization: Protocol, Metrics, and Datasets

New Definitions and Evaluations for Saliency Methods: Staying Intrinsic, Complete and Sound


This repository contains the code for Instance Credibility Inference (ICI).

Iterative label cleaning for transductive and semi-supervised few-shot learning

How to trust unlabeled data? Instance Credibility Inference for Few-Shot Learning

Realistic Evaluation of Transductive Few-Shot Learning


Code and workloads from the Learned Cardinalities paper (https://arxiv.org/abs/1809.00677)

Learned Cardinalities: Estimating Correlated Joins with Deep Learning

An End-to-End Learning-based Cost Estimator

Deep Unsupervised Cardinality Estimation

Are We Ready For Learned Cardinality Estimation?

A Unified Deep Model of Learning from both Data and Queries for Cardinality Estimation

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

PRICE: A Pretrained Model for Cross-Database Cardinality Estimation


Pytorch reimplementation for "Gradient Surgery for Multi-Task Learning"

One Policy to Dress Them All: Learning to Dress People with Diverse Poses and Garments

PiCor: Multi-Task Deep Reinforcement Learning with Policy Correction

Proceedings of the AAAI Conference on Artificial Intelligence


The implementation of "Bootstrapping Semantic Segmentation with Regional Contrast" [ICLR 2022].

Semi-supervised semantic segmentation needs strong, varied perturbations

ClassMix: Segmentation-Based Data Augmentation for Semi-Supervised Learning


Benchmarks for the Unit Commitment Problem

Applying reinforcement learning and tree search to the unit commitment problem

Convex Polar Second-Order Taylor Approximation of AC Power Flows: A Unit Commitment Study


To address some of the failure modes in training of physics informed neural networks, a Lagrangian architecture is designed to conform to the direction of travel of information in convection-diffusion equations, i.e., method of characteristic; The repository includes a pytorch implementation of PINN and proposed LPINN with periodic boundary conditions

Physics Informed Deep Learning (Part II): Data-driven Discovery of Nonlinear Partial Differential Equations

PyHessian: Neural Networks Through the Lens of the Hessian

Respecting causality is all you need for training physics-informed neural networks

Lagrangian PINNs: A causality-conforming solution to failure modes of physics-informed neural networks

Computer Methods in Applied Mechanics and Engineering


ISTA-Net: Interpretable Optimization-Inspired Deep Network for Image Compressive Sensing

MR Image Reconstruction Using Deep Density Priors

Stabilizing Deep Tomographic Reconstruction

CS-GAN for High-Quality Diffusion Tensor Imaging

Invertible Diffusion Models for Compressed Sensing


Manually annotated chord data set of US pop songs and Popular Music Collection of RWC Music Database

A Bi-directional Transformer for Musical Chord Recognition

Improved Chord Recognition by Combining Duration and Harmonic Language Models

Personalized Popular Music Generation Using Imitation and Structure

Large Vocabulary Automatic Chord Estimation Using Deep Neural Nets: Design Framework, System Variations and Limitations

DECIBEL: Improving Audio Chord Estimation for Popular Music by Alignment and Integration of Crowd-Sourced Symbolic Representations


A Matlab package for probabilistic modeling of circular data with mixtures of von Mises distributions.

Egocentric boundary vector tuning of the retrosplenial cortex

Human interictal epileptiform discharges are bidirectional traveling waves echoing ictal discharges

Dynamic Distortion of Orientation Representation after Learning in the Mouse Primary Visual Cortex

Learning the Vector Coding of Egocentric Boundary Cells from Visual Data


Belief matching framework official implementation

Being Bayesian about Categorical Probability

Prior and Posterior Networks: A Survey on Evidential Deep Learning Methods For Uncertainty Estimation

Function-Space Regularization for Deep Bayesian Classification


QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis

QTLseqr: An R package for bulk segregant analysis with next-generation sequencing

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

A graph-based genome and pan-genome variation of the model plant Setaria

Optimizing bulk segregant analysis of drug resistance using Plasmodium falciparum genetic crosses conducted in humanized mice

Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle

BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima


A curated list of awesome serverless research works, including papers and open-sourced projects.

Pocket: Elastic Ephemeral Storage for Serverless Analytics

Catalyzer: Sub-millisecond Startup for Serverless Computing with Initialization-less Booting

TWENTY-FIFTH INTERNATIONAL CONFERENCE ON ARCHITECTURAL SUPPORT FOR PROGRAMMING LANGUAGES AND OPERATING SYSTEMS (ASPLOS XXV)

Cloudburst: Stateful Functions-as-a-Service

Architectural Implications of Function-as-a-Service Computing

Sprocket

Characterizing serverless platforms with serverlessbench

Benchmarking, analysis, and optimization of serverless function snapshots

International Conference on Architectural Support for Programming Languages and Operating Systems

SEUSS: skip redundant paths to make serverless fast

PROCEEDINGS OF THE FIFTEENTH EUROPEAN CONFERENCE ON COMPUTER SYSTEMS (EUROSYS'20)

Formal foundations of serverless computing

Proceedings of the ACM on Programming Languages

Replayable Execution Optimized for Page Sharing for a Managed Runtime Environment

Proceedings of the Fourteenth EuroSys Conference 2019


Benchmark quantum circuits before and after optimization.

t|ket⟩: a retargetable compiler for NISQ devices

Reducing the number of non-Clifford gates in quantum circuits

An Efficient Quantum Compiler that reduces T count

Fast and effective techniques for T-count reduction via spider nest identities

Using Spectral Graph Theory to Map Qubits onto Connectivity-limited Devices


Ælæctra was created as part of a Cognitive Science bachelor thesis, in the attempt to enhance the Danish NLP community with a more efficient Transformer-based language model.

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

ELECTRA: Pre-training Text Encoders as Discriminators Rather Than Generators

DaCy: A Unified Framework for Danish NLP


An approximate sequence pattern matcher for FASTQ/FASTA files.

An Illumina metabarcoding pipeline for fungi

Oomycete-specific ITS primers for identification and metabarcoding

Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils

Zenodo (CERN European Organization for Nuclear Research)

Fast sequence-based microsatellite genotyping development workflow

Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests

Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil

Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types

Phylogenetic studies uncover a predominantly African lineage in a widely distributed lichen-forming fungal species

What determines plant species diversity along the Modern Silk Road in the east?


SPICE: Semantic Propositional Image Caption Evaluation

Improved Image Captioning via Policy Gradient optimization of SPIDEr

International Conference on Computer Vision

VIFIDEL: Evaluating the Visual Fidelity of Image Descriptions

Towards Understanding Sample Variance in Visually Grounded Language Generation: Evaluations and Observations


[ICLR 2024] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations

The Open Catalyst 2020 (OC20) Dataset and Community Challenges

Proceedings of the International Conference on Electrocatalysis for Energy Applications and Sustainable Chemicals

Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs

Reducing SO(3) Convolutions to SO(2) for Efficient Equivariant GNNs


Differentially Private Conditional Generative Adversarial Network

InfoGAN: Interpretable Representation Learning by Information Maximizing Generative Adversarial Nets

DP-CGAN: Differentially Private Synthetic Data and Label Generation

GS-WGAN: A Gradient-Sanitized Approach for Learning Differentially Private Generators

Private Set Generation with Discriminative Information

A Unified View of Differentially Private Deep Generative Modeling


a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome

Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.

Automated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel

Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus


This dataset contains all the COVID-19 related data from the paper "An Augmented Multilingual Twitter Dataset for Studying the COVID-19 Infodemic"

BB_twtr at SemEval-2017 Task 4: Twitter Sentiment Analysis with CNNs and LSTMs

Understanding the perception of COVID-19 policies by mining a multilanguage Twitter dataset

An intelligent early warning system of analyzing Twitter data using machine learning on COVID-19 surveillance in the US

Data-driven multiscale modelling and analysis of COVID-19 spatiotemporal evolution using explainable AI


Bridge Correlational Neural Networks for Multilingual Multimodal Representation Learning

Towards Zero-shot Cross-lingual Image Retrieval and Tagging


A collection of LUTs for ImageJ/Fiji

In vitro endoderm emergence and self-organisation in the absence of extraembryonic tissues and embryonic architecture

HSP90 Modulates T2R Bitter Taste Receptor Nitric Oxide Production and Innate Immune Responses in Human Airway Epithelial Cells and Macrophages

A timer gene network is spatially regulated by the terminal system in the Drosophila embryo

Rab10 regulates the sorting of internalised TrkB for retrograde axonal transport

Botulinum neurotoxin A modulates the axonal release of pathological tau in hippocampal neurons

Apolipoprotein A1 and high-density lipoprotein limit low-density lipoprotein transcytosis by binding SR-B1

Quantitative study of alpha-synuclein prion-like spreading in fully oriented reconstructed neural networks reveals non-synaptic dissemination of seeding aggregates


DeepInspect code release

Men Also Like Shopping: Reducing Gender Bias Amplification using Corpus-level Constraints

MixTrain: Scalable Training of Verifiably Robust Neural Networks

Testing DNN Image Classifiers for Confusion & Bias Errors

Proceedings of the ACM/IEEE 42nd International Conference on Software Engineering: Companion Proceedings

Fairness Testing: A Comprehensive Survey and Analysis of Trends


Quantum algorithms for the simulation of Hamiltonian dynamics.

Toward the first quantum simulation with quantum speedup

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

Practical Quantum Computing: Solving the Wave Equation Using a Quantum Approach

Empirical determination of the simulation capacity of a near-term quantum computer


Plant small RNA target prediction tool

Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana

P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design

Small RNAs from the wheat stripe rust fungus (Puccinia striiformis f.sp. tritici)

Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris)

International journal of molecular sciences

Transcriptome-Wide Identification and Characterization of Circular RNAs in Leaves of Chinese Cabbage (Brassica rapa L. ssp. pekinensis) in Response to Calcium Deficiency-Induced Tip-burn

Long noncoding RNAs in the model species Brachypodium distachyon

A novel miRNA analysis framework to analyze differential biological networks

Identification of miRNA–mRNA Regulatory Modules Involved in Lipid Metabolism and Seed Development in a Woody Oil Tree (Camellia oleifera)

Identification of Grafting-Responsive MicroRNAs Associated with Growth Regulation in Pecan [Carya illinoinensis (Wangenh.) K. Koch]

Genome-wide identification of microRNAs involved in the somatic embryogenesis of Eucalyptus


A pytorch toolbox designed for experimentation using a generalization of the Resnet design.

Stable Architectures for Deep Neural Networks

Deep Neural Networks Motivated by Partial Differential Equations

Reversible Architectures for Arbitrarily Deep Residual Neural Networks


Predicting Factuality of Reporting and Bias of News Media Sources

What Was Written vs. Who Read It: News Media Profiling Using Text Analysis and Social Media Context

Tackling Fake News Detection by Continually Improving Social Context Representations using Graph Neural Networks

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

Tackling Fake News Detection by Interactively Learning Representations using Graph Neural Networks

Proceedings of the First Workshop on Interactive Learning for Natural Language Processing

Interactively Learning Social Media Representations Improves News Source Factuality Detection

Reliability Estimation of News Media Sources: Birds of a Feather Flock Together

The Challenges of Machine Learning for Trust and Safety: A Case Study on Misinformation Detection


[CIKM 2018] Weakly-Supervised Neural Text Classification

International Conference on Information and Knowledge Management

Fine-Tuning Pre-trained Language Model with Weak Supervision: A Contrastive-Regularized Self-Training Approach

Contextualized Weak Supervision for Text Classification

Meeting of the Association for Computational Linguistics

Calibrated Language Model Fine-Tuning for In- and Out-of-Distribution Data

HiGitClass: Keyword-Driven Hierarchical Classification of GitHub Repositories

META: Metadata-Empowered Weak Supervision for Text Classification

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

MotifClass: Weakly Supervised Text Classification with Higher-order Metadata Information

vONTSS: vMF based semi-supervised neural topic modeling with optimal transport

Weakly supervised prototype topic model with discriminative seed words: modifying the category prior by self-exploring supervised signals

Towards Weakly-Supervised Hate Speech Classification Across Datasets


Hexnet - The Hexagonal Image Processing Framework

Improving automated visual fault inspection for semiconductor manufacturing using a hybrid multistage system of deep neural networks

Hexagonal Image Processing in the Context of Machine Learning: Conception of a Biologically Inspired Hexagonal Deep Learning Framework

International Conference on Machine Learning and Applications

Biologically Inspired Hexagonal Deep Learning for Hexagonal Image Generation

International Conference on Information Photonics

Visual acuity prediction on real-life patient data using a machine learning based multistage system


BERT pre-training in Thai language

Neural Machine Translation of Rare Words with Subword Units

Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation

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

WangchanBERTa: Pretraining transformer-based Thai Language Models

Detecting Depression in Thai Blog Posts: a Dataset and a Baseline

A Comparative Study of Pretrained Language Models on Thai Social Text Categorization

CMTA: COVID-19 Misinformation Multilingual Analysis on Twitter

International Joint Conference on Natural Language Processing

MUCS@Text-LT-EDI@ACL 2022: Detecting Sign of Depression from Social Media Text using Supervised Learning Approach

Proceedings of the Second Workshop on Language Technology for Equality, Diversity and Inclusion

Looking for COVID-19 misinformation in multilingual social media texts


A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes

Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes

Decoding huge phage diversity: a taxonomic classification of Lak megaphages

Predicting stop codon reassignment improves functional annotation of bacteriophages

bioRxiv : the preprint server for biology

Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages


Episodic Control

Neural Episodic Control

Model-Free Episodic Control

Memory-Efficient Episodic Control Reinforcement Learning with Dynamic Online k-means

Successor Feature Neural Episodic Control

Sample-Efficient Reinforcement Learning with Maximum Entropy Mellowmax Episodic Control


A full pipeline to finetune Alpaca LLM with LoRA and RLHF on consumer hardware. Implementation of RLHF (Reinforcement Learning with Human Feedback) on top of the Alpaca architecture. Basically ChatGPT but with Alpaca

LoRA: Low-Rank Adaptation of Large Language Models

Fine-Tuning Language Models from Human Preferences

Efficient and Effective Text Encoding for Chinese LLaMA and Alpaca

LLM-Adapters: An Adapter Family for Parameter-Efficient Fine-Tuning of Large Language Models


Gradient boosted decision trees for multiple outputs. Better generalization ability, faster training and inference.

GBDT-MO: Gradient Boosted Decision Trees for Multiple Outputs

SketchBoost: Fast Gradient Boosted Decision Tree for Multioutput Problems


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

Speech Commands: A Dataset for Limited-Vocabulary Speech Recognition

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

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

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


A fast transit-fitting algorithm to search for transits of exomoons

Pandora: A fast open-source exomoon transit detection algorithm

Large exomoons unlikely around Kepler-1625 b and Kepler-1708 b


Optimizing Sequential Experimental Design with Deep Reinforcement Learning

Variational Sequential Optimal Experimental Design using Reinforcement Learning