Reaver: Modular Deep Reinforcement Learning Framework. Focused on StarCraft II. Supports Gym, Atari, and MuJoCo.

Proximal Policy Optimization Algorithms

Deep Reinforcement Learning that Matters

StarCraft II: A New Challenge for Reinforcement Learning

Relational Deep Reinforcement Learning

Hierarchical Reinforcement Learning in StarCraft II with Human Expertise in Subgoals Selection

Adversary agent reinforcement learning for pursuit-evasion

Outcome-Guided Counterfactuals for Reinforcement Learning Agents from a Jointly Trained Generative Latent Space


SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension

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

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Differential transcript expression profiles of susceptible and resistant pigeonpea cultivars at an early time point during Fusarium udum infection

Comprehensive phenomic and genomic studies of the species, Pectobacterium cacticida and proposal for reclassification as Alcorniella cacticida comb. nov

Comparative genomics, pangenomics, and phenomic studies of Pectobacterium betavasculorum strains isolated from sugar beet, potato, sunflower, and artichoke: insights into pathogenicity, virulence determinants, and adaptation to the host plant


[CVPR 2022] POCO: Point Convolution for Surface Reconstruction

Neural Kernel Surface Reconstruction

ALTO: Alternating Latent Topologies for Implicit 3D Reconstruction


Some code for processing and analysing UK Biobank cardiac MR images.

Automated cardiovascular magnetic resonance image analysis with fully convolutional networks

Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach

Deep-Learning Segmentation of Epicardial Adipose Tissue Using Four-Chamber Cardiac Magnetic Resonance Imaging

Deep learning for image segmentation: veritable or overhyped?

Identification of Circulating Plasma Proteins as a Mediator of Hypertension-Driven Cardiac Remodeling: A Mediation Mendelian Randomization Study


Creative Commons Attribution Share Alike 4.0 International

StereoSet: Measuring stereotypical bias in pretrained language models

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

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

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

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

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

An Efficient Multilingual Language Model Compression through Vocabulary Trimming

Robust Evaluation Measures for Evaluating Social Biases in Masked Language Models

How Different Is Stereotypical Bias Across Languages?


Learning Deep Representations of Fine-grained Visual Descriptions

Prototypical Networks for Few-shot Learning

Fine-Grained Image Classification via Combining Vision and Language

ZSCRGAN: A GAN-based Expectation Maximization Model for Zero-Shot Retrieval of Images from Textual Descriptions


This repository has implementations of data augmentation for NLP for Japanese.

EDA: Easy Data Augmentation Techniques for Boosting Performance on Text Classification Tasks

Data Augmentation using Pre-trained Transformer Models

An Analysis of Simple Data Augmentation for Named Entity Recognition


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

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

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

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

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

Genome-wide association study of cooking-caused grain expansion in rice (Oryza sativa L.)


[CVPR 2022] PointCLIP: Point Cloud Understanding by CLIP

PointCLIP V2: Prompting CLIP and GPT for Powerful 3D Open-world Learning

Exploiting GPT-4 Vision for Zero-shot Point Cloud Understanding


Pytorch Implementation of DOLG (ICCV 2021)

DOLG: Single-Stage Image Retrieval with Deep Orthogonal Fusion of Local and Global Features


MATLAB-based solver package of Maxwell's equations by the FDFD method

Inverse design of large-area metasurfaces

Nanophotonic media for artificial neural inference

Cross-Correlated Contrast Source Inversion

IEEE Transactions on Antennas and Propagation

Linearized 3-D Electromagnetic Contrast Source Inversion and Its Applications to Half-Space Configurations

IEEE Transactions on Geoscience and Remote Sensing

Optical analogues to the equatorial Kerr–Newman black hole


TensorFlow implementations of Graph Neural Networks

Deep Learning on Graphs: A Survey

Adversarial Examples for Models of Code

GNN-FiLM: Graph Neural Networks with Feature-wise Linear Modulation

Graph-based Molecular Representation Learning

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


Lstm variational auto-encoder for time series anomaly detection and features extraction

Tutorial on Variational Autoencoders

A Multimodal Anomaly Detector for Robot-Assisted Feeding Using an LSTM-based Variational Autoencoder

An Evaluation of Anomaly Detection and Diagnosis in Multivariate Time Series

IEEE transactions on neural networks and learning systems

Time-Series Anomaly Detection with Implicit Neural Representation

Anomaly Detection for Multivariate Time Series on Large-scale Fluid Handling Plant Using Two-stage Autoencoder

21ST IEEE INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS ICDMW 2021

Practical Anomaly Detection over Multivariate Monitoring Metrics for Online Services

Assessing Unsupervised Machine Learning solutions for Anomaly Detection in Cloud Gaming Sessions

Conference on Network and Service Management


DDPO for finetuning diffusion models, implemented in PyTorch with LoRA support

Training Diffusion Models with Reinforcement Learning

Directly Fine-Tuning Diffusion Models on Differentiable Rewards

Feedback Efficient Online Fine-Tuning of Diffusion Models

RL for Consistency Models: Faster Reward Guided Text-to-Image Generation


Source code for Neural Information Processing Systems (NeurIPS) 2018 paper "Multi-Task Learning as Multi-Objective Optimization"

Revisiting Scalarization in Multi-Task Learning: A Theoretical Perspective

Stochastic Multiple Target Sampling Gradient Descent

Differentiable Random Partition Models

Analytical Uncertainty-Based Loss Weighting in Multi-Task Learning


NAACL2021 - COIL Contextualized Lexical Retriever

COIL: Revisit Exact Lexical Match in Information Retrieval with Contextualized Inverted List

A Few Brief Notes on DeepImpact, COIL, and a Conceptual Framework for Information Retrieval Techniques

Fast Passage Re-ranking with Contextualized Exact Term Matching and Efficient Passage Expansion

Faster Learned Sparse Retrieval with Guided Traversal

CITADEL: Conditional Token Interaction via Dynamic Lexical Routing for Efficient and Effective Multi-Vector Retrieval

SpaDE: Improving Sparse Representations using a Dual Document Encoder for First-stage Retrieval

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

A Dense Representation Framework for Lexical and Semantic Matching

An Analysis on Matching Mechanisms and Token Pruning for Late-interaction Models

ACM transactions on office information systems


Exact Combinatorial Optimization with Graph Convolutional Neural Networks (NeurIPS 2019)

Ecole: A Gym-like Library for Machine Learning in Combinatorial Optimization Solvers

Learning a Large Neighborhood Search Algorithm for Mixed Integer Programs

Learning Cut Selection for Mixed-Integer Linear Programming via Hierarchical Sequence Model

Lookback for Learning to Branch

A Fast Graph Neural Network-Based Method for Winner Determination in Multi-Unit Combinatorial Auctions

Promoting Generalization for Exact Solvers via Adversarial Instance Augmentation

Rethinking the Capacity of Graph Neural Networks for Branching Strategy

Distributional MIPLIB: a Multi-Domain Library for Advancing ML-Guided
  MILP Methods


Fader Networks: Manipulating Images by Sliding Attributes - NIPS 2017

AttGAN: Facial Attribute Editing by Only Changing What You Want

DeepFakes and Beyond: A Survey of Face Manipulation and Fake Detection

Preliminary Forensics Analysis of DeepFake Images

Latent Space Factorisation and Manipulation via Matrix Subspace Projection

An Introduction to Digital Face Manipulation

Handbook of Digital Face Manipulation and Detection


Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

Comprehensive identification of transposable element insertions using multiple sequencing technologies

Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder

Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology


CASCADE Server

Cybercompetitions: A survey of competitions, tools, and systems to support cybersecurity education

Cyber Attack and Defense Emulation Agents

ProblemChild: Discovering Anomalous Patterns based on Parent-Child Process Relationships


DialoGLUE: A Natural Language Understanding Benchmark for Task-Oriented Dialogue

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

Example-Driven Intent Prediction with Observers

ConvFiT: Conversational Fine-Tuning of Pretrained Language Models


MiVOLO age & gender transformer neural network

MiVOLO: Multi-input Transformer for Age and Gender Estimation

Mobile Foundation Model as Firmware

Beyond Specialization: Assessing the Capabilities of MLLMs in Age and
  Gender Estimation


Qoala-T is a supervised-learning tool for quality control of FreeSurfer segmented MRI data

The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism

Qoala-T: A supervised-learning tool for quality control of FreeSurfer segmented MRI data

Different brain responses during empathy in autism spectrum disorders versus conduct disorder and callous-unemotional traits

Journal of child psychology and psychiatry, and allied disciplines

Brain structure is linked to the association between family environment and behavioral problems in children in the ABCD study

Linked patterns of biological and environmental covariation with brain structure in adolescence: a population-based longitudinal study

Identification of Two Distinct Working Memory-Related Brain Networks in Healthy Young Adults

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


Genome-wide contact analysis using sklearn

A supervised learning framework for chromatin loop detection in genome-wide contact maps

Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin

Machine and deep learning methods for predicting 3D genome organization


Discrete Graph Structure Learning for Forecasting Multiple Time Series, ICLR 2021.

Pre-training Enhanced Spatial-temporal Graph Neural Network for Multivariate Time Series Forecasting

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

A Survey on Graph Neural Networks for Time Series: Forecasting, Classification, Imputation, and Anomaly Detection

Online Metro Origin-Destination Prediction via Heterogeneous Information Aggregation

Sparse Graph Learning from Spatiotemporal Time Series

MBrain: A Multi-channel Self-Supervised Learning Framework for Brain Signals

RadNet: Incident Prediction in Spatio-Temporal Road Graph Networks Using Traffic Forecasting

Enhancing Spatio-temporal Traffic Prediction through Urban Human Activity Analysis

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


A Survey of Algorithms for Black-Box Safety Validation of Cyber-Physical Systems

A survey of challenges for runtime verification from advanced application domains (beyond software)

Two-Layered Falsification of Hybrid Systems Guided by Monte Carlo Tree Search

Multi-Armed Bandits for Boolean Connectives in Hybrid System Falsification (Extended Version)

Fast Falsification of Hybrid Systems using Probabilistically Adaptive Input

Algebraic Quantitative Semantics for Efficient Online Temporal Monitoring

Tools and Algorithms for Construction and Analysis of Systems

Constrained Optimization for Hybrid System Falsification and Application to Conjunctive Synthesis

Ensuring Reliable Robot Task Performance through Probabilistic Rare-Event Verification and Synthesis


Audio super resolution using neural networks

Audio Super Resolution using Neural Networks

Temporal FiLM: Capturing Long-Range Sequence Dependencies with Feature-Wise Modulations

WSRGlow: A Glow-based Waveform Generative Model for Audio Super-Resolution

Enabling Real-Time On-Chip Audio Super Resolution for Bone-Conduction Microphones

Explicit Estimation of Magnitude and Phase Spectra in Parallel for High-Quality Speech Enhancement


tf-trusted allows you to run TensorFlow models in secure enclaves

CrypTen: Secure Multi-Party Computation Meets Machine Learning

Mind Your Weight(s): A Large-scale Study on Insufficient Machine Learning Model Protection in Mobile Apps

ShadowNet: A Secure and Efficient On-device Model Inference System for Convolutional Neural Networks

Serdab: An IoT Framework for Partitioning Neural Networks Computation across Multiple Enclaves

Smart App Attack: Hacking Deep Learning Models in Android Apps

A Systematic Comparison of Encrypted Machine Learning Solutions for Image Classification

Proceedings of the 2020 Workshop on Privacy-Preserving Machine Learning in Practice

Accelerating 2PC-based ML with Limited Trusted Hardware


Python wrapper for the Elexon/BMRS API

A Collection and Categorization of Open-Source Wind and Wind Power Datasets


Public Health England SNP calling pipeline.

Evolution of Streptococcus pneumoniae Serotype 3 in England and Wales: A Major Vaccine Evader

Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP

Dynamic Transmission of Staphylococcus Aureus in the Intensive Care Unit

International journal of environmental research and public health

Genetic diversity and delineation of Salmonella Agona outbreak strains by next generation sequencing, Bavaria, Germany, 1993 to 2018

Sources of Multidrug Resistance in Patients With Previous Isoniazid-Resistant Tuberculosis Identified Using Whole Genome Sequencing: A Longitudinal Cohort Study

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Genomic Comparison of Salmonella Enteritidis Strains Isolated from Laying Hens and Humans in the Abruzzi Region during 2018

Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019

Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation

Targeted sequencing from cerebrospinal fluid for rapid identification of drug-resistant tuberculous meningitis

Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin


Newton and Quasi-Newton optimization with PyTorch

TTOpt: A Maximum Volume Quantized Tensor Train-based Optimization and its Application to Reinforcement Learning

Drivable Avatar Clothing: Faithful Full-Body Telepresence with Dynamic Clothing Driven by Sparse RGB-D Input

Automatic Differentiation for Inverse Problems in X-ray Imaging and Microscopy

Anisotropic power diagrams for polycrystal modelling: Efficient generation of curved grains via optimal transport

Machine learning stochastic differential equations for the evolution of
  order parameters of classical many-body systems in and out of equilibrium


Discontinuous Data-Oriented Parsing

The Paradox of the Compositionality of Natural Language: A Neural Machine Translation Case Study

Data-oriented parsing with discontinuous constituents and function tags

Discontinuous Parsing with an Efficient and Accurate DOP Model

International Workshop/Conference on Parsing Technologies

Span-based discontinuous constituency parsing: a family of exact chart-based algorithms with time complexities from O(n^6) down to O(n^3)

Multitask Pointer Network for Multi-Representational Parsing

Unlexicalized Transition-based Discontinuous Constituency Parsing

Discontinuous Constituent Parsing with Pointer Networks

Discontinuous Data-Oriented Parsing: A mildly context-sensitive all-fragments grammar

Discontinuous Constituent Parsing as Sequence Labeling

Efficient Discontinuous Phrase-Structure Parsing via the Generalized Maximum Spanning Arborescence

Empirical Methods in Natural Language Processing


Mem2Seq: Effectively Incorporating Knowledge Bases into End-to-End Task-Oriented Dialog Systems

A Survey of Knowledge-enhanced Text Generation

Multi-Level Memory for Task Oriented Dialogs

North American Chapter of the Association for Computational Linguistics

A Working Memory Model for Task-oriented Dialog Response Generation

Meeting of the Association for Computational Linguistics

Scaling Multi-Domain Dialogue State Tracking via Query Reformulation

Learning to Memorize in Neural Task-Oriented Dialogue Systems


Lattice methods in TensorFlow

Deontological Ethics By Monotonicity Shape Constraints

Feature Necessity & Relevancy in ML Classifier Explanations

Signal Combination for Language Identification

Interpretable Set Functions


This is a Genome Annotation Framework developed with the goal of annotating VCF files (Exomes or Genomes) from patients with Mendelian Disorders.

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

Characterising and Predicting Haploinsufficiency in the Human Genome

A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root

The human gene damage index as a gene-level approach to prioritizing exome variants

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

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

Calculating the statistical significance of rare variants causal for Mendelian and complex disorders

Mendel,MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders


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

Sequential enhancer state remodelling defines human germline competence and specification

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

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

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

International journal of molecular sciences


Entity disambiguation evaluation and error analysis tool

Improving broad-coverage medical entity linking with semantic type prediction and large-scale datasets

Fast and Effective Biomedical Entity Linking Using a Dual Encoder

Revisiting the Evaluation for Cross Document Event Coreference

International Conference on Computational Linguistics

Combining Open Source Annotators for Entity Linking through Weighted Voting

Joint Conference on Lexical and Computational Semantics

Framing Named Entity Linking Error Types

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

Stacking With Auxiliary Features

Visual Error Analysis for Entity Linking

PROCEEDINGS OF THE 53RD ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS AND THE 7TH INTERNATIONAL JOINT CONFERENCE ON NATURAL LANGUAGE PROCESSING (ACL-IJCNLP 2015): SYSTEM DEMONSTRATIONS

Supervised and Unsupervised Ensembling for Knowledge Base Population

Hedwig: A Named Entity Linker

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


A Resistance Capacitance Model for an Energetic Simulation of a Building


A SciUnit library for validation testing of spiking neural network models.

Reproducible Neural Network Simulations: Statistical Methods for Model Validation on the Level of Network Activity Data

Rigorous Neural Network Simulations: A Model Substantiation Methodology for Increasing the Correctness of Simulation Results in the Absence of Experimental Validation Data

Prominent characteristics of recurrent neuronal networks are robust against low synaptic weight resolution

A System-on-Chip Based Hybrid Neuromorphic Compute Node Architecture for Reproducible Hyper-Real-Time Simulations of Spiking Neural Networks

Evaluating the statistical similarity of neural network activity and connectivity via eigenvector angles


Uncertainty Quantification 360 (UQ360) is an extensible open-source toolkit that can help you estimate, communicate and use uncertainty in machine learning model predictions.

Building Calibrated Deep Models via Uncertainty Matching with Auxiliary Interval Predictors

Uncertainty Quantification 360: A Holistic Toolkit for Quantifying and Communicating the Uncertainty of AI

Data-IQ: Characterizing subgroups with heterogeneous outcomes in tabular data

MAPIE: an open-source library for distribution-free uncertainty quantification

Data-SUITE: Data-centric identification of in-distribution incongruous examples

Uncertainty Quantification 360: A Hands-on Tutorial

Proceedings of the 5th Joint International Conference on Data Science & Management of Data (9th ACM IKDD CODS and 27th COMAD)

Uncertainty Characteristics Curves: A Systematic Assessment of Prediction Intervals

TRIAGE: Characterizing and auditing training data for improved regression


An Automated Theorem Prover for Classical Higher-Order Logic with Henkin Semantics

The Higher-Order Prover Leo-II

The Higher-Order Prover Leo-III

Theorem Provers For Every Normal Modal Logic

Logic Programming and Automated Reasoning

Extensional Higher-Order Paramodulation in Leo-III

Agent-Based HOL Reasoning

The MET: The Art of Flexible Reasoning with Modalities

Rules and Rule Markup Languages for the Semantic Web

Leo-III Version 1.1 (System description)

Going Polymorphic - TH1 Reasoning for Leo-III


MQT QECC - Tools for Quantum Error Correcting Codes

Decoding algorithms for surface codes

Decoding quantum color codes with MaxSAT

Software Tools for Decoding Quantum Low-Density Parity-Check Codes

Automatic Implementation and Evaluation of Error-Correcting Codes for Quantum Computing: An Open-Source Framework for Quantum Error Correction

Analog information decoding of bosonic quantum LDPC codes

Automated Synthesis of Fault-Tolerant State Preparation Circuits for
  Quantum Error Correction Codes


An application to remove PCR duplicates from high throughput sequencing runs.

Super deduper, fast PCR duplicate detection in fastq files

International Conference on Bioinformatics

Subtyping analysis reveals new variants and accelerated evolution of Clostridioides difficile toxin B

Genomic basis of homoploid hybrid speciation within chestnut trees

The genomics of rapid climatic adaptation and parallel evolution in North American house mice

A Comprehensive Multi-Omic Approach Reveals a Relatively Simple Venom in a Diet Generalist, the Northern Short-Tailed Shrew, Blarina brevicauda

Mating system is correlated with immunogenetic diversity in sympatric species of Peromyscine mice


Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109

Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation

Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling

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

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


SNIRF Format Specification

Best practices for fNIRS publications

Wearable, high-density fNIRS and diffuse optical tomography technologies: a perspective

Introduction to the shared near infrared spectroscopy format

Using preregistration as a tool for transparent fNIRS study design

The IPASC data format: A consensus data format for photoacoustic imaging

Open Access Multimodal fNIRS Resting State Dataset With and Without Synthetic Hemodynamic Responses

Open access dataset of task-free hemodynamic activity in 4-month-old infants during sleep using fNIRS

Shedding light on functional near-infrared spectroscopy and open science practices

Assessment of Surgical Tasks Using Neuroimaging Dataset (ASTaUND)


Build a partitioned pangenome graph from microbial genomes

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Interactions between pili affect the outcome of bacterial competition driven by the type VI secretion system

panModule: detecting conserved modules in the variable regions of a pangenome graph

Strain-level Screening of Human Gut Microbes Identifies Blautia Producta as a Novel Anti-hyperlipidemic Probiotic Via the Production of 12-methylmyristic Acid


Python distribution of the MatLab package UTide

Modelling the barotropic sea level in the Mediterranean Sea using data assimilation

HIDRA2: deep-learning ensemble sea level and storm tide forecasting in the presence of seiches – the case of the northern Adriatic

Testing Ocean Software with Metamorphic Testing

Proceedings of the 7th International Workshop on Metamorphic Testing


oneAPI Collective Communications Library (oneCCL)

Optimizing Deep Learning Recommender Systems' Training On CPU Cluster Architectures

Enabling Compute-Communication Overlap in Distributed Deep Learning Training Platforms

International Symposium on Computer Architecture

Tensor Processing Primitives: A Programming Abstraction for Efficiency and Portability in Deep Learning Workloads

Efficient Direct-Connect Topologies for Collective Communications

Efficient All-to-All Collective Communication Schedules for Direct-Connect Topologies

Gleam: An RDMA-accelerated Multicast Protocol for Datacenter Networks

FastSample: Accelerating Distributed Graph Neural Network Training for Billion-Scale Graphs


Analysis components from Oxford Nanopore Research

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Novel Insights and Features of the NDM-5-Producing Escherichia coli Sequence Type 167 High-Risk Clone

Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit

Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere

Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach

Chromosome-Scale Genome Assembly of Two Australian Nannochloropsis oceanica Isolates Exhibiting Superior Lipid Characteristics

MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution

High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria

Rapid genotyping of porcine reproductive and respiratory syndrome virus (PRRSV) using MinION nanopore sequencing


Repository for the Tetrad Project, www.phil.cmu.edu/tetrad.

Causality-based Feature Selection: Methods and Evaluations

Beware of the Simulated DAG! Causal Discovery Benchmarks May Be Easy To Game

Scaling up Greedy Causal Search for Continuous Variables

A Survey on Causal Discovery Methods for I.I.D. and Time Series Data

Explaining the Behavior of Black-Box Prediction Algorithms with Causal Learning

Improving Accuracy and Scalability of the PC Algorithm by Maximizing P-value

Causal Discovery of Feedback Networks with Functional Magnetic Resonance Imaging

A Hybrid Causal Structure Learning Algorithm for Mixed-Type Data

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

A Causal Approach to Detecting Multivariate Time-series Anomalies and Root Causes

Mixed Graphical Models for Causal Analysis of Multi-modal Variables


DSPy: The framework for programming—not prompting—foundation models

What Makes Good In-Context Examples for GPT-3?

Demonstrate-Search-Predict: Composing retrieval and language models for knowledge-intensive NLP

Enhancing Retrieval-Augmented Large Language Models with Iterative Retrieval-Generation Synergy

DSPy: Compiling Declarative Language Model Calls into Self-Improving Pipelines

Cognitive Architectures for Language Agents

Diagnostic reasoning prompts reveal the potential for large language model interpretability in medicine

Reliable, Adaptable, and Attributable Language Models with Retrieval

DSPy Assertions: Computational Constraints for Self-Refining Language Model Pipelines

Optimizing Instructions and Demonstrations for Multi-Stage Language Model Programs

Adapting LLMs for Efficient, Personalized Information Retrieval: Methods and Implications


JavaScript 3D Library.

Viewport-aware adaptive 360° video streaming using tiles for virtual reality

ScrollyVis: Interactive Visual Authoring of Guided Dynamic Narratives for Scientific Scrollytelling

VMesh: Hybrid Volume-Mesh Representation for Efficient View Synthesis

Professional Differences: A Comparative Study of Visualization Task Performance and Spatial Ability Across Disciplines

3D WebGIS: From Visualization to Analysis. An Efficient Browser-Based 3D Line-of-Sight Analysis

ISPRS International Journal of Geo-Information

From one to hundreds: multi-licensing in the JavaScript ecosystem

Chemozart: a web-based 3D molecular structure editor and visualizer platform

THE CASE FOR LOW-COST, PERSONALIZED VISUALIZATION FOR ENHANCING NATURAL HAZARD PREPAREDNESS

The international archives of the photogrammetry, remote sensing and spatial information sciences/International archives of the photogrammetry, remote sensing and spatial information sciences

Emotion-aware music tower blocks (EmoMTB ): an intelligent audiovisual interface for music discovery and recommendation

International journal of multimedia information retrieval

Exploring AI-assisted Ideation and Prototyping for Choreography

Companion Proceedings of the 29th International Conference on Intelligent User Interfaces


The project is an official implementation of our CVPR2020 paper "Attention Mechanism Exploits Temporal Contexts: Real-time 3D Human Pose Reconstruction"

Attention Mechanism Exploits Temporal Contexts: Real-Time 3D Human Pose Reconstruction

Recent Advances in Monocular 2D and 3D Human Pose Estimation: A Deep Learning Perspective

Enhanced 3D Human Pose Estimation from Videos by Using Attention-Based Neural Network with Dilated Convolutions


Official implementation of the paper WAV2CLIP: LEARNING ROBUST AUDIO REPRESENTATIONS FROM CLIP

Wav2CLIP: Learning Robust Audio Representations From CLIP

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

How to Listen? Rethinking Visual Sound Localization

Exploring Efficient-Tuned Learning Audio Representation Method from BriVL


Unsupervised  Extractive Summarization based on Position-Augmented Centrality

TLDR: Extreme Summarization of Scientific Documents

Sentence Centrality Revisited for Unsupervised Summarization

Discourse-Aware Unsupervised Summarization of Long Scientific Documents

Extractive is not Faithful: An Investigation of Broad Unfaithfulness Problems in Extractive Summarization

HipoRank: Incorporating Hierarchical and Positional Information into Graph-based Unsupervised Long Document Extractive Summarization

Applicability of large language models and generative models for legal case judgement summarization

GOAL: Towards Benchmarking Few-Shot Sports Game Summarization


Implementation for <Large-Margin Softmax Loss for Convolutional Neural Networks> in ICML'16.

OLÉ: Orthogonal Low-rank Embedding, A Plug and Play Geometric Loss for Deep Learning

Ensemble Soft-Margin Softmax Loss for Image Classification


[CVPR 2020 Workshop] A PyTorch GAN library that reproduces research results for popular GANs.

Pros and Cons of GAN Evaluation Measures: New Developments

InfoMax-GAN: Improved Adversarial Image Generation via Information Maximization and Contrastive Learning

A Systematic Survey of Regularization and Normalization in GANs

A New Perspective on Stabilizing GANs Training: Direct Adversarial Training

Mimicry: Towards the Reproducibility of GAN Research

Exploring the Effect of High-frequency Components in GANs Training

On Sampling with Approximate Transport Maps

Local-Global MCMC kernels: the best of both worlds

BIGRoC: Boosting Image Generation via a Robust Classifier


A pipeline used to identify different modes of duplicated gene pairs

Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants

A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

The Cycas genome and the early evolution of seed plants

Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature

Genome-Wide Identification and Characterization of FBA Gene Family in Polyploid Crop Brassica napus

International journal of molecular sciences

Genome-Wide Identification and Functional Investigation of 1-Aminocyclopropane-1-carboxylic Acid Oxidase (ACO) Genes in Cotton

A Comprehensive Identification and Function Analysis of Serine/Arginine-Rich (SR) Proteins in Cotton (Gossypium spp.)

The Origin and Evolution of RNase T2 Family and Gametophytic Self-incompatibility System in Plants

Multi-Omics Analysis Reveals the Dynamic Changes of RNA N6-Methyladenosine in Pear (Pyrus bretschneideri) Defense Responses to Erwinia amylovora Pathogen Infection

Genome-wide identification and expression analysis of the response regulator gene family in alfalfa (Medicago sativa L.) reveals their multifarious roles in stress response


Easily identify and label sentence intervals using various taggers.

A Domain-independent Rule-based Framework for Event Extraction

Odin's Runes: A Rule Language for Information Extraction

Description of the Odin Event Extraction Framework and Rule Language


An implementation of the BADGE batch active learning algorithm.

Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds

SIMILAR: Submodular Information Measures Based Active Learning In Realistic Scenarios

Gone Fishing: Neural Active Learning with Fisher Embeddings

Effective Evaluation of Deep Active Learning on Image Classification Tasks

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

Streaming Active Learning with Deep Neural Networks

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

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

Low-Regret Active learning

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


Code of NIPS18 Paper: BRITS: Bidirectional Recurrent Imputation for Time Series

SAITS: Self-Attention-based Imputation for Time Series

Filling the G_ap_s: Multivariate Time Series Imputation by Graph Neural Networks

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

Networked Time Series Imputation via Position-aware Graph Enhanced Variational Autoencoders

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

Gradient Importance Learning for Incomplete Observations

PulseImpute: A Novel Benchmark Task for Pulsative Physiological Signal Imputation

Graph-based Virtual Sensing from Sparse and Partial Multivariate
  Observations

SRI-EEG: State-Based Recurrent Imputation for EEG Artifact Correction


Code for "Black-box Adversarial Attacks with Limited Queries and Information" (http://arxiv.org/abs/1804.08598)

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

Making Targeted Black-box Evasion Attacks Effective and Efficient

Proceedings of the 12th ACM Workshop on Artificial Intelligence and Security

On Robustness of Lane Detection Models to Physical-World Adversarial Attacks in Autonomous Driving


Safe RLHF: Constrained Value Alignment via Safe Reinforcement Learning from Human Feedback

OPT: Open Pre-trained Transformer Language Models

Safe RLHF: Safe Reinforcement Learning from Human Feedback

Is DPO Superior to PPO for LLM Alignment? A Comprehensive Study

Beyond One-Preference-Fits-All Alignment: Multi-Objective Direct Preference Optimization

Human-Instruction-Free LLM Self-Alignment with Limited Samples

Panacea: Pareto Alignment via Preference Adaptation for LLMs

Unmasking and Improving Data Credibility: A Study with Datasets for Training Harmless Language Models

Negating Negatives: Alignment without Human Positive Samples via
  Distributional Dispreference Optimization

RLHFPoison: Reward Poisoning Attack for Reinforcement Learning with Human Feedback in Large Language Models

Red Teaming Game: A Game-Theoretic Framework for Red Teaming Language Models


Explore and share your scRNAseq clustering results

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling

scClustViz – Single-cell RNAseq cluster assessment and visualization


SBX: Stable Baselines Jax (SB3 + Jax)

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

Controlling Overestimation Bias with Truncated Mixture of Continuous Distributional Quantile Critics

Dropout Q-Functions for Doubly Efficient Reinforcement Learning

Smooth Exploration for Robotic Reinforcement Learning

CrossQ: Batch Normalization in Deep Reinforcement Learning for Greater Sample Efficiency and Simplicity


NEural Minimizer for pytOrch

Technical Report: NEMO DNN Quantization for Deployment Model

Self-Supervised Learning of Visual Robot Localization Using LED State Prediction as a Pretext Task

A Deep Learning-Based Face Mask Detector for Autonomous Nano-Drones (Student Abstract)


A data-driven method combining symbolic regression and compressed sensing for accurate & interpretable models.

SISSO: A compressed-sensing method for identifying the best low-dimensional descriptor in an immensity of offered candidates

Big-Data Science in Porous Materials: Materials Genomics and Machine Learning

Simultaneous learning of several materials properties from incomplete databases with multi-task SISSO

Efficient machine-learning model for fast assessment of elastic properties of high-entropy alloys

High-throughput computation and structure prototype analysis for two-dimensional ferromagnetic materials

Distilling Accurate Descriptors from Multi-Source Experimental Data for Discovering Highly Active Perovskite OER Catalysts

SISSO++: A C++ Implementation of the Sure-Independence Screening and Sparsifying Operator Approach

Data-driven equation for drug-membrane permeability across drugs and membranes.

Dimerization of sub-nanoscale molecular clusters affords broadly tuneable viscoelasticity above the glass transition temperature


Repository for the paper "Planning to Explore via Self-Supervised World Models"

Model-Based Active Exploration

Curiosity-Driven Exploration via Latent Bayesian Surprise

Reparameterized Policy Learning for Multimodal Trajectory Optimization


REBEL is a seq2seq model that simplifies Relation Extraction (EMNLP 2021).

REBEL: Relation Extraction By End-to-end Language generation

Findings of the Association for Computational Linguistics: EMNLP 2021

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

Sequence Generation with Label Augmentation for Relation Extraction

Beyond Rule-based Named Entity Recognition and Relation Extraction for Process Model Generation from Natural Language Text

Towards Relation Extraction From Speech

REDFM: a Filtered and Multilingual Relation Extraction Dataset

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


A package for single-cell Hi-C data clustering and downstream analysis.

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

bioRxiv : the preprint server for biology

Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering

Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection


This package implements both the discrete and continuous maximum likelihood estimators for fitting the power-law distribution to data. Additionally, a goodness-of-fit based approach is used to estimate the lower cutoff for the scaling region.

The precision of the arithmetic mean, geometric mean and percentiles for citation data: An experimental simulation modelling approach

Are the discretised lognormal and hooked power law distributions plausible for citation data?

Are there too many uncited articles? Zero inflated variants of the discretised lognormal and hooked power law distributions


Spike sorting benchmarking system

An Emergent Neural Coactivity Code for Dynamic Memory

Integrating new memories into the hippocampal network activity space

Coordinating brain-distributed network activities in memory resistant to extinction


All image quality metrics you need in one package.

Misusing Tools in Large Language Models With Visual Adversarial Examples

Information Encoding in Bursting Spiking Neural Network Modulated by Astrocytes

DualFlow: Generating imperceptible adversarial examples by flow field and normalize flow-based model

Markup-to-Image Diffusion Models with Scheduled Sampling

Face Beneath the Ink: Synthetic Data and Tattoo Removal with Application to Face Recognition

AFLOW: Developing Adversarial Examples under Extremely Noise-limited Settings

On the Efficacy of Metrics to Describe Adversarial Attacks


CSI: Novelty Detection via Contrastive Learning on Distributionally Shifted Instances (NeurIPS 2020)

OpenMatch: Open-set Consistency Regularization for Semi-supervised Learning with Outliers

OODformer: Out-Of-Distribution Detection Transformer

Out-of-Distribution Detection Without Class Labels

Dissolving Is Amplifying: Towards Fine-Grained Anomaly Detection

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


DifFace: Blind Face Restoration with Diffused Error Contraction (TPAMI, 2024)

DiffBIR: Towards Blind Image Restoration with Generative Diffusion Prior

On the Vulnerability of Deepfake Detectors to Attacks Generated by Denoising Diffusion Models


A tiny library for coding with large language models.

Chain-of-Thought Prompting Elicits Reasoning in Large Language Models

PAL: Program-aided Language Models

Bridging the Novice-Expert Gap via Models of Decision-Making: A Case Study on Remediating Math Mistakes

Tree Prompting: Efficient Task Adaptation without Fine-Tuning

A Taxonomy of Foundation Model based Systems through the Lens of Software Architecture

From Decoding to Meta-Generation: Inference-time Algorithms for Large Language Models

Backtracing: Retrieving the Cause of the Query


Sen1Floods11: a georeferenced dataset to train and test deep learning flood algorithms for Sentinel-1

Enhancement of Detecting Permanent Water and Temporary Water in Flood Disasters by Fusing Sentinel-1 and Sentinel-2 Imagery Using Deep Learning Algorithms: Demonstration of Sen1Floods11 Benchmark Datasets

Foundation Models for Generalist Geospatial Artificial Intelligence

Q-Seg: Quantum Annealing-Based Unsupervised Image Segmentation

When are Foundation Models Effective? Understanding the Suitability for
  Pixel-Level Classification Using Multispectral Imagery


ReAct: Synergizing Reasoning and Acting in Language Models

AgentBoard: An Analytical Evaluation Board of Multi-turn LLM Agents

AgentGym: Evolving Large Language Model-based Agents across Diverse
  Environments


Video embeddings for retrieval with natural language queries

Squeeze-and-Excitation Networks

Use What You Have: Video Retrieval Using Representations From Collaborative Experts

TEACHTEXT: CrossModal Generalized Distillation for Text-Video Retrieval

The End-of-End-to-End: A Video Understanding Pentathlon Challenge (2020)


Workflow Description Language (WDL) scripts for common vg workflows

Benchmarking challenging small variants with linked and long reads

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

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

Personalized Pangenome References


AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community.

Experimentally validated geometrically exact model for extreme nonlinear motions of cantilevers

Methods of continuation and their implementation in the COCO software platform with application to delay differential equations

Nonlinear damping in micromachined bridge resonators

The Role of Sea-ice Processes on the Probability of AMOC Transitions

Travelling waves in a PDE-ODE coupled system with nonlinear diffusion

Modeling of dual frequency combs and bistable solitons in third-harmonic generation


Indonesian stemmer. Python port of PHP Sastrawi project.

Multi-label Hate Speech and Abusive Language Detection in Indonesian Twitter

THIRD WORKSHOP ON ABUSIVE LANGUAGE ONLINE

Clickbait Headline Detection in Indonesian News Sites using Multilingual Bidirectional Encoder Representations from Transformers (M-BERT)

Implementation of Stacking Ensemble Classifier for Multi-class Classification of COVID-19 Vaccines Topics on Twitter

Aspect-based Sentiment Analysis on Indonesia’s Tourism Destinations Based on Google Maps User Code-Mixed Reviews (Study Case: Borobudur and Prambanan Temples)

Pacific Asia Conference on Language, Information, and Computation

Topic Modeling of Online Media News Titles during COVID-19 Emergency Response in Indonesia Using the Latent Dirichlet Allocation (LDA) Algorithm

A stance dataset with aspect-based sentiment information from Indonesian COVID-19 vaccination-related tweets

Knowing Right from Wrong: Should We Use More Complex Models for Automatic Short-Answer Scoring in Bahasa Indonesia?

Empirical Methods in Natural Language Processing


Some C++ example code to demonstrate how to perform code similarity searches using SimHashing.

Deep Graph Similarity Learning: A Survey

HEBCS: A High-Efficiency Binary Code Search Method


Multiple Automatically Generated Templates brain segmentation algorithm

Warping an atlas derived from serial histology to 5 high-resolution MRIs

Linking persistent negative symptoms to amygdala–hippocampus structure in first-episode psychosis

Manual-Protocol Inspired Technique for Improving Automated MR Image Segmentation during Label Fusion

Habenular Involvement in Response to Subcallosal Cingulate Deep Brain Stimulation for Depression

Examining litter specific variability in mice and its impact on neurodevelopmental studies

Deformation-based shape analysis of the hippocampus in the semantic variant of primary progressive aphasia and Alzheimer’s disease

XKR4 Gene Effects on Cerebellar Development Are Not Specific to ADHD

Variation in subcortical anatomy: relating interspecies differences, heritability, and brain-behavior relationships


Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

Prediction of acute myeloid leukaemia risk in healthy individuals

Tobacco smoking and somatic mutations in human bronchial epithelium

Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study

Mechanisms of APOBEC3 mutagenesis in human cancer cells

Recurrent intragenic rearrangements of EGFR and BRAF in soft tissue tumors of infants

A recurrent novel MGA-NUTM1 fusion identifies a new subtype of high-grade spindle cell sarcoma

Single cell derived mRNA signals across human kidney tumors

Abnormal oxidative metabolism in a quiet genomic background underlies clear cell papillary renal cell carcinoma

Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers

A living biobank of patient-derived ductal carcinoma in situ mouse-intraductal xenografts identifies risk factors for invasive progression


Open Source Photometric classification https://supernnova.readthedocs.io

SuperNNova: an open-source framework for Bayesian, neural network-based supernova classification

Monthly Notices of the Royal Astronomical Society

The Dark Energy Survey: Cosmology Results With ~1500 New High-redshift Type Ia Supernovae Using The Full 5-year Dataset

The Dark Energy Survey supernova program: cosmological biases from supernova photometric classification

Exempla Gratis (E.G.): Code Examples for Free

The Dark Energy Survey Supernova Program: Cosmological Analysis and Systematic Uncertainties

The Dark Energy Survey Supernova Program: Light curves and 5-Year data
  release

The dark energy survey supernova program: investigating beyond-ΛCDM

Recovered supernova Ia rate from simulated LSST images


Generating bash command from natural language https://arxiv.org/abs/1802.08979

Neural Machine Translation by Jointly Learning to Align and Translate

Incorporating Copying Mechanism in Sequence-to-Sequence Learning

NL2Bash: A Corpus and Semantic Parser for Natural Language Interface to the Linux Operating System

Neural Machine Translation for Code Generation

LogPrécis: Unleashing Language Models for Automated Shell Log Analysis


SALMONN: Speech Audio Language Music Open Neural Network

SALMONN: Towards Generic Hearing Abilities for Large Language Models

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

video-SALMONN: Speech-Enhanced Audio-Visual Large Language Models

AffectGPT: Dataset and Framework for Explainable Multimodal Emotion
  Recognition


Many-body dispersion library

Long-range dispersion-inclusive machine learning potentials for structure search and optimization of hybrid organic-inorganic interfaces

Ab Initio Evaluation of Henry Coefficients Using Importance Sampling

Journal of chemical theory and computation

libMBD: A general-purpose package for scalable quantum many-body dispersion calculations


Mixed Precision DNNs: All you need is a good parametrization

Densely connected multidilated convolutional networks for dense prediction tasks

D3Net: Densely connected multidilated DenseNet for music source separation

All for One and One for All: Improving Music Separation by Bridging Networks

Multi-Task Audio Source Separation

Data Cleansing for Deep Neural Networks with Storage-efficient Approximation of Influence Functions

Towards Robust FastSpeech 2 by Modelling Residual Multimodality

Feature-informed Latent Space Regularization for Music Source Separation


Framework-agnostic implementation for state-of-the-art saliency methods (XRAI, BlurIG, SmoothGrad, and more).

SmoothGrad: removing noise by adding noise

Toward Trustworthy AI Development: Mechanisms for Supporting Verifiable Claims

XRAI: Better Attributions Through Regions

A Survey of Deep Learning for Scientific Discovery

Guided Integrated Gradients: An Adaptive Path Method for Removing Noise

Attribution in Scale and Space

Detection of signs of disease in external photographs of the eyes via deep learning

Understanding Impacts of High-Order Loss Approximations and Features in Deep Learning Interpretation

Shared Interest: Measuring Human-AI Alignment to Identify Recurring Patterns in Model Behavior

A Primer on the Inner Workings of Transformer-based Language Models


Generalized and Efficient Blackbox Optimization System

OpenBox: A Generalized Black-box Optimization Service

Automated Hyperparameter Optimization Challenge at CIKM 2021 AnalyticCup

OpenBox: A Python Toolkit for Generalized Black-box Optimization


Rembg is a tool to remove images background

ICON: Implicit Clothed humans Obtained from Normals

ECON: Explicit Clothed humans Optimized via Normal integration

OmniObject3D: Large-Vocabulary 3D Object Dataset for Realistic Perception, Reconstruction and Generation

PF-LRM: Pose-Free Large Reconstruction Model for Joint Pose and Shape Prediction

Towards Open-World Text-Guided Face Image Generation and Manipulation

TediGAN: Text-Guided Diverse Image Generation and Manipulation

SeSDF: Self-evolved Signed Distance Field for Implicit 3D Clothed Human Reconstruction

Scrape, Cut, Paste and Learn: Automated Dataset Generation Applied to Parcel Logistics

ConTex-Human: Free-View Rendering of Human from a Single Image with Texture-Consistent Synthesis

PLA4D: Pixel-Level Alignments for Text-to-4D Gaussian Splatting


Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

Comparative Analysis of Single-Cell RNA Sequencing Methods.

A comparison of single-cell trajectory inference methods

An accurate and robust imputation method scImpute for single-cell RNA-seq data

Bias, robustness and scalability in single-cell differential expression analysis

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

Design and computational analysis of single-cell RNA-sequencing experiments

Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models


RFCs for changes to Rust

Leveraging Rust Types for Modular Specification and Verification

Proceedings of the ACM on Programming Languages

Putting the Semantics into Semantic Versioning

Rusty Variation: Deadlock-free Sessions with Failure in Rust

The Usability of Ownership

Knowing when to ask: sound scheduling of name resolution in type checkers derived from declarative specifications

Dependent Type Systems as Macros

An Empirical Study of Yanked Releases in the Rust Package Registry

IEEE Transactions on Software Engineering

Rust Distilled: An Expressive Tower of Languages

Borrowing Safe Pointers from Rust in SPARK

Unboxed Data Constructors: Or, How cpp Decides a Halting Problem


Cross-platform software to draw phylogenetic trees

Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella

High-resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences

Niche and ecosystem preference of earliest diverging fungi in soils

Mycology&#58 An International Journal on Fungal Biology

AutoPhy: Automated phylogenetic identification of novel protein subfamilies


MetricGAN: Generative Adversarial Networks based Black-box Metric Scores Optimization for Speech Enhancement (ICML 2019, with Travel awards)

MetricGAN+: An Improved Version of MetricGAN for Speech Enhancement

Improving Character Error Rate Is Not Equal to Having Clean Speech: Speech Enhancement for ASR Systems with Black-box Acoustic Models


TeCNO: Surgical Phase Recognition with Multi-Stage Temporal Convolutional Networks

Trans-SVNet: Accurate Phase Recognition from Surgical Videos via Hybrid Embedding Aggregation Transformer

TUNeS: A Temporal U-Net with Self-Attention for Video-based Surgical Phase Recognition


[Official] Exploring Temporal Coherence for More General Video Face Forgery Detection(ICCV 2021)

Detecting Deepfakes with Self-Blended Images

Leveraging Real Talking Faces via Self-Supervision for Robust Forgery Detection

Adversarially Robust Deepfake Detection via Adversarial Feature Similarity Learning

Generalizable Deepfake Detection with Phase-Based Motion Analysis

DeepFake-O-Meter v2.0: An Open Platform for DeepFake Detection


Representation learning on dynamic graphs using self-attention networks

Dynamic Network Embedding Survey

Understanding graph embedding methods and their applications

Dynamic Graph Representation Learning via Self-Attention Networks

TCL: Transformer-based Dynamic Graph Modelling via Contrastive Learning

Dynamic Graph Representation Learning via Graph Transformer Networks

Link prediction in dynamic networks using random dot product graphs

VStreamDRLS: Dynamic Graph Representation Learning with Self-Attention for Enterprise Distributed Video Streaming Solutions

EGAD: Evolving Graph Representation Learning with Self-Attention and Knowledge Distillation for Live Video Streaming Events

Meta-Reinforcement Learning via Buffering Graph Signatures for Live Video Streaming Events

A Deep Graph Reinforcement Learning Model for Improving User Experience in Live Video Streaming


DeepStack: Ensembling Keras Deep Learning Models into the next Performance Level

DeepCOVID-XR: An Artificial Intelligence Algorithm to Detect COVID-19 on Chest Radiographs Trained and Tested on a Large U.S. Clinical Data Set.

Deep Ensemble Learning-Based Models for Diagnosis of COVID-19 from Chest CT Images

Hand Gesture Recognition with Two Stage Approach Using Transfer Learning and Deep Ensemble Learning


Filter SAM file for soft and hard clipped alignments

Bactopia: a flexible pipeline for complete analysis of bacterial genomes

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines

Nanopore sequencing of RNA and cDNA molecules in Escherichia coli

Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome

A single unidirectional piRNA cluster similar to the flamenco locus is the major source of EVE-derived transcription and small RNAs in Aedes aegypti mosquitoes

Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group III Bacillus cereus Sensu Lato Facilitate the Transition between Emetic and Diarrheal Foodborne Pathogens

The Paracaedibacter-like endosymbiont of Bodo saltans (Kinetoplastida) uses multiple putative toxin-antitoxin systems to maintain its host association

Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood


Bridging Vision and Language Model

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

WenLan: Bridging Vision and Language by Large-Scale Multi-Modal Pre-Training

Multi-Modal Experience Inspired AI Creation

Proceedings of the 30th ACM International Conference on Multimedia

UniBriVL: Robust Universal Representation and Generation of Audio Driven Diffusion Models

Exploring Efficient-Tuned Learning Audio Representation Method from BriVL


The Dynamic Embedded Topic Model

Topic Modeling in Embedding Spaces

What Does the Indian Parliament Discuss? An Exploratory Analysis of the Question Hour in the Lok Sabha

Improving Diachronic Word Sense Induction with a Nonparametric Bayesian method

Findings of the Association for Computational Linguistics: ACL 2023


LOcal Rule-based Exlanations

Counterfactuals and Causability in Explainable Artificial Intelligence: Theory, Algorithms, and Applications

Towards Transparent Healthcare: Advancing Local Explanation Methods in Explainable Artificial Intelligence

counterfactuals: An R Package for Counterfactual Explanation Methods

Counterfactual Metarules for Local and Global Recourse


Code for http://saliency.mit.edu/

What do different evaluation metrics tell us about saliency models?

Spatially Adaptive Computation Time for Residual Networks

How is Gaze Influenced by Image Transformations? Dataset and Model

Meaning guides attention in real-world scene images: Evidence from eye movements and meaning maps

BubbleView: a validation of a mouse-contingent interface for crowdsourcing image importance and tracking visual attention

ACM Transactions on Computer-Human Interaction

SalFBNet: Learning Pseudo-Saliency Distribution via Feedback Convolutional Networks

Center Bias Does Not Account for the Advantage of Meaning Over Salience in Attentional Guidance During Scene Viewing

Saliency prediction based on multi-channel models of visual processing

A Gated Fusion Network for Dynamic Saliency Prediction

Invariance Analysis of Saliency Models versus Human Gaze During Scene Free Viewing


Bitcoin and Blockchain Simulator

Hybrid-IoT: Hybrid Blockchain Architecture for Internet of Things - PoW Sub-blockchains

Blockchain Evaluation Approaches: State-of-the-Art and Future Perspective


SCOPS: Self-Supervised Co-Part Segmentation (CVPR'19)

Motion-supervised Co-Part Segmentation

Unsupervised Part Segmentation through Disentangling Appearance and Shape


IGRINS pipeline package v3

ZODIACAL EXOPLANETS IN TIME (ZEIT). III. A SHORT-PERIOD PLANET ORBITING A PRE-MAIN-SEQUENCE STAR IN THE UPPER SCORPIUS OB ASSOCIATION

ZODIACAL EXOPLANETS IN TIME (ZEIT). I. A NEPTUNE-SIZED PLANET ORBITING AN M4.5 DWARF IN THE HYADES STAR CLUSTER

A solar C/O and sub-solar metallicity in a hot Jupiter atmosphere

ZODIACAL EXOPLANETS IN TIME (ZEIT). IV. SEVEN TRANSITING PLANETS IN THE PRAESEPE CLUSTER

A CANDIDATE YOUNG MASSIVE PLANET IN ORBIT AROUND THE CLASSICAL T TAURI STAR CI TAU

Zodiacal Exoplanets in Time (ZEIT). VI. A Three-planet System in the Hyades Cluster Including an Earth-sized Planet

Magnetic Inflation and Stellar Mass. II. On the Radii of Single, Rapidly Rotating, Fully Convective M-Dwarf Stars

TESS Hunt for Young and Maturing Exoplanets (THYME). VI. An 11 Myr Giant Planet Transiting a Very-low-mass Star in Lower Centaurus Crux

2 PLANETS AROUND LOW-MASS STARS (PALMS). VI. DISCOVERY OF A REMARKABLY RED PLANETARY-MASS COMPANION TO THE AB DOR MOVING GROUP CANDIDATE 2MASS J22362452+4751425

Zodiacal exoplanets in time (ZEIT) - II. A 'super-Earth' orbiting a young K dwarf in the Pleiades Neighbourhood


Numbers Station Text to SQL model code.

A Benchmark to Understand the Role of Knowledge Graphs on Large Language Model's Accuracy for Question Answering on Enterprise SQL Databases

Fine-Tuning Language Models for Context-Specific SQL Query Generation

Enhancing Text-to-SQL Translation for Financial System Design

Lucy: Think and Reason to Solve Text-to-SQL


GenMap - Fast and Exact Computation of Genome Mappability

GenMap: ultra-fast computation of genome mappability

Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics

Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks

GenMap: Fast and Exact Computation of Genome Mappability

Pan‐Cancer Single‐Nucleus Total RNA Sequencing Using snHH‐Seq


DeepFilterNet2: Towards Real-Time Speech Enhancement on Embedded Devices for Full-Band Audio

HGCN: Harmonic gated compensation network for speech enhancement

Complex Spectral Mapping With Attention Based Convolution Recurrent Neural Network for Speech Enhancement

TENET: A Time-reversal Enhancement Network for Noise-robust ASR

Quantitative Evidence on Overlooked Aspects of Enrollment Speaker Embeddings for Target Speaker Separation

DDS: A new device-degraded speech dataset for speech enhancement


All languages stopwords collection

COVID-19 Vaccination Awareness and Aftermath: Public Sentiment Analysis on Twitter Data and Vaccinated Population Prediction in the USA

MultiAzterTest: a Multilingual Analyzer on Multiple Levels of Language for Readability Assessment

Constructing Geospatial Concept Graphs from Tagged Images for Geo-Aware Fine-Grained Image Recognition

ISPRS International Journal of Geo-Information

Constructing Geographic Dictionary from Streaming Geotagged Tweets

Supervised Machine Learning mit Nutzergenerierten Inhalten: Oversampling für nicht balancierte Trainingsdaten

LAMPAT: Low-Rank Adaption for Multilingual Paraphrasing Using Adversarial Training

Can Domains Be Transferred Across Languages in Multi-Domain Multilingual Neural Machine Translation?


ICRA 2018 "Sparse-to-Dense: Depth Prediction from Sparse Depth Samples and a Single Image" (PyTorch Implementation)

Deeper Depth Prediction with Fully Convolutional Residual Networks

Fast Robust Monocular Depth Estimation for Obstacle Detection with Fully Convolutional Networks

Parse Geometry from a Line: Monocular Depth Estimation with Partial Laser Observation

Towards Real-Time Monocular Depth Estimation for Robotics: A Survey

The Aleatoric Uncertainty Estimation Using a Separate Formulation with Virtual Residuals


Hetionet: an integrative network of disease

TISSUES 2.0: an integrative web resource on mammalian tissue expression

Database : the journal of biological databases and curation

Knowledge-based Biomedical Data Science 2019

Scientific Language Models for Biomedical Knowledge Base Completion: An Empirical Study

Graph Chain-of-Thought: Augmenting Large Language Models by Reasoning on Graphs

An open source knowledge graph ecosystem for the life sciences

Establish the expected number of induced motifs on unlabeled graphs through analytical models

An Open-Source Knowledge Graph Ecosystem for the Life Sciences


This is a Pytorch implementation of paper: DropEdge: Towards Deep Graph Convolutional Networks on Node Classification

Simple and Deep Graph Convolutional Networks

Graph-based Semi-supervised Learning: A Comprehensive Review

Interpreting and Unifying Graph Neural Networks with An Optimization Framework

G-Mixup: Graph Data Augmentation for Graph Classification

Multi-hop Attention Graph Neural Networks

PROCEEDINGS OF THE THIRTIETH INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE, IJCAI 2021

Sparse Graph Attention Networks

Graph-Coupled Oscillator Networks

Feature Overcorrelation in Deep Graph Neural Networks: A New Perspective

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

SE-GSL: A General and Effective Graph Structure Learning Framework through Structural Entropy Optimization


A toolbox for comparative genomics.

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels

Methanotrophy across a natural permafrost thaw environment

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants

Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes


NeuS: Learning Neural Implicit Surfaces by Volume Rendering for Multi-view Reconstruction

Multiview Neural Surface Reconstruction by Disentangling Geometry and Appearance

NeRS: Neural Reflectance Surfaces for Sparse-view 3D Reconstruction in the Wild

Multi-View Mesh Reconstruction with Neural Deferred Shading


IRGAN SIGIR paper experimental code

IRGAN: A Minimax Game for Unifying Generative and Discriminative Information Retrieval Models

SIGIR'17: PROCEEDINGS OF THE 40TH INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL

Adversarial Personalized Ranking for Recommendation

International ACM SIGIR Conference on Research and Development in Information Retrieval

Adversarial Sampling and Training for Semi-Supervised Information Retrieval

WEB CONFERENCE 2019: PROCEEDINGS OF THE WORLD WIDE WEB CONFERENCE (WWW 2019)

Sampling-Decomposable Generative Adversarial Recommender

Generative Adversarial Nets for Information Retrieval: Fundamentals and Advances

Leveraging Long and Short-term Information in Content-aware Movie Recommendation


Deep Reinforcement Learning for Mention-Ranking Coreference Models

Improving Coreference Resolution by Learning Entity-Level Distributed Representations

Automated Data-Driven Generation of Personalized Pedagogical Interventions in Intelligent Tutoring Systems

International Journal of Artificial Intelligence in Education

Conundrums in Entity Coreference Resolution: Making Sense of the State of the Art

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

Coreference Resolution Using Neural MCDM and Fuzzy Weighting Technique

International Journal of Computational Intelligence Systems

Use Generalized Representations, But Do Not Forget Surface Features


Flip-flop basecaller for Oxford Nanopore reads

Recent advances in the detection of base modifications using the Nanopore sequencer

A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field

A new era of long-read sequencing for cancer genomics

An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations

Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling

On Coding for an Abstracted Nanopore Channel for DNA Storage

High Diversity of Type I Polyketide Genes in Bacidia rubella as Revealed by the Comparative Analysis of 23 Lichen Genomes


Kernel Density Estimation and (re)sampling

Gravitational self-lensing in populations of massive black hole binaries

Monthly Notices of the Royal Astronomical Society

Basic considerations for the observability of kinematically offset binary AGN

Zenodo (CERN European Organization for Nuclear Research)

Mass Ratios of Merging Double Neutron Stars as Implied by the Milky Way Population

The optical properties of three Type II supernovae: 2014cx, 2014cy, and 2015cz


WordNet-LMF formats

Open Dutch WordNet

Building the Cantonese Wordnet

Some Issues with Building a Multilingual Wordnet

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

Pinchah Kristang: A Dictionary of Kristang

Building the Old Javanese Wordnet

The Making of Coptic Wordnet

Abui Wordnet: Using a Toolbox Dictionary to develop a wordnet for a low-resource language

Enriching Linguistic Representation in the Cantonese Wordnet and Building the New Cantonese Wordnet Corpus

LREC 2022: THIRTEEN INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION


Code Release for MViTv2 on Image Recognition.

Multiscale Vision Transformers

MViTv2: Improved Multiscale Vision Transformers for Classification and Detection

Reversible Vision Transformers

Bringing Image Scene Structure to Video via Frame-Clip Consistency of Object Tokens

PromptonomyViT: Multi-Task Prompt Learning Improves Video Transformers using Synthetic Scene Data

Visual Concept Connectome (VCC): Open World Concept Discovery and their
  Interlayer Connections in Deep Models


PyTorch Re-Implementation of "Generating Sentences from a Continuous Space" by Bowman et al 2015 https://arxiv.org/abs/1511.06349

Unsupervised Paraphrasing by Simulated Annealing

A Stable Variational Autoencoder for Text Modelling

Improving Variational Autoencoder for Text Modelling with Timestep-Wise Regularisation

Text Morphing

Russian Natural Language Generation: Creation of a Language Modelling Dataset and Evaluation with Modern Neural Architectures


Bayesian demographic estimation and forecasting.

Obesity and occupation in Thailand: using a Bayesian hierarchical model to obtain prevalence estimates from the National Health Examination Survey

A Computationally Efficient Approach to Fully Bayesian Benchmarking


A novel embedding training algorithm leveraging ANN search and achieved SOTA retrieval on Trec DL 2019 and OpenQA benchmarks

Approximate Nearest Neighbor Negative Contrastive Learning for Dense Text Retrieval

Few-Shot Conversational Dense Retrieval

SIGIR '21 - PROCEEDINGS OF THE 44TH INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL

A Neural Corpus Indexer for Document Retrieval

Adversarial Retriever-Ranker for dense text retrieval

Simplified Data Wrangling with ir_datasets

Zero-Shot Dense Retrieval with Momentum Adversarial Domain Invariant Representations

More Robust Dense Retrieval with Contrastive Dual Learning

Improving Query Representations for Dense Retrieval with Pseudo Relevance Feedback: A Reproducibility Study

HLATR: Enhance Multi-stage Text Retrieval with Hybrid List Aware Transformer Reranking


SIMD-accelerated UTF-8 validation for Rust.

Transcoding Billions of Unicode Characters per Second with SIMD Instructions

Transcoding Unicode Characters with AVX-512 Instructions

Unicode at Gigabytes per Second

String Processing and Information Retrieval


S2ORC: The Semantic Scholar Open Research Corpus:  https://www.aclweb.org/anthology/2020.acl-main.447/

Lifelong Pretraining: Continually Adapting Language Models to Emerging Corpora

A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language

The Semantic Scholar Open Data Platform

Nougat: Neural Optical Understanding for Academic Documents

Explaining Relationships Between Scientific Documents

SciFact-Open: Towards open-domain scientific claim verification

CiteWorth: Cite-Worthiness Detection for Improved Scientific Document Understanding

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

Arctic-Embed: Scalable, Efficient, and Accurate Text Embedding Models


PCAtools: everything Principal Components Analysis

Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection

Myelin insulation as a risk factor for axonal degeneration in autoimmune demyelinating disease

Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex

Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs

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

Analysis of systemic epigenetic alterations in inflammatory bowel disease: defining geographical, genetic, and immune-inflammatory influences on the circulating methylome

Integrated Analysis of a Risk Score System Predicting Prognosis and a ceRNA Network for Differentially Expressed lncRNAs in Multiple Myeloma

Diversity and Differential Expression of MicroRNAs in the Human Skeletal Muscle with Distinct Fiber Type Composition

Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR

Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO2 during early development

Transposable elements are associated with the variable response to influenza infection


cortex lab code for electrophysiology

Chronically-implanted Neuropixels probes enable high yield recordings in freely moving mice

Distance-tuned neurons drive specialized path integration calculations in medial entorhinal cortex

Mouse entorhinal cortex encodes a diverse repertoire of self-motion signals

Binocular Suppression in the Macaque Lateral Geniculate Nucleus Reveals Early Competitive Interactions between the Eyes

3D printed guide tube system for acute Neuropixels probe recordings in non-human primates

Oxytocin induces the formation of distinctive cortical representations and cognitions biased toward familiar mice


Models and Simulations for the Photometric LSST Astronomical Time Series Classification Challenge (PLAsTiCC)

Publications of the Astronomical Society of the Pacific

VBBinaryLensing: a public package for microlensing light-curve computation

Monthly notices of the Royal Astronomical Society

ROME/REA: A Gravitational Microlensing Search for Exoplanets Beyond the Snow Line on a Global Network of Robotic Telescopes

Measuring the Microlensing Parallax from Various Space Observatories

A public code for astrometric microlensing with contour integration

Reconciling the Predictions of Microlensing Analysis with Radial Velocity Measurements for OGLE-2011-BLG-0417

Confirmation of the Stellar Binary Microlensing Event, Macho 97-BLG-28

Estimating Microlensing Parameters from Observables and Stellar Isochrones with pyLIMASS


license

Spatially Explicit Soil Compaction Risk Assessment of Arable Soils at Regional Scale: The SaSCiA-Model

Temporal Sensitivity Analysis of the MONICA Model: Application of Two Global Approaches to Analyze the Dynamics of Parameter Sensitivity


A computationally efficient and robust LiDAR-inertial odometry (LIO) package

FAST-LIO: A Fast, Robust LiDAR-Inertial Odometry Package by Tightly-Coupled Iterated Kalman Filter

ikd-Tree: An Incremental K-D Tree for Robotic Applications

LLOL: Low-Latency Odometry for Spinning Lidars

PALoc: Advancing SLAM Benchmarking with Prior-Assisted 6-DoF Trajectory
  Generation and Uncertainty Estimation


Creating heat and power demand profiles from annual values.

Speed of technological transformations required in Europe to achieve different climate goals

The potential role of a hydrogen network in Europe


REL: Radboud Entity Linker

REL: An Entity Linker Standing on the Shoulders of Giants

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

Entity Linking Meets Deep Learning: Techniques and Solutions

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

TweetNERD - End to End Entity Linking Benchmark for Tweets

Pre-training Language Models with Deterministic Factual Knowledge

OpenEL: An Annotated Corpus for Entity Linking and Discourse in Open Domain Dialogue

MMEAD: MS MARCO Entity Annotations and Disambiguations

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


Gym environments and agents for autonomous driving.

BARK: Open Behavior Benchmarking in Multi-Agent Environments

An Introduction to Multi-Agent Reinforcement Learning and Review of its Application to Autonomous Mobility

Counterfactual Policy Evaluation for Decision-Making in Autonomous Driving

Causal Reinforcement Learning: A Survey

Using Counterfactual Reasoning and Reinforcement Learning for Decision-Making in Autonomous Driving.


A differentiable PDE solving framework for machine learning

Solver-in-the-Loop: Learning from Differentiable Physics to Interact with Iterative PDE-Solvers

Message Passing Neural PDE Solvers

Learning to Control PDEs with Differentiable Physics

Physics-based Deep Learning

Towards Multi-spatiotemporal-scale Generalized PDE Modeling

Clifford Neural Layers for PDE Modeling

Meta-Learning Dynamics Forecasting Using Task Inference

Learning to Accelerate Partial Differential Equations via Latent Global Evolution

Geometric Clifford Algebra Networks

MAgNet: Mesh Agnostic Neural PDE Solver


TextWorld is a sandbox learning environment for the training and evaluation of reinforcement learning (RL) agents on text-based games.

Modeling Worlds in Text

Situated Language Learning via Interactive Narratives

A survey of benchmarks for reinforcement learning algorithms


Additional themes, scales, and geoms for ggplot2

Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface

Frontiers in cellular and infection microbiology

Characterization and Tissue Tropism of Newly Identified Iflavirus and Negeviruses in Glossina morsitans morsitans Tsetse Flies

Fat body phospholipid state dictates hunger-driven feeding behavior

Training machine learning algorithms for automatic facial coding: The role of emotional facial expressions’ prototypicality

Mutational signatures representative transcriptomic perturbations in hepatocellular carcinoma


Self-describing content-addressed identifiers for distributed systems

GLASS: A Citizen-Centric Distributed Data-Sharing Model within an e-Governance Architecture

A Fully Decentralized Triplestore Managed via the Ethereum Blockchain

A Privacy-Preserving Platform for Recording COVID-19 Vaccine Passports

Transforming EU Governance: The Digital Integration Through EBSI and GLASS


Contains the REMIND-specific routines for data and model output manipulation.


PyTorch Wildlife: a Collaborative Deep Learning Framework for Conservation.

A deep active learning system for species identification and counting in camera trap images

Efficient Pipeline for Camera Trap Image Review

Perspectives on Individual Animal Identification from Biology and Computer Vision

Efficient Pipeline for Automating Species ID in new Camera Trap Projects

Biodiversity Information Science and Standards

The iWildCam 2019 Challenge Dataset

Automated wildlife image classification: An active learning tool for ecological applications

U-Infuse: Democratization of Customizable Deep Learning for Object Detection

Fisheye transformation enhances deep-learning-based single-cell phenotyping by including cellular microenvironment

Pytorch-Wildlife: A Collaborative Deep Learning Framework for Conservation


Apache Mesos

A Comprehensive Feature Comparison Study of Open-Source Container Orchestration Frameworks

On Byzantine fault tolerance in multi-master Kubernetes clusters

Multitenant Containers as a Service (CaaS) for Clouds and Edge Clouds

Empirical Analysis of Software Vulnerabilities Causing Timing Side Channels


Code for our CVPR 2021 Paper "Self-Supervised Learning for Semi-Supervised Temporal Action Proposal".

SlowFast Networks for Video Recognition

Proposal Relation Network for Temporal Action Detection

CBR-Net: Cascade Boundary Refinement Network for Action Detection: Submission to ActivityNet Challenge 2020 (Task 1)


Defense-GAN: Protecting Classifiers Against Adversarial Attacks Using Generative Models (published in ICLR2018)

Robustifying Models Against Adversarial Attacks by Langevin Dynamics

Defense-VAE: A Fast and Accurate Defense against Adversarial Attacks

AID-Purifier: A Light Auxiliary Network for Boosting Adversarial Defense

Effective and Robust Detection of Adversarial Examples via Benford-Fourier Coefficients

Perturbations are not Enough: Generating Adversarial Examples with Spatial Distortions


PyTorch Face Recognizer based on 'VGGFace2: A dataset for recognising faces across pose and age'

Joint Face Detection and Alignment Using Multitask Cascaded Convolutional Networks

Mitigating dataset harms requires stewardship: Lessons from 1000 papers

Deep Learning for Face Recognition: Pride or Prejudiced?

M3ED: Multi-modal Multi-scene Multi-label Emotional Dialogue Database

Latent Diffusion Counterfactual Explanations


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

Phrase-Based & Neural Unsupervised Machine Translation

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

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

Learning Implicit Text Generation via Feature Matching


SoundNet: Learning Sound Representations from Unlabeled Video. NIPS 2016

AudioCaps: Generating Captions for Audios in The Wild

North American Chapter of the Association for Computational Linguistics

Learning Joint Embedding for Cross-Modal Retrieval


Improved Techniques for Training GANs

Generating Long Sequences with Sparse Transformers

Towards Accurate Generative Models of Video: A New Metric & Challenges

VideoGPT: Video Generation using VQ-VAE and Transformers

CogVideo: Large-scale Pretraining for Text-to-Video Generation via Transformers

PV3D: A 3D Generative Model for Portrait Video Generation

Diffusion Reward: Learning Rewards via Conditional Video Diffusion

POS: A Prompts Optimization Suite for Augmenting Text-to-Video Generation


Assembly by Reduced Complexity (ARC)

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

Dietary breadth is positively correlated with venom complexity in cone snails

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

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

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

Complete Mitochondrial Genome Sequence of Bighorn Sheep

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


Image Captioning Using Transformer

On Vision Features in Multimodal Machine Translation

YOLOR-Based Multi-Task Learning

Semi-Supervised Cross-Modal Salient Object Detection with U-Structure Networks


Easy Bootstrap Resampling and Approximate Randomization for BLEU, METEOR, and TER using Multiple Optimizer Runs. This implements "Better Hypothesis Testing for Statistical Machine Translation: Controlling for Optimizer Instability" from ACL 2011.

A Call for Clarity in Reporting BLEU Scores

Meeting of the Association for Computational Linguistics

Neural Paraphrase Generation with Stacked Residual LSTM Networks

A Deep Generative Framework for Paraphrase Generation

A Shared Task on Multimodal Machine Translation and Crosslingual Image Description

Proceedings of the First Conference on Machine Translation: Volume 2,
          Shared Task Papers

A Systematic Comparison of Smoothing Techniques for Sentence-Level BLEU

Workshop on Statistical Machine Translation

Ask the Right Questions: Active Question Reformulation with Reinforcement Learning

Fill-up versus interpolation methods for phrase-based SMT adaptation

International Workshop on Spoken Language Translation

Multimodal Pivots for Image Caption Translation

PROCEEDINGS OF THE 54TH ANNUAL MEETING OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS, VOL 1

Scientific Credibility of Machine Translation Research: A Meta-Evaluation of 769 Papers


Quantized Neural Networks: Training Neural Networks with Low Precision Weights and Activations

Binarized Neural Networks: Training Deep Neural Networks with Weights and Activations Constrained to +1 or -1

LightNN: Filling the Gap between Conventional Deep Neural Networks and Binarized Networks

Espresso: Efficient Forward Propagation for BCNNs

PocketNN: Integer-only Training and Inference of Neural Networks via Direct Feedback Alignment and Pocket Activations in Pure C++


GAIA, with the full name Generic AIOps Atlas, is an overall dataset for analyzing operation problems such as anomaly detection, log analysis, fault localization, etc.

Robust Failure Diagnosis of Microservice System Through Multimodal Data

LogFormer: A Pre-train and Tuning Pipeline for Log Anomaly Detection


Codebase, data and models for the SummaC paper in TACL

SummaC: Re-Visiting NLI-based Models for Inconsistency Detection in Summarization

TRUE: Re-evaluating Factual Consistency Evaluation

SummEdits: Measuring LLM Ability at Factual Reasoning Through The Lens of Summarization

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

ECTSum: A New Benchmark Dataset For Bullet Point Summarization of Long Earnings Call Transcripts

LLMs as Factual Reasoners: Insights from Existing Benchmarks and Beyond

TofuEval: Evaluating Hallucinations of LLMs on Topic-Focused Dialogue
  Summarization

Revisiting text decomposition methods for NLI-based factuality scoring of summaries

Leveraging Summary Guidance on Medical Report Summarization

Applicability of large language models and generative models for legal case judgement summarization

Aligning Factual Consistency for Clinical Studies Summarization through Reinforcement Learning

Proceedings of the 5th Clinical Natural Language Processing Workshop


Subgraph Neural Networks (NeurIPS 2020)

Subgraph Neural Networks

State of the Art and Potentialities of Graph-level Learning

Position-Aware Subgraph Neural Networks with Data-Efficient Learning

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

Models and Benchmarks for Representation Learning of Partially Observed Subgraphs


This is the Army Research Laboratory (ARL) EEGModels Project: A Collection of Convolutional Neural Network (CNN) models for EEG signal classification, using Keras and Tensorflow

EEGNet: a compact convolutional neural network for EEG-based brain–computer interfaces

Compact convolutional neural networks for classification of asynchronous steady-state visual evoked potentials

Deep Learning Based on Event-Related EEG Differentiates Children with ADHD from Healthy Controls

EEG-Based Cross-Subject Driver Drowsiness Recognition With an Interpretable Convolutional Neural Network

Decoding Movement From Electrocorticographic Activity: A Review

Data Augmentation: Using Channel-Level Recombination to Improve Classification Performance for Motor Imagery EEG

Decoding P300 Variability Using Convolutional Neural Networks

Toward reliable signals decoding for electroencephalogram: A benchmark study to EEGNeX

A few filters are enough: Convolutional Neural Network for P300 Detection

Priming Cross-Session Motor Imagery Classification with A Universal Deep Domain Adaptation Framework


Software Development Vehicles to enable extended and early co-design: a RISC-V and HPC case of study


Toolkit for building machine learning models that generalize to unseen domains and are robust to privacy and other attacks.

Domain Generalization using Causal Matching

Alleviating Privacy Attacks via Causal Learning

Hierarchical Variational Auto-Encoding for Unsupervised Domain Generalization

The Connection between Out-of-Distribution Generalization and Privacy of ML Models


MuCGEC中文纠错数据集及文本纠错SOTA模型开源；Code & Data for our NAACL 2022 Paper "MuCGEC: a Multi-Reference Multi-Source Evaluation Dataset for Chinese Grammatical Error Correction"

LawBench: Benchmarking Legal Knowledge of Large Language Models

GrammarGPT: Exploring Open-Source LLMs for Native Chinese Grammatical Error Correction with Supervised Fine-Tuning

Evaluating the Capability of Large-scale Language Models on Chinese Grammatical Error Correction Task

FlaCGEC: A Chinese Grammatical Error Correction Dataset with Fine-grained Linguistic Annotation

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

Mining Error Templates for Grammatical Error Correction

Are Pre-trained Language Models Useful for Model Ensemble in Chinese Grammatical Error Correction?


A generalised, dynamic DNA reference library for metabarcoding of fishes

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

Surveillance of fish species composition using environmental DNA

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea).

Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes.


MFannot is a program for the annotation of mitochondrial and plastid genomes

Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts

Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

Chloroplast Genomes for Five Skeletonema Species: Comparative and Phylogenetic Analysis

RecombineX: A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis

Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation

Comparative Analysis of Chloroplast Genomes of Seven Chaetoceros Species Revealed Variation Hotspots and Speciation Time

Genomic Characterization of Parengyodontium torokii sp. nov., a Biofilm-Forming Fungus Isolated from Mars 2020 Assembly Facility


BioModelos is a collaborative online system to map species distributions. This repository stores functions to automate the construction of Species Distribution Models (SDM) from databases gathered, managed and curated by The Alexander Von Humboldt Institute and a network of experts in order to be evaluated and refined.

A practical guide to MaxEnt for modeling species' distributions: what it does, and why inputs and settings matter

Simple Features for R: Standardized Support for Spatial Vector Data

spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models

The importance of correcting for sampling bias in MaxEnt species distribution models

kuenm: an R package for detailed development of ecological niche models using Maxent

CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases

ntbox: An r package with graphical user interface for modelling and evaluating multidimensional ecological niches

BioModelos: A collaborative online system to map species distributions


Python interface to RADEX

Temperature, Mass, and Turbulence: A Spatially Resolved Multiband Non-LTE Analysis of CS in TW Hya

Temperature structures in Galactic center clouds. Direct evidence for gas heating via turbulence

Warm and cold molecular gas conditions modelled in 87 galaxies observed by the Herschel SPIRE Fourier transform spectrometer

Monthly Notices of the Royal Astronomical Society

Recovering the Physical Properties of Molecular Gas in Galaxies from CO SLED Modeling

Dense Molecular Gas Properties of the Central Kiloparsec of Nearby Ultraluminous Infrared Galaxies Constrained by ALMA Three Transition-line Observations

Cold Deuterium Fractionation in the Nearest Planet-forming Disk

Massive Molecular Gas Reservoir in a Luminous Submillimeter Galaxy during Cosmic Noon

ALMA 0.5 kpc Resolution Spatially Resolved Investigations of Nuclear Dense Molecular Gas Properties in Nearby Ultraluminous Infrared Galaxies Based on HCN and HCO^+ Three Transition Line Data


Easy access to high-resolution daily climate data for Europe


Active Learning for Convolutional Neural Networks: A Core-Set Approach

Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds

Discriminative Active Learning

Active Discriminative Text Representation Learning

Scalable k-Means Clustering via Lightweight Coresets

Revisiting Uncertainty-based Query Strategies for Active Learning with Transformers

Similarity Search for Efficient Active Learning and Search of Rare Concepts

Small-Text: Active Learning for Text Classification in Python

AnchorAL: Computationally Efficient Active Learning for Large and
  Imbalanced Datasets


LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data

Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization

Most large structural variants in cancer genomes can be detected without long reads


autodp: A flexible and easy-to-use package for differential privacy

Subsampled Rényi Differential Privacy and Analytical Moments Accountant

Survey on Federated Learning Threats: concepts, taxonomy on attacks and defences, experimental study and challenges

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

Fast-adapting and privacy-preserving federated recommender system

Poission Subsampled Rényi Differential Privacy

International Conference on Machine Learning

Optimal Accounting of Differential Privacy via Characteristic Function

GAP: Differentially Private Graph Neural Networks with Aggregation Perturbation

Mixed Differential Privacy in Computer Vision

Pre-trained Perceptual Features Improve Differentially Private Image Generation

Advancing Differential Privacy: Where We Are Now and Future Directions for Real-World Deployment