This repo is the official implementation of "Mask-based Latent Reconstruction for Reinforcement Learning" (NeurIPS 2022).

CURL: Contrastive Unsupervised Representations for Reinforcement Learning

Image Augmentation Is All You Need: Regularizing Deep Reinforcement Learning from Pixels

PlayVirtual: Augmenting Cycle-Consistent Virtual Trajectories for Reinforcement Learning


Open Platform for Energy Networks


CoLight: Learning Network-level Cooperation for Traffic Signal Control

PROCEEDINGS OF THE 28TH ACM INTERNATIONAL CONFERENCE ON INFORMATION & KNOWLEDGE MANAGEMENT (CIKM '19)

STMARL: A Spatio-Temporal Multi-Agent Reinforcement Learning Approach for Cooperative Traffic Light Control

MetaVIM: Meta Variationally Intrinsic Motivated Reinforcement Learning for Decentralized Traffic Signal Control

Independent Reinforcement Learning for Weakly Cooperative Multiagent Traffic Control Problem

TinyLight: Adaptive Traffic Signal Control on Devices with Extremely Limited Resources

Large-Scale Traffic Signal Control Using Constrained Network Partition and Adaptive Deep Reinforcement Learning


PyTorch bottom-up attention with Detectron2

Multimodal Learning for Hateful Memes Detection

Hierarchical Object-oriented Spatio-Temporal Reasoning for Video Question Answering

M5Product: Self-harmonized Contrastive Learning for E-commercial Multi-modal Pretraining

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

Decoding the Underlying Meaning of Multimodal Hateful Memes

Object-Centric Representation Learning for Video Question Answering


A python based, MPI enabled, Monte-Carlo calculation of 2D system using Metropolis algorithm.

Ferroelectricity and Phase Transitions in Monolayer Group-IV Monochalcogenides

Promising ferroelectricity in 2D group IV tellurides: a first-principles study

Tunable ferroelectricity and anisotropic electric transport in monolayer β -GeSe


A collection of graph neural networks implementations in JAX

Semi-Supervised Classification with Graph Convolutional Networks

Graph Attention Networks

How Powerful are Graph Neural Networks?

Gated Graph Sequence Neural Networks

Principal Neighbourhood Aggregation for Graph Nets


MATLAB package of iterative regularization methods and large-scale test problems. This software is described in the paper "IR Tools: A MATLAB Package of Iterative Regularization Methods and Large-Scale Test Problems" that will be published in Numerical Algorithms, 2018.

Tensor Arnoldi–Tikhonov and GMRES-Type Methods for Ill-Posed Problems with a t-Product Structure

Computational Methods for Large-Scale Inverse Problems: A Survey on Hybrid Projection Methods

Gauss-Newton Optimization for Phase Recovery from the Bispectrum

Randomized core reduction for discrete ill-posed problem

On Non-Negative Quadratic Programming in Geometric Optimization


Quasi-Periodic Parallel WaveGAN Pytorch implementation

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

IEICE Transactions on Information and Systems

Parallel WaveGAN: A fast waveform generation model based on generative adversarial networks with multi-resolution spectrogram

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

IEEE/ACM Transactions on Audio, Speech, and Language Processing

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

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


Clustering-based methods for overlapping diarization

GPU-accelerated Guided Source Separation for Meeting Transcription

One Model to Rule Them All ? Towards End-to-End Joint Speaker Diarization and Speech Recognition

Low-Latency Speech Separation Guided Diarization for Telephone Conversations

An Experimental Review of Speaker Diarization methods with application to Two-Speaker Conversational Telephone Speech recordings

Geodesic interpolation of frame-wise speaker embeddings for the diarization of meeting scenarios


C API drivers for PYNQ FPGA board

A Configurable RO-PUF for Securing Embedded Systems Implemented on Programmable Devices

Multi-Unit Serial Polynomial Multiplier to Accelerate NTRU-Based Cryptographic Schemes in IoT Embedded Systems

On-Line Evaluation and Monitoring of Security Features of an RO-Based PUF/TRNG for IoT Devices

Task‐based preemptive scheduling on FPGAs leveraging partial reconfiguration


SmoothGrad implementation in PyTorch

Grad-CAM: Visual Explanations from Deep Networks via Gradient-Based Localization

International Journal of Computer Vision

Deep Inside Convolutional Networks: Visualising Image Classification Models and Saliency Maps

Striving for Simplicity: The All Convolutional Net

SmoothGrad: removing noise by adding noise

Drone Model Classification Using Convolutional Neural Network Trained on Synthetic Data


Effective Algebraic Topology in Haskell

Polynomial-time computation of homotopy groups and Postnikov systems in fixed dimension

Computing all maps into a sphere

Polynomial-time homology for simplicial Eilenberg-MacLane spaces

Computing the homology of groups: the geometric way

Effective homotopy of fibrations

Applicable Algebra in Engineering, Communication and Computing

The Hochschild complex of a twisting cochain

Computing the first stages of the Bousfield-Kan spectral sequence

A Combinatorial Tool for Computing the Effective Homotopy of Iterated Loop Spaces

Effective chain complexes for twisted products

A Bousfield–Kan Algorithm for Computing the Effective Homotopy of a Space

Foundations of Computational Mathematics


CAQE is a solver for quantified Boolean formulas

Clausal Abstraction for DQBF (full version)

Positional Games and QBF: The Corrective Encoding

Solving Explainability Queries with Quantification: The Case of Feature Relevancy

THIRTY-SEVENTH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE, VOL 37 NO 4

Making = Practical: Efficient Interactive Protocols for BDD Algorithms


Graph Auto-Encoder in PyTorch

Variational Graph Auto-Encoders

Better with Less: A Data-Active Perspective on Pre-Training Graph Neural Networks

GenCAT: Generating Attributed Graphs with Controlled Relationships between Classes, Attributes, and Topology

DINE: Dimensional Interpretability of Node Embeddings

Link Prediction without Graph Neural Networks


The official PyTorch implementation of the paper "SAITS: Self-Attention-based Imputation for Time Series". A fast and state-of-the-art (SOTA) deep-learning neural network model for efficient time-series imputation (impute multivariate incomplete time series containing NaN missing data/values with machine learning). https://arxiv.org/abs/2202.08516

BRITS: Bidirectional Recurrent Imputation for Time Series

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

GP-VAE: Deep Probabilistic Time Series Imputation

Learning to Reconstruct Missing Data from Spatiotemporal Graphs with Sparse Observations

Deep Learning for Multivariate Time Series Imputation: A Survey

Graph-based Virtual Sensing from Sparse and Partial Multivariate
  Observations

An End-to-End Time Series Model for Simultaneous Imputation and Forecast

TSI-Bench: Benchmarking Time Series Imputation


Nonparametric group variable selection with multivariate response for connectome-based modelling of cognitive scores

Journal of the Royal Statistical Society Series C: Applied Statistics

SoftBart: Soft Bayesian Additive Regression Trees

Gibbs Priors for Bayesian Nonparametric Variable Selection with Weak Learners

Journal of Computational and Graphical Statistics


Jointly Modelling Aspects, Ratings and Sentiments for Movie Recommendation (JMARS)

Is Attention Interpretable?

Fastformer: Additive Attention Can Be All You Need

Hi-Transformer: Hierarchical Interactive Transformer for Efficient and Effective Long Document Modeling

Attentive Pooling with Learnable Norms for Text Representation

Meeting of the Association for Computational Linguistics

Smart Bird: Learnable Sparse Attention for Efficient and Effective Transformer


VideoCLIP: Contrastive Pre-training for Zero-shot Video-Text Understanding

UniVL: A Unified Video and Language Pre-Training Model for Multimodal Understanding and Generation

Cross-task weakly supervised learning from instructional videos

VLM: Task-agnostic Video-Language Model Pre-training for Video Understanding

A Benchmark for Structured Procedural Knowledge Extraction from Cooking Videos

Non-Sequential Graph Script Induction via Multimedia Grounding

Beyond Instructional Videos: Probing for More Diverse Visual-Textual Grounding on YouTube


PyTorch-1.0 implementation for the adversarial training on MNIST/CIFAR-10 and visualization on robustness classifier.

Robustness May Be at Odds with Accuracy

AdamP: Slowing Down the Slowdown for Momentum Optimizers on Scale-invariant Weights

On the Generalization Properties of Adversarial Training

Slowing Down the Weight Norm Increase in Momentum-based Optimizers


Biomedical Question Answering Datasets.

PubMedQA: A Dataset for Biomedical Research Question Answering

Constructing Datasets for Multi-hop Reading Comprehension Across Documents

What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams

Modeling Biological Processes for Reading Comprehension

Empirical Methods in Natural Language Processing

emrQA: A Large Corpus for Question Answering on Electronic Medical Records

Overview of the MEDIQA 2019 Shared Task on Textual Inference, Question Entailment and Question Answering

SIGBIOMED WORKSHOP ON BIOMEDICAL NATURAL LANGUAGE PROCESSING (BIONLP 2019)

Infusing Disease Knowledge into BERT for Health Question Answering, Medical Inference and Disease Name Recognition

Medical Visual Question Answering via Conditional Reasoning

MM '20: PROCEEDINGS OF THE 28TH ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA

CliCR: A Dataset of Clinical Case Reports for Machine Reading Comprehension

CAiRE-COVID: A Question Answering and Query-focused Multi-Document Summarization System for COVID-19 Scholarly Information Management


vessel segmentation, artery and vein, optic disc, vascular feature analysis

A foundation model for generalizable disease detection from retinal images

AutoMorph: Automated Retinal Vascular Morphology Quantification Via a Deep Learning Pipeline

Comparison of Retinal Imaging Techniques in Individuals with Pulmonary Artery Hypertension Using Vessel Generation Analysis


Pytorch implementation of GANimation with pretrained weights.

GANimation: Anatomically-aware Facial Animation from a Single Image

SepMark: Deep Separable Watermarking for Unified Source Tracing and Deepfake Detection

Label-Noise Robust Multi-Domain Image-to-Image Translation


Simulation-Enabled Estimation of Kinetic Rates - Version 2

SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning

Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach

The journal of physical chemistry letters

Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach

Journal of chemical theory and computation

SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine

Journal of chemical information and modeling


Persian (Farsi) Question Answering Dataset (+ Models)

PQuAD: A Persian Question Answering Dataset

Khayyam Challenge (PersianMMLU): Is Your LLM Truly Wise to The Persian
  Language?

PCoQA: Persian Conversational Question Answering Dataset


Code repository for Ensemble Bayesian Optimization

Batched Large-scale Bayesian Optimization in High-dimensional Spaces

Re-Examining Linear Embeddings for High-Dimensional Bayesian Optimization

Sample-Then-Optimize Batch Neural Thompson Sampling

Comparison of High-Dimensional Bayesian Optimization Algorithms on BBOB

Pseudo-Bayesian Optimization


Streamlined neural network training.

Jet flavour tagging for future colliders with fast simulation

Attention to the strengths of physical interactions: Transformer and graph-based event classification for particle physics experiments

Classify the Higgs decays with the PFN and ParticleNet at electron-positron colliders

Optimizing High-Throughput Inference on Graph Neural Networks at Shared Computing Facilities with the NVIDIA Triton Inference Server


LaNMT: Latent-variable Non-autoregressive Neural Machine Translation with Deterministic Inference

Latent-Variable Non-Autoregressive Neural Machine Translation with Deterministic Inference Using a Delta Posterior

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


Recommendation algorithms for large graphs

On the Equivalence of Decoupled Graph Convolution Network and Label Propagation

pygrank: A Python Package for Graph Node Ranking

Unsupervised evaluation of multiple node ranks by reconstructing local structures


Few-shot Learning of GPT-3

Language Models are Few-Shot Learners

Calibrate Before Use: Improving Few-Shot Performance of Language Models

kNN Prompting: Beyond-Context Learning with Calibration-Free Nearest Neighbor Inference

Prototypical Calibration for Few-shot Learning of Language Models

Towards Informative Few-Shot Prompt with Maximum Information Gain for In-Context Learning

Enhancing In-context Learning via Linear Probe Calibration


AssemblyNet: 3D Whole Brain MRI segmentation pipeline

Hippocampal‐amygdalo‐ventricular atrophy score: Alzheimer disease detection using normative and pathological lifespan models

Interpretable differential diagnosis for Alzheimer's disease and Frontotemporal dementia

Deep grading for MRI-based differential diagnosis of Alzheimer's disease and Frontotemporal dementia

Brain Structure Ages -- A new biomarker for multi-disease classification

Lifespan neurodegeneration of the human brain in multiple sclerosis

bioRxiv : the preprint server for biology

Towards better Interpretable and Generalizable AD detection using Collective Artificial Intelligence

Staging of progressive supranuclear palsy-Richardson syndrome using MRI brain charts for the human lifespan


Cooperative Vision-and-Dialog Navigation

Vision-and-Dialog Navigation

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

ESceme: Vision-and-Language Navigation with Episodic Scene Memory


Measure the similarity of text corpora for 74 languages

Representations of Language Varieties Are Reliable Given Corpus Similarity Measures

Register Variation Remains Stable Across 60 Languages

Corpus Similarity Measures Remain Robust Across Diverse Languages

Predicting Embedding Reliability in Low-Resource Settings Using Corpus Similarity Measures


The official implementation of our ICLR2024 paper "AutoDAN: Generating Stealthy Jailbreak Prompts on Aligned Large Language Models".

Defending Large Language Models against Jailbreak Attacks via Semantic
  Smoothing

Gradient Cuff: Detecting Jailbreak Attacks on Large Language Models by
  Exploring Refusal Loss Landscapes

Defensive Prompt Patch: A Robust and Interpretable Defense of LLMs
  against Jailbreak Attacks

Uncovering Safety Risks in Open-source LLMs through Concept Activation
  Vector

Enhancing the Capability and Robustness of Large Language Models through
  Reinforcement Learning-Driven Query Refinement


SustainBench: Benchmarks for Monitoring the Sustainable Development Goals with Machine Learning


This is the reference implementation of commonly used coreference metrics.

Event Coreference Resolution by Iteratively Unfolding Inter-dependencies among Events

DWIE: an entity-centric dataset for multi-task document-level information extraction

Joint Inference for Event Coreference Resolution

International Conference on Computational Linguistics

Multilingual Coreference Resolution with Harmonized Annotations

Multi-source annotation projection of coreference chains: assessing strategies and testing opportunities

Proceedings of the 2nd Workshop on Coreference Resolution Beyond
          OntoNotes (CORBON 2017)

CORBON 2017 Shared Task: Projection-Based Coreference Resolution

CEREC: A Corpus for Entity Resolution in Email Conversations

Event co-reference resolution via a multi-loss neural network without using argument information

Capturing the Content of a Document through Complex Event Identification

Proceedings of the 11th Joint Conference on Lexical and Computational Semantics


Classification of low quality cells from single-cell RNA-seq data

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq

Journal of translational genetics and genomics


[NeurIPS 2021] Large Scale Learning on Non-Homophilous Graphs: New Benchmarks and Strong Simple Methods

Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited

Augmentation-Free Graph Contrastive Learning with Performance Guarantee

EvenNet: Ignoring Odd-Hop Neighbors Improves Robustness of Graph Neural Networks

Demystifying Structural Disparity in Graph Neural Networks: Can One Size Fit All?

Label-Wise Graph Convolutional Network for Heterophilic Graphs

AGNN: Alternating Graph-Regularized Neural Networks to Alleviate Over-Smoothing

Single-Pass Contrastive Learning Can Work for Both Homophilic and Heterophilic Graph

Simple and Asymmetric Graph Contrastive Learning without Augmentations

Position: Graph Foundation Models are Already Here


Traceability Transformed: Generating more Accurate Links with Pre-Trained BERT Models

EALink: An Efficient and Accurate Pre-Trained Framework for Issue-Commit Link Recovery


Creative Commons Attribution 4.0 International

Copora for evaluating NLU Services/Platforms such as Dialogflow, LUIS, Watson, Rasa etc.

Benchmarking Natural Language Understanding Services for building Conversational Agents

CG-BERT: Conditional Text Generation with BERT for Generalized Few-shot Intent Detection

Intent Mining from past conversations for conversational agent

Composed Variational Natural Language Generation for Few-shot Intents

LabelVizier: Interactive Validation and Relabeling for Technical Text Annotations

One System to Rule them All: a Universal Intent Recognition System for Customer Service Chatbots

BlendX: Complex Multi-Intent Detection with Blended Patterns


ManiSkill-Learn is a framework for training agents on SAPIEN Open-Source Manipulation Skill Challenge (ManiSkill Challenge), a physics-rich manipulation skill benchmark with large-scale demonstrations.

Conservative Q-Learning for Offline Reinforcement Learning

Off-Policy Deep Reinforcement Learning without Exploration

Pseudo-LiDAR from Visual Depth Estimation: Bridging the Gap in 3D Object Detection for Autonomous Driving

A Minimalist Approach to Offline Reinforcement Learning

ManiSkill: Generalizable Manipulation Skill Benchmark with Large-Scale Demonstrations


Mean-Shifted Contrastive Loss for Anomaly Detection (AAAI 2023)

Attribute-based Representations for Accurate and Interpretable Video Anomaly Detection

No Free Lunch: The Hazards of Over-Expressive Representations in Anomaly Detection


A spatially explicit trait- and individual-based microbial systems modelling framework

A trait-based approach for modelling microbial litter decomposition.

Consequences of drought tolerance traits for microbial decomposition in the DEMENT model

Emergent properties of organic matter decomposition by soil enzymes

Drought legacies mediated by trait trade‐offs in soil microbiomes


Benchmarking Suite for BDD packages

Parallel disk-based computation for large, monolithic binary decision diagrams

Efficient Binary Decision Diagram Manipulation in External Memory

Adiar 1.1.0 : Experiment Data

Zenodo (CERN European Organization for Nuclear Research)


DRLinFluids: An open-source Python platform of coupling deep reinforcement learning and OpenFOAM

Dynamic feature-based deep reinforcement learning for flow control of circular cylinder with sparse surface pressure sensing

Robust and adaptive deep reinforcement learning for enhancing flow control around a square cylinder with varying Reynolds numbers

Deep reinforcement learning-based active flow control of an elliptical cylinder: Transitioning from an elliptical cylinder to a circular cylinder and a flat plate

Effect of Synthetic Jets Actuator Parameters on Deep Reinforcement
  Learning-Based Flow Control Performance in a Square Cylinder


GLObal Coastal Ocean Flood Forecasting System: An ADCIRC-based global storm tide modeling system providing real-time forecasts of coastal flooding

OceanMesh2D 1.0: MATLAB-based software for two-dimensional unstructured mesh generation in coastal ocean modeling

Global storm tide modeling with ADCIRC v55: unstructured mesh design and performance


Scene-Graph Augmented Data-Driven Risk Assessment of Autonomous Vehicle Decisions

Spatio-Temporal Scene-Graph Embedding for Autonomous Vehicle Collision Prediction

roadscene2vec: A Tool for Extracting and Embedding Road Scene-Graphs


Automatically harvested multilingual contrastive word sense disambiguation test sets for machine translation

The MuCoW Test Suite at WMT 2019: Automatically Harvested Multilingual Contrastive Word Sense Disambiguation Test Sets for Machine Translation

Proceedings of the Fourth Conference on Machine Translation (Volume 2: Shared Task Papers, Day 1)

An Evaluation Benchmark for Testing the Word Sense Disambiguation Capabilities of Machine Translation Systems

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

Democratizing neural machine translation with OPUS-MT

The MUCOW word sense disambiguation test suite at WMT 2020

A Comparison between Pre-training and Large-scale Back-translation for Neural Machine Translation


Official TagMe API wrapper for Python.

Learning to Retrieve Reasoning Paths over Wikipedia Graph for Question Answering

Multi-Task Learning with Multi-View Attention for Answer Selection and Knowledge Base Question Answering

Contextualized Knowledge-aware Attentive Neural Network: Enhancing Answer Selection with Knowledge

Knowledge Rumination for Pre-trained Language Models


Evaluating Deep Neural Networks Trained on Clinical Images in Dermatology with the Fitzpatrick 17k Dataset

MEDFAIR: Benchmarking Fairness for Medical Imaging

A deep-learning algorithm to classify skin lesions from mpox virus infection

Towards Transparency in Dermatology Image Datasets with Skin Tone Annotations by Experts, Crowds, and an Algorithm

Skin Lesion Classification and Detection Using Machine Learning Techniques: A Systematic Review

Meaningfully Explaining Model Mistakes Using Conceptual Counterfactuals.

The Role of Subgroup Separability in Group-Fair Medical Image Classification

FairTune: Optimizing Parameter Efficient Fine Tuning for Fairness in Medical Image Analysis

Domain Generalization for Medical Image Analysis: A Survey

Optimizing skin disease diagnosis: harnessing online community data with contrastive learning and clustering techniques


(ECCVW 2020) Joint Denoising and SR in Microscopy Imaging

Fully Unsupervised Diversity Denoising with Convolutional Variational Autoencoders

Improving Blind Spot Denoising for Microscopy

W2S: Microscopy Data with Joint Denoising and Super-Resolution for Widefield to SIM Mapping

Joint self-supervised blind denoising and noise estimation


Robust Compressed Sensing MRI with Deep Generative Priors

Decomposed Diffusion Sampler for Accelerating Large-Scale Inverse Problems

A Regularized Conditional GAN for Posterior Sampling in Image Recovery Problems

Mining the manifolds of deep generative models for multiple data-consistent solutions of ill-posed tomographic imaging problems

Score-based Generative Priors Guided Model-driven Network for MRI
  Reconstruction


Classify output of AmpliconArchitect to detect types of focal amplifications present

The landscape of extrachromosomal circular DNA in medulloblastoma

Coordinated inheritance of extrachromosomal DNA species in human cancer cells

Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors

Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer


PyTrx is a Python object-oriented programme created for the purpose of calculating real-world measurements from oblique images and time-lapse image series. Its primary purpose is to obtain velocities, surface areas, and distances from oblique, optical imagery of glacial environments.

Calving controlled by melt-under-cutting: detailed calving styles revealed through time-lapse observations

Rapidly changing subglacial hydrological pathways at a tidewater glacier revealed through simultaneous observations of water pressure, supraglacial lakes, meltwater plumes and surface velocities

PyTrx: A Python-Based Monoscopic Terrestrial Photogrammetry Toolset for Glaciology

PyTrx: A Python toolbox for deriving velocities, surface areas and
line measurements from oblique imagery in glacial environments


methods for functional summary-based imputation

Transcriptome-wide association study identifies new susceptibility genes and pathways for depression

Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration

Association Between Brain Structure and Alcohol Use Behaviors in Adults

Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation

Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton

Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits

Novel insight into the etiology of ischemic stroke gained by integrative multiome-wide association study

Harnessing transcriptomic signals for amyotrophic lateral sclerosis to identify novel drugs and enhance risk prediction

medRxiv : the preprint server for health sciences

Genome-wide meta-analysis of pneumonia suggests a role for mucin biology and provides novel drug repurposing opportunities

Novel insight into the etiology of ischemic stroke gained by integrative transcriptome-wide association study


Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy

Functional CRISPR dissection of gene networks controlling human regulatory T cell identity

Modulation of myeloid and T cells in vivo by Bruton's tyrosine kinase inhibitor ibrutinib in patients with metastatic pancreatic ductal adenocarcinoma

Immune Modulation with RANKL Blockade through Denosumab Treatment in Patients with Cancer


Global Maps of Potential Natural Vegetation based on Machine Learning

Global mapping of potential natural vegetation: an assessment of Machine Learning algorithms for estimating land potential


A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.

Uncovering new families and folds in the natural protein universe

Geometricus Represents Protein Structures as Shape-mers Derived from Moment Invariants

Fast and adaptive protein structure representations for machine learning


making synthetic spectra from libraries

The Gaia DR2 parallax zero-point: hierarchical modelling of red clump stars

Monthly notices of the Royal Astronomical Society

A Panchromatic Study of Massive Stars in the Extremely Metal-Poor Local Group Dwarf Galaxy Leo A

High mass function ellipsoidal variables in the Gaia Focused Product Release: searching for black hole candidates in the binary zoo

A hidden population of massive white dwarfs: two spotted K+WD binaries


MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

MolTrans: Molecular Interaction Transformer for drug–target interaction prediction

Interpretable bilinear attention network with domain adaptation improves drug-target prediction

A brief review of protein–ligand interaction prediction

Computational and structural biotechnology journal

FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for
  Drug-Target Interaction


Clustering and Predictions with Multi-Task Gaussian Processes

MAGMA: Inference and Prediction with Multi-Task Gaussian Processes

Cluster-Specific Predictions with Multi-Task Gaussian Processes


The repo contains SDK for Penglai Enclave (based on RISC-V TVM).


Python bindings for YMW16, NE2001 and YT2020 electron density models

A comparison of Galactic electron density models using PyGEDM

Publications of the Astronomical Society of Australia

A Large-scale Magneto-ionic Fluctuation in the Local Environment of Periodic Fast Radio Burst Source FRB 20180916B

The MSPSRπ catalogue: VLBA astrometry of 18 millisecond pulsars

A Data-driven Technique Using Millisecond Transients to Measure the Milky Way Halo

Revealing the Dynamic Magnetoionic Environments of Repeating Fast Radio Burst Sources through Multiyear Polarimetric Monitoring with CHIME/FRB

The eccentric millisecond pulsar, PSR J0955−6150

The Green Bank North Celestial Cap Survey. VIII. 21 New Pulsar Timing Solutions

TRAPUM search for pulsars in supernova remnants and pulsar wind nebulae − I. Survey description and initial discoveries

On the Initial Spin Period Distribution of Neutron Stars


Deep Articulatory Synthesis and Inversion

Speaker-Independent Acoustic-to-Articulatory Speech Inversion

Deep Speech Synthesis from Articulatory Representations

Evidence of Vocal Tract Articulation in Self-Supervised Learning of Speech

Deep Speech Synthesis from MRI-Based Articulatory Representations


Download and Visualize Essential Global Heating Data in R


This repo contains a set of neural transducer, e.g. sequence-to-sequence model, focusing on character-level tasks.

Applying the Transformer to Character-level Transduction

Exact Hard Monotonic Attention for Character-Level Transduction

Hard Non-Monotonic Attention for Character-Level Transduction

Can a Transformer Pass the Wug Test? Tuning Copying Bias in Neural Morphological Inflection Models

Morphological Irregularity Correlates with Frequency

Differentiable Generative Phonology

Sample-efficient Linguistic Generalizations through Program Synthesis: Experiments with Phonology Problems


Evolving Directed Acyclic Graph

EvoDAG: A semantic Genetic Programming Python library

IEEE International Autumn Meeting on Power, Electronics and Computing

Semantic Genetic Programming for Sentiment Analysis

EvoMSA: A Multilingual Evolutionary Approach for Sentiment Analysis

IEEE Computational Intelligence Magazine

INGEOTEC at SemEval 2017 Task 4: A B4MSA Ensemble based on Genetic Programming for Twitter Sentiment Analysis

Meeting of the Association for Computational Linguistics

NEO 2015

NEO 2015 - Numerical and Evolutionary Optimization

INGEOTEC at SemEval-2019 Task 5 and Task 6: A Genetic Programming Approach for Text Classification

North American Chapter of the Association for Computational Linguistics

Selection Heuristics on Semantic Genetic Programming for Classification Problems

INGEOTEC at SemEval-2018 Task 1: EvoMSA and μTC for Sentiment Analysis


REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability

Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease

The role of the NMD factor UPF3B in olfactory sensory neurons

SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis

Alterations in oligodendrocyte transcriptional networks reveal region-specific vulnerabilities to neurological disease


Natural Language Processing Tutorial for MindSpore Users

Attention Is All You Need

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

Sequence to Sequence Learning with Neural Networks

Convolutional Neural Networks for Sentence Classification

word2vec Parameter Learning Explained


Self-supervised contrastive learning for time series via time-frequency consistency

Self-Supervised Contrastive Pre-Training For Time Series via Time-Frequency Consistency

A Survey on Time-Series Pre-Trained Models

A Co-training Approach for Noisy Time Series Learning

Proceedings of the 32nd ACM International Conference on Information and Knowledge Management

Evaluating Large Language Models as Virtual Annotators for Time-series
  Physical Sensing Data


BABILong is a benchmark for LLM evaluation using the needle-in-a-haystack approach.

Towards AI-Complete Question Answering: A Set of Prerequisite Toy Tasks

In Search of Needles in a 10M Haystack: Recurrent Memory Finds What LLMs
  Miss

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


PyORBIT: a code for exoplanet orbital parameters and stellar activity.

An Ultra-short Period Rocky Super-Earth with a Secondary Eclipse and a Neptune-like Companion around K2-141

The GAPS programme with HARPS-N at TNG XI. Pr~0211 in M~44: the first multi-planet system in an open cluster

The Kepler-19 System: A Thick-envelope Super-Earth with Two Neptune-mass Companions Characterized Using Radial Velocities and Transit Timing Variations

The GAPS Programme at TNG

A PSF-based Approach to TESS High quality data Of Stellar clusters (PATHOS) -- II. Search for exoplanets in open clusters of the southern ecliptic hemisphere and their frequency

Monthly Notices of the Royal Astronomical Society

An unusually low density ultra-short period super-Earth and three mini-Neptunes around the old star TOI-561

The GAPS Programme with HARPS-N at TNG XVII. Line profile indicators and kernel regression as diagnostics of radial-velocity variations due to stellar activity in solar-like stars

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

A PSF-based Approach to TESS High quality data Of Stellar clusters (PATHOS) - III. Exploring the properties of young associations through their variables, dippers, and candidate exoplanets

A PSF-based Approach to TESS High quality data Of Stellar clusters (PATHOS) - IV. Candidate exoplanets around stars in open clusters: frequency and age-planetary radius distribution


Computing landscape metrics in the Python ecosystem


Tools and libraries for processing Planet SkySat imagery, including camera model refinement, stereo reconstruction, and orthomosaic production

An automated, open-source pipeline for mass production of digital elevation models (DEMs) from very-high-resolution commercial stereo satellite imagery

ISPRS Journal of Photogrammetry and Remote Sensing

The Ames Stereo Pipeline: NASA's Open Source Software for Deriving and Processing Terrain Data

Automated digital elevation model (DEM) generation from very-high-resolution Planet SkySat triplet stereo and video imagery

NeoGeographyToolkit/StereoPipeline 2.7.0


Python implementation of 'Scalable Recommendation with Hierarchical Poisson Factorization'.

Scalable Recommendation with Poisson Factorization

LensKit for Python: Next-Generation Software for Recommender Systems Experiments

International Conference on Information and Knowledge Management

Characterizing and Predicting Repeat Food Consumption Behavior for Just-in-Time Interventions

Proceedings of the 9th International Conference on Digital Public Health

Deep Determinantal Point Processes

Fast Non-Bayesian Poisson Factorization for Implicit-Feedback Recommendations


This is a Julia package of nonlinear solvers. These codes are used in my book, Solving Nonlinear Equations with Iterative Methods: Solvers and Examples in Julia.

Convergence Analysis for Anderson Acceleration

Numerical methods for nonlinear equations

A Quasi–Monte Carlo Method With Krylov Linear Solvers for Multigroup Neutron Transport Simulations


Lesion to Symptom Mapping in R

Relative contributions of lesion location and lesion size to predictions of varied language deficits in post-stroke aphasia

White matter disconnection of left multiple demand network is associated with post-lesion deficits in cognitive control

Behavioural and neural structure of fluent speech production deficits in aphasia

A presurgical voxel-wise predictive model for cerebellar mutism syndrome in children with posterior fossa tumors


Beyond I.I.D.: Three Levels of Generalization for Question Answering on Knowledge Bases

Would You Ask it that Way?

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

Combining Transfer Learning with In-context Learning using Blackbox LLMs for Zero-shot Knowledge Base Question Answering


Fluency-related Temporal Features and Syllable Prominence as Prosodic Proficiency Predictors for Learners of English with Different Language Backgrounds

BERT, can HE predict contrastive focus? Predicting and controlling prominence in neural TTS using a language model

Speech prosody enhances the neural processing of syntax


A parallel python Milne Eddington synthesis framework

Spicules and downflows in the solar chromosphere

Signatures of ubiquitous magnetic reconnection in the lower solar atmosphere

Heating of the solar chromosphere through current dissipation

Active region chromospheric magnetic fields

High-resolution observations of the solar photosphere, chromosphere, and transition region

Signatures of ubiquitous magnetic reconnection in the deep atmosphere of sunspot penumbrae

The Chromosphere Underneath a Coronal Bright Point

Properties of ubiquitous magnetic reconnection events in the lower solar atmosphere

Properties of shock waves in the quiet-Sun chromosphere

Magnetic Fields in Solar Plage Regions: Insights from High-sensitivity Spectropolarimetry


Weekly visualization report of Open LLM model performance based on 4 metrics.

Survey on Factuality in Large Language Models: Knowledge, Retrieval and Domain-Specificity

LLM4SecHW: Leveraging Domain-Specific Large Language Model for Hardware Debugging

Asian Hardware-Oriented Security and Trust Symposium

A Systematic Literature Review on Explainability for Machine/Deep
  Learning-based Software Engineering Research

Evaluating the Retrieval Component in LLM-Based Question Answering Systems


code of CycleGT

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

CycleGT: Unsupervised Graph-to-Text and Text-to-Graph Generation via Cycle Training

EventNarrative: A large-scale Event-centric Dataset for Knowledge Graph-to-Text Generation

Fork or Fail: Cycle-Consistent Training with Many-to-One Mappings


UCCA Documentation

Refining Implicit Argument Annotation for UCCA

Comparison by Conversion: Reverse-Engineering UCCA from Syntax and Lexical Semantics

UCCA's Foundational Layer: Annotation Guidelines v2.1

SemEval 2019 Shared Task: Cross-lingual Semantic Parsing with UCCA - Call for Participation


Positively Split Ewald

Leveraging collective effects in externally driven colloidal suspensions: experiments and simulations

Current Opinion in Colloid & Interface Science

Large Scale Brownian Dynamics of Confined Suspensions of Rigid Particles

Efficient reactive Brownian dynamics

Driven dynamics in dense suspensions of microrollers

A fast spectral method for electrostatics in doubly periodic slit channels

A fluctuating boundary integral method for Brownian suspensions

Diffusion and sedimentation in colloidal suspensions using multiparticle collision dynamics with a discrete particle model.

Hydrodynamic fluctuations in quasi-two dimensional diffusion

Journal of Statistical Mechanics: Theory and Experiment

Computing hydrodynamic interactions in confined doubly periodic geometries in linear time.


An ultrafast optimal aligner for mapping large NGS data to large genome databases.

Evaluating the Information Content of Shallow Shotgun Metagenomics

Technology dictates algorithms: Recent developments in read alignment

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics

BURST enables mathematically optimal short-read alignment for big data

Characterization of the Oral Microbiome Among Children With Type 1 Diabetes Compared With Healthy Children

Alteration of the Gut Microbiome in Normal and Overweight School Children from Selangor with Lactobacillus Fermented Milk Administration

Heterogeneity of gut microbial responses in healthy household dogs transitioning from an extruded to a mildly cooked diet


Code and data for reproducing baselines for TopiOCQA, an open-domain conversational question-answering dataset

TopiOCQA: Open-domain Conversational Question Answering with Topic Switching

INSCIT: Information-Seeking Conversations with Mixed-Initiative Interactions

Can Long-Context Language Models Subsume Retrieval, RAG, SQL, and More?


SemiBin: metagenomics binning with self-supervised deep learning

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments

SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing

SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)


Retrieve data from thousands of mesonet stations as Polars DataFrames from Synoptic's Weather API.


The SETimes.HR+ Croatian dependency treebank

Multilingual Projection for Parsing Truly Low-Resource Languages

Transactions of the Association for Computational Linguistics

New Inflectional Lexicons and Training Corpora for Improved Morphosyntactic Annotation of Croatian and Serbian

Universal Dependencies for Croatian (that work for Serbian, too)

A Legal Perspective on Training Models for Natural Language Processing

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

Collaborative Development of a Rule-Based Machine Translator between Croatian and Serbian

European Association for Machine Translation Conferences/Workshops

Regional Linguistic Data Initiative (ReLDI)


Character-based word embeddings model based on RNN for handling real world texts

A Universal Question-Answering Platform for Knowledge Graphs

Form2Seq : A Framework for Higher-Order Form Structure Extraction

Multi-Modal Association based Grouping for Form Structure Extraction


A toolkit for automated local phylogenomic analyses, or ALPHA

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

A Draft Sequence of the Neandertal Genome

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Testing for Ancient Admixture between Closely Related Populations

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

WABI - DGEN: A Test Statistic for Detection of General Introgression Scenarios

ALPHA: a toolkit for Automated Local PHylogenomic Analyses


Scripts and libraries for Environmental Genomics

The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes

piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions

Host Specificity of the Dickeya Bacteriophage PP35 Is Directed by a Tail Spike Interaction With Bacterial O-Antigen, Enabling the Infection of Alternative Non-pathogenic Bacterial Host

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase

Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus

A dataset of four probiotic Bifidobacterium strains genome assemblies

Draft Genome Sequence of Rhodococcus erythropolis HX7, a Psychrotolerant Soil-Derived Oil Degrader

Data on draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia)


The ideal tool for exploring global marine biogeochemical cycles.

GNOM v1.0: An optimized steady-state model of the modern marine neodymium cycle

AIBECS.jl: A tool for exploring global marine biogeochemical cycles.


[CVPR2022] DanceTrack: Multiple Object Tracking in Uniform Appearance and Diverse Motion

DanceTrack: Multi-Object Tracking in Uniform Appearance and Diverse Motion

MOTRv2: Bootstrapping End-to-End Multi-Object Tracking by Pretrained Object Detectors

MOTRv3: Release-Fetch Supervision for End-to-End Multi-Object Tracking

UTOPIA: Unconstrained Tracking Objects without Preliminary Examination via Cross-Domain Adaptation


A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data

Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal

Listeria monocytogenes, Escherichia coli and Coagulase Positive Staphylococci in Cured Raw Milk Cheese from Alentejo Region, Portugal

Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. in Two Natural Conservation Centers of Wildlife in Portugal: Genotypic and Phenotypic Characterization

Zenodo (CERN European Organization for Nuclear Research)

Genome mining reveals the prevalence and extensive diversity of toxin–antitoxin systems in Staphylococcus aureus


NuDup -- Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.

Genomic–transcriptomic evolution in lung cancer and metastasis

Functional characterization of a ‘plant-like’ HYL1 homolog in the cnidarian Nematostella vectensis indicates a conserved involvement in microRNA biogenesis

Cell Type-Specific Oxidative Stress Genomic Signatures in the Globus Pallidus of Dopamine-Depleted Mice

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

Multi-omic identification of key transcriptional regulatory programs during endurance exercise training

bioRxiv : the preprint server for biology

Dynamic antagonism between key repressive pathways maintains the placental epigenome


Application and data for analyzing and structuring portfolios for climate investing.


For calculating global feature importance using Shapley values.

Understanding Global Feature Contributions With Additive Importance Measures

Explaining by Removing: A Unified Framework for Model Explanation

Improving KernelSHAP: Practical Shapley Value Estimation via Linear Regression

Shapley variable importance clouds for interpretable machine learning

Understanding Global Feature Contributions Through Additive Importance Measures

DCI-ES: An Extended Disentanglement Framework with Connections to Identifiability

Information decomposition in complex systems via machine learning

Marginal Contribution Feature Importance -- an Axiomatic Approach for
  The Natural Case


A software tool for personalized and allele-specific CRISPR editing.

SNP-CRISPR: A Web Tool for SNP-Specific Genome Editing

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models

International journal of molecular sciences


A plugin to use Nvidia GPU in PySCF package

BAMBOO: a predictive and transferable machine learning force field
  framework for liquid electrolyte development

Python-Based Quantum Chemistry Calculations with GPU Acceleration


ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnrich provide functions to import any in-house catalogue, automate and plot the enrichment analysis for genomic regions.

Sequential enhancer state remodelling defines human germline competence and specification

Survivin promotes a glycolytic switch in CD4+ T cells by suppressing the transcription of PFKFB3 in rheumatoid arthritis

Survivin prevents the polycomb repressor complex 2 from methylating histone 3 lysine 27

Short Interrupted Repeat Cassette (SIRC)—Novel Type of Repetitive DNA Element Found in Arabidopsis thaliana


:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Plastic-degrading potential across the global microbiome correlates with recent pollution trends

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics

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


Multi-subject Single Cell Deconvolution

Resolving the immune landscape of human prostate at a single-cell level in health and cancer

Comprehensive evaluation of deconvolution methods for human brain gene expression

Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research

Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures

Exploring Additional Valuable Information From Single-Cell RNA-Seq Data

Frontiers in cell and developmental biology

DAISM-DNNXMBD: Highly accurate cell type proportion estimation with in silico data augmentation and deep neural networks

Strategies for cellular deconvolution in human brain RNA sequencing data

Deconvolution of a Large Cohort of Placental Microarray Data Reveals Clinically Distinct Subtypes of Preeclampsia

Frontiers in bioengineering and biotechnology

Single-cell RNA sequencing reveals in vivo osteoimmunology interactions between the immune and skeletal systems

A transcriptomic based deconvolution framework for assessing differentiation stages and drug responses of AML


A phenology modelling framework in R


Overview of the HECKTOR Challenge at MICCAI 2021: Automatic Head and Neck Tumor Segmentation and Outcome Prediction in PET/CT Images

Progression Free Survival Prediction for Head and Neck Cancer using Deep Learning based on Clinical and PET-CT Imaging Data

Head and Neck Cancer Primary Tumor Auto Segmentation using Model Ensembling of Deep Learning in PET-CT Images

MLC at HECKTOR 2022: The Effect and Importance of Training Data when Analyzing Cases of Head and Neck Tumors using Machine Learning


POET pipeline for reduction of Spitzer data

Absence of a thick atmosphere on the terrestrial exoplanet LHS 3844b

TESS Hunt for Young and Maturing Exoplanets (THYME). II. A 17 Myr Old Transiting Hot Jupiter in the Sco-Cen Association

TESS Hunt for Young and Maturing Exoplanets (THYME). V. A Sub-Neptune Transiting a Young Star in a Newly Discovered 250 Myr Association

K2 and Spitzer phase curves of the rocky ultra-short-period planet K2-141 b hint at a tenuous rock vapor atmosphere

The First Habitable-zone Earth-sized Planet from TESS. II. Spitzer Confirms TOI-700 d

Introducing a New Spitzer Master BLISS Map to Remove the Instrument Systematic Phase-curve-parameter Degeneracy, as Demonstrated by a Reanalysis of the 4.5 μm WASP-43b Phase Curve

Phase Curves of Hot Neptune LTT 9779b Suggest a High-metallicity Atmosphere

A Mirage or an Oasis? Water Vapor in the Atmosphere of the Warm Neptune TOI-674 b

Wolf 503 b: Characterization of a Sub-Neptune Orbiting a Metal-poor K Dwarf

Hazy with a Chance of Star Spots: Constraining the Atmosphere of Young Planet K2-33b


Composable Sparse Fine-Tuning for Cross-Lingual Transfer

AmericasNLI: Evaluating Zero-shot Natural Language Understanding of Pretrained Multilingual Models in Truly Low-resource Languages

Findings of the AmericasNLP 2021 Shared Task on Open Machine Translation for Indigenous Languages of the Americas

Proceedings of the First Workshop on Natural Language Processing for Indigenous Languages of the Americas

NRC-CNRC Machine Translation Systems for the 2021 AmericasNLP Shared Task

Peru is Multilingual, Its Machine Translation Should Be Too?

Distilling Efficient Language-Specific Models for Cross-Lingual Transfer


Repository for supplemental material of manuscripts

MEK inhibitors activate Wnt signalling and induce stem cell plasticity in colorectal cancer

Toward an integrated map of genetic interactions in cancer cells

Widespread Rewiring of Genetic Networks upon Cancer Signaling Pathway Activation

Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library

Time-resolved mapping of genetic interactions to model rewiring of signaling pathways

Detection of mutational patterns in cell‐free DNA of colorectal cancer by custom amplicon sequencing

Multi-omics integration identifies a selective vulnerability of colorectal cancer subtypes to YM155.

Pooled CRISPR screening at high sensitivity with an empirically designed sgRNA library


Tools for Easier Analysis of Meteorological Fields


The Rolling Hough Transform

Inference of the chromospheric magnetic field orientation in the Ca II 8542 Å line fibrils

Magnetically aligned straight depolarization canals and the rolling Hough transform

Turbulence and Energetic Particles in Radiative Shock Waves in the Cygnus Loop. II. Development of Postshock Turbulence

Multi-tracer analysis of straight depolarisation canals in the surroundings of the 3C 196 field

A Comparison of Multiphase Magnetic Field Tracers in a High Galactic Latitude Region of the Filamentary Interstellar Medium

HI filaments as potential compass needles? Comparing the magnetic field structure of the Small Magellanic Cloud to the orientation of GASKAP-HI filaments

MaLeFiSenta: Machine Learning for FilamentS Identification and Orientation in the ISM


Open mesh-to-mesh registration framework

Insights into the genetic architecture of the human face

MeshMonk: Open-source large-scale intensive 3D phenotyping

Precise modulation of transcription factor levels identifies features underlying dosage sensitivity

Precise modulation of transcription factor levels reveals drivers of dosage sensitivity

Three-dimensional facial capture using a custom-built photogrammetry setup: Design, performance, and cost

American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics


diploid SNV caller for error-prone reads

Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer

Longshot: accurate variant calling in diploid genomes using single-molecule long read sequencing

Sequencing of Monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection

Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq


Quantitative features for mass spectrometry data

Replication of single-cell proteomics data reveals important computational challenges

The current state of single-cell proteomics data analysis

DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data


A python tool that ingests WUDAPT information into WRF.

Local Climate Zones for Urban Temperature Studies

Bulletin of the American Meteorological Society

Evaluation of the ‘local climate zone’ scheme using temperature observations and model simulations

WUDAPT: An Urban Weather, Climate, and Environmental Modeling Infrastructure for the Anthropocene

WUDAPT, an efficient land use producing data tool for mesoscale models? Integration of urban LCZ in WRF over Madrid

Mapping Europe into local climate zones

LCZ Generator: A Web Application to Create Local Climate Zone Maps

Combining expert and crowd-sourced training data to map urban form and functions for the continental US

Evaluating the performance of a novel WUDAPT averaging technique to define urban morphology with mesoscale models


Temporal Network Tools

From static to temporal network theory: Applications to functional brain connectivity

Temporal flow of hubs and connectivity in the human brain

Brain network segregation and integration during painful thermal stimulation

Multiple spatial scale mapping of time-resolved brain network reconfiguration during evoked pain in patients with rheumatoid arthritis


A Python library for Secure and Explainable Machine Learning

Technical Report on the CleverHans v2.1.0 Adversarial Examples Library

Foolbox: A Python toolbox to benchmark the robustness of machine learning models

secml: Secure and explainable machine learning in Python

Combining Generators of Adversarial Malware Examples to Increase Evasion Rate


TransferAttack is a pytorch framework to boost the adversarial transferability for image classification.

Explaining and Harnessing Adversarial Examples

Adversarial examples in the physical world

Boosting Adversarial Attacks with Momentum

Improving Transferability of Adversarial Examples with Input Diversity

Evading Defenses to Transferable Adversarial Examples by Translation-Invariant Attacks

Nesterov Accelerated Gradient and Scale Invariance for Adversarial Attacks

Enhancing the Transferability of Adversarial Attacks through Variance Tuning

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

Enhancing Adversarial Example Transferability with an Intermediate Level Attack

Feature Importance-aware Transferable Adversarial Attacks


Train or evolve controllable and diverse level-generators.

PCGRL: Procedural Content Generation via Reinforcement Learning

Illuminating Diverse Neural Cellular Automata for Level Generation

Learning Controllable Content Generators

Learning Controllable 3D Level Generators

Tree Search vs Optimization Approaches for Map Generation


A repository for the BCIO ontology

Representation of behaviour change interventions and their evaluation: Development of the Upper Level of the Behaviour Change Intervention Ontology

The Behaviour Change Technique Ontology: Transforming the Behaviour Change Technique Taxonomy v1

Specifying who delivers behaviour change interventions: development of an Intervention Source Ontology

Specifying how intervention content is communicated: Development of a Style of Delivery Ontology


pyDVL is a library of stable implementations of algorithms for data valuation and influence function computation

Understanding Black-box Predictions via Influence Functions

Optimizing Neural Networks with Kronecker-factored Approximate Curvature

Data Shapley: Equitable Valuation of Data for Machine Learning

Towards Efficient Data Valuation Based on the Shapley Value

Second-Order Stochastic Optimization for Machine Learning in Linear Time

Efficient Task-Specific Data Valuation for Nearest Neighbor Algorithms

Fast Approximate Natural Gradient Descent in a Kronecker-factored Eigenbasis

Beta Shapley: a Unified and Noise-reduced Data Valuation Framework for Machine Learning

Data Banzhaf: A Robust Data Valuation Framework for Machine Learning

Scaling Up Influence Functions


Python code for downloading PV data from PVOutput.org


A Large Quadcopter Swarm

CrazyChoir: Flying Swarms of Crazyflie Quadrotors in ROS 2

GCBF+: A Neural Graph Control Barrier Function Framework for Distributed
  Safe Multi-Agent Control


MATLAB / Octave tools for BIDS datasets

Open and reproducible neuroimaging: From study inception to publication

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

Good scientific practice in EEG and MEG research: Progress and perspectives

Neural and physiological data from participants listening to affective music

BIDS-EEG: an extension to the Brain Imaging Data Structure (BIDS) Specification for electroencephalography

Intracranial electrophysiological recordings from the human brain during memory tasks with pupillometry


Code for "Prior Convictions: Black-Box Adversarial Attacks with Bandits and Priors"

Square Attack: a query-efficient black-box adversarial attack via random search

AdvSim: Generating Safety-Critical Scenarios for Self-Driving Vehicles

Projection & Probability-Driven Black-Box Attack

Black-box Adversarial Attacks with Bayesian Optimization

Adversarial Attack on Attackers: Post-Process to Mitigate Black-Box Score-Based Query Attacks

On the Effectiveness of Small Input Noise for Defending Against Query-based Black-Box Attacks


An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

Assemblathon 1: A competitive assessment of de novo short read assembly methods

GemSIM: general, error-model based simulator of next-generation sequencing data

Estimating telomere length from whole genome sequence data

CLEVER: Clique-Enumerating Variant Finder

De novo assembly of viral quasispecies using overlap graphs

Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan

Unraveling long non-coding RNAs through analysis of high-throughput RNA-sequencing data

Variant profiling of evolving prokaryotic populations

AMYCNE: Confident copy number assessment using whole genome sequencing data


DAGGEN: A synthethic task graph generator

A Comparison of Random Task Graph Generation Methods for Scheduling Problems

An improved Monte Carlo Tree Search approach to workflow scheduling

Limited Duplication-Based List Scheduling Algorithm for Heterogeneous Computing System


NeuroDebian packaging of SPM12 (official repo at https://github.com/spm)

fNIRS Optodes’ Location Decider (fOLD): a toolbox for probe arrangement guided by brain regions-of-interest

Blood-brain barrier imaging as a potential biomarker for bipolar disorder progression

Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and neurodegeneration: a prospective cross-sectional study


PyTorch implementation of Audio Flamingo: A Novel Audio Language Model with Few-Shot Learning and Dialogue Abilities.

Listen, Think, and Understand

LLark: A Multimodal Foundation Model for Music

Improving Text-To-Audio Models with Synthetic Captions


Learning Adversarially Fair and Transferable Representations

Controllable Guarantees for Fair Outcomes via Contrastive Information Estimation

Learning fair representation with a parametric integral probability metric

Learning Fair Rule Lists


CoAID: COVID-19 Healthcare Misinformation Dataset

Automated Classification of Fake News Spreaders to Break the Misinformation Chain

Analysing the Effect of Recommendation Algorithms on the Amplification of Misinformation

ARCNN framework for multimodal infodemic detection

Neural networks : the official journal of the International Neural Network Society

Multi-modal Misinformation Detection: Approaches, Challenges and Opportunities

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

People Still Care About Facts: Twitter Users Engage More with Factual Discourse than Misinformation--A Comparison Between COVID and General Narratives on Twitter


The official implementation of NeMo: Neural Mesh Models of Contrastive Features for Robust 3D Pose Estimation [ICLR-2021].  https://arxiv.org/pdf/2101.12378.pdf

OOD-CV: A Benchmark for Robustness to Out-of-Distribution Shifts of Individual Nuisances in Natural Images

OOD-CV-v2: An extended Benchmark for Robustness to Out-of-Distribution Shifts of Individual Nuisances in Natural Images


Official project website for the CVPR 2021 paper "Exploring intermediate representation for monocular vehicle pose estimation"

M3D-RPN: Monocular 3D Region Proposal Network for Object Detection

MonoPair: Monocular 3D Object Detection Using Pairwise Spatial Relationships

Kinematic 3D Object Detection in Monocular Video


PyTorch Implementation of Meta-StyleSpeech : Multi-Speaker Adaptive Text-to-Speech Generation

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

FastSpeech: Fast, Robust and Controllable Text to Speech

StyleTTS: A Style-Based Generative Model for Natural and Diverse Text-to-Speech Synthesis

SNAC: Speaker-Normalized Affine Coupling Layer in Flow-Based Architecture for Zero-Shot Multi-Speaker Text-to-Speech


transform-average-concatenate (TAC) method for end-to-end microphone permutation and number invariant ad-hoc beamforming.

Dual-path RNN: efficient long sequence modeling for time-domain single-channel speech separation

End-to-end Microphone Permutation and Number Invariant Multi-channel Speech Separation

FaSNet: Low-latency Adaptive Beamforming for Multi-microphone Audio Processing

L3DAS21 Challenge: Machine Learning for 3D Audio Signal Processing

Group Communication With Context Codec for Lightweight Source Separation

IEEE/ACM Transactions on Audio, Speech, and Language Processing

DESNet: A Multi-channel Network for Simultaneous Speech Dereverberation, Enhancement and Separation

A Time-Domain Real-Valued Generalized Wiener Filter for Multi-Channel Neural Separation Systems

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

Microphone Array Generalization for Multichannel Narrowband Deep Speech Enhancement

Implicit Filter-and-sum Network for Multi-channel Speech Separation


PyTorch code for EMNLP 2020 paper "X-LXMERT: Paint, Caption and Answer Questions with Multi-Modal Transformers"

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

Unifying Multimodal Transformer for Bi-directional Image and Text Generation

PROCEEDINGS OF THE 29TH ACM INTERNATIONAL CONFERENCE ON MULTIMEDIA, MM 2021


Code and data for ACL20 paper "Incorporating External Knowledge through Pre-training for Natural Language to Code Generation"

In-IDE Code Generation from Natural Language: Promise and Challenges

StructVAE: Tree-structured Latent Variable Models for Semi-supervised Semantic Parsing


A user friendly tools using Monte Carlo simulations for estimation of Curie temperature

Giant valley splitting in a MoTe2/MnSe2 van der Waals heterostructure with room-temperature ferromagnetism

Achieving High-Temperature Ferromagnetism by Means of Magnetic Ion Dimerization in the Graphene-like Mn2N6C6 Monolayer

Atomic Intercalation Induced Spin-Flip Transition in Bilayer CrI3

Tetragonal Mexican-Hat Dispersion and Switchable Half-Metal State with Multiple Anisotropic Weyl Fermions in Penta-Graphene


REFIT: A Unified Watermark Removal Framework For Deep Learning Systems With Limited Data

TATTOOED: A Robust Deep Neural Network Watermarking Scheme based on Spread-Spectrum Channel Coding

Non-Transferable Learning: A New Approach for Model Verification and Authorization.


CLIP+MLP Aesthetic Score Predictor

Optimizing Prompts for Text-to-Image Generation

LayoutLLM-T2I: Eliciting Layout Guidance from LLM for Text-to-Image Generation

Restart Sampling for Improving Generative Processes

HyperHuman: Hyper-Realistic Human Generation with Latent Structural Diffusion

X-IQE: eXplainable Image Quality Evaluation for Text-to-Image Generation with Visual Large Language Models

DEADiff: An Efficient Stylization Diffusion Model with Disentangled
  Representations

Quality and Quantity: Unveiling a Million High-Quality Images for Text-to-Image Synthesis in Fashion Design

Sampler Scheduler for Diffusion Models

PanGu-Draw: Advancing Resource-Efficient Text-to-Image Synthesis with Time-Decoupled Training and Reusable Coop-Diffusion


an easy-to-use interface to fine-tuned BERT models for computing semantic similarity in clinical and web text. that's it.

A Comparison of Document Similarity Algorithms

Commit Messages in the Age of Large Language Models

CultureBERT: Measuring Corporate Culture With Transformer-Based Language Models


[CVPR 2023] 3D Representation Learning via Foreground Aware Feature Contrast

PointRCNN: 3D Object Proposal Generation and Detection from Point Cloud

PV-RCNN: Point-Voxel Feature Set Abstraction for 3D Object Detection

From Points to Parts: 3D Object Detection from Point Cloud with Part-aware and Part-aggregation Network

Voxel R-CNN: Towards High Performance Voxel-based 3D Object Detection

Generalized 3D Self-supervised Learning Framework via Prompted Foreground-Aware Feature Contrast


Atwell et al data

Fast and flexible linear mixed models for genome-wide genetics

Subset-based genomic prediction provides insights into the genetic architecture of free amino acid levels in dry Arabidopsis thaliana seeds

Combining Sparse Group Lasso and Linear Mixed Model Improves Power to Detect Genetic Variants Underlying Quantitative Traits

Bivariate genomic analysis identifies a hidden locus associated with bacteria hypersensitive response in Arabidopsis thaliana


AudioMNIST: Exploring Explainable Artificial Intelligence for audio analysis on a simple benchmark

Unified Probabilistic Deep Continual Learning through Generative Replay and Open Set Recognition

Side Eye: Characterizing the Limits of POV Acoustic Eavesdropping from Smartphone Cameras with Rolling Shutters and Movable Lenses

SymJAX: symbolic CPU/GPU/TPU programming

Learnable filter-banks for CNN-based audio applications

Proceedings of the Northern Lights Deep Learning Workshop

Improving Compositionality of Neural Networks by Decoding Representations to Inputs

Disentangling Quantum and Classical Contributions in Hybrid Quantum Machine Learning Architectures


PTE: Predictive Text Embedding through Large-scale Heterogeneous Text Networks

Weakly-Supervised Neural Text Classification

International Conference on Information and Knowledge Management

Graph-based Semi-supervised Learning: A Comprehensive Review

VGCN-BERT: Augmenting BERT with Graph Embedding for Text Classification

HeteGCN: Heterogeneous Graph Convolutional Networks for Text Classification

Hierarchical Heterogeneous Graph Representation Learning for Short Text Classification

Graph Convolutional Network Based on Multi-Head Pooling for Short Text Classification

A Sequential Graph Neural Network for Short Text Classification

Representation Learning for Short Text Clustering


Practical Detection of Trojan Neural Networks: Data-Limited and Data-Free Cases

AEVA: Black-box Backdoor Detection Using Adversarial Extreme Value Analysis

Handcrafted Backdoors in Deep Neural Networks

Trigger Hunting with a Topological Prior for Trojan Detection

FreeEagle: Detecting Complex Neural Trojans in Data-Free Cases

Learning Topological Representations for Deep Image Understanding


Hiding Among the Clones: A Simple and Nearly Optimal Analysis of Privacy Amplification by Shuffling

Differentially Private Triangle and 4-Cycle Counting in the Shuffle Model

Differentially Private Synthetic Data via Foundation Model APIs 2: Text

Private Federated Statistics in an Interactive Setting


Single cell RNA Seq data analysis with quantitative phenotypes

Large-scale simultaneous measurement of epitopes and transcriptomes in single cells

Analysing high-throughput sequencing data in Python with HTSeq 2.0

Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue

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

Single-cell transcriptional dynamics of flavivirus infection

Pancreas patch-seq links physiologic dysfunction in diabetes to single-cell transcriptomic phenotypes

Northstar enables automatic classification of known and novel cell types from tumor samples

Developmental diversity and unique sensitivity to injury of lung endothelial subtypes during postnatal growth


neural variational document model

Neural Variational Inference for Text Processing

Pre-training is a Hot Topic: Contextualized Document Embeddings Improve Topic Coherence

Spherical Latent Spaces for Stable Variational Autoencoders

Neural Topic Modeling with Bidirectional Adversarial Training

ATM:Adversarial-neural Topic Model

Short Text Topic Modeling with Topic Distribution Quantization and Negative Sampling Decoder

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

Sparsemax and Relaxed Wasserstein for Topic Sparsity

Neural Topic Modeling with Cycle-Consistent Adversarial Training

Context Reinforced Neural Topic Modeling over Short Texts

Neural Mixed Counting Models for Dispersed Topic Discovery

Meeting of the Association for Computational Linguistics


LLM Self Defense: By Self Examination, LLMs know they are being tricked

LLM Self Defense: By Self Examination, LLMs Know They Are Being Tricked

Protecting Your LLMs with Information Bottleneck

On the Intrinsic Self-Correction Capability of LLMs: Uncertainty and Latent Concept


Pytorch Implementation of Knowing When to Look: Adaptive Attention via A Visual Sentinel for Image Captioning

Incorporating Sememes into Chinese Definition Modeling

Diversity as a By-Product: Goal-oriented Language Generation Leads to Linguistic Variation

Decoupling Pragmatics: Discriminative Decoding for Referring Expression Generation


OCR for DjVu

Kleister: Key Information Extraction Datasets Involving Long Documents with Complex Layouts

Kleister: A novel task for Information Extraction involving Long Documents with Complex Layout

CCpdf: Building a High Quality Corpus for Visually Rich Documents from Web Crawl Data


This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.

Automated high throughput animal CO1 metabarcode classification

DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness

Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments

Automated high throughput animal DNA metabarcode classification

Unveiling invasive insect threats to plant biodiversity: Leveraging eDNA metabarcoding and saturated salt trap solutions for biosurveillance

taxalogue: a toolkit to create comprehensive CO1 reference databases


code for "Fully Neural Network based Model for General Temporal Point Processes"

Intensity-Free Learning of Temporal Point Processes

Using Deep Learning for Flexible and Scalable Earthquake Forecasting

An Empirical Study: Extensive Deep Temporal Point Process


Acoustic mosquito detection code with Bayesian Neural Networks

Learning to detect an animal sound from five examples

HumBugDB: A Large-scale Acoustic Mosquito Dataset

Few-shot bioacoustic event detection at the DCASE 2022 challenge


Python library to convert textual numbers to integers

MCScript: A Novel Dataset for Assessing Machine Comprehension Using Script Knowledge

Revisiting Challenges in Data-to-Text Generation with Fact Grounding

International Conference on Natural Language Generation

From Characters to Time Intervals: New Paradigms for Evaluation and Neural Parsing of Time Normalizations

Transactions of the Association for Computational Linguistics


Papers of ComputerVision x Surgery

Surgical process modelling: a review

International Journal of Computer Assisted Radiology and Surgery

Exploiting the potential of unlabeled endoscopic video data with self-supervised learning

Objective Assessment of Surgical Technical Skill and Competency in the Operating Room

“Deep-Onto” network for surgical workflow and context recognition

International journal of computer assisted radiology and surgery

Real-Time Dense Stereo Reconstruction Using Convex Optimisation with a Cost-Volume for Image-Guided Robotic Surgery

Medical Image Computing and Computer-Assisted Intervention

Data-driven spatio-temporal RGBD feature encoding for action recognition in operating rooms

Surgical Tool Tracking and Pose Estimation in Retinal Microsurgery

Automatic phase prediction from low-level surgical activities

Automatic Operating Room Surgical Activity Recognition for Robot-Assisted Surgery

Deep Neural Networks Predict Remaining Surgery Duration from Cholecystectomy Videos


A Dual Reinforcement Learning Framework for Unsupervised Text Style Transfer (IJCAI 2019)

Phrase-Based & Neural Unsupervised Machine Translation

NAST: A Non-Autoregressive Generator with Word Alignment for Unsupervised Text Style Transfer

Adapter-TST: A Parameter Efficient Method for Multiple-Attribute Text Style Transfer

Learning Implicit Text Generation via Feature Matching


Insightface Keras implementation

MagFace: A Universal Representation for Face Recognition and Quality Assessment

AdaFace: Quality Adaptive Margin for Face Recognition

Mitigating dataset harms requires stewardship: Lessons from 1000 papers

LCAM: Low-Complexity Attention Module for Lightweight Face Recognition Networks


INTeractive learning via REPresentatIon Discovery

Is Q-learning Provably Efficient?

Provable Safe Reinforcement Learning with Binary Feedback

Towards Principled Representation Learning from Videos for Reinforcement
  Learning

Provable Interactive Learning with Hindsight Instruction Feedback


10W首中文歌词数据库

ChipSong: A Controllable Lyric Generation System for Chinese Popular Song

Proceedings of the First Workshop on Intelligent and Interactive Writing Assistants (In2Writing 2022)

Songs Across Borders: Singable and Controllable Neural Lyric Translation

CMDAG: A Chinese Metaphor Dataset with Annotated Grounds as CoT for
  Boosting Metaphor Generation


A heuristic solver for the set cover problem

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

Monthly Notices of the Royal Astronomical Society

What's The Latest? A Question-driven News Chatbot

Performance of the Quasar Spectral Templates for the Dark Energy Spectroscopic Instrument

A New View of Classification in Astronomy with the Archetype Technique: An Astronomical Case of the NP-complete Set Cover Problem

Modeling the Spectral Diversity of Quasars in the Sixteenth Data Release from the Sloan Digital Sky Survey


Fast underwater image enhancement for Improved Visual Perception. #TensorFlow #PyTorch #RAL2020

Fast Underwater Image Enhancement for Improved Visual Perception

A Generative Approach for Detection-driven Underwater Image Enhancement

DGD-cGAN: A Dual Generator for Image Dewatering and Restoration


Mass-editing thousands of facts into a transformer memory (ICLR 2023)

Mass-Editing Memory in a Transformer

Detecting Edit Failures In Large Language Models: An Improved Specificity Benchmark

Model Editing at Scale leads to Gradual and Catastrophic Forgetting

Untying the Reversal Curse via Bidirectional Language Model Editing

Model Editing Can Hurt General Abilities of Large Language Models

See the Unseen: Better Context-Consistent Knowledge-Editing by Noises

Empirical Study on Updating Key-Value Memories in Transformer
  Feed-forward Layers

Neighboring Perturbations of Knowledge Editing on Large Language Models

The Missing Piece in Model Editing: A Deep Dive into the Hidden Damage
  Brought By Model Editing

WikiFactDiff: A Large, Realistic, and Temporally Adaptable Dataset for
  Atomic Factual Knowledge Update in Causal Language Models


Deep Reinforcement Learning for Continuous Control in PyTorch

Continuous control with deep reinforcement learning

Soft Actor-Critic: Off-Policy Maximum Entropy Deep Reinforcement Learning with a Stochastic Actor

Addressing Function Approximation Error in Actor-Critic Methods

Continuous Deep Q-Learning with Model-based Acceleration

GRAC: Self-Guided and Self-Regularized Actor-Critic

Towards Automatic Actor-Critic Solutions to Continuous Control

A Closer Look at Advantage-Filtered Behavioral Cloning in High-Noise Datasets


A Persistent Weisfeiler–Lehman Procedure for Graph Classification

International Conference on Machine Learning

State of the Art and Potentialities of Graph-level Learning

Contrastive Graph Few-Shot Learning


Code for our paper "SimCLS: A Simple Framework for Contrastive Learning of Abstractive Summarization", ACL 2021

Expand, Rerank, and Retrieve: Query Reranking for Open-Domain Question Answering

GUMSum: Multi-Genre Data and Evaluation for English Abstractive Summarization


Crosslingual Generalization through Multitask Finetuning

Instruction Tuning for Large Language Models: A Survey

Scaling Up Models and Data with  and

A Survey of Large Language Models for Healthcare: from Data, Technology, and Applications to Accountability and Ethics

M4: Multi-generator, Multi-domain, and Multi-lingual Black-Box Machine-Generated Text Detection


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

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

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

PyAutoLens: Open-Source Strong Gravitational Lensing

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

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


Lifelong Learning with Dynamically Expandable Networks, ICLR 2018

Learn to Grow: A Continual Structure Learning Framework for Overcoming Catastrophic Forgetting

Bayesian Structure Adaptation for Continual Learning

TAME: Task Agnostic Continual Learning using Multiple Experts


This project develops the program FORGE. It allows to calculate gene p-values from Genome-Wide Association Data using multivariate methods. The gene-level statistics can be used for pathway or other system biology analyses (check out sister project for additional on pathway analysis with GWAS data: https://github.com/inti/GeneSetAnalysis/wiki). Check our Wiki for more details

Reduced Anxiety and Depression-Like Behaviours in the Circadian Period Mutant Mouse Afterhours

FORGE: multivariate calculation of gene-wide p-values from Genome-Wide Association Studies


VMD plugin to calculate and visualize clusters of conformations for a trajectory

Probing protein flexibility reveals a mechanism for selective promiscuity

Conformational and Immunogenicity Studies of the Shigella flexneri Serogroup 6 O-Antigen: The Effect of O-Acetylation

Subunit-Specific Photocontrol of Glycine Receptors by Azobenzene-Nitrazepam Photoswitcher


Mathematical notes and papers

Internal Universes in Models of Homotopy Type Theory

A cubical model of homotopy type theory

Strict universes for Grothendieck topoi

Sheaf semantics of termination-insensitive noninterference

Kripke-Joyal forcing for type theory and uniform fibrations

A Cubical Language for Bishop Sets

Denotational semantics of general store and polymorphism

Oracle modalities

Definable and Non-definable Notions of Structure

Double negation stable h-propositions in cubical sets


A tool for automatic spelling normalization

A Large-Scale Comparison of Historical Text Normalization Systems

North American Chapter of the Association for Computational Linguistics

Improving historical spelling normalization with bi-directional LSTMs and multi-task learning

Normalizing Medieval German Texts: from rules to deep learning

Learning attention for historical text normalization by learning to pronounce

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

Cross-lingual Cross-temporal Summarization: Dataset, Models, Evaluation


NeurIPS 2017 best paper. An interpretable linear-time kernel goodness-of-fit test.

A Linear-Time Kernel Goodness-of-Fit Test

Informative Features for Model Comparison

Denoising Score Matching with Random Fourier Features


Channel Reconstruction Network implemented in PyTorch

Multi-resolution CSI Feedback with deep learning in Massive MIMO System

Overview of Deep Learning-based CSI Feedback in Massive MIMO Systems

CLNet: Complex Input Lightweight Neural Network Designed for Massive MIMO CSI Feedback


Peak calling tool for CLIP-seq data

Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control

The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition

The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages

Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing

miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles

Improving CLIP-seq data analysis by incorporating transcript information

Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis

RNA damage compartmentalization by DHX9 stress granules

Time-Resolved Analysis of N-RNA Interactions during RVFV Infection Shows Qualitative and Quantitative Shifts in RNA Encapsidation and Packaging

Peakachu peaks of human uvCLAP datasets.

Zenodo (CERN European Organization for Nuclear Research)


Implementation of fast exact k-means algorithms

Fast K-Means with Accurate Bounds

Nested Mini-Batch K-Means


Code for fine-tuning Platypus fam LLMs using LoRA

LoRA: Low-Rank Adaptation of Large Language Models

Platypus: Quick, Cheap, and Powerful Refinement of LLMs


v1.5 and v1.6 OCPP implementation in Golang


Python library for analysing faces using PyTorch

RetinaFace: Single-stage Dense Face Localisation in the Wild

AdaFace: Quality Adaptive Margin for Face Recognition

Classifying Emotions and Engagement in Online Learning Based on a Single Facial Expression Recognition Neural Network

IEEE Transactions on Affective Computing

Facial expression and attributes recognition based on multi-task learning of lightweight neural networks

Symposium on Intelligent Systems and Informatics

Learning Multi-dimensional Edge Feature-based AU Relation Graph for Facial Action Unit Recognition

Synergy between 3DMM and 3D Landmarks for Accurate 3D Facial Geometry

Frame-level Prediction of Facial Expressions, Valence, Arousal and Action Units for Mobile Devices

Pre-training strategies and datasets for facial representation learning

Optimal Transport-based Identity Matching for Identity-invariant Facial Expression Recognition

Unified Negative Pair Generation toward Well-discriminative Feature Space for Face Recognition


This is the GitHub repository of the Building Efficiency Targeting Tool for Energy Retrofits (BETTER)


DeepWalk implementation in C++

VERSE: Versatile Graph Embeddings from Similarity Measures

WEB CONFERENCE 2018: PROCEEDINGS OF THE WORLD WIDE WEB CONFERENCE (WWW2018)

FREDE: Anytime Graph Embeddings

An open source knowledge graph ecosystem for the life sciences

Node Embedding with Adaptive Similarities for Scalable Learning over Graphs

Massively Parallel Graph Drawing and Representation Learning

Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome

Evaluating Scholarly Impact: Towards Content-Aware Bibliometrics

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

An Open-Source Knowledge Graph Ecosystem for the Life Sciences


A PyTorch Implementation of FastFusionNet on SQuAD 1.1

FusionNet: Fusing via Fully-Aware Attention with Application to Machine Comprehension

Can Small and Synthetic Benchmarks Drive Modeling Innovation? A Retrospective Study of Question Answering Modeling Approaches.

Fast Reading Comprehension with ConvNets

Do Question Answering Modeling Improvements Hold Across Benchmarks?

FastFusionNet: New State-of-the-Art for DAWNBench SQuAD

Integrated Triaging for Fast Reading Comprehension


The implementation of "A Weakly-supervised Framework for COVID-19 Classification and Lesion Localization from Chest CT"

Deep Learning-based Detection for COVID-19 from Chest CT using Weak Label

A Weakly-Supervised Framework for COVID-19 Classification and Lesion Localization From Chest CT

COVID-19 Control by Computer Vision Approaches: A Survey

IEEE access : practical innovations, open solutions

A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19

Computer Vision For COVID-19 Control: A Survey

Comparison and ensemble of 2D and 3D approaches for COVID-19 detection in CT images

Unsupervised Deep learning-based Feature Fusion Approach for Detection and Analysis of COVID-19 using X-ray and CT Images


A Framework for Textual Entailment based Zero Shot text classification

Label Verbalization and Entailment for Effective Zero and Few-Shot Relation Extraction

Aligning Instruction Tasks Unlocks Large Language Models as Zero-Shot Relation Extractors

Summarization as Indirect Supervision for Relation Extraction

Textual Entailment for Event Argument Extraction: Zero- and Few-Shot with Multi-Source Learning

Ask2Transformers: Zero-Shot Domain labelling with Pre-trained Language Models

Generative Prompt Tuning for Relation Classification

ZS4IE: A toolkit for Zero-Shot Information Extraction with simple Verbalizations


An implementation of the BADGE batch active learning algorithm.

Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds

SIMILAR: Submodular Information Measures Based Active Learning In Realistic Scenarios

Gone Fishing: Neural Active Learning with Fisher Embeddings

Effective Evaluation of Deep Active Learning on Image Classification Tasks

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

Streaming Active Learning with Deep Neural Networks

Unifying Approaches in Active Learning and Active Sampling via Fisher Information and Information-Theoretic Quantities

Advancing Deep Active Learning & Data Subset Selection: Unifying Principles with Information-Theory Intuitions

Low-Regret Active learning

Pareto Optimization for Active Learning under Out-of-Distribution Data Scenarios


Entity Abstraction in Visual Model-Based Reinforcement Learning

Physion: Evaluating Physical Prediction from Vision in Humans and Machines

GATSBI: Generative Agent-centric Spatio-temporal Object Interaction


LASER multilingual sentence embeddings as a pip package

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

NewsEmbed: Modeling News through Pre-trained Document Representations

Democratizing neural machine translation with OPUS-MT

Building Neural Machine Translation Systems for Multilingual Participatory Spaces


Very fast greedy diffeomorphic registration code

The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: advanced MRI, clinical, genomics, & radiomics

The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

NODEO: A Neural Ordinary Differential Equation Based Optimization Framework for Deformable Image Registration

Unsupervised Denoising of Retinal OCT with Diffusion Probabilistic Model

Direct and specific assessment of axonal injury and spinal cord microenvironments using diffusion correlation imaging

Unsupervised machine learning using K-means identifies radiomic subgroups of pediatric low-grade gliomas that correlate with key molecular markers

Accurate and Robust Alignment of Differently Stained Histologic Images Based on Greedy Diffeomorphic Registration

Accurate and Robust Alignment of Variable-stained Histologic Images Using a General-purpose Greedy Diffeomorphic Registration Tool

iEEG-recon: A Fast and Scalable Pipeline for Accurate Reconstruction of Intracranial Electrodes and Implantable Devices

medRxiv : the preprint server for health sciences

Clinically Deployed Computational Assessment of Multiple Sclerosis Lesions


Data, metadata, and software tools for the COSORE database of continuous soil respiration measurements

COSORE: A community database for continuous soil respiration and other soil‐atmosphere greenhouse gas flux data


node2vec implementation in C++

node2vec: Scalable Feature Learning for Networks

VERSE: Versatile Graph Embeddings from Similarity Measures

Massively Parallel Graph Drawing and Representation Learning


Power Law Distribution Fitting in python (and fortran and cython)

ALMA Observations of Massive Clouds in the Central Molecular Zone: Jeans Fragmentation and Cluster Formation

THE BOLOCAM GALACTIC PLANE SURVEY. XIII. PHYSICAL PROPERTIES AND MASS FUNCTIONS OF DENSE MOLECULAR CLOUD STRUCTURES

Protostellar Cores in Sagittarius B2 N and M


Tools/resources for journalism, media, communication, computational social science

Quantitative analysis of large amounts of journalistic texts using topic modelling

Data ex Machina: Introduction to Big Data

Large-Scale Computerized Text Analysis in Political Science: Opportunities and Challenges

Taking Stock of the Toolkit

Teaching the Computer to Code Frames in News: Comparing Two Supervised Machine Learning Approaches to Frame Analysis

Automated Text Classification of News Articles: A Practical Guide


A Novel Embedding Model for Knowledge Base Completion Based on Convolutional Neural Network (NAACL 2018) (Pytorch and Tensorflow)

A Capsule Network-based Embedding Model for Knowledge Graph Completion and Search Personalization

A Re-evaluation of Knowledge Graph Completion Methods

GreenKGC: A Lightweight Knowledge Graph Completion Method


Python implementation of the monster group

The maximal subgroups of the Monster

A computer-friendly construction of the monster

A fast implementation of the Monster group


General Use Binary Asteroid Simulator

Momentum transfer from the DART mission kinetic impact on asteroid Dimorphos

The excited spin state of Dimorphos resulting from the DART impact

Predictions for the Dynamical States of the Didymos System before and after the Planned DART Impact

Doubly synchronous binary asteroid mass parameter observability

Dynamical Evolution of the Didymos−Dimorphos Binary Asteroid as Rubble Piles following the DART Impact

High-fidelity Modeling of Rotationally Fissioned Asteroids

The accuracy of mutual potential approximations in simulations of binary asteroids


Scripts for analysis used during the course

Polygenic adaptation from standing genetic variation allows rapid ecotype formation

Whole-genome Analyses Reveal Past Population Fluctuations and Low Genetic Diversities of the North Pacific Albatrosses

Molecular Signatures of Reticulate Evolution within the Complex of European Pine Taxa


Feature extractor for DL speech processing.

Very Deep Convolutional Networks for Large-Scale Image Recognition

Deep speech inpainting of time-frequency masks

Anti-Transfer Learning for Task Invariance in Convolutional Neural Networks for Speech Processing

Word-Level Embeddings for Cross-Task Transfer Learning in Speech Processing

A novel audio representation using space filling curves


An Automated Scanning Transmission Electron Microscope Guided by Sparse Data Analytics

Towards Automating Structural Discovery in Scanning Transmission Electron Microscopy

Towards Augmented Microscopy with Reinforcement Learning-Enhanced Workflows

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

Probe microscopy is all you need

Machine Learning: Science and Technology


Scikit-learn friendly library to interpret, and prompt-engineer text datasets using large language models.

Explaining Patterns in Data with Language Models via Interpretable Autoprompting

Explaining black box text modules in natural language with language models

Augmenting Interpretable Models with LLMs during Training

Rethinking Interpretability in the Era of Large Language Models

Auto-Instruct: Automatic Instruction Generation and Ranking for Black-Box Language Models


A PyTorch library for two-sample tests

Generating Multivariate Load States Using a Conditional Variational Autoencoder

GANs with Conditional Independence Graphs: On Subadditivity of Probability Divergences


Measure instruction latency and throughput

Automated Instruction Stream Throughput Prediction for Intel and AMD Microarchitectures

PROCEEDINGS OF 2018 IEEE/ACM PERFORMANCE MODELING, BENCHMARKING AND SIMULATION OF HIGH PERFORMANCE COMPUTER SYSTEMS (PMBS 2018)

Automatic Throughput and Critical Path Analysis of x86 and ARM Assembly Kernels

PROCEEDINGS OF 2019 IEEE/ACM PERFORMANCE MODELING, BENCHMARKING AND SIMULATION OF HIGH PERFORMANCE COMPUTER SYSTEMS (PMBS 2019)

Execution‐Cache‐Memory modeling and performance tuning of sparse matrix‐vector multiplication and Lattice quantum chromodynamics on A64FX

Performance Modeling of Streaming Kernels and Sparse Matrix-Vector Multiplication on A64FX

PROCEEDINGS OF 2020 IEEE/ACM PERFORMANCE MODELING, BENCHMARKING AND SIMULATION OF HIGH PERFORMANCE COMPUTER SYSTEMS (PMBS 2020)

Bridging the Architecture Gap: Abstracting Performance-Relevant Properties of Modern Server Processors

Supercomputing Frontiers and Innovations


Interactive hydrodynamic solver for pipe and channel networks


Model compression by constrained optimization, using the Learning-Compression (LC) algorithm

Low-Rank Compression of Neural Nets: Learning the Rank of Each Layer

Model compression as constrained optimization, with application to neural nets. Part II: quantization

Model compression as constrained optimization, with application to neural nets. Part I: general framework

More General and Effective Model Compression via an Additive Combination of Compressions

LC: A Flexible, Extensible Open-Source Toolkit for Model Compression

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

A flexible, extensible software framework for model compression based on the LC algorithm