A continually expanding collection of cancer genomics notes and data

Robust enumeration of cell subsets from tissue expression profiles

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

Inferring tumour purity and stromal and immune cell admixture from expression data

UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses

GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

The prognostic landscape of genes and infiltrating immune cells across human cancers

Next-generation characterization of the Cancer Cell Line Encyclopedia

Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning


G-SchNet - a generative model for 3d molecular structures

Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules

MDM: Molecular Diffusion Model for 3D Molecule Generation

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

Symphony: Symmetry-Equivariant Point-Centered Spherical Harmonics for Molecule Generation


A code generator for grid-based PDE solving on CPUs and GPUs

Constraining axion inflation with gravitational waves from preheating

Constraining Axion Inflation with Gravitational Waves across 29 Decades in Frequency

Constraining early dark energy with gravitational waves before recombination

Nonperturbative structure in coupled axion sectors and implications for direct detection

Probing the electroweak symmetry breaking history with gravitational waves

Gauge preheating with full general relativity


Event network analyzer (eventnet): statistical analysis of networks of relational events.

Reliability of relational event model estimates under sampling: How to fit a relational event model to 360 million dyadic events

Dynamic network analysis of contact diaries

Micro-level network dynamics of scientific collaboration and impact: Relational hyperevent models for the analysis of coauthor networks

Relational hyperevent models for polyadic interaction networks

Relational hyperevent models for the coevolution of coauthoring and citation networks

Replication data for: Occupations and their impact on the spreading of COVID-19 in urban communities

Zenodo (CERN European Organization for Nuclear Research)


Translating Embeddings for Modeling Multi-relational Data

Learning Entity and Relation Embeddings for Knowledge Graph Completion

Proceedings of the AAAI Conference on Artificial Intelligence

Knowledge Graph Embedding by Translating on Hyperplanes

Knowledge Graph Embedding via Dynamic Mapping Matrix

PROCEEDINGS OF THE 53RD ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS AND THE 7TH INTERNATIONAL JOINT CONFERENCE ON NATURAL LANGUAGE PROCESSING, VOL 1


source code for paper "Riemannian Preconditioned LoRA for Fine-Tuning Foundation Models"

LoRA: Low-Rank Adaptation of Large Language Models

Mix-of-Show: Decentralized Low-Rank Adaptation for Multi-Concept Customization of Diffusion Models

Low-Rank Matrix Recovery with Scaled Subgradient Methods: Fast and Robust Convergence Without the Condition Number


An initial conditions generator for Gadget, modified from N-GenIC

The BAHAMAS project: Calibrated hydrodynamical simulations for large-scale structure cosmology

An efficient implementation of massive neutrinos in non-linear structure formation simulations

Monthly Notices of the Royal Astronomical Society - The BAHAMAS project: the CMB-large-scale structure tension and the roles of massive neutrinos and galaxy formation

MassiveNuS: cosmological massive neutrino simulations

Journal of Cosmology and Astroparticle Physics

Non-linear evolution of the cosmic neutrino background

The separate and combined effects of baryon physics and neutrino free streaming on large-scale structure

A hydrodynamical halo model for weak-lensing cross correlations

Connecting the structure of dark matter haloes to the primordial power spectrum

Monthly notices of the Royal Astronomical Society

SP(k) – a hydrodynamical simulation-based model for the impact of baryon physics on the non-linear matter power spectrum

Cosmology with velocity dispersion counts: an alternative to measuring cluster halo masses


Interactive multivariate data analysis in R implemented in shiny.

Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer

Genomic, Proteomic, and Metabolomic Data Integration Strategies

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

Understanding the response to endurance exercise using a systems biology approach: combining blood metabolomics, transcriptomics and miRNomics in horses

Commensal microbiota-derived metabolite agmatine triggers inflammation to promote colorectal tumorigenesis


Code for Paper (ReMax: A Simple, Efficient and Effective Reinforcement Learning Method for Aligning Large Language Models)

ReMax: A Simple, Effective, and Efficient Reinforcement Learning Method for Aligning Large Language Models

Adam-mini: Use Fewer Learning Rates To Gain More


Public repository for the work on bandit problems

Variational inference for the multi-armed contextual bandit

Bayesian bandits: balancing the exploration-exploitation tradeoff via double sampling

Nonparametric Gaussian Mixture Models for the Multi-Armed Bandit


Harassment Lexicon and Corpus

A Quality Type-aware Annotated Corpus and Lexicon for Harassment Research

Towards multidomain and multilingual abusive language detection: a survey

Analyzing and learning the language for different types of harassment

Hate Speech Detection via Dual Contrastive Learning


Code for measuring bispectra from cosmological simulation snapshots

Accurate initial conditions for cosmological N-body simulations: minimizing truncation and discreteness errors

A flexible modelling of galaxy assembly bias

Baryonic effects on the matter bispectrum

Simultaneous modelling of matter power spectrum and bispectrum in the presence of baryons

Three-point intrinsic alignments of dark matter haloes in the IllustrisTNG simulation

The halo bispectrum as a sensitive probe of massive neutrinos and baryon physics


RISC-V Instruction Set Simulator (Built for education).

A Survey of the RISC-V Architecture Software Support


Natural Gradient, Variational Inference

Optimizing Neural Networks with Kronecker-factored Approximate Curvature

Noisy Natural Gradient as Variational Inference

Eigenvalue Corrected Noisy Natural Gradient

Predictive Uncertainty Quantification with Compound Density Networks

Walsh-Hadamard Variational Inference for Bayesian Deep Learning


Strongest attack against Feature Scatter and Adversarial Interpolation

Defense Against Adversarial Attacks Using Feature Scattering-based Adversarial Training

Boosting Adversarial Training with Hypersphere Embedding

Bilateral Adversarial Training: Towards Fast Training of More Robust Models Against Adversarial Attacks

Adversarial Distributional Training for Robust Deep Learning

Improving Adversarial Robustness via Guided Complement Entropy


Arioc:  GPU-accelerated DNA short-read alignment

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Arioc: GPU-accelerated alignment of short bisulfite-treated reads

Arioc: High-concurrency short-read alignment on multiple GPUs


Curated List of papers on Time Series Analysis

Deep learning for time series classification: a review

Transfer Learning for Financial Time Series Forecasting

Pacific Rim International Conference on Artificial Intelligence

Multi-source transfer learning of time series in cyclical manufacturing

Generative Adversarial Networks for Failure Prediction

Multivariate Time Series as Images: Imputation Using Convolutional Denoising Autoencoder

Analysis of Wide and Deep Echo State Networks for Multiscale Spatiotemporal Time Series Forecasting

Proceedings of the 7th Annual Neuro-inspired Computational Elements Workshop


Official code for "CoDi: Co-evolving Contrastive Diffusion Models for Mixed-type Tabular Synthesis", ICML 2023

Mixed-Type Tabular Data Synthesis with Score-based Diffusion in Latent Space

Diffusion Models for Tabular Data Imputation and Synthetic Data
  Generation


Generating Information-Seeking Conversations from Unlabeled Documents (EMNLP 2022).

Longformer: The Long-Document Transformer

FewshotQA: A simple framework for few-shot learning of question answering tasks using pre-trained text-to-text models

Book2Dial: Generating Teacher-Student Interactions from Textbooks for
  Cost-Effective Development of Educational Chatbots


Notes on SNP-related tools and genome variation analysis

DELLY: structural variant discovery by integrated paired-end and split-read analysis

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

LUMPY: A probabilistic framework for structural variant discovery

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

A universal SNP and small-indel variant caller using deep neural networks

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis

International journal of methods in psychiatric research


A CIFAR10-like galaxy image dataset

Scaling Laws for Galaxy Images


On-Premise DeepFake Detection SDK for Linux

Taming Transformers for High-Resolution Image Synthesis

FaceForensics++: Learning to Detect Manipulated Facial Images

MesoNet: a Compact Facial Video Forgery Detection Network

International Workshop on Information Forensics and Security

Unmasking DeepFakes with simple Features

Rethinking the Up-Sampling Operations in CNN-based Generative Network for Generalizable Deepfake Detection


Conservative Q-Learning for Offline Reinforcement Learning

Critic Regularized Regression

Offline Prioritized Experience Replay

Improving and Benchmarking Offline Reinforcement Learning Algorithms


Intelligent Health Care: Applications of Deep Learning in Computational Medicine

DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening

基因组蛋白质组与生物信息学报

Trends and Potential of Machine Learning and Deep Learning in Drug Study at Single-Cell Level

A computational framework of host-based drug repositioning for broad-spectrum antivirals against RNA viruses

An in silico drug repositioning workflow for host-based antivirals


Official Code for our MICCAI 2022 paper "Exploring Smoothness and Class-Separation for Semi-supervised Medical Image Segmentation"

Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective

Cross-Adversarial Local Distribution Regularization for Semi-supervised Medical Image Segmentation


Kilonova models associated to papers using POSSIS

Optical follow-up of the neutron star–black hole mergers S200105ae and S200115j

The critical role of nuclear heating rates, thermalization efficiencies, and opacities for kilonova modelling and parameter inference

Detectability of kilonovae in optical surveys: post-mortem examination of the LVC O3 run follow-up

Polarized kilonovae from black hole–neutron star mergers

Predicting electromagnetic counterparts using low-latency gravitational-wave data products

Impact of jets on kilonova photometric and polarimetric emission from binary neutron star mergers

A search for the afterglows, kilonovae, and host galaxies of two short GRBs: GRB 211106A and GRB 211227A

Predictions for electromagnetic counterparts to Neutron Star mergers discovered during LIGO-Virgo-KAGRA observing runs 4 and 5

Kilonova-Targeting Lightcurve Classification for Wide Field Survey Telescope


Small collection of random useful perl scripts

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches

Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus


MRAugment: physics-aware data augmentation for deep learning based accelerated MRI reconstruction

fastMRI: An Open Dataset and Benchmarks for Accelerated MRI

End-to-End Variational Networks for Accelerated MRI Reconstruction

Data augmentation for deep learning based accelerated MRI reconstruction with limited data


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

Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer–Giedion syndrome and Cornelia de Lange syndrome-4

Biallelic structural variations within FGF12 detected by long-read sequencing in epilepsy

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

Finding rearrangements in nanopore DNA reads with last and dnarrange


Code for "Efficient Relation-aware Scoring Function Search for Knowledge Graph Embedding" ICDE 2021

NSCaching: Simple and Efficient Negative Sampling for Knowledge Graph Embedding

AutoSF: Searching Scoring Functions for Knowledge Graph Embedding

Interstellar: Searching Recurrent Architecture for Knowledge Graph Embedding


Image-to-Image Translation with Conditional Adversarial Networks

Skin Lesion Synthesis with Generative Adversarial Networks

OR 2.0 CONTEXT-AWARE OPERATING THEATERS, COMPUTER ASSISTED ROBOTIC ENDOSCOPY, CLINICAL IMAGE-BASED PROCEDURES, AND SKIN IMAGE ANALYSIS, OR 2.0 2018

Skin cancer segmentation and classification with improved deep convolutional neural network

SLSNet: Skin lesion segmentation using a lightweight generative adversarial network

Segmentation of skin lesions and their attributes using Generative Adversarial Networks


STOPGAP is a MATLAB-based package for subtomogram averaging.

A modular platform for automated cryo-FIB workflows

In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli

Structures of the eukaryotic ribosome and its translational states in situ

STOPGAP: an open-source package for template matching, subtomogram alignment and classification

bioRxiv : the preprint server for biology

In situ architecture of the ciliary base reveals the stepwise assembly of IFT trains


Open source code for ACL 2020 Paper "Dynamic Fusion Network for Multi-Domain End-to-end Task-Oriented Dialog"

Global-to-local Memory Pointer Networks for Task-Oriented Dialogue

Learning Knowledge Bases with Parameters for Task-Oriented Dialogue Systems

Intention Reasoning Network for Multi-Domain End-to-end Task-Oriented Dialogue

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


Reinforcement Learning based 'Learning' of Dynamic Sepsis Treatment Strategies

Off-Policy Deep Reinforcement Learning without Exploration

Benchmarking Batch Deep Reinforcement Learning Algorithms

Unifying Cardiovascular Modelling with Deep Reinforcement Learning for Uncertainty Aware Control of Sepsis Treatment


Machine Learning for Genomics and Therapeutics Resources (Cell Patterns)

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection

DeepCRISPR: optimized CRISPR guide RNA design by deep learning

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

Predicting tumor cell line response to drug pairs with deep learning

MethylNet: an automated and modular deep learning approach for DNA methylation analysis

Melissa: Bayesian clustering and imputation of single-cell methylomes

Extracting microRNA-gene relations from biomedical literature using distant supervision

Machine Learning Applications for Therapeutic Tasks with Genomics Data


This repository contains code to apply vision transformers on surface data

Surface Vision Transformers: Attention-Based Modelling applied to Cortical Analysis

Surface Analysis with Vision Transformers

Surface Vision Transformers: Flexible Attention-Based Modelling of Biomedical Surfaces

The Multiscale Surface Vision Transformer


ESC: Redesigning WSD with Extractive Sense Comprehension

North American Chapter of the Association for Computational Linguistics

ConSeC: Word Sense Disambiguation as Continuous Sense Comprehension

Nibbling at the Hard Core of Word Sense Disambiguation

WiC = TSV = WSD: On the Equivalence of Three Semantic Tasks

LexicoMatic: Automatic Creation of Multilingual Lexical-Semantic Dictionaries

Proceedings of the 13th International Joint Conference on Natural Language Processing and the 3rd Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics (Volume 1: Long Papers)


Codebase for GANITE: Estimation of Individualized Treatment Effects using GANs - ICLR 2018

A Survey of Deep Causal Models and Their Industrial Applications

Learning to Infer Counterfactuals: Meta-Learning for Estimating Multiple Imbalanced Treatment Effects

Causal Effect Estimation using Variational Information Bottleneck


QuickerADC is an implementation of highly-efficient product quantizers leveraging SIMD shuffle instructions integrated into FAISS

Product Quantization for Nearest Neighbor Search

IEEE transactions on pattern analysis and machine intelligence

Efficient and Robust Approximate Nearest Neighbor Search Using Hierarchical Navigable Small World Graphs

The Inverted Multi-Index

Accelerated Nearest Neighbor Search with Quick ADC

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

Quicker ADC : Unlocking the Hidden Potential of Product Quantization With SIMD


Multi-threaded implementation of the Tsetlin Machine, Convolutional Tsetlin Machine, Regression Tsetlin Machine, and Weighted Tsetlin Machine, with support for continuous features and multigranularity.

The Tsetlin Machine - A Game Theoretic Bandit Driven Approach to Optimal Pattern Recognition with Propositional Logic

The Convolutional Tsetlin Machine

Extending the Tsetlin Machine With Integer-Weighted Clauses for Increased Interpretability

Explainable Tsetlin Machine Framework for Fake News Detection with Credibility Score Assessment

On the Convergence of Tsetlin Machines for the XOR Operator

Measuring the Novelty of Natural Language Text Using the Conjunctive Clauses of a Tsetlin Machine Text Classifier

A Scheme for Continuous Input to the Tsetlin Machine with Applications to Forecasting Disease Outbreaks

Coalesced Multi-Output Tsetlin Machines with Clause Sharing

A Tsetlin Machine with Multigranular Clauses

Word-level human interpretable scoring mechanism for novel text detection using Tsetlin Machines


Statistical Recurrent Unit based time series generative models for detecting nonlinear Granger causality

Economy Statistical Recurrent Units For Inferring Nonlinear Granger Causality

Interpretable Models for Granger Causality Using Self-explaining Neural Networks

Rhino: Deep Causal Temporal Relationship Learning With History-dependent Noise

Learning interaction rules from multi-animal trajectories via augmented behavioral models


Python 3 support for the MS COCO caption evaluation tools

CIDEr: Consensus-based Image Description Evaluation

Microsoft COCO Captions: Data Collection and Evaluation Server

SPICE: Semantic Propositional Image Caption Evaluation

CLIPScore: A Reference-free Evaluation Metric for Image Captioning

Visual Captioning at Will: Describing Images and Videos Guided by a Few Stylized Sentences


[ICML 2022] Graph Stochastic Attention (GSAT) for interpretable and generalizable graph learning.

Parameterized Explainer for Graph Neural Network

Interpretable and Generalizable Graph Learning via Stochastic Attention Mechanism

Learning Invariant Molecular Representation in Latent Discrete Space

Interpretable Prototype-based Graph Information Bottleneck


Characterizing Entities in the Bitcoin Blockchain

A Probabilistic Model of the Bitcoin Blockchain


Code to run submissions for the Atlantic Causal Inference Competition

Automated versus Do-It-Yourself Methods for Causal Inference: Lessons Learned from a Data Analysis Competition

Treatment effect estimation with disentangled latent factors

On Inductive Biases for Heterogeneous Treatment Effect Estimation

A Unified Survey of Treatment Effect Heterogeneity Modelling and Uplift Modelling

Counterfactual Representation Learning with Balancing Weights

In Search of Insights, Not Magic Bullets: Towards Demystification of the Model Selection Dilemma in Heterogeneous Treatment Effect Estimation

A unified survey of treatment effect heterogeneity modeling and uplift modeling

Estimating causal effects with optimization-based methods: A review and empirical comparison

European Journal of Operational Research

Doing Great at Estimating CATE? On the Neglected Assumptions in Benchmark Comparisons of Treatment Effect Estimators

Ensemble Method for Estimating Individualized Treatment Effects


Code to accompany "Reversing unknown quantum transformations: A universal protocol for inverting general unitary operations"

Probabilistic exact universal quantum circuits for transforming unitary operations

Universal construction of decoders from encoding black boxes


NetVLAD: CNN architecture for weakly supervised place recognition

NetVLAD: CNN Architecture for Weakly Supervised Place Recognition

Robust Image Retrieval-based Visual Localization using Kapture

Benchmarking Image Retrieval for Visual Localization

Hyperdimensional computing as a framework for systematic aggregation of image descriptors

Investigating the Role of Image Retrieval for Visual Localization

International Journal of Computer Vision

Sequential Place Learning: Heuristic-Free High-Performance Long-Term Place Recognition

VLAD-BuFF: Burst-Aware Fast Feature Aggregation for Visual Place Recognition


Kosp2e: Korean Speech to English Translation Corpus

Open Korean Corpora: A Practical Report

Proceedings of Second Workshop for NLP Open Source Software (NLP-OSS)

mHuBERT-147: A Compact Multilingual HuBERT Model


The code repo contains multiple code reproduction processes of various SOTA deep learning algorithms

Attention Is All You Need

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

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

Off-Policy Deep Reinforcement Learning without Exploration

Distributed Distributional Deterministic Policy Gradients

AWAC: Accelerating Online Reinforcement Learning with Offline Datasets


A toolkit for testing machine translation [ICSE'20, '21, ESEC/FSE'20]

Structure-Invariant Testing for Machine Translation

SemMT: A Semantic-Based Testing Approach for Machine Translation Systems

Machine Translation Testing via Syntactic Tree Pruning


The associated repo for paper "Data-Efficient Learning of Natural Language to Linear Temporal Logic Translators for Robot Task Specification"

Language Models are Few-Shot Learners

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

Planning with State Abstractions for Non-Markovian Task Specifications


Official repository for the paper "Neural Differential Equations for Learning to Program Neural Nets Through Continuous Learning Rules" (NeurIPS 2022)

Linear Transformers Are Secretly Fast Weight Programmers

Going Beyond Linear Transformers with Recurrent Fast Weight Programmers

A Modern Self-Referential Weight Matrix That Learns to Modify Itself


HANNA, a large annotated dataset of Human-ANnotated NArratives for ASG evaluation.

RoBERTa: A Robustly Optimized BERT Pretraining Approach

CTRL: A Conditional Transformer Language Model for Controllable Generation

Of Human Criteria and Automatic Metrics: A Benchmark of the Evaluation of Story Generation

A Temporal Variational Model for Story Generation

Do Language Models Enjoy Their Own Stories? Prompting Large Language Models for Automatic Story Evaluation


A set of scripts for calculating pairwise SNP distance

Fast and flexible bacterial genomic epidemiology with PopPUNK

Dissemination of Mycobacterium abscessus via global transmission networks

Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial

Population structure and transmission of Mycobacterium bovis in Ethiopia

Genomic surveillance of multidrug-resistant Klebsiella in Wales reveals persistent spread of Klebsiella pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids

Epidemiologic and Genomic Reidentification of Yaws, Liberia

Detection of SARS-CoV-2 infection clusters: The useful combination of spatiotemporal clustering and genomic analyses

Colonization and transmission of Staphylococcus aureus in schools: a citizen science project

Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage


SSRNET for hyperspectral and multispectral image fusion.

Deep Learning in Multimodal Remote Sensing Data Fusion: A Comprehensive Review

SSR-NET: Spatial–Spectral Reconstruction Network for Hyperspectral and Multispectral Image Fusion

IEEE Transactions on Geoscience and Remote Sensing

Hyperspectral and Multispectral Image Fusion Using the Conditional Denoising Diffusion Probabilistic Model

Crossed Dual-Branch U-Net for Hyperspectral Image Super-Resolution

IEEE journal of selected topics in applied earth observations and remote sensing


Code for paper "Adversarial Support Alignment"

Domain-Adversarial Training of Neural Networks

A DIRT-T Approach to Unsupervised Domain Adaptation

Domain Adaptation with Conditional Distribution Matching and Generalized Label Shift

Domain Adaptation with Asymmetrically-Relaxed Distribution Alignment

Adversarial Support Alignment


[ICCV'19] Improving Adversarial Robustness via Guided Complement Entropy

Explaining and Harnessing Adversarial Examples

Towards Deep Learning Models Resistant to Adversarial Attacks

Boosting Adversarial Attacks with Momentum


Learning to Drop: Robust Graph Neural Network via Topological Denoising & Robust Graph Representation Learning via Neural Sparsification

Sparse Graph Attention Networks

Robust Preference-Guided Denoising for Graph based Social Recommendation

Adversarially Robust Neural Architecture Search for Graph Neural Networks

Finding Heterophilic Neighbors via Confidence-based Subgraph Matching for Semi-supervised Node Classification

Proceedings of the 31st ACM International Conference on Information & Knowledge Management

Data Augmentation for Graph Data: Recent Advancements

Combating Bilateral Edge Noise for Robust Link Prediction

A Comparative Study on Robust Graph Neural Networks to Structural Noises

Improving Signed Propagation for Graph Neural Networks


Author implementation of "Learning Recurrent Span Representations for Extractive Question Answering" (Lee et al. 2016)

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

Learning to Search in Long Documents Using Document Structure

Do Question Answering Modeling Improvements Hold Across Benchmarks?


Code to accompany the paper 'Improving model calibration with accuracy versus uncertainty optimization'.

Can You Trust Your Model's Uncertainty? Evaluating Predictive Uncertainty Under Dataset Shift

Evaluating Bayesian Deep Learning Methods for Semantic Segmentation

Loss-Calibrated Approximate Inference in Bayesian Neural Networks


[NeurIPS'22] What Makes a "Good" Data Augmentation in Knowledge Distillation -- A Statistical Perspective

mixup: Beyond Empirical Risk Minimization

Improved Regularization of Convolutional Neural Networks with Cutout

AutoAugment: Learning Augmentation Policies from Data


Alternative chill models and functions to handle or download weather data


Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file

The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization

The tuatara genome reveals ancient features of amniote evolution

Comparative genomics of 10 new Caenorhabditis species

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution

Zenodo (CERN European Organization for Nuclear Research)

Whole-genome microsynteny-based phylogeny of angiosperms

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

Continental-Scale Gene Flow Prevents Allopatric Divergence of Pelagic Freshwater Bacteria

The Genome of Caenorhabditis bovis

Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities

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

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event


SRS - Fast Approximate Nearest Neighbor Search in High Dimensional Euclidean Space With a Tiny Index

Approximate Nearest Neighbor Search on High Dimensional Data — Experiments, Analyses, and Improvement

IEEE Transactions on Knowledge and Data Engineering

Locality-Sensitive Hashing Scheme based on Longest Circular Co-Substring

Approximate Nearest Neighbor Search on High Dimensional Data --- Experiments, Analyses, and Improvement (v1.0)


[NeurIPS 2021] Better Safe Than Sorry: Preventing Delusive Adversaries with Adversarial Training

Image Shortcut Squeezing: Countering Perturbative Availability Poisons with Compression

Learning the Unlearnable: Adversarial Augmentations Suppress Unlearnable Example Attacks

Corrupting Convolution-based Unlearnable Datasets with Pixel-based Image Transformations


[IEEE Access] "Head Network Distillation: Splitting Distilled Deep Neural Networks for Resource-constrained Edge Computing Systems" and [ACM MobiCom HotEdgeVideo 2019] "Distilled Split Deep Neural Networks for Edge-assisted Real-time Systems"

Split Computing and Early Exiting for Deep Learning Applications: Survey and Research Challenges

Distilled Split Deep Neural Networks for Edge-Assisted Real-Time Systems

Proceedings of the 2019 Workshop on Hot Topics in Video Analytics and Intelligent Edges

Head Network Distillation: Splitting Distilled Deep Neural Networks for Resource-Constrained Edge Computing Systems

BottleFit: Learning Compressed Representations in Deep Neural Networks for Effective and Efficient Split Computing

IEEE International Symposium on a World of Wireless, Mobile and Multimedia Networks


Evaluating video predictions from the standpoint of a robot making action decisions

Deep Visual Foresight for Planning Robot Motion

Predicting Deeper into the Future of Semantic Segmentation

Action-conditioned Benchmarking of Robotic Video Prediction Models: a Comparative Study


Verilog implementation of the symmetric block cipher AES (Advanced Encryption Standard) as specified in NIST FIPS 197. This implementation supports 128 and 256 bit keys.

OpenABC-D: A Large-Scale Dataset For Machine Learning Guided Integrated Circuit Synthesis

An Experimental Study of Building Blocks of Lattice-Based NIST Post-Quantum Cryptographic Algorithms

A Scalable Formal Verification Methodology for Data-Oblivious Hardware

Too Big to Fail? Active Few-Shot Learning Guided Logic Synthesis


Omnigrok: Grokking Beyond Algorithmic Data

Grokking: Generalization Beyond Overfitting on Small Algorithmic Datasets

Identifying Equivalent Training Dynamics


GMSS2.0 is a software package for implementing stochastic ground motion simulation using finite-fault sources.

An Updated Corner-Frequency Model for Stochastic Finite-Fault Ground-Motion Simulation

Bulletin of the Seismological Society of America

A Computational Tool for Ground-Motion Simulations Incorporating Regional Crustal Conditions

GMSS2.0: An Enhanced Software Program for Stochastic Finite-Fault Ground-Motion Simulation


Implementation of BFT consensus protocols based on the Narwhal mempool.

Narwhal and Tusk: A DAG-based Mempool and Efficient BFT Consensus

Bullshark: DAG BFT Protocols Made Practical

Sui Lutris: A Blockchain Combining Broadcast and Consensus

Motorway: Seamless high speed BFT

JUMBO: Fully Asynchronous BFT Consensus Made Truly Scalable


Python interface to synchrotron libraries

A snapshot of the oldest AGN feedback phases

A population of galaxy-scale jets discovered using LOFAR

Monthly Notices of the Royal Astronomical Society

The nature of compact radio sources: the case of FR0 radio galaxies

Investigating the spectra and physical nature of galaxy scale jets

Unmasking the history of 3C 293 with LOFAR sub-arcsecond imaging

AGN feedback in the FR II galaxy 3C 220.1

Monthly notices of the Royal Astronomical Society

Relic jet activity in 'Hanny's Voorwerp' revealed by the LOFAR two metre sky survey

Seeing the forest and the trees: A radio investigation of the ULIRG Mrk 273

Re-energisation of AGN head-tail radio galaxies in the galaxy cluster ZwCl0634.1+47474

LOFAR discovery and wide-band characterisation of an ultra-steep spectrum AGN radio remnant associated with Abell 1318


Taxi Traffic Speed/Flow Prediction Benchmark(based on Shanghai Taxi Dataset)

Spatio-Temporal Graph Convolutional Networks: A Deep Learning Framework for Traffic Forecasting

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

Graph WaveNet for Deep Spatial-Temporal Graph Modeling


Collection of Paper Ranking method implementations

BIP4COVID19: Impact metrics and indicators for coronavirus related publications


Unofficial implementation of some fantastic shallow domain adaptation (SDA) methods.

Joint Geometrical and Statistical Alignment for Visual Domain Adaptation

Discriminative Transfer Subspace Learning via Low-Rank and Sparse Representation

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

Domain Invariant and Class Discriminative Feature Learning for Visual Domain Adaptation

Unsupervised Domain Adaptation via Structured Prediction Based Selective Pseudo-Labeling

Visual domain adaptation via transfer feature learning

Aggregating Randomized Clustering-Promoting Invariant Projections for Domain Adaptation

IEEE transactions on pattern analysis and machine intelligence

Discriminative and Geometry-Aware Unsupervised Domain Adaptation

Active Transfer Learning

IEEE Transactions on Circuits and Systems for Video Technology

Discriminant Geometrical and Statistical Alignment With Density Peaks for Domain Adaptation

Maximum Mean and Covariance Discrepancy for Unsupervised Domain Adaptation


Official implementation of Learning The Pareto Front With HyperNetworks [ICLR 2021]

Learning the Pareto Front with Hypernetworks

Controllable Pareto Multi-Task Learning

Scalable Unidirectional Pareto Optimality for Multi-Task Learning with Constraints

Multi-Task Learning with Multi-Task Optimization


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


High Relative Degree Control Barrier Functions Under Input Constraints

Control Barrier Functions in Sampled-Data Systems

Guaranteed Safe Spacecraft Docking With Control Barrier Functions

Compositions of Multiple Control Barrier Functions Under Input Constraints

Predictive Control Barrier Functions for Online Safety Critical Control

Safety-Critical Control for Systems With Impulsive Actuators and Dwell Time Constraints

Robust Safety-Critical Control for Systems With Sporadic Measurements and Dwell-Time Constraints


This repository contains code used for the fly brain activity experiments

Fast near-whole–brain imaging in adult Drosophila during responses to stimuli and behavior

Valence and State-Dependent Population Coding in Dopaminergic Neurons in the Fly Mushroom Body

Global change in brain state during spontaneous and forced walk in Drosophila is composed of combined activity patterns of different neuron classes

A dopamine-gated learning circuit underpins reproductive state-dependent odor preference in Drosophila females


X-Class: Text Classification with Extremely Weak Supervision

MEGClass: Extremely Weakly Supervised Text Classification via Mutually-Enhancing Text Granularities

XAI-CLASS: Explanation-Enhanced Text Classification with Extremely Weak Supervision

Towards Weakly-Supervised Hate Speech Classification Across Datasets


Spatial Temporal Graph Convolutional Networks (ST-GCN) for Skeleton-Based Action Recognition in PyTorch

A Comprehensive Survey on Graph Neural Networks

IEEE transactions on neural networks and learning systems

Graph Neural Networks: A Review of Methods and Applications

Spatial Temporal Graph Convolutional Networks for Skeleton-Based Action Recognition

Graph Embedded Pose Clustering for Anomaly Detection

Human in Events: A Large-Scale Benchmark for Human-centric Video Analysis in Complex Events

Spatial-Temporal Graph Convolutional Networks for Sign Language Recognition

Mimetics: Towards Understanding Human Actions Out of Context

Normalizing Flows for Human Pose Anomaly Detection

GeomNet: A Neural Network Based on Riemannian Geometries of SPD Matrix Space and Cholesky Space for 3D Skeleton-Based Interaction Recognition

IEEE International Conference on Computer Vision

Hierarchically Self-Supervised Transformer for Human Skeleton Representation Learning


Correlation-consistent Gaussian basis sets for solids made simple

Ground-State Properties of Metallic Solids from Ab Initio Coupled-Cluster Theory.

Double-Hybrid DFT Functionals for the Condensed Phase: Gaussian and Plane Waves Implementation and Evaluation

Integral-direct Hartree-Fock and Møller-Plesset Perturbation Theory for Periodic Systems with Density Fitting: Application to the Benzene Crystal

Exploring cesium-tellurium phase space via high-throughput calculations beyond semi-local density-functional theory.

Optical Properties of Defects in Solids via Quantum Embedding with Good Active Space Orbitals

Accurate, fast and generalisable first principles simulation of aqueous lithium chloride

Ab Initio Quantum-Mechanical Predictions of Semiconducting Photocathode Materials

Ab initio quantum many-body description of superconducting trends in the cuprates

CO Adsorption on the Surface of MgO from Periodic Coupled-Cluster Theory with Local Natural Orbitals: Adding to the Consensus


Author Disambiguation using Knowledge Graph Embeddings with Literals

Complex Embeddings for Simple Link Prediction

Embedding Entities and Relations for Learning and Inference in Knowledge Bases

SPECTER: Document-level Representation Learning using Citation-informed Transformers

A knowledge graph embeddings based approach for author name disambiguation using literals

AMiner-534K - Dataset

OC-782K: Knowledge Graph of "Scientometrics" modelled according to the OpenCitations Data Model

Dataset for paper: " Knowledge Graph Embeddings based Approach for Author Name Disambiguation using Literals"


Code to read/write tables of rotation measures following the proposed standard.

The Galactic Faraday rotation sky 2020

Magnetism Science with the Square Kilometre Array

The POlarised GLEAM Survey (POGS) II: Results from an all-sky rotation measure synthesis survey at long wavelengths

Publications of the Astronomical Society of Australia

Discovery of ASKAP J173608.2–321635 as a Highly Polarized Transient Point Source with the Australian SKA Pathfinder

The Faraday Rotation Measure Grid of the LOFAR Two-metre Sky Survey: Data Release 2

Revisiting Rotation Measures from the Canadian Galactic Plane Survey: the Magnetic Field in the Disk of the Outer Galaxy

The Astrophysical Journal Supplement Series

RMTable2023 and PolSpectra2023: Standards for Reporting Polarization and Faraday Rotation Measurements of Radio Sources

The Rapid ASKAP Continuum Survey III: Spectra and Polarisation In Cutouts of Extragalactic Sources (SPICE-RACS) first data release

The Global Magneto-Ionic Medium Survey (GMIMS): the brightest polarized region in the southern sky at 75 cm and its implications for Radio Loop II

Prototype Faraday rotation measure catalogs from the Polarisation Sky
  Survey of the Universe's Magnetism (POSSUM) pilot observations


DMRGPy is a Python library to compute quasi-one-dimensional spin chains and fermionic systems using matrix product states with DMRG as implemented in ITensor. Most of the computations can be performed both with DMRG and exact diagonalization for small systems, which allows one to benchmark the results.

Topological spin excitations in Harper-Heisenberg spin chains

Non-Hermitian many-body topological excitations in interacting quantum dots

Lee-Yang theory of criticality in interacting quantum many-body systems

Inducing a many-body topological state of matter through Coulomb-engineered local interactions

Topological phase diagrams of exactly solvable non-Hermitian interacting Kitaev chains

Designing quantum many-body matter with conditional generative adversarial networks

Solitonic in-gap modes in a superconductor-quantum antiferromagnet interface

Dynamical topological excitations in parafermion chains

Kondo lattice mediated interactions in flat-band systems

Real-space imaging of dispersive triplon excitations in engineered quantum magnets


Learning from Indirect Observations

Learning Noise Transition Matrix from Only Noisy Labels via Total Variation Regularization

Learning from Aggregate Observations

Approximating Instance-Dependent Noise via Instance-Confidence Embedding

Learning from Indirect Observations


A journey into Convolutional Neural Network visualization

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

International Journal of Computer Vision

Learning Deep Features for Discriminative Localization

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


Probabilistic Programming eXecution protocol (PPX)

Technology Readiness Levels for Machine Learning Systems

Efficient Probabilistic Inference in the Quest for Physics Beyond the Standard Model

Planning as Inference in Epidemiological Models

Probabilistic Surrogate Networks for Simulators with Unbounded Randomness


Burgess et al. "MONet: Unsupervised Scene Decomposition and Representation"

On the Relationship Between Variational Inference and Auto-Associative Memory

Compositional Image Decomposition with Diffusion Models


Creative Commons Attribution Share Alike 4.0 International

GEMBA — GPT Estimation Metric Based Assessment

Large Language Models Are State-of-the-Art Evaluators of Translation Quality

GEMBA-MQM: Detecting Translation Quality Error Spans with GPT-4

The Eval4NLP 2023 Shared Task on Prompting Large Language Models as Explainable Metrics

Not All Metrics Are Guilty: Improving NLG Evaluation by Diversifying References

Beyond Correlation: Interpretable Evaluation of Machine Translation Metrics


Evolve Me A Cluster of StarS

The devil is in the tails: the role of globular cluster mass evolution on stream properties

Towards an N-body model for the globular cluster M4

A prescription and fast code for the long-term evolution of star clusters - III. Unequal masses and stellar evolution

The initial conditions of observed star clusters - I. Method description and validation


Zero-Shot Cross-Lingual Semantic Parsing (Sherborne & Lapata, ACL 2022)

Zero-Shot Cross-lingual Semantic Parsing

Bootstrapping a Crosslingual Semantic Parser

Extrinsic Evaluation of Machine Translation Metrics

On Evaluating Multilingual Compositional Generalization with Translated Datasets


Code to prepare and use common datasets for scene analysis tasks

Efficient RGB-D Semantic Segmentation for Indoor Scene Analysis

Efficient Multi-Task RGB-D Scene Analysis for Indoor Environments

Efficient Multi-Task Scene Analysis with RGB-D Transformers

PanopticNDT: Efficient and Robust Panoptic Mapping


32 projects in the framework of Deep Reinforcement Learning algorithms: Q-learning, DQN, PPO, DDPG, TD3, SAC, A2C and others. Each project is provided with a detailed training log.

Proximal Policy Optimization Algorithms

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

Addressing Function Approximation Error in Actor-Critic Methods

FORK: A FORward-looKing Actor for Model-Free Reinforcement Learning


code for generating metrics of forest vertical structure from airborne LiDAR data


Processing and analysis of proteomics data

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

Proteomic and phosphoproteomic landscapes of acute myeloid leukemia

Inflammatory osteolysis is regulated by site-specific ISGylation of the scaffold protein NEMO

Immune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infection

Loss of KMT2C reprograms the epigenomic landscape in hPSCs resulting in NODAL overexpression and a failure of hemogenic endothelium specification

Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses

KDM6A knockout in human iPSCs alters the genome-wide histone methylation profile at active and poised enhancers, activating expression of ectoderm gene expression pathways


PyTorch code for our CoLLAs-2022 paper "Online Continual Learning for Embedded Devices"

F-SIOL-310: A Robotic Dataset and Benchmark for Few-Shot Incremental Object Learning

Continual Learning for Autonomous Robots: A Prototype-based Approach


MM-Vet: Evaluating Large Multimodal Models for Integrated Capabilities (ICML 2024)

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

MM-Vet v2: A Challenging Benchmark to Evaluate Large Multimodal Models for Integrated Capabilities


Code for the paper "Disentanglement by Nonlinear ICA with General Incompressible-flow Networks (GIN)" (2020)

On the Identifiability of Nonlinear ICA: Sparsity and Beyond

Generalizing Nonlinear ICA Beyond Structural Sparsity


A Generalized Web Component for Domain-Independent Smart Assistants

A Semantic Web Framework for Automated Smart Assistants: A Case Study for Public Health

A Semantic Web Framework for Automated Smart Assistants: COVID-19 Case Study


"Learning to Generate Realistic Noisy Images via Pixel-level Noise-aware Adversarial Training" (NeurIPS 2021)

Toward Convolutional Blind Denoising of Real Photographs

Unprocessing Images for Learned Raw Denoising

Dual Adversarial Network: Toward Real-world Noise Removal and Noise Generation

GRDN:Grouped Residual Dense Network for Real Image Denoising and GAN-based Real-world Noise Modeling


Code deobfuscation framework to simplify Mixed Boolean-Arithmetic (MBA) expressions

Binary Code Similarity Detection

Efficient Deobfuscation of Linear Mixed Boolean-Arithmetic Expressions

Semdiff: Binary Similarity Detection by Diffing Key-Semantics Graphs

Simplification of General Mixed Boolean-Arithmetic Expressions: GAMBA


SportVU movement tracking data.

Multi-Modal Trajectory Prediction of NBA Players

Group Activity Recognition in Basketball Tracking Data -- Neural Embeddings in Team Sports (NETS)

ESTA: An Esports Trajectory and Action Dataset


Theory and operational rules for the discrete Hankel transform

Journal of the Optical Society of America. A, Optics, image science, and vision

Matlab code for the Discrete Hankel Transform

The Discrete Hankel Transform


The COVID-19 Real World Worry Datasets

COVID-19 open source data sets: a comprehensive survey

Measuring Emotions in the COVID-19 Real World Worry Dataset

Covid-19: Open-Data Resources for Monitoring, Modeling, and Forecasting the Epidemic

Multilingual topic modeling for tracking COVID-19 trends based on Facebook data analysis

Applied intelligence (Dordrecht, Netherlands)

Open Data Resources for Fighting COVID-19


Multilinear PageRank

Multilinear PageRank

SIAM Journal on Matrix Analysis and Applications

Perron‐based algorithms for the multilinear PageRank

Numerical Linear Algebra with Applications


[ICML 2020] "When Does Self-Supervision Help Graph Convolutional Networks?" by Yuning You, Tianlong Chen, Zhangyang Wang, Yang Shen

Graph Self-Supervised Learning: A Survey

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

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


German Text Embedding Clustering Benchmark

MTEB: Massive Text Embedding Benchmark

TSDAE: Using Transformer-based Sequential Denoising Auto-Encoder for Unsupervised Sentence Embedding Learning


Recursive Diffeomorphism-Based Regression for Shape Functions

Multiresolution mode decomposition for adaptive time series analysis

A Fast Algorithm for Multiresolution Mode Decomposition


Taskmaster-1: Toward a Realistic and Diverse Dialog Dataset

Findings of the WMT 2024 Shared Task on Chat Translation

Tencent AI Lab Machine Translation Systems for WMT20 Chat Translation Task

Empirical Methods in Natural Language Processing

Modeling Bilingual Conversational Characteristics for Neural Chat Translation

Towards Making the Most of Dialogue Characteristics for Neural Chat Translation

Scheduled Multi-task Learning for Neural Chat Translation

The University of Edinburgh-Uppsala University’s Submission to the WMT 2020 Chat Translation Task

HAL (Le Centre pour la Communication Scientifique Directe)

Recent Advances in Dialogue Machine Translation

Low Resource Chat Translation: A Benchmark for Hindi–English Language Pair

Conference of the Association for Machine Translation in the Americas

A Multi-Task Multi-Stage Transitional Training Framework for Neural Chat Translation


WordBias: Visualizing Intersectional Social biases encoded in Word Embeddings

WordBias: An Interactive Visual Tool for Discovering Intersectional Biases Encoded in Word Embeddings

STILE: Exploring and Debugging Social Biases in Pre-trained Text Representations

Proceedings of the CHI Conference on Human Factors in Computing Systems

Towards Fair and Explainable AI using a Human-Centered AI Approach


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

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

Bayesian Optimization over Discrete and Mixed Spaces via Probabilistic Reparameterization

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

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

Domain-Agnostic Batch Bayesian Optimization with Diverse Constraints via Bayesian Quadrature

A Quadrature Approach for General-Purpose Batch Bayesian Optimization
  via Probabilistic Lifting

BruSLeAttack: A Query-Efficient Score-Based Black-Box Sparse Adversarial
  Attack


Creative Commons Attribution 4.0 International

This repository holds the code for my master thesis entitles "The Association of Gender Bias with BERT - Measuring, Mitigating and Cross-lingual portability"

Unmasking Contextual Stereotypes: Measuring and Mitigating BERT's Gender Bias.

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

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

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

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


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

Deep Learning for General Game Playing with Ludii and Polygames

Biasing MCTS with Features for General Games

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


Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

Somatic Hypermutation in Enhancer Regions Shapes Non-Coding Myeloma Genome, Generating DNA Breaks and Driving Etiology through Mutation and Structural Variation

Whole-Genome Sequencing Identifies Structural Variation As a Key Driver of Disease Relapse and Aggressive Clinical Behavior in Multiple Myeloma


Supervised Predictive Medical Image Registration Model

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

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

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


General-Purpose Reinforcement Learning

Deep Residual Learning for Image Recognition

Squeeze-and-Excitation Networks

MobileNetV2: Inverted Residuals and Linear Bottlenecks

CBAM: Convolutional Block Attention Module

Identity Mappings in Deep Residual Networks

Effective Approaches to Attention-based Neural Machine Translation

Searching for MobileNetV3

Hybrid computing using a neural network with dynamic external memory

Human-level performance in 3D multiplayer games with population-based reinforcement learning


Versatile FASTA/FASTQ demultiplexer.

An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing

Differential Modulation of the European Sea Bass Gut Microbiota by Distinct Insect Meals

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem

Soil warming increases the number of growing bacterial taxa but not their growth rates

Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan’s Great Rift Valley


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

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

SAITS: Self-Attention-based Imputation for Time Series

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

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


OPT-IML: Scaling Language Model Instruction Meta Learning through the Lens of Generalization

StylePTB: A Compositional Benchmark for Fine-grained Controllable Text Style Transfer

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

Towards Zero-Shot Functional Compositionality of Language Models


Safety Score for Pre-Trained Language Models

Baichuan 2: Open Large-scale Language Models

Textbooks Are All You Need II: phi-1.5 technical report

An Empirical Study of Metrics to Measure Representational Harms in Pre-Trained Language Models

Examining Forgetting in Continual Pre-training of Aligned Large Language Models


Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.

Rapid evolution of piRNA clusters in theDrosophila melanogasterovary

bioRxiv : the preprint server for biology

Transposable elements generate regulatory novelty in a tissue-specific fashion

Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration

Confined migration induces heterochromatin formation and alters chromatin accessibility

Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression

A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development.

WEE1 inhibition induces anti-tumor immunity by activating ERV and the dsRNA pathway

Evolution of mouse circadian enhancers from transposable elements

Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape

Transposable Elements Continuously Remodel the Regulatory Landscape, Transcriptome, and Function of Decidual Stromal Cells


Bag of MLP

MLP-Mixer: An all-MLP Architecture for Vision

ResMLP: Feedforward networks for image classification with data-efficient training

Pay Attention to MLPs


A set of instruments to design the sustainability-quality concerns at the software architecture level, and define and operationalize them

Characterizing the contribution of quality requirements to software sustainability

Architecture Design Decision Maps for Software Sustainability

International Conference on Software Engineering

An Action Research for Improving the Sustainability Assessment Framework Instruments

Towards a Software Sustainability-Quality Model: Insights from a Multi-Case Study

Research Challenges in Information Science

Sustainability Competencies and Skills in Software Engineering: An Industry Perspective

Sustainability in Software Architecture: A Systematic Mapping Study

The Sustainability Assessment Framework Toolkit: A Decade of Modeling
  Experience


Implementation of the paper "Adversarial Attacks on Neural Networks for Graph Data".

Deep Learning on Graphs: A Survey

Adversarial Attack and Defense on Graph Data: A Survey

Adversarial Attacks and Defenses on Graphs: A Review and Empirical Study

Are Defenses for Graph Neural Networks Robust?

Graph Sanitation with Application to Node Classification

Efficient, Direct, and Restricted Black-Box Graph Evasion Attacks to Any-Layer Graph Neural Networks via Influence Function

Topological Effects on Attacks Against Vertex Classification

A Systematic Review of Deep Graph Neural Networks: Challenges, Classification, Architectures, Applications & Potential Utility in Bioinformatics


A Python implementation of the rough Bergomi model.

Turbocharging Monte Carlo pricing for the rough Bergomi model

Non-adversarial training of Neural SDEs with signature kernel scores

A path-dependent PDE solver based on signature kernels

Bartlett's Delta revisited: Variance-optimal hedging in the lognormal SABR and in the rough Bergomi model


[PAKDD 2021] Graph InfoClust: Leveraging cluster-level node information for unsupervised graph representation learning

Graph Self-Supervised Learning: A Survey

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

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

Graph InfoClust: Maximizing Coarse-Grain Mutual Information in Graphs

Pacific-Asia Conference on Knowledge Discovery and Data Mining

HeMI: Multi-view Embedding in Heterogeneous Graphs


Code for MedCPT, a model for zero-shot biomedical information retrieval.

MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval

Improving medical reasoning through retrieval and self-reflection with retrieval-augmented large language models

AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale
  Clinical Tool Learning


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

Multiplex Heterogeneous Graph Convolutional Network

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

Subset Node Representation Learning over Large Dynamic Graphs

Accelerating Dynamic Network Embedding with Billions of Parameter Updates to Milliseconds

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


Pytorch implementation of Hebbian learning algorithms to train deep convolutional neural networks.

Hebbian Semi-Supervised Learning in a Sample Efficiency Setting

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

Comparing the performance of Hebbian against backpropagation learning using convolutional neural networks

Deep Features for CBIR with Scarce Data using Hebbian Learning

Training Convolutional Neural Networks With Hebbian Principal Component Analysis


Dataset of 11,072 radiocarbon dates from the Near East from the Late Pleistocene until the Late Holocene (15 - 1.5 cal. kyr BP).

Human responses and non-responses to climatic variations during the last Glacial-Interglacial transition in the eastern Mediterranean

Holocene regional population dynamics and climatic trends in the Near East: A first comparison using archaeo-demographic proxies

Collapse and continuity: A multi-proxy reconstruction of settlement organization and population trajectories in the Northern Fertile Crescent during the 4.2kya Rapid Climate Change event


Code accompanying the NeurIPS 2019 paper "GOT: An Optimal Transport framework for Graph comparison"

Fast and Robust Comparison of Probability Measures in Heterogeneous Spaces

FGOT: Graph Distances based on Filters and Optimal Transport


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


Implementation of the multiple sequential markovian coalescent

Stairway Plot 2: demographic history inference with folded SNP frequency spectra

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

MSMC and MSMC2: The Multiple Sequentially Markovian Coalescent

Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant

Intra-species differences in population size shape life history and genome evolution

Limits and Convergence properties of the Sequentially Markovian Coalescent

Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events

Protocol to analyze population structure and migration history based on human genome variation data


Codebase for Generative Adversarial Imputation Networks (GAIN) - ICML 2018

GAIN: Missing Data Imputation using Generative Adversarial Nets

MisGAN: Learning from Incomplete Data with Generative Adversarial Networks

Variational Autoencoder with Arbitrary Conditioning

Handling Missing Data with Graph Representation Learning

Missing Data Imputation using Optimal Transport

Imputation of Missing Data with Class Imbalance using Conditional Generative Adversarial Networks

Why Not to Use Zero Imputation? Correcting Sparsity Bias in Training Neural Networks

Deep learning-based phenotype imputation on population-scale biobank data increases genetic discoveries

Deep Generative Pattern-Set Mixture Models for Nonignorable Missingness

Handling Missing Data via Max-Entropy Regularized Graph Autoencoder


Media Forensics / Fake Detection experiments in PyTorch. Implements Fighting Fake News: Image Splice Detection via Learned Self-Consistency

Media Forensics and DeepFakes: an overview

A Survey of Machine Learning Techniques in Adversarial Image Forensics

Adversarial Attack on Deep Learning-Based Splice Localization


Input Purification Defense Against Trojan Attacks on Deep Neural Network Systems

Towards Effective and Robust Neural Trojan Defenses via Input Filtering

Watch Out! Simple Horizontal Class Backdoor Can Trivially Evade Defense

DataElixir: Purifying Poisoned Dataset to Mitigate Backdoor Attacks via Diffusion Models


Official PyTorch Implementation of Long-Short Transformer (NeurIPS 2021).

Long-Short Transformer: Efficient Transformers for Language and Vision

Temporal Latent Bottleneck: Synthesis of Fast and Slow Processing Mechanisms in Sequence Learning

A Primal-Dual Framework for Transformers and Neural Networks


Improving Scene Text Image Super-Resolution via  Dual Prior Modulation Network (AAAI 2023)

Scene Text Image Super-Resolution in the Wild

Improving Scene Text Image Super-resolution via Dual Prior Modulation Network

PEAN: A Diffusion-based Prior-Enhanced Attention Network for Scene Text Image Super-Resolution


Pytorch notebook with One Cycle Policy implementation (https://arxiv.org/abs/1803.09820)

Cyclical Learning Rates for Training Neural Networks

A disciplined approach to neural network hyper-parameters: Part 1 -- learning rate, batch size, momentum, and weight decay

Wide-minima Density Hypothesis and the Explore-Exploit Learning Rate Schedule


The analysis of satellite imagery can provide vital insights in various corporate and governmental application areas. Semantic segmentation of satellite imagery provides dense pixel-wise knowledge, which is necessary to facilitate such analysis. Deep convolutional neural networks are state of the art, when it comes to semantic segmentation of digital images. However, characteristics unique to satellite imagery like their high-resolution, multi-channel input and limited availability of data-sets challenge the designing, parametrizing and training of the neural network model.

MobileNetV2: Inverted Residuals and Linear Bottlenecks

Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation

Rethinking Atrous Convolution for Semantic Image Segmentation


Facial image inpainting is a task of filling visually realistic and semantically meaningful contents for missing or masked pixels in a face image. This paper presents EXE-GAN, a novel diverse and interactive facial inpainting framework, which can not only preserve the high-quality visual effect of the whole image but also complete the face image with exemplar-like facial attributes.

Paint by Example: Exemplar-based Image Editing with Diffusion Models

Reference-Guided Large-Scale Face Inpainting With Identity and Texture Control

Do Inpainting Yourself: Generative Facial Inpainting Guided by Exemplars

PATMAT: Person Aware Tuning of Mask-Aware Transformer for Face inpainting


[T-IFS] RNN-SM: Fast Steganalysis of VoIP Streams Using Recurrent Neural Network

IEEE Transactions on Information Forensics and Security

Fast Steganalysis Method for VoIP Streams

FCEM: A Novel Fast Correlation Extract Model For Real Time Steganalysis of VoIP Stream via Multi-head Attention

Hierarchical Representation Network for Steganalysis of QIM Steganography in Low-Bit-Rate Speech Signals

Real-Time Steganalysis for Stream Media Based on Multi-channel Convolutional Sliding Windows

F3SNet: A Four-Step Strategy for QIM Steganalysis of Compressed Speech Based on Hierarchical Attention Network


Training a MNIST classifier, and use it to compute inception score (ICP)

ALICE: Towards Understanding Adversarial Learning for Joint Distribution Matching

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

G-PATE: Scalable Differentially Private Data Generator via Private Aggregation of Teacher Discriminators

DataLens: Scalable Privacy Preserving Training via Gradient Compression and Aggregation

Conference on Computer and Communications Security


Visual question answering for CVPR16 VQA Challenge.

Dynamic Memory Networks for Visual and Textual Question Answering

Generating Factoid Questions With Recurrent Neural Networks: The 30M Factoid Question-Answer Corpus

Open-Ended Visual Question-Answering


Time-Aware LSTM

Patient Subtyping via Time-Aware LSTM Networks

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

CATNet: Cross-event Attention-based Time-aware Network for Medical Event Prediction


compute bolometric corrections and synthetic colours for input values of stellar parameters

On the use of Gaia magnitudes and new tables of bolometric corrections

Monthly Notices of the Royal Astronomical Society: Letters

Synthetic Stellar Photometry - II. Testing the bolometric flux scale and tables of bolometric corrections for the Hipparcos/Tycho, Pan-STARRS1, SkyMapper, and JWST systems

The GALAH survey: effective temperature calibration from the InfraRed Flux Method in the Gaia system

The all-sky PLATO input catalogue

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

Fundamental stellar parameters of benchmark stars from CHARA interferometry

Precision angular diameters for 16 southern stars with VLTI/PIONIER

Characterization of 92 southern TESS candidate planet hosts and a new photometric [Fe/H] relation for cool dwarfs

Analysis of eclipsing binaries in multiple stellar systems: the case of V1200 Centauri

Titans metal-poor reference stars II. Red giants and CEMP stars


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

GloDyNE: Global Topology Preserving Dynamic Network Embedding

IEEE Transactions on Knowledge and Data Engineering

Accelerating Dynamic Network Embedding with Billions of Parameter Updates to Milliseconds

Robust Dynamic Network Embedding via Ensembles


BCP-MAPF – branch-and-cut-and-price for multi-agent path finding

Priority Inheritance with Backtracking for Iterative Multi-agent Path Finding

Improving LaCAM for Scalable Eventually Optimal Multi-Agent Pathfinding

Tracking Progress in Multi-Agent Path Finding


a reimplementation of Holistically-Nested Edge Detection in PyTorch

Holistically-Nested Edge Detection

Unsupervised Domain Generalization by Learning a Bridge Across Domains

Edge Augmentation for Large-Scale Sketch Recognition without Sketches

Layout Aware Inpainting for Automated Furniture Removal in Indoor Scenes

Dark Side Augmentation: Generating Diverse Night Examples for Metric Learning

Shape Defense Against Adversarial Attacks

Automated Grain Boundary (GB) Segmentation and Microstructural Analysis in 347H Stainless Steel Using Deep Learning and Multimodal Microscopy


Toolbox with R scripts

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

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

Sexually dimorphic activation of innate antitumor immunity prevents adrenocortical carcinoma development

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

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

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


[Paper][SIGIR2022] Meta-Knowledge Transfer for Inductive Knowledge Graph Embedding

Inductive Relation Prediction by Subgraph Reasoning

Contrastive Learning with Generated Representations for Inductive Knowledge Graph Embedding

Findings of the Association for Computational Linguistics: ACL 2023

Task-Oriented GNNs Training on Large Knowledge Graphs for Accurate and Efficient Modeling


Self-supervised pre-training method to fuse LiDAR and camera features.

Masked Autoencoders Are Scalable Vision Learners

CrossViT: Cross-Attention Multi-Scale Vision Transformer for Image Classification


A benchmark for the task of translation suggestion

WeTS: A Benchmark for Translation Suggestion

TSMind: Alibaba and Soochow University's Submission to the WMT22 Translation Suggestion Task

Easy Guided Decoding in Providing Suggestions for Interactive Machine Translation


Component data sheets, busbars and files needed to build no-weld BMS DKblock style battery packs.   Here is a YouTube video, courtesy of Nick Jobbitt of a 10 block build, sped up: https://www.youtube.com/watch?v=V05_WOhEqQg&feature=youtu.be    ................    DKblock2 parts available on ebay search "DKblock


(NeurIPS 2021) Revisiting Deep Learning Models for Tabular Data

Transfer Learning with Deep Tabular Models

Towards Cross-Table Masked Pretraining for Web Data Mining

UniTabE: Pretraining a Unified Tabular Encoder for Heterogeneous Tabular Data

A Performance-Driven Benchmark for Feature Selection in Tabular Deep Learning

Learning Active Subspaces and Discovering Important Features with Gaussian Radial Basis Functions Neural Networks

Tabdoor: Backdoor Vulnerabilities in Transformer-based Neural Networks for Tabular Data

Tabular Data: Is Attention All You Need?


Augmented halo model for accurate non-linear matter power spectrum calculations

Constraints on Cosmology and Baryonic Feedback with the Deep Lens Survey Using Galaxy–Galaxy and Galaxy–Mass Power Spectra

An accurate halo model for fitting non-linear cosmological power spectra and baryonic feedback models

KiDS-450+2dFLenS: Cosmological parameter constraints from weak gravitational lensing tomography and overlapping redshift-space galaxy clustering

CFHTLenS revisited: assessing concordance with Planck including astrophysical systematics

Dark Energy Survey Year 3 results: Cosmology from cosmic shear and robustness to modeling uncertainty

Accurate halo-model matter power spectra with dark energy, massive neutrinos and modified gravitational forces

HMCODE-2020: improved modelling of non-linear cosmological power spectra with baryonic feedback

Monthly notices of the Royal Astronomical Society

The Uchuu simulations: Data Release 1 and dark matter halo concentrations

Modelling baryonic physics in future weak lensing surveys

Dark energy survey year 3 results: cosmological constraints from the analysis of cosmic shear in harmonic space


Forward and inverse problems in asteroseismology

FUNDAMENTAL PARAMETERS OF MAIN-SEQUENCE STARS IN AN INSTANT WITH MACHINE LEARNING

Stellar Parameters in an Instant with Machine Learning - Application to Kepler LEGACY Targets

Relevance of the small frequency separation for asteroseismic stellar age, mass, and radius

Inverse Problems in Asteroseismology


Package pymcd

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

VoiceCraft: Zero-Shot Speech Editing and Text-to-Speech in the Wild

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


stream processing reading list

S-Store: Streaming Meets Transaction Processing

Grizzly: Efficient Stream Processing Through Adaptive Query Compilation

SIGMOD'20: PROCEEDINGS OF THE 2020 ACM SIGMOD INTERNATIONAL CONFERENCE ON MANAGEMENT OF DATA

LightSaber: Efficient Window Aggregation on Multi-core Processors

Parallel Index-based Stream Join on a Multicore CPU

Hardware-Conscious Stream Processing: A Survey

FlowDB: Integrating Stream Processing and Consistent State Management

A Scalable Software Framework for Stateful Stream Data Processing on Multiple GPUs and Applications

Deterministic Model for Distributed Speculative Stream Processing

Symposium on Advances in Databases and Information Systems


Differentially Private Conditional Generative Adversarial Network

InfoGAN: Interpretable Representation Learning by Information Maximizing Generative Adversarial Nets

DP-CGAN: Differentially Private Synthetic Data and Label Generation

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

Private Set Generation with Discriminative Information

A Unified View of Differentially Private Deep Generative Modeling


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

The Application of Deep Learning in Cancer Prognosis Prediction

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

IEEE/ACM transactions on computational biology and bioinformatics

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


A collection of differentiable SVD methods and ICCV21 "Why Approximate Matrix Square Root Outperforms Accurate SVD in Global Covariance Pooling?"

Backpropagation-Friendly Eigendecomposition

Robust Differentiable SVD

IEEE transactions on pattern analysis and machine intelligence

On the Eigenvalues of Global Covariance Pooling for Fine-Grained Visual Recognition

Fast Differentiable Matrix Square Root


My collection of Python tools!

The Design of the Fifth Answer Set Programming Competition

A Trajectory Calculus for Qualitative Spatial Reasoning Using Answer Set Programming

Theory and Practice of Logic Programming

Preliminary Report on WASP 2.0

Inconsistency Proofs for ASP: The ASP-DRUPE Format

A Generalised Approach for Encoding and Reasoning with Qualitative Theories in Answer Set Programming

Static Analysis and Stochastic Search for Reachability Problem

Evaluating Datalog Tools for Meta-reasoning over OWL 2 QL


Multi^2OIE: Multilingual Open Information Extraction Based on Multi-Head Attention with BERT (Findings of ACL: EMNLP 2020)

OIE@OIA: an Adaptable and Efficient Open Information Extraction Framework

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

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


Contrastive Learning for Domain Adaptation of Time Series

Deep Domain Confusion: Maximizing for Domain Invariance

On Minimum Discrepancy Estimation for Deep Domain Adaptation

A Survey on Time-Series Pre-Trained Models

Contrastive Learning for Unsupervised Domain Adaptation of Time Series


Analysing Metagenomic Species (MGS)

A new genomic blueprint of the human gut microbiota

Packaging research artefacts with RO-Crate

DeepMicrobes: taxonomic classification for metagenomics with deep learning

MetaTransformer: deep metagenomic sequencing read classification using self-attention models


Datasets: road-scene-infrared-visible-images, for feature matching, image registration, and image fusion

U2Fusion: A Unified Unsupervised Image Fusion Network

FusionDN: A Unified Densely Connected Network for Image Fusion

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

SwinFuse: A Residual Swin Transformer Fusion Network for Infrared and Visible Images

Unsupervised Misaligned Infrared and Visible Image Fusion via Cross-Modality Image Generation and Registration

An Interactively Reinforced Paradigm for Joint Infrared-Visible Image Fusion and Saliency Object Detection

Infrared and Visible Image Fusion via Interactive Compensatory Attention Adversarial Learning

Infrared and Visible Image Fusion with Hybrid Image Filtering

Advanced Driving Assistance Based on the Fusion of Infrared and Visible Images

Image Fusion via Vision-Language Model

Improving Misaligned Multi-modality Image Fusion with One-stage Progressive Dense Registration


A Light CNN for Deep Face Representation with Noisy Labels, TIFS 2018

A Light CNN for Deep Face Representation With Noisy Labels

Biometric Face Presentation Attack Detection With Multi-Channel Convolutional Neural Network

Disentangled Variational Representation for Heterogeneous Face Recognition

Mitigating dataset harms requires stewardship: Lessons from 1000 papers

Dual-Attention GAN for Large-Pose Face Frontalization

Deep Learning for Face Recognition: Pride or Prejudiced?

ReMix: Towards Image-to-Image Translation with Limited Data

A Community Detection Approach to Cleaning Extremely Large Face Database

Computational intelligence and neuroscience

M2FPA: A Multi-Yaw Multi-Pitch High-Quality Database and Benchmark for Facial Pose Analysis

Multispectral Face Recognition Using Transfer Learning with Adaptation of Domain Specific Units


Implementation of several Bayesian multi-target tracking algorithms, including Poisson multi-Bernoulli mixture filters for sets of targets and sets of trajectories. The repository also includes the GOSPA metric and a metric for sets of trajectories to evaluate performance.

Poisson Multi-Bernoulli Mixture Filter: Direct Derivation and Implementation

IEEE Transactions on Aerospace and Electronic Systems

Multiple Target Tracking Based on Sets of Trajectories

A Metric on the Space of Finite Sets of Trajectories for Evaluation of Multi-Target Tracking Algorithms

Trajectory PHD and CPHD Filters

Poisson multi-Bernoulli mixture trackers: continuity through random finite sets of trajectories

Gaussian implementation of the multi-Bernoulli mixture filter

Poisson Multi-Bernoulli Mixtures for Sets of Trajectories

Continuous-Discrete Multiple Target Tracking With Out-of-Sequence Measurements

Tracking Multiple Spawning Targets Using Poisson Multi-Bernoulli Mixtures on Sets of Tree Trajectories

A comparison between PMBM Bayesian track initiation and labelled RFS adaptive birth


BERT pre-training in Thai language

Neural Machine Translation of Rare Words with Subword Units

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

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

WangchanBERTa: Pretraining transformer-based Thai Language Models

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

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

CMTA: COVID-19 Misinformation Multilingual Analysis on Twitter

International Joint Conference on Natural Language Processing

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

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

Looking for COVID-19 misinformation in multilingual social media texts


Open set classification of car models. This 3-step classifier solves the problem where dogs are classified as cars, by first filtering these images out using ResNet CNNs transfer-trained on different datasets.

Towards Open Set Deep Networks

Reducing Network Agnostophobia

Learning a Neural-network-based Representation for Open Set Recognition


Molecular Explanation Generator

Optimization of Molecules via Deep Reinforcement Learning

MEG: Generating Molecular Counterfactual Explanations for Deep Graph Networks

Counterfactual Learning on Graphs: A Survey

Explaining Deep Graph Networks with Molecular Counterfactuals


plant NGS analysis

Linking key steps of microRNA biogenesis by TREX-2 and the nuclear pore complex in Arabidopsis

Anterograde signaling controls plastid transcription via sigma factors separately from nuclear photosynthesis genes

Transcriptome-wide analyses of RNA m6A methylation in hexaploid wheat reveal its roles in mRNA translation regulation

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation

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


CORE: COnsistent REpresentation Learning for Face Forgery Detection, CVPRW 22

CORE: Consistent Representation Learning for Face Forgery Detection

DeepfakeBench: A Comprehensive Benchmark of Deepfake Detection

AI-Face: A Million-Scale Demographically Annotated AI-Generated Face Dataset and Fairness Benchmark


Playing Text-Adventure Games with Graph-Based Deep Reinforcement Learning

Reinforcement learning on graphs: A survey

Transfer in Deep Reinforcement Learning using Knowledge Graphs


SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

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

Network Inference with Granger Causality Ensembles on Single-Cell Transcriptomic Data

Inferring Gene Regulatory Networks From Single-Cell Transcriptomic Data Using Bidirectional RNN

Reconstructing gene regulatory networks in single-cell transcriptomic data analysis


An Online Algorithm for Constrained Face Clustering in Videos

AN ONLINE ALGORITHM FOR CONSTRAINED FACE CLUSTERING IN VIDEOS

International Conference on Information Photonics

Dynamic Character Graph via Online Face Clustering for Movie Analysis

A Bibliographic View on Constrained Clustering


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

Fixing Data Augmentation to Improve Adversarial Robustness

Toward Understanding Generative Data Augmentation


DP-Rewrite: Towards Reproducibility and Transparency in Differentially Private Text Rewriting

Snips Voice Platform: an embedded Spoken Language Understanding system for private-by-design voice interfaces

ADePT: Auto-encoder based Differentially Private Text Transformation

When differential privacy meets NLP: The devil is in the detail


The best solution of the Weather Prediction track in the Yandex Shifts challenge

On the Variance of the Adaptive Learning Rate and Beyond

Shifts: A Dataset of Real Distributional Shift Across Multiple Large-Scale Tasks

More layers! End-to-end regression and uncertainty on tabular data with deep learning


Demonstration of the PIPG algorithm for trajectory optimization

Proportional-Integral Projected Gradient Method for Model Predictive Control

A Customised First-Order Solver for Real-Time Powered-Descent Guidance

Extrapolated Proportional-Integral Projected Gradient Method for Conic Optimization

Proportional-Integral Projected Gradient Method for Infeasibility Detection in Conic Optimization


Code for DeCoAR (ICASSP 2020) and BERTphone (Odyssey 2020)

Deep Contextualized Acoustic Representations for Semi-Supervised Speech Recognition

International Conference on Acoustics, Speech, and Signal Processing

DeCoAR 2.0: Deep Contextualized Acoustic Representations with Vector Quantization

Probing Acoustic Representations for Phonetic Properties

BERTphone: Phonetically-aware Encoder Representations for Utterance-level Speaker and Language Recognition

The Speaker and Language Recognition Workshop (Odyssey 2020)

Bridging the Gap: Using Deep Acoustic Representations to Learn Grounded Language from Percepts and Raw Speech


Compact Matlab code for the computation of the 1- and 2-Wasserstein distances in 1D

Learning interaction kernels in mean-field equations of 1st-order systems of interacting particles

Multi-timescale reinforcement learning in the brain

bioRxiv : the preprint server for biology

Spatial accuracy evaluation of magnetic source imaging methods on OPM-based MEG

Asymmetry and Condition Number of an Elliptic-Parabolic System for Biological Network Formation

Unsupervised learning of observation functions in state-space models by nonparametric moment methods


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

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

Striving for Simplicity: The All Convolutional Net

LARNN: Linear Attention Recurrent Neural Network


[ICPR 2022] Data, code and pretrained models for Deep Surface Reconstruction from Point Clouds with Visibility Information

Occupancy Networks: Learning 3D Reconstruction in Function Space

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

Convolutional Occupancy Networks


AdaSpeech 2: Adaptive Text to Speech with Untranscribed Data

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

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


CLIPfa: Connecting Farsi Text and Images

Learning Transferable Visual Models From Natural Language Supervision

SRCB at SemEval-2023 Task 1: Prompt Based and Cross-Modal Retrieval Enhanced Visual Word Sense Disambiguation

Proceedings of the The 17th International Workshop on Semantic Evaluation (SemEval-2023)

UAlberta at SemEval-2023 Task 1: Context Augmentation and Translation for Multilingual Visual Word Sense Disambiguation


Here, we provide mappings to DBpedia resources of items in well known datasets to evaluate recommender systems. This can allows practitioners in the field to evaluate and compare their algorithms with existing approaches.

Linked open data to support content-based recommender systems

Top-N recommendations from implicit feedback leveraging linked open data

Auto-Encoding User Ratings via Knowledge Graphs in Recommendation Scenarios

Tinderbook: Fall in Love with Culture


The official RBG release repository.

Regular Boardgames

Efficient Reasoning in Regular Boardgames

Split Moves for Monte-Carlo Tree Search

Experimental Studies in General Game Playing: An Experience Report

A note on the empirical comparison of RBG and Ludii


Testing the consistency of binary classification performance scores reported in papers

mlscorecheck: Testing the consistency of reported performance scores and experiments in machine learning

Testing the Consistency of Performance Scores Reported for Binary Classification Problems

Enumerating the k-fold configurations in multi-class classification problems


Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations in protein-protein and protein-ligand systems

In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2

Computational Analysis of the Interactions between the S100B Extracellular Chaperone and Its Amyloid β Peptide Client

International journal of molecular sciences

Predicting stable binding modes from simulated dimers of the D76N mutant of β2-microglobulin

Interfacial Dynamics and Growth Modes of β2-Microglobulin Dimers


Public code developed during my MSc study at University of Bologna

A Formalization of the Process Algebra CCS in HOL4

Further Formalization of the Process Algebra CCS in HOL4

Formalized Lambek Calculus in Higher Order Logic (HOL4)

A Formalization of Unique Solutions of Equations in Process Algebra


Unsupervised speech enhancement using DVAEs

Unsupervised Speech Enhancement Using Dynamical Variational Autoencoders

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

Audio-Visual Speech Enhancement with a Deep Kalman Filter Generative Model

Unsupervised speech enhancement with diffusion-based generative models


Pytorch code of  "Revisiting Local Descriptor based Image-to-Class Measure for Few-shot Learning", CVPR 2019.

Matching Networks for One Shot Learning

Meta-Learning for Semi-Supervised Few-Shot Classification

Low-Rank Pairwise Alignment Bilinear Network For Few-Shot Fine-Grained Image Classification


[CVPR 2021] CDFI: Compression-Driven Network Design for Frame Interpolation

LDMVFI: Video Frame Interpolation with Latent Diffusion Models

Sparsity-guided Network Design for Frame Interpolation


Transfer Feature Learning with Joint Distribution Adaptation

International Conference on Computer Vision

Balanced Distribution Adaptation for Transfer Learning

On the application of domain adaptation in structural health monitoring

Mechanical systems and signal processing

Foundations of population-based SHM, Part III: Heterogeneous populations – Mapping and transfer

Machine learning at the interface of structural health monitoring and non-destructive evaluation

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Overcoming the problem of repair in structural health monitoring: Metric-informed transfer learning

On the application of kernelised Bayesian transfer learning to population-based structural health monitoring


An Urban Morphogenesis Model Capturing Interactions between Networks and Territories

Unveiling co-evolutionary patterns in systems of cities: a systematic exploration of the SimpopNet model

An Applied Knowledge Framework to Study Complex Systems

Models Coupling Urban Growth and Transportation Network Growth : An Algorithmic Systematic Review Approach

Second-order control of complex systems with correlated synthetic data

Characterising and modeling the co-evolution of transportation networks and territories

Evolving accessibility landscapes: mutations of transportation networks in China

A systematic review and meta-analysis of interaction models between transportation networks and territories


[ACL2024] A Codebase for Incremental Learning with Large Language Models; Official released code for "Learn or Recall? Revisiting Incremental Learning with Pre-trained Language Models (ACL 2024)", "Incremental Sequence Labeling: A Tale of Two Shifts (ACL 2024 Findings)", and "Concept-1K: A Novel Benchmark for Instance Incremental Learning (arxiv)"

Can LLMs Learn New Concepts Incrementally without Forgetting?


pytorch implementation of Domain-Adversarial Training of Neural Networks

Unsupervised Domain Adaptation by Backpropagation

Accounting for Unobserved Confounding in Domain Generalization

Latent-Optimized Adversarial Neural Transfer for Sarcasm Detection

Co-Teaching for Unsupervised Domain Adaptation and Expansion


PubMedQA: A Dataset for Biomedical Research Question Answering

DataComp-LM: In search of the next generation of training sets for
  language models

Leveraging Biomolecule and Natural Language through Multi-Modal
  Learning: A Survey

SentiMedQAer: A Transfer Learning-Based Sentiment-Aware Model for Biomedical Question Answering

MediSwift: Efficient Sparse Pre-trained Biomedical Language Models


The Kinetics Human Action Video Dataset

A Closer Look at Spatiotemporal Convolutions for Action Recognition

How Severe is Benchmark-Sensitivity in Video Self-Supervised Learning?

Tubelet-Contrastive Self-Supervision for Video-Efficient Generalization


A PyTorch implementation for PyramidNets (Deep Pyramidal Residual Networks, https://arxiv.org/abs/1610.02915)

Deep Pyramidal Residual Networks

Fairness Through Robustness: Investigating Robustness Disparity in Deep Learning

Low-Pass Filtering SGD for Recovering Flat Optima in the Deep Learning Optimization Landscape

Ensemble Model Patching: A Parameter-Efficient Variational Bayesian Neural Network

Bio-inspired Min-Nets Improve the Performance and Robustness of Deep Networks

End-to-End Learning-Based Wireless Image Recognition Using the PyramidNet in Edge Intelligence


A Capsule Network-based framework for identification of COVID-19 cases from chest X-ray Images

COVID-CAPS: A Capsule Network-based Framework for Identification of COVID-19 cases from X-ray Images

COVID-19 open source data sets: a comprehensive survey

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


ChID: A Large-scale Chinese IDiom Dataset for Cloze Test

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

Teaching Machines to Read and Comprehend

EasyNLP: A Comprehensive and Easy-to-use Toolkit for Natural Language Processing

A BERT-based Dual Embedding Model for Chinese Idiom Prediction


Japanese Moral Foundations Dictionary (J-MFD)

Development and validation of the Japanese Moral Foundations Dictionary

Morality-Based Assertion and Homophily on Social Media: A Cultural Comparison Between English and Japanese Languages

Appraisal of the Fairness Moral Foundation Predicts the Language Use Involving Moral Issues on Twitter Among Japanese


A collection of Meta-Reinforcement Learning algorithms in PyTorch

A Simple Neural Attentive Meta-Learner

RL^2: Fast Reinforcement Learning via Slow Reinforcement Learning

Learning to reinforcement learn

Meta-Gradient Reinforcement Learning


Mapping, filtering, and data hub visualisation pipeline for DNase, ATAC, ChIP data

DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation

BET inhibition disrupts transcription but retains enhancer-promoter contact

H3K79me2/3 controls enhancer–promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells

NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

On-microscope staging of live cells reveals changes in the dynamics of transcriptional bursting during differentiation


Python port of the Twokenize class of ark-tweet-nlp

Improving Twitter Named Entity Recognition using Word Representations

Proceedings of the Workshop on Noisy User-generated Text

IIIDYT at IEST 2018: Implicit Emotion Classification With Deep Contextualized Word Representations

ÚFAL at MultiLexNorm 2021: Improving Multilingual Lexical Normalization by Fine-tuning ByT5

The Role of Features and Context on Suicide Ideation Detection

Australasian Language Technology Association Workshop

Topic and audience effects on distinctively Scottish vocabulary usage in Twitter data

Proceedings of the Workshop on Stylistic Variation

Modeling Temporal Evidence from External Collections

Utterance Emotion Dynamics in Children's Poems: Emotional Changes Across Age

Using Social Networks to Improve Language Variety Identification with Neural Networks

Learning Representations of Social Media Users

CoLi at UdS at SemEval-2020 Task 12: Offensive Tweet Detection with Ensembling

International Workshop on Semantic Evaluation


Machine learning to predict future number Covid19 Daily Cases (7-day moving average). Long Short Term Memory (LSTM) Predictor and Reinforcement Learning (RL) Prescription with Oxford Dataset

Evolutionary Neural AutoML for Deep Learning

From Prediction to Prescription: Evolutionary Optimization of Non-Pharmaceutical Interventions in the COVID-19 Pandemic

Effective Reinforcement Learning through Evolutionary Surrogate-Assisted Prescription


This project is the Torch implementation of our  accepted CVPR 2019 paper,  Iterative Normalization: Beyond Standardization towards Efficient Whitening

Decorrelated Batch Normalization

Approximated Orthonormal Normalisation in Training Neural Networks


A hierarchical deep learning framework for ncRNA-protein interaction prediction.

Predicting RNA-Protein Interactions Using Only Sequence Information

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information

NPInter v2.0: an updated database of ncRNA interactions

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction

RPITER: A Hierarchical Deep Learning Framework for ncRNA–Protein Interaction Prediction