Force Fields

Preliminary Structure–Activity Relationship Study of the MMV Pathogen Box Compound MMV675968 (2,4-Diaminoquinazoline) Unveils Novel Inhibitors of Trypanosoma brucei brucei

Molecular dynamics simulations of the flexibility and inhibition of SARS-CoV-2 NSP 13 helicase

Journal of molecular graphics & modelling

Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds

International journal of molecular sciences

Structure-Based Experimental Datasets for Benchmarking of Protein Simulation Force Fields


Code for reproducing Manifold Mixup results (ICML 2019)

Manifold Mixup: Better Representations by Interpolating Hidden States

Manifold Mixup: Learning Better Representations by Interpolating Hidden States

k-Mixup Regularization for Deep Learning via Optimal Transport


NeurIPS'18: Co-teaching: Robust Training of Deep Neural Networks with Extremely Noisy Labels

Learning from Noisy Labels with Deep Neural Networks: A Survey

Masking: A New Perspective of Noisy Supervision

Decoupled Knowledge Distillation

Searching to Exploit Memorization Effect in Learning from Corrupted Labels

FINE Samples for Learning with Noisy Labels

Wasserstein Adversarial Regularization (WAR) on label noise

Robustness to Label Noise Depends on the Shape of the Noise Distribution in Feature Space

Combating Bilateral Edge Noise for Robust Link Prediction

Label Noise-Robust Learning using a Confidence-Based Sieving Strategy


Deep Speaker: an End-to-End Neural Speaker Embedding System.

STYLER: Style Factor Modeling with Rapidity and Robustness via Speech Decomposition for Expressive and Controllable Neural Text to Speech

MERBench: A Unified Evaluation Benchmark for Multimodal Emotion Recognition

MER 2024: Semi-Supervised Learning, Noise Robustness, and Open-Vocabulary Multimodal Emotion Recognition

Jointly Trained Conversion Model With LPCNet for Any-to-One Voice Conversion Using Speaker-Independent Linguistic Features


A space to log issues, updates, and software related to the ATLAS (Anatomical Tracings of Lesions After Stroke) database.

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

Automatic Segmentation and Quantitative Assessment of Stroke Lesions on MR Images

Coupled-Projection Residual Network for MRI Super-Resolution

A standardized protocol for manually segmenting stroke lesions on high-resolution T1-weighted MR images


Segment-Anything + 3D. Let's lift anything to 3D.

Anything-3D: Towards Single-view Anything Reconstruction in the Wild

Black-box Targeted Adversarial Attack on Segment Anything (SAM)

Segment Anything Meets Universal Adversarial Perturbation


Several data modalities for KBs (visual, numerical, temporal, etc.)

Learning Sequence Encoders for Temporal Knowledge Graph Completion

Representation Learning for Dynamic Graphs: A Survey

MMKG: Multi-Modal Knowledge Graphs

KBLRN : End-to-End Learning of Knowledge Base Representations with Latent, Relational, and Numerical Features

Time-aware Graph Neural Network for Entity Alignment between Temporal Knowledge Graphs

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

Answering Visual-Relational Queries in Web-Extracted Knowledge Graphs

Attribute-Consistent Knowledge Graph Representation Learning for Multi-Modal Entity Alignment

Few-Shot Inductive Learning on Temporal Knowledge Graphs using Concept-Aware Information

Meta-Learning Based Knowledge Extrapolation for Temporal Knowledge Graph

EasyDGL: Encode, Train and Interpret for Continuous-time Dynamic Graph Learning


Simple heat and power model of Germany


The Data Cards Playbook helps dataset producers and publishers adopt a people-centered approach to transparency in dataset documentation.

Model Cards for Model Reporting

Proceedings of the Conference on Fairness, Accountability, and Transparency

Data Cards: Purposeful and Transparent Dataset Documentation for Responsible AI

Healthsheet: Development of a Transparency Artifact for Health Datasets

Leveraging LLMs for Synthesizing Training Data Across Many Languages in Multilingual Dense Retrieval


Tools for tissue image stain normalisation and augmentation in Python 3

Staining Invariant Features for Improving Generalization of Deep Convolutional Neural Networks in Computational Pathology

Frontiers in bioengineering and biotechnology

Predicting molecular phenotypes from histopathology images: a transcriptome-wide expression-morphology analysis in breast cancer

HistoCartography: A Toolkit for Graph Analytics in Digital Pathology

Breast cancer histopathology image-based gene expression prediction using spatial transcriptomics data and deep learning

Artificial Intelligence-based Tumor Segmentation in Mouse Models of Lung Adenocarcinoma

Predicting colorectal cancer microsatellite instability with a self-attention-enabled convolutional neural network

Hybrid guiding: A multi-resolution refinement approach for semantic segmentation of gigapixel histopathological images

PatchSorter: a high throughput deep learning digital pathology tool for object labeling

Towards a representative reference for MRI-based human axon radius assessment using light microscopy

Multi-domain stain normalization for digital pathology: A cycle-consistent adversarial network for whole slide images


Access to Biological Collection Data (ABCD)

Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs?

A story of data won, data lost and data re-found: the realities of ecological data preservation

ABCD 3.0 Ready to Use

Biodiversity Information Science and Standards

Essential Annotation Schema for Ecology (EASE)—A framework supporting the efficient data annotation and faceted navigation in ecology


Helper package with multiple U-Net implementations in Keras as well as useful utility tools helpful when working with image semantic segmentation tasks. This library and underlying tools come from multiple projects I performed working on semantic segmentation tasks

U-Net: Convolutional Networks for Biomedical Image Segmentation

Automatic Segmentation of Retinal Fluid and Photoreceptor Layer from Optical Coherence Tomography Images of Diabetic Macular Edema Patients Using Deep Learning and Associations with Visual Acuity

ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic

������������: An eXplainable Framework to Map Bark Beetle Infestation in Sentinel-2 Images

IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing

Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint

Sea ice concentration estimation techniques using machine learning: an end-to-end workflow for estimating concentration maps from SAR images

Leveraging Sentinel-2 time series for bark beetle-induced forest dieback inventory


A C++ library for Quadratic Programming which implements the Goldfarb-Idnani active-set dual method.

LEoPart: a particle library for FEniCS

Computers and Mathematics with Applications

A model predictive control (MPC)-integrated multiphase immersed boundary (IB) framework for simulating wave energy converters (WECs)

Real-Time Model Predictive Control for Industrial Manipulators with Singularity-Tolerant Hierarchical Task Control


Group ICA/IVA software (MATLAB)

Clinical and Cortical Similarities Identified Between Bipolar Disorder I and Schizophrenia: A Multivariate Approach

Searching Reproducible Brain Features using NeuroMark: Templates for Different Age Populations and Imaging Modalities

Dynamic spectral signatures of mirror movements in the sensorimotor functional connectivity network of patients with Kallmann syndrome


An implementation of KFAC for TensorFlow

Optimizing Neural Networks with Kronecker-factored Approximate Curvature

Estimating Model Uncertainty of Neural Networks in Sparse Information Form

M-FAC: Efficient Matrix-Free Approximations of Second-Order Information

Convolutional Neural Network Training with Distributed K-FAC

Small Steps and Giant Leaps: Minimal Newton Solvers for Deep Learning

Gradient Descent on Neurons and its Link to Approximate Second-Order Optimization

Network Automatic Pruning: Start NAP and Take a Nap

Component-Wise Natural Gradient Descent - An Efficient Neural Network Optimization


Torch implementation of "Enhanced Deep Residual Networks for Single Image Super-Resolution"

Image Super-Resolution by Neural Texture Transfer

Noise Conditional Flow Model for Learning the Super-Resolution Space

FS-NCSR: Increasing Diversity of the Super-Resolution Space via Frequency Separation and Noise-Conditioned Normalizing Flow

Super-Resolving Beyond Satellite Hardware Using Realistically Degraded Images


Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Genetic identification of brain cell types underlying schizophrenia

Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq

Regional brain iron and gene expression provide insights into neurodegeneration in Parkinson’s disease

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

Differences in network controllability and regional gene expression underlie hallucinations in Parkinson’s disease

Genes influenced by MEF2C contribute to neurodevelopmental disease via gene expression changes that affect multiple types of cortical excitatory neurons

Heterogeneous somatostatin-expressing neuron population in mouse ventral tegmental area

Genetic topography and cortical cell loss in Huntington's disease link development and neurodegeneration

An Integrated Genomic Approach to Dissect the Genetic Landscape Regulating the Cell-to-Cell Transfer of α-Synuclein

Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into the complex genetic architecture


Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

JAFFAL: detecting fusion genes with long-read transcriptome sequencing

Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing

Detection of alternative isoforms of gene fusions from long-read RNA-seq with FLAIR-fusion

Identifying N6-Methyladenosine Sites in HepG2 Cell Lines Using Oxford Nanopore Technology

The Singapore Nanopore Expression Project (SG-NEx) data pre-release v0.1

Zenodo (CERN European Organization for Nuclear Research)

Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework

bioRxiv : the preprint server for biology


Compute distance between sequences. 30+ algorithms, pure python implementation, common interface, optional external libs usage.

Automated Extraction of Chemical Synthesis Actions from Experimental Procedures

DualSC: Automatic Generation and Summarization of Shellcode via Transformer and Dual Learning

BashExplainer: Retrieval-Augmented Bash Code Comment Generation based on Fine-tuned CodeBERT

ACES: Translation Accuracy Challenge Sets for Evaluating Machine Translation Metrics

Factorizing Content and Budget Decisions in Abstractive Summarization of Long Documents

FigurA11y: AI Assistance for Writing Scientific Alt Text

Proceedings of the 29th International Conference on Intelligent User Interfaces

Iterative Genetic Improvement: Scaling Stochastic Program Synthesis

Leveraging Task Information in Grammatical Error Correction for Short Answer Assessment through Context-based Reranking


LLM-jp: A Cross-organizational Project for the Research and Development of Fully Open Japanese LLMs

Building a Large Japanese Web Corpus for Large Language Models

Analyzing Social Biases in Japanese Large Language Models


Import, manipulate and explore the results of an Antares simulation


[ACL 2024] An Easy-to-use Knowledge Editing Framework for LLMs.

Editing Large Language Models: Problems, Methods, and Opportunities

A Comprehensive Study of Knowledge Editing for Large Language Models

EasyEdit: An Easy-to-use Knowledge Editing Framework for Large Language Models

Detoxifying Large Language Models via Knowledge Editing

What does the Knowledge Neuron Thesis Have to do with Knowledge?

Can We Edit Multimodal Large Language Models?

Cross-Lingual Knowledge Editing in Large Language Models

The Butterfly Effect of Model Editing: Few Edits Can Trigger Large Language Models Collapse

WISE: Rethinking the Knowledge Memory for Lifelong Model Editing of
  Large Language Models

Editing Conceptual Knowledge for Large Language Models


:stuck_out_tongue_closed_eyes: TensorFlowTTS: Real-Time State-of-the-art Speech Synthesis for Tensorflow 2 (supported including English, French, Korean, Chinese, German and Easy to adapt for other languages)

Natural TTS Synthesis by Conditioning WaveNet on Mel Spectrogram Predictions

Tacotron: Towards End-to-End Speech Synthesis

HiFi-GAN: Generative Adversarial Networks for Efficient and High Fidelity Speech Synthesis

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

MelGAN: Generative Adversarial Networks for Conditional Waveform Synthesis

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

FastSpeech: Fast, Robust and Controllable Text to Speech

A Survey on Neural Speech Synthesis

ESPnet2-TTS: Extending the Edge of TTS Research

"Hello, It's Me": Deep Learning-based Speech Synthesis Attacks in the Real World

Conference on Computer and Communications Security


An algorithm for recovering haplotypes from metagenomes

On the complexity of haplotyping a microbial community

Recovery of gene haplotypes from a metagenome

Computational haplotype recovery and long-read validation identiﬁes novel isoforms of industrially relevant enzymes from natural microbial communities

Aberystwyth Research portal (Aberystwyth University)

Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

Probabilistic recovery of cryptic haplotypes from metagenomic data

Advances in the recovery of haplotypes from the metagenome


Calculating carbon emissions in R


Code for experiments regarding importance sampling for training neural networks

Not All Samples Are Created Equal: Deep Learning with Importance Sampling

Variance Reduction in SGD by Distributed Importance Sampling

Biased Importance Sampling for Deep Neural Network Training

Supercharging Imbalanced Data Learning With Energy-based Contrastive Representation Transfer


Event Extraction by Answering (Almost) Natural Questions

DEGREE: A Data-Efficient Generation-Based Event Extraction Model

Prompt for Extraction? PAIE: Prompting Argument Interaction for Event Argument Extraction

PHEE: A Dataset for Pharmacovigilance Event Extraction from Text

DEGREE: A Data-Efficient Generative Event Extraction Model

The Devil is in the Details: On the Pitfalls of Event Extraction Evaluation

TextEE: Benchmark, Reevaluation, Reflections, and Future Challenges in Event Extraction

Few-shot Event Detection: An Empirical Study and a Unified View

Role Knowledge Prompting for Document-Level Event Argument Extraction


Identifying Mislabeled Data using the Area Under the Margin Ranking

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

Dissecting Sample Hardness: A Fine-Grained Analysis of Hardness
  Characterization Methods for Data-Centric AI

Denoising after Entropy-based Debiasing A Robust Training Method for Dataset Bias with Noisy Labels


Code and data for MedQA

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

Benchmarking Retrieval-Augmented Generation for Medicine

Kformer: Knowledge Injection in Transformer Feed-Forward Layers

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

Small Language Models Learn Enhanced Reasoning Skills from Medical
  Textbooks

MedAdapter: Efficient Test-Time Adaptation of Large Language Models towards Medical Reasoning

PsyEval: A Comprehensive Large Language Model Evaluation Benchmark for Mental Health

An Automatic Evaluation Framework for Multi-turn Medical Consultations Capabilities of Large Language Models

Examining User-Friendly and Open-Sourced Large GPT Models: A Survey on Language, Multimodal, and Scientific GPT Models

Automatic Interactive Evaluation for Large Language Models with State Aware Patient Simulator


Implementation of the Convolution Neural Network for factoid QA on the answer sentence selection task

aNMM: Ranking Short Answer Texts with Attention-Based Neural Matching Model

Neural Information Retrieval: A Literature Review

Cross-Pair Text Representations for Answer Sentence Selection

Empirical Methods in Natural Language Processing

Injecting Relational Structural Representation in Neural Networks for Question Similarity


CWL+Singularity implementation of an RNA editing workflow

Singularity: Scientific containers for mobility of compute

Common Workflow Language, v1.0

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis

Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing


source code for the paper Deep Knowledge Tracing

Deep Knowledge Tracing

A Self-Attentive model for Knowledge Tracing

EdNet: A Large-Scale Hierarchical Dataset in Education

Knowledge Tracing with Sequential Key-Value Memory Networks

PROCEEDINGS OF THE 42ND INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL (SIGIR '19)

Knowledge Tracing: A Survey

Knowledge Query Network: How Knowledge Interacts with Skills

Domain Adaption for Knowledge Tracing

DBE-KT22: A Knowledge Tracing Dataset Based on Online Student Evaluation

DAGKT: Difficulty and Attempts Boosted Graph-based Knowledge Tracing

Empirical Evaluation of Deep Learning Models for Knowledge Tracing: Of Hyperparameters and Metrics on Performance and Replicability


Code regarding to our paper "N-ary Relation Extraction using Graph State LSTM"

Graph Convolution over Multiple Dependency Sub-graphs for Relation Extraction

International Conference on Computational Linguistics

Tackling Graphical NLP problems with Graph Recurrent Networks

A Comprehensive Survey of Document-level Relation Extraction (2016-2023)


Implementation of the KDD 2020 paper "Graph Structure Learning for Robust Graph Neural Networks"

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

Compact Graph Structure Learning via Mutual Information Compression

Graph Sanitation with Application to Node Classification

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

How does Heterophily Impact the Robustness of Graph Neural Networks?

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

Adversarial Robustness in Graph Neural Networks: A Hamiltonian Approach

GARNET: Reduced-Rank Topology Learning for Robust and Scalable Graph Neural Networks

Quasi-framelets: robust graph neural networks via adaptive framelet convolution

Data Augmentation for Graph Data: Recent Advancements


[NeurIPS2023,ICML2024] Multiparameter Persistence for Machine Learning

Stable Vectorization of Multiparameter Persistent Homology using Signed Barcodes as Measures

A Framework for Fast and Stable Representations of Multiparameter Persistent Homology Decompositions

Euler Characteristic Tools For Topological Data Analysis

Fast, Stable and Efficient Approximation of Multi-parameter Persistence Modules with MMA


Graph Auto-Encoder in PyTorch

Variational Graph Auto-Encoders

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

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

DINE: Dimensional Interpretability of Node Embeddings

Link Prediction without Graph Neural Networks


Code for the ICML 2020 paper: Leveraging Frequency Analysis for Deep Fake Image Recognition.

Countering Malicious DeepFakes: Survey, Battleground, and Horizon

RepMix: Representation Mixing for Robust Attribution of Synthesized Images


Meta-Learning with Differentiable Convex Optimization

Meta-Learning with Latent Embedding Optimization

Leveraging the Feature Distribution in Transfer-based Few-Shot Learning

Few-Shot Learning by Integrating Spatial and Frequency Representation


Scaleogram plot for Continuous Wavelet Transform made easy

Classifying Be star variability with TESS I: the southern ecliptic

A comparison of three heart rate detection algorithms over ballistocardiogram signals

Biomedical Signal Processing and Control

Short-term variability and mass loss in Be stars VI. Frequency groups in
  γ Cas detected by TESS

Monthly Notices of the Royal Astronomical Society

DMPP-4: Candidate sub-Neptune mass planets orbiting a naked-eye star


[CVPR 2019]: Pluralistic Image Completion

Pluralistic Image Completion

Text-Guided Neural Image Inpainting

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

Iterative facial image inpainting based on an encoder-generator architecture

Conditional Image Generation by Conditioning Variational Auto-Encoders

Neural Image Inpainting Guided with Descriptive Text

Generative Data Augmentation for Vehicle Detection in Aerial Images

Pluralistic Image Completion with Probabilistic Mixture-of-Experts

Towards robustness under occlusion for face recognition


Visualization toolkit for neural networks in PyTorch! Demo -->

Very Deep Convolutional Networks for Large-Scale Image Recognition

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

Striving for Simplicity: The All Convolutional Net

One weird trick for parallelizing convolutional neural networks

Rethinking the Trigger of Backdoor Attack

Open-Set Text Recognition via Character-Context Decoupling

Towards automatic detection of wildlife trade using machine vision models


Code related to analyzing the Natural Scenes Dataset

A massive 7T fMRI dataset to bridge cognitive neuroscience and artificial intelligence

The transition from vision to language: Distinct patterns of functional connectivity for subregions of the visual word form area

Dissociable contributions of the medial parietal cortex to recognition memory


Resources for the MRQA 2019 Shared Task

SpanBERT: Improving Pre-training by Representing and Predicting Spans

CTRL: A Conditional Transformer Language Model for Controllable Generation

MRQA 2019 Shared Task: Evaluating Generalization in Reading Comprehension

Look at the First Sentence: Position Bias in Question Answering

Conditionally Adaptive Multi-Task Learning: Improving Transfer Learning in NLP Using Fewer Parameters & Less Data

Generalizing Question Answering System with Pre-trained Language Model Fine-tuning

Contextualized Representations Using Textual Encyclopedic Knowledge

Dynamic Sampling Strategies for Multi-Task Reading Comprehension

Meeting of the Association for Computational Linguistics

Ensemble Learning-Based Approach for Improving Generalization Capability of Machine Reading Comprehension Systems

Continual Domain Adaptation for Machine Reading Comprehension

International Conference on Information and Knowledge Management


Code for "ATISS: Autoregressive Transformers for Indoor Scene Synthesis", NeurIPS 2021

Fast and Flexible Indoor Scene Synthesis via Deep Convolutional Generative Models

SceneFormer: Indoor Scene Generation with Transformers

MIME: Human-Aware 3D Scene Generation

InstructScene: Instruction-Driven 3D Indoor Scene Synthesis with
  Semantic Graph Prior

CLIP-Layout: Style-Consistent Indoor Scene Synthesis with Semantic Furniture Embedding

COFS: COntrollable Furniture layout Synthesis


A Survey of Knowledge-enhanced Text Generation

Grounded Conversation Generation as Guided Traverses in Commonsense Knowledge Graphs

Emp-RFT: Empathetic Response Generation via Recognizing Feature Transitions between Utterances

Enhancing Dialogue Generation with Conversational Concept Flows

Findings of the Association for Computational Linguistics: EACL 2023

Guiding Topic Flows in the Generative Chatbot by Enhancing the ConceptNet with the Conversation Corpora


BLOCK (AAAI 2019), with a multimodal fusion library for deep learning models

BLOCK: Bilinear Superdiagonal Fusion for Visual Question Answering and Visual Relationship Detection

RTIC: Residual Learning for Text and Image Composition using Graph Convolutional Network

Accuracy vs. Complexity: A Trade-off in Visual Question Answering Models

Question-Agnostic Attention for Visual Question Answering

International Conference on Pattern Recognition

Fashion-IQ 2020 Challenge 2nd Place Team's Solution

Surgical-VQLA++: Adversarial contrastive learning for calibrated robust visual question-localized answering in robotic surgery


Package for Neural Posterior Estimation and Importance Sampling focused on Astronomical Applications

Deep Residual Learning for Image Recognition

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

Masked Autoregressive Flow for Density Estimation

nbi: the Astronomer's Package for Neural Posterior Estimation

Stellar Spectra Fitting with Amortized Neural Posterior Estimation and nbi


Phased assembly variant caller

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

Cas9 targeted enrichment of mobile elements using nanopore sequencing

Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

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

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Structural polymorphism and diversity of human segmental duplications


Codon Usage Analysis and Prediction  of Gene Expressivity

Translation and natural selection of micropeptides from long non-canonical RNAs

DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors

Predicting the animal hosts of coronaviruses from compositional biases of spike protein and whole genome sequences through machine learning

Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective

International journal of molecular sciences

Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Codon usage bias and dinucleotide preference in 29 Drosophila species

Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics

Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China

Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field


Research code for pixel-based encoders of language (PIXEL)

Masked Autoencoders Are Scalable Vision Learners

Language Modelling with Pixels

Text Rendering Strategies for Pixel Language Models

PHD: Pixel-Based Language Modeling of Historical Documents


Dataset with 5 million images depicting human-made and natural landmarks spanning 200 thousand classes.

Google Landmarks Dataset v2 -- A Large-Scale Benchmark for Instance-Level Recognition and Retrieval

Federated Visual Classification with Real-World Data Distribution

Computationally Budgeted Continual Learning: What Does Matter?

A linearized framework and a new benchmark for model selection for fine-tuning

Motley: Benchmarking Heterogeneity and Personalization in Federated Learning

Large-scale Landmark Retrieval/Recognition under a Noisy and Diverse Dataset

Two-stage Discriminative Re-ranking for Large-scale Landmark Retrieval

Online Continual Learning Without the Storage Constraint

Image Retrieval using Multi-scale CNN Features Pooling

DALG: Deep Attentive Local and Global Modeling for Image Retrieval


MIDAS (Modular Integrated Distributed Analysis System)

MIDAS: Open-source framework for distributed online analysis of data streams

PeyeDF: an Eye-Tracking Application for Reading and Self-Indexing Research

A short review and primer on online processing of multiple signal sources in human computer interaction applications


SimSpin - A package for the kinematic analysis of galaxy simulations

Recovering λR and V/σ from seeing-dominated IFS data

The MAGPI survey: Science goals, design, observing strategy, early results and theoretical framework

Publications of the Astronomical Society of Australia

A numerical twist on the spin parameter, λR

SimSpin—Constructing mock IFS kinematic data cubes

Realistic synthetic integral field spectroscopy with RealSim-IFS

SimSpin v2.6.0—constructing synthetic spectral IFU cubes for comparison with observational surveys

Application of dimensionality reduction and clustering algorithms for the classification of kinematic morphologies of galaxies


A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

mockrobiota: a public resource for microbiome bioinformatics benchmarking

Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data

ReprDB and panDB: minimalist databases with maximal microbial representation

LEMMI: a continuous benchmarking platform for metagenomics classifiers


A symbolic time series representation building Brownian bridges

ABBA: Adaptive Brownian bridge-based symbolic aggregation of time series


lamtram: A toolkit for neural language and translation modeling

A Syntactic Neural Model for General-Purpose Code Generation

DyNet: The Dynamic Neural Network Toolkit

TRANX: A Transition-based Neural Abstract Syntax Parser for Semantic Parsing and Code Generation

Correcting Length Bias in Neural Machine Translation

Stronger Baselines for Trustable Results in Neural Machine Translation

Neural Lattice-to-Sequence Models for Uncertain Inputs

Neural Reranking Improves Subjective Quality of Machine Translation: NAIST at WAT2015

Learning to Generate Corrective Patches using Neural Machine Translation

A User-Study on Online Adaptation of Neural Machine Translation to Human Post-Edits

Lexicons and Minimum Risk Training for Neural Machine Translation: NAIST-CMU at WAT2016


a library to measure the python energy consumption of python code

GNNear: Accelerating Full-Batch Training of Graph Neural Networks with Near-Memory Processing

Energon: Towards Efficient Acceleration of Transformers Using Dynamic Sparse Attention

Energy-Efficient and Federated Meta-Learning via Projected Stochastic Gradient Ascent


A gap-closing software tool that uses long reads to enhance genome assembly.

TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina

Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation

Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium

Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in Lactobacillus salivarius

The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China

Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics


A library for X-ray matter interaction cross sections for X-ray fluorescence applications

Monte Carlo simulation of X-ray imaging and spectroscopy experiments using quadric geometry and variance reduction techniques

X-ray radiative transfer in protoplanetary disks - The role of dust and X-ray background fields

Examining molecular clouds in the Galactic Centre region using X-ray reflection spectra simulations

Measuring the Thickness of Metal Films: A Selection Guide to the Most Suitable Technique

2nd Coatings and Interfaces Web Conference (CIWC-2 2020)

Beamline simulations using monochromators with high d-spacing crystals.


General tools for Astronomical Time Series in Python

PERIODOGRAMS FOR MULTIBAND ASTRONOMICAL TIME SERIES

Inferring probabilistic stellar rotation periods using Gaussian processes

K2 Rotation Periods for Low-mass Hyads and a Quantitative Comparison of the Distribution of Slow Rotators in the Hyades and Praesepe

Poking the Beehive from Space: K2 Rotation Periods for Praesepe

K2 ROTATION PERIODS FOR LOW-MASS HYADS AND THE IMPLICATIONS FOR GYROCHRONOLOGY

The heart of the swarm: K2 photometry and rotational characteristics of 56 Jovian Trojan asteroids

SYSTEMATICS-INSENSITIVE PERIODIC SIGNAL SEARCH WITH K2

Uninterrupted optical light curves of main-belt asteroids from the K2 mission

Properties of the Irregular Satellite System around Uranus Inferred from K2, Herschel, and Spitzer Observations

Zwicky Transient Facility and Globular Clusters: The RR Lyrae gri-band Period–Luminosity–Metallicity and Period–Wesenheit–Metallicity Relations


Generates inputs for and runs the coupled groundwater-surface water model "GSFLOW"


A suite of convenience functions for working with hydrology data in an interactive Python session.

Automated Water Level Monitoring at the Continental Scale from ICESat-2 Photons


The main distribution of NuWro

Electroweak single-pion production off the nucleon: From threshold to high invariant masses

Pion production within the hybrid relativistic plane wave impulse approximation model at MiniBooNE and MINERvA kinematics

Neutrino energy reconstruction from semi-inclusive samples

Data-based two-body current contribution to the neutrino-nucleus cross section

Second class currents, axial mass, and nuclear effects in hyperon production

Monte Carlo event generation of neutrino-electron scattering

Journal of Physics G: Nuclear and Particle Physics

Modeling neutrino-nucleus interaction at intermediate energies

Proceedings of The 19th International Workshop on Neutrinos from Accelerators NUFACT2017 — PoS(NuFact2017)

Comparing generator predictions of transverse kinematic imbalance in neutrino-argon scattering


Python module for stochastic residential occupancy behavior for both building and district energy simulations.

A Markov Process Approach to Ensemble Control of Smart Buildings


museval - source separation evaluation tools for python

Music Source Separation With Band-Split RNN

Demucs: Deep Extractor for Music Sources with extra unlabeled data remixed

Investigating U-Nets with various Intermediate Blocks for Spectrogram-based Singing Voice Separation

Class-conditional embeddings for music source separation

Denoising Auto-encoder with Recurrent Skip Connections and Residual Regression for Music Source Separation

Dilated Convolution with Dilated GRU for Music Source Separation

LaSAFT: Latent Source Attentive Frequency Transformation for Conditioned Source Separation

Diffiner: A Versatile Diffusion-based Generative Refiner for Speech Enhancement

Universal Source Separation with Weakly Labelled Data

Switching Independent Vector Analysis and its Extension to Blind and Spatially Guided Convolutional Beamforming Algorithms


Parallel nested sampling

Properties and astrophysical implications of the 150 Msun binary black hole merger GW190521.

Time-domain effective-one-body gravitational waveforms for coalescing compact binaries with nonprecessing spins, tides, and self-spin effects

Analysis of Ringdown Overtones in GW150914

Constraining astrophysical observables of galaxy and supermassive black hole binary mergers using pulsar timing arrays

Monthly notices of the Royal Astronomical Society

Stellar binary black holes in the LISA band: a new class of standard sirens

Enhancing modified gravity detection from gravitational-wave observations using the parametrized ringdown spin expansion coeffcients formalism

Constraints on Kerr-Newman black holes from merger-ringdown gravitational-wave observations

No tension between assembly models of super massive black hole binaries and pulsar observations

Accelerating the evaluation of inspiral-merger-ringdown waveforms with adapted grids

Probing the assembly history and dynamical evolution of massive black hole binaries with pulsar timing arrays


DL1 HDF5 format IACT data writer + reader + processor

Studying deep convolutional neural networks with hexagonal lattices for imaging atmospheric Cherenkov telescope event reconstruction

CTLearn: Deep Learning for Gamma-ray Astronomy

Reconstruction of stereoscopic CTA events using deep learning with CTLearn

IACT event analysis with the MAGIC telescopes using deep convolutional neural networks with CTLearn

The performance of the MAGIC telescopes using deep convolutional neural networks with CTLearn

Prospects for the Use of Photosensor Timing Information with Machine Learning Techniques in Background Rejection


Genome Assembly and Annotation Service code

Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss

Evolutionary History of the Marchantia polymorpha Complex

Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species

LGAAP: Leishmaniinae Genome Assembly and Annotation Pipeline

The first genome for the Cape Primrose Streptocarpus rexii (Gesneriaceae), a model plant for studying meristem-driven shoot diversity

Pan-genome analysis of six completeParacoccustype strain genomes from hybrid next generation sequencing

Pan-genome analysis of six Paracoccus type strain genomes reveal lifestyle traits


Data Analysis with Bootstrapped ESTimation

Distinct actin–tropomyosin cofilament populations drive the functional diversification of cytoskeletal myosin motor complexes

Ferroptosis Induction and YAP Inhibition as New Therapeutic Targets in Gastrointestinal Stromal Tumors (GISTs)

Long range temporal correlations (LRTCs) in MEG-data during emerging psychosis: Relationship to symptoms, medication-status and clinical trajectory

Energetic determinants of animal cell polarity regulator Par-3 interaction with the Par complex

Cooperative regulation of C1-domain membrane recruitment polarizes atypical protein kinase C

OSS Effort Estimation Using Software Features Similarity and Developer Activity-Based Metrics

ACM Transactions on Software Engineering and Methodology

PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration


Python Financial ENGineering (PyFENG package in PyPI.org)

A Black-Scholes user's guide to the Bachelier model

The equivalent constant-elasticity-of-variance (CEV) volatility of the stochastic-alpha-beta-rho (SABR) model

A note on the option price and 'Mass at zero in the uncorrelated SABR model and implied volatility asymptotics'

Tighter 'uniform bounds for Black-Scholes implied volatility' and the applications to root-finding


GridCal, a cross-platform power systems software written in Python with user interface, used in academia and industry.

Pandapower—An Open-Source Python Tool for Convenient Modeling, Analysis, and Optimization of Electric Power Systems

PyPSA: Python for Power System Analysis

Opening the black box of energy modelling: Strategies and lessons learned

Vectorized Calculation of Short Circuit Currents Considering Distributed Generation - An Open Source Implementation of IEC 60909

Consensus based phase connectivity identification for distribution network with limited observability

PyPSA: Open Source Python Tool for Load Flow Study

Guidelines and Use Cases for Power Systems Dynamic Modeling and Model Verification using Modelica and OpenIPSL

Linköping electronic conference proceedings


Diffusion Policies as an Expressive Policy Class for Offline Reinforcement Learning

Boosting Continuous Control with Consistency Policy

Memory-Consistent Neural Networks for Imitation Learning

Iteratively Refined Behavior Regularization for Offline Reinforcement Learning

Efficient Planning with Latent Diffusion


[NeurIPS 2024 Spotlight] Buffer of Thoughts: Thought-Augmented Reasoning with Large Language Models

Beyond the Imitation Game: Quantifying and extrapolating the capabilities of language models

Challenging BIG-Bench Tasks and Whether Chain-of-Thought Can Solve Them


Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks

Coupled Generative Adversarial Networks

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

On Scalable and Efficient Computation of Large Scale Optimal Transport

Generative Adversarial Networks for Image Augmentation in Agriculture: A Systematic Review


Review article: the human intestinal virome in health and disease

Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut

Overview of Virus Metagenomic Classification Methods and Their Biological Applications

VIP: an integrated pipeline for metagenomics of virus identification and discovery

Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice

Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era

Vector-Borne Diseases - Recent Developments in Epidemiology and Control

Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome


中文领域心理健康对话大模型SoulChat

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

SoulChat: Improving LLMs' Empathy, Listening, and Comfort Abilities through Fine-tuning with Multi-turn Empathy Conversations


Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.

Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits

The Time Sequence of Gene Expression Changes after Spinal Cord Injury

Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition

Long-Term, Simultaneous Impact of Antimicrobials on the Efficiency of Anaerobic Digestion of Sewage Sludge and Changes in the Microbial Community

Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics


Pytorch implementation of GRU-ODE-Bayes

GRU-ODE-Bayes: Continuous modeling of sporadically-observed time series

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

Neural Jump Ordinary Differential Equations: Consistent Continuous-Time Prediction and Filtering

Neural Ordinary Differential Equations for Intervention Modeling

Prediction of Cardiovascular Complication in Patients with Newly Diagnosed Type 2 Diabetes Using an XGBoost/GRU-ODE-Bayes-Based Machine-Learning Algorithm

Endocrinology and metabolism (Seoul, Korea)


ICLR 2018 Quick-Thought vectors

Contrastive Learning with Hard Negative Samples

An efficient framework for learning sentence representations

Debiased Contrastive Learning

RUSE: Regressor Using Sentence Embeddings for Automatic Machine Translation Evaluation

Proceedings of the Third Conference on Machine Translation: Shared Task Papers

Hard Negative Sampling Strategies for Contrastive Representation Learning

A Comparative Study on Structural and Semantic Properties of Sentence Embeddings

Clustering and Network Analysis for the Embedding Spaces of Sentences and Sub-Sentences


syntactically controlled paraphrase networks

Adversarial Example Generation with Syntactically Controlled Paraphrase Networks

Towards a Robust Deep Neural Network in Texts: A Survey

Generating Syntactically Controlled Paraphrases without Using Annotated Parallel Pairs

GCPG: A General Framework for Controllable Paraphrase Generation

Findings of the Association for Computational Linguistics: ACL 2022

Syntactically-Informed Unsupervised Paraphrasing with Non-Parallel Data

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

Unsupervised Syntactically Controlled Paraphrase Generation with Abstract Meaning Representations

Identifying Adversarial Sentences by Analyzing Text Complexity

Perceptual Models of Machine-Edited Text

Meeting of the Association for Computational Linguistics


A program for detection of tRNA genes

Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery

A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa

A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.

Genomic Insights and Synthetic Biology Applications of Marine Actinomycete Streptomyces griseoincarnatus HNS054


PyTorch Code of NAACL 2019 paper "Learning to Navigate Unseen Environments: Back Translation with Environmental Dropout"

How Much Can CLIP Benefit Vision-and-Language Tasks?

Improving Cross-Modal Alignment in Vision Language Navigation via Syntactic Information

Structure-Encoding Auxiliary Tasks for Improved Visual Representation in Vision-and-Language Navigation


PMP-Net: Point Cloud Completion by Learning Multi-step Point Moving Paths

PMP-Net++: Point Cloud Completion by Transformer-Enhanced Multi-step Point Moving Paths

Learning Self-Prior for Mesh Inpainting Using Self-Supervised Graph Convolutional Networks


Software implementing the Latent Causal Variable Model

GWAS of peptic ulcer disease implicates Helicobacter pylori infection, other gastrointestinal disorders and depression

Investigation of glycaemic traits in psychiatric disorders using Mendelian randomisation revealed a causal relationship with anorexia nervosa

Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology

Empirical comparisons of multiple Mendelian randomization approaches in the presence of assortative mating

Genetic association and causal inference converge on hyperglycaemia as a modifiable factor to improve lung function

Genetic analyses identify pleiotropy and causality for blood proteins and highlight Wnt/β-catenin signalling in migraine

The genetic architecture of human amygdala volumes and their overlap with common brain disorders

Investigating the effect of glycaemic traits on the risk of psychiatric illness using Mendelian randomisation

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

Genetically informed precision drug repurposing for lung function and implications for respiratory infection

Genetic and epidemiological analyses of infection load and its relationship with psychiatric disorders


Miscellaneous functions for metagenomic analysis.

Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents

Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species

Randomized Double-Blind Crossover Study for Evaluating a Probiotic Mixture on Gastrointestinal and Behavioral Symptoms of Autistic Children

Trachymyrmex septentrionalisants promote fungus garden hygiene usingTrichoderma-derived metabolite cues

Comparative analysis of scalp and gut microbiome in androgenetic alopecia: A Korean cross-sectional study

Broad Dissemination of Plasmids across Groundwater-Fed Rapid Sand Filter Microbiomes

Characterization of the Soil Bacterial Community from Selected Boxwood Gardens across the United States

Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode

Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp.


Bayesian Deep Learning Benchmarks

A Systematic Comparison of Bayesian Deep Learning Robustness in Diabetic Retinopathy Tasks

On the Expressiveness of Approximate Inference in Bayesian Neural Networks

Depth Uncertainty in Neural Networks

Wat zei je? Detecting Out-of-Distribution Translations with Variational Transformers

Pathologies of Factorised Gaussian and MC Dropout Posteriors in Bayesian Neural Networks.

Beyond Marginal Uncertainty: How Accurately can Bayesian Regression Models Estimate Posterior Predictive Correlations?

A Decoupled Uncertainty Model for MRI Segmentation Quality Estimation


D2-Net: A Trainable CNN for Joint Description and Detection of Local Features

D2-Net: A Trainable CNN for Joint Detection and Description of Local Features

Review of Wide-Baseline Stereo Image Matching Based on Deep Learning

Content-Adaptive Downsampling in Convolutional Neural Networks


PyTorch re-implementation of DeepLab v2 on COCO-Stuff / PASCAL VOC datasets

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

COCO-Stuff: Thing and Stuff Classes in Context

Contrastive Learning for Unpaired Image-to-Image Translation

Anti-Adversarially Manipulated Attributions for Weakly and Semi-Supervised Semantic Segmentation

BBAM: Bounding Box Attribution Map for Weakly Supervised Semantic and Instance Segmentation

Collaborative Global-Local Networks for Memory-Efficient Segmentation of Ultra-High Resolution Images

Reducing Information Bottleneck for Weakly Supervised Semantic Segmentation

Discriminative Region Suppression for Weakly-Supervised Semantic Segmentation

CLIMS: Cross Language Image Matching for Weakly Supervised Semantic Segmentation

GANcraft: Unsupervised 3D Neural Rendering of Minecraft Worlds


Generalized lasso implementations

Fast and Flexible ADMM Algorithms for Trend Filtering

False discovery rate smoothing

A Fast and Flexible Algorithm for the Graph-Fused Lasso

Multiscale Spatial Density Smoothing: An Application to Large-Scale Radiological Survey and Anomaly Detection

Journal of the American Statistical Association

Mixtures, envelopes, and hierarchical duality

Nonparametric density estimation by histogram trend filtering


GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training @ KDD 2020

Graph Self-Supervised Learning: A Survey

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

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

GraphControl: Adding Conditional Control to Universal Graph Pre-trained Models for Graph Domain Transfer Learning

Domain Adaptive Graph Infomax via Conditional Adversarial Networks

IEEE Transactions on Network Science and Engineering

State of the Art and Potentialities of Graph-level Learning

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

Spectral Augmentations for Graph Contrastive Learning

Spatial Autoregressive Coding for Graph Neural Recommendation


A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution

Impact of sequencing depth and technology on de novo RNA-Seq assembly

Chlorogenic Acid Alleviates Colon Mucosal Damage Induced by a High-Fat Diet via Gut Microflora Adjustment to Increase Short-Chain Fatty Acid Accumulation in Rats

Oxidative medicine and cellular longevity

Spatial control of potato tuberization by the TCP transcription factor BRANCHED1b

De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar ‘Tieguanyin’ compared with cultivar ‘Benshan’

On the origin and evolution of RNA editing in metazoans

Adipose tissue-derived neurotrophic factor 3 regulates sympathetic innervation and thermogenesis in adipose tissue

The DNA dioxygenase Tet1 regulates H3K27 modification and embryonic stem cell biology independent of its catalytic activity

A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data


Concept Bottleneck Models, ICML 2020

Concept Bottleneck Models

Now You See Me (CME): Concept-based Model Extraction

Concept Bottleneck Model with Additional Unsupervised Concepts


A BERT-based Chinese Text Encoder Enhanced by N-gram Representations

ZEN: Pre-training Chinese Text Encoder Enhanced by N-gram Representations

Named Entity Recognition for Social Media Texts with Semantic Augmentation

Improving Named Entity Recognition with Attentive Ensemble of Syntactic Information

Summarizing Medical Conversations via Identifying Important Utterances

International Conference on Computational Linguistics

Joint Chinese Word Segmentation and Part-of-speech Tagging via Two-way Attentions of Auto-analyzed Knowledge

Improving Constituency Parsing with Span Attention

Joint Chinese Word Segmentation and Part-of-speech Tagging via Multi-channel Attention of Character N-grams


Brain Surrogate Maps with Autocorrelated Spatial Heterogeneity

Overcoming bias in gene-set enrichment analyses of brain-wide transcriptomic data

Homotopic functional connectivity disruptions in schizophrenia and their associated gene expression

Resting-state brain functional alterations and their genetic mechanisms in drug-naive first-episode psychosis

A phylogenetically-conserved axis of thalamocortical connectivity in the human brain

Molecular mechanisms underlying resting-state brain functional correlates of behavioral inhibition

Regional gene expression patterns are associated with task-specific brain activation during reward and emotion processing measured with functional MRI

Transcriptional signatures of the whole-brain voxel-wise resting-state functional network centrality alterations in schizophrenia

A latent clinical-anatomical dimension relating metabolic syndrome to brain structure and cognition

bioRxiv : the preprint server for biology

Indirect evidence for altered dopaminergic neurotransmission in very premature‐born adults


The RefinedWeb Dataset for Falcon LLM: Outperforming Curated Corpora with Web Data, and Web Data Only

Deduplicating Training Data Makes Language Models Better

A Survey on Data Selection for Language Models

The Responsible Foundation Model Development Cheatsheet: A Review of Tools & Resources


Neural Question Generation using the SQuAD and NewsQA datasets

SQuAD: 100,000+ Questions for Machine Comprehension of Text

Learning to Ask: Neural Question Generation for Reading Comprehension

Machine Comprehension by Text-to-Text Neural Question Generation


Learn and L3 embedding from audio/video pairs

Look, Listen and Learn

Self-supervised audio representation learning for mobile devices

Learnable Irrelevant Modality Dropout for Multimodal Action Recognition on Modality-Specific Annotated Videos


Learning Named Entity Tagger from Domain-Specific Dictionary

Automated Phrase Mining from Massive Text Corpora

Learning Named Entity Tagger using Domain-Specific Dictionary

BOND: BERT-Assisted Open-Domain Named Entity Recognition with Distant Supervision

Distantly-Supervised Named Entity Recognition with Noise-Robust Learning and Language Model Augmented Self-Training

Optimizing Bi-Encoder for Named Entity Recognition via Contrastive Learning

Distantly Supervised Named Entity Recognition via Confidence-Based Multi-Class Positive and Unlabeled Learning


Portable C implementation of Ed25519, a high-speed high-security public-key signature system.

CURE: A Security Architecture with CUstomizable and Resilient Enclaves

Secure Boot and Remote Attestation in the Sanctum Processor.

IEEE Computer Security Foundations Symposium

Citadel: Enclaves with Strong Microarchitectural Isolation and Secure Shared Memory on a Speculative Out-of-Order Processor


Differentiable controlled differential equation solvers for PyTorch with GPU support and memory-efficient adjoint backpropagation.

Latent ODEs for Irregularly-Sampled Time Series

Neural Controlled Differential Equations for Irregular Time Series

On Neural Differential Equations

Neural Rough Differential Equations for Long Time Series

Signatory: differentiable computations of the signature and logsignature transforms, on both CPU and GPU

Efficient and Accurate Gradients for Neural SDEs

Neural Controlled Differential Equations for Online Prediction Tasks

PriSTI: A Conditional Diffusion Framework for Spatiotemporal Imputation

NRTSI: Non-Recurrent Time Series Imputation

Stable Neural Stochastic Differential Equations in Analyzing Irregular
  Time Series Data


Soft Actor-Critic

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

Addressing Function Approximation Error in Actor-Critic Methods

Latent Space Policies for Hierarchical Reinforcement Learning

Establishing Appropriate Trust via Critical States

Regularization Matters in Policy Optimization

Policy Optimization as Wasserstein Gradient Flows

Dynamics-aware Embeddings

VIREL: A Variational Inference Framework for Reinforcement Learning

For SALE: State-Action Representation Learning for Deep Reinforcement Learning

Deep Reinforcement Learning


Official Implementation of StyleTTS

StarGANv2-VC: A Diverse, Unsupervised, Non-parallel Framework for Natural-Sounding Voice Conversion

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

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


End-To-End Memory Network using Tensorflow

End-To-End Memory Networks

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

Multi-Relational Question Answering from Narratives: Machine Reading and Reasoning in Simulated Worlds

t-Exponential Memory Networks for Question-Answering Machines

Learning to Organize Knowledge with N-Gram Machines

Think Visually: Question Answering through Virtual Imagery

Learning to Organize Knowledge and Answer Questions with N-Gram Machines

A2P-MANN: Adaptive Attention Inference Hops Pruned Memory-Augmented Neural Networks.


[NeurIPS'23 Spotlight] "Mind2Web: Towards a Generalist Agent for the Web"

DeBERTa: Decoding-enhanced BERT with Disentangled Attention

Dual-View Visual Contextualization for Web Navigation


Hydrodynamic coefficients viewer and converter for Boundary Element Method solver formats


Deep and Machine Learning for Microscopy

Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles

An Introduction to Variational Autoencoders

Foundations and Trends® in Machine Learning

Averaging Weights Leads to Wider Optima and Better Generalization

Deep Kernel Learning

Recent advances and applications of deep learning methods in materials science

Automated and Autonomous Experiments in Electron and Scanning Probe Microscopy

AtomAI: A Deep Learning Framework for Analysis of Image and Spectroscopy Data in (Scanning) Transmission Electron Microscopy and Beyond

Exploring order parameters and dynamic processes in disordered systems via variational autoencoders

Ensemble learning-iterative training machine learning for uncertainty quantification and automated experiment in atom-resolved microscopy

Disentangling ferroelectric domain wall geometries and pathways in dynamic piezoresponse force microscopy via unsupervised machine learning


PROTEUS - The Dynamic Surface Water eXtent from Harmonized Landsat and Sentinel-2 (DSWx-HLS) Science Application Software (SAS)


Clustering through Imputation and Dimensionality Reduction

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

Fast and precise single-cell data analysis using a hierarchical autoencoder

Self-supervised contrastive learning for integrative single cell RNA-seq data analysis

Deep Learning in Single-Cell Analysis

Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning

scEFSC: Accurate single-cell RNA-seq data analysis via ensemble consensus clustering based on multiple feature selections

Computational and structural biotechnology journal

Fast and precise single-cell data analysis using hierarchical autoencoder

Imputation Methods for scRNA Sequencing Data


Guess gender from first name in Python 2 and 3

Evaluating Saliency Methods for Neural Language Models

A Bag of Tricks for Dialogue Summarization

Worldwide Gender Differences in Public Code Contributions and how they have been affected by the COVID-19 pandemic

Proceedings of the 2022 ACM/IEEE 44th International Conference on Software Engineering: Software Engineering in Society

Gender-Related Differences in Online Comment Sections: Findings From a Large-Scale Content Analysis of Commenting Behavior

Authorship in top-ranked mathematical and physical journals: Role of gender on self-perceptions and bibliographic evidence

Bias, Fairness, and Accountability with AI and ML Algorithms

From Asking to Answering: Getting More Involved on Stack Overflow


Python package for analyzing and visualizing iModulons

Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks

Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa

Pan-Genome Analysis of Transcriptional Regulation in Six Salmonella enterica Serovar Typhimurium Strains Reveals Their Different Regulatory Structures

Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

Machine learning uncovers the Pseudomonas syringae transcriptome in microbial communities and during infection


De novo spatial reconstruction of single-cell gene expression.

Charting human development using a multi-endodermal organ atlas and organoid models

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

Zenodo (CERN European Organization for Nuclear Research)

Computational methods for the integrative analysis of single-cell data

Spatio-temporal, optogenetic control of gene expression in organoids

An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine

SpaDiT: Diffusion Transformer for Spatial Gene Expression Prediction using scRNA-seq


Segment Anything in Medical Images

Segment Anything in Medical Images

One Model to Rule them All: Towards Universal Segmentation for Medical Images with Text Prompts

Segment Anything in Medical Images and Videos: Benchmark and Deployment

Exploring SAM Ablations for Enhancing Medical Segmentation in Radiology and Pathology

FairMedFM: Fairness Benchmarking for Medical Imaging Foundation Models


A library for manipulating DMRS structures

Functional Distributional Semantics

A Proposition-Based Abstractive Summariser

Semantic Composition via Probabilistic Model Theory

Graph- and surface-level sentence chunking

Variational Inference for Logical Inference


TensorFlow port of PyTorch Image Models (timm) - image models with pretrained weights.

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

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

A ConvNet for the 2020s

Segment Anything

Pyramid Vision Transformer: A Versatile Backbone for Dense Prediction without Convolutions

MLP-Mixer: An all-MLP Architecture for Vision

PVT v2: Improved baselines with Pyramid Vision Transformer

Going deeper with Image Transformers

MetaFormer is Actually What You Need for Vision

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


Multilingual word vectors in 78 languages

Enriching Word Vectors with Subword Information

Exploiting Similarities among Languages for Machine Translation

A Survey Of Cross-lingual Word Embedding Models

Offline bilingual word vectors, orthogonal transformations and the inverted softmax

Improving zero-shot learning by mitigating the hubness problem

Unsupervised Cross-Lingual Information Retrieval using Monolingual Data Only

Cross-Lingual Syntactic Transfer through Unsupervised Adaptation of Invertible Projections

Transliteration Better than Translation? Answering Code-mixed Questions over a Knowledge Base

Aggression Identification and Multi Lingual Word Embeddings

Debiasing Multilingual Word Embeddings: A Case Study of Three Indian Languages


Rigorous Global Branch-and-Bound Optimizer

Sound Mixed-Precision Optimization with Rewriting

On Sound Relative Error Bounds for Floating-Point Arithmetic

An Interval Arithmetic for Robust Error Estimation


Topology Optimization using Python

TopologyGAN: Topology Optimization Using Generative Adversarial Networks Based on Physical Fields Over the Initial Domain

3D Topology Optimization using Convolutional Neural Networks

A Comparative Study of the Application of Different Commercial Software for Topology Optimization

From Concept to Manufacturing: Evaluating Vision-Language Models for Engineering Design

Sensitivity Analysis of Key Formulations of Topology Optimization on an Example of Cantilever Bending Beam

Topology optimization using PETSc: a Python wrapper and extended functionality

Structural and Multidisciplinary Optimization


Multi-Worm Behaviour Tracker


A proxy app for the Monte Carlo Transport Code, Mercury.  LLNL-CODE-684037

GPA: A GPU Performance Advisor Based on Instruction Sampling

Measurement and analysis of GPU-accelerated applications with HPCToolkit

Evaluation of Single-Node Performance of Parallel Algorithms for Multigroup Monte Carlo Particle Transport Methods

Power Constrained Autotuning using Graph Neural Networks


Next generation sequencing reads de novo assembler.

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

An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)

Prevalence and Genetic Diversity of Listeria monocytogenes Isolated From Retail Pork in Wuhan, China

Molecular Characteristics of Brucella Isolates Collected From Humans in Hainan Province, China

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Population Genomic Approaches for Weed Science

The Gut Microbiota Determines the High-Altitude Adaptability of Tibetan Wild Asses (Equus kiang) in Qinghai-Tibet Plateau

GAAP: A Genome Assembly + Annotation Pipeline

Development of Sequence-Tagged Site Marker Set for Identification of J, JS, and St Sub-genomes of Thinopyrum intermedium in Wheat Background

The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean


Tarski - An AI Planning Modeling Framework

Approximate Novelty Search

Semantic Attachments for HTN Planning

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

Sampling from Pre-Images to Learn Heuristic Functions for Classical Planning

Synthesis of Procedural Models for Deterministic Transition Systems


distributed trainer for LLMs

MEDITRON-70B: Scaling Medical Pretraining for Large Language Models

Executable Code Actions Elicit Better LLM Agents

Tower: An Open Multilingual Large Language Model for Translation-Related Tasks

Visually Descriptive Language Model for Vector Graphics Reasoning

Sailor: Open Language Models for South-East Asia

A Single Transformer for Scalable Vision-Language Modeling

MedCalc-Bench: Evaluating Large Language Models for Medical Calculations


A 256-RISC-V-core system with low-latency access into shared L1 memory.

Assessment of Reinforcement Learning for Macro Placement

MemPool: A Scalable Manycore Architecture With a Low-Latency Shared L1 Memory

Spatz: A Compact Vector Processing Unit for High-Performance and Energy-Efficient Shared-L1 Clusters

MemPool-3D: Boosting Performance and Efficiency of Shared-L1 Memory Many-Core Clusters with 3D Integration

Hier-RTLMP: A Hierarchical Automatic Macro Placer for Large-scale Complex IP Blocks


RNA Interference Strategies for Future Management of Plant Pathogenic Fungi: Prospects and Challenges

Concepts and considerations for enhancing RNAi efficiency in phytopathogenic fungi for RNAi-based crop protection using nanocarrier-mediated dsRNA delivery systems

Recent Progress on Nanocarriers for Topical-Mediated RNAi Strategies for Crop Protection—A Review

Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling

Evaluation of RNA Interference for Control of the Grape Mealybug Pseudococcus maritimus (Hemiptera: Pseudococcidae)


Simplified Action Decoder for Deep Multi-Agent Reinforcement Learning

"Other-Play" for Zero-Shot Coordination

Improving Policies via Search in Cooperative Partially Observable Games

Off-Belief Learning

Generalized Beliefs for Cooperative AI


FairFace: Face Attribute Dataset for Balanced Race, Gender, and Age for Bias Measurement and Mitigation

Workshop on Applications of Computer Vision

Fair Diffusion: Instructing Text-to-Image Generation Models on Fairness

Algorithmic fairness datasets: the story so far

Understanding Fairness of Gender Classification Algorithms Across Gender-Race Groups

Learning Fair Classifiers with Partially Annotated Group Labels

Human-Centric Multimodal Machine Learning: Recent Advances and Testbed on AI-based Recruitment

Transferring Fairness under Distribution Shifts via Fair Consistency Regularization

The Bias Amplification Paradox in Text-to-Image Generation

OpenFilter: A Framework to Democratize Research Access to Social Media AR Filters


[CVPR22] Official Implementation of DAFormer: Improving Network Architectures and Training Strategies for Domain-Adaptive Semantic Segmentation

Refign: Align and Refine for Adaptation of Semantic Segmentation to Adverse Conditions

Domain Adaptive and Generalizable Network Architectures and Training Strategies for Semantic Image Segmentation

VBLC: Visibility Boosting and Logit-Constraint Learning for Domain Adaptive Semantic Segmentation under Adverse Conditions

VisDA 2022 Challenge: Domain Adaptation for Industrial Waste Sorting

Consistency Regularization for Domain Adaptation


ADer (https://arxiv.org/abs/2406.03262) is an open source visual anomaly detection toolbox based on PyTorch, which supports multiple popular AD datasets and approaches.

Real-IAD: A Real-World Multi-View Dataset for Benchmarking Versatile Industrial Anomaly Detection

Exploring Plain ViT Reconstruction for Multi-class Unsupervised Anomaly Detection

MambaAD: Exploring State Space Models for Multi-class Unsupervised
  Anomaly Detection

A Comprehensive Library for Benchmarking Multi-class Visual Anomaly Detection

Learning Feature Inversion for Multi-class Anomaly Detection under
  General-purpose COCO-AD Benchmark


A service that lists all available and registered STAC catalogs and APIs.


code for our NAACL 2019 paper: "BERT Post-Training for Review Reading Comprehension and Aspect-based Sentiment Analysis"

Conditional Augmentation for Aspect Term Extraction via Masked Sequence-to-Sequence Generation

DomBERT: Domain-oriented Language Model for Aspect-based Sentiment Analysis

Understanding Pre-trained BERT for Aspect-based Sentiment Analysis

Constituency Lattice Encoding for Aspect Term Extraction

A Failure of Aspect Sentiment Classifiers and an Adaptive Re-weighting Solution


Neural architecture search(NAS)

DARTS: Differentiable Architecture Search

FBNet: Hardware-Aware Efficient ConvNet Design via Differentiable Neural Architecture Search

SNAS: Stochastic Neural Architecture Search


Code for paper "Which Training Methods for GANs do actually Converge? (ICML 2018)"

StarGAN v2: Diverse Image Synthesis for Multiple Domains

Unsupervised Object Learning via Common Fate

CAM-GAN: Continual Adaptation Modules for Generative Adversarial Networks

Gradient Descent-Ascent Provably Converges to Strict Local Minmax Equilibria with a Finite Timescale Separation


Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons

Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

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

Delaying chloroplast turnover increases water-deficit stress tolerance through the enhancement of nitrogen assimilation in rice

RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression

Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Targeted gene disruption in a marsupial, Monodelphis domestica, by CRISPR/Cas9 genome editing

Unexpected binding behaviors of bacterial Argonautes in human cells cast doubts on their use as targetable gene regulators

Low recovery of bacterial community after an extreme salinization-desalinization cycle


Personalizing Dialogue Agents via Meta-Learning

Will I Sound Like Me? Improving Persona Consistency in Dialogues through Pragmatic Self-Consciousness

Meta-Learning the Difference: Preparing Large Language Models for Efficient Adaptation


Poisson pseudo-likelihood regression with multiple levels of fixed effects

ppmlhdfe: Fast Poisson Estimation with High-Dimensional Fixed Effects

Verifying the existence of maximum likelihood estimates for generalized linear models


Peak calling tool for CLIP-seq data

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

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

The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages

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

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

Improving CLIP-seq data analysis by incorporating transcript information

RNA damage compartmentalization by DHX9 stress granules

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

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


Position-aware Graph Neural Networks

Position-aware Graph Neural Networks

Distance Encoding: Design Provably More Powerful Neural Networks for Graph Representation Learning

Equivariant and Stable Positional Encoding for More Powerful Graph Neural Networks

Distance Encoding -- Design Provably More Powerful GNNs for Structural Representation Learning

Hierarchical message-passing graph neural networks

Adversarial Permutation Guided Node Representations for Link Prediction

A Simple and General Graph Neural Network with Stochastic Message Passing

Permutation-equivariant and Proximity-aware Graph Neural Networks with Stochastic Message Passing


This is the code for our KILT leaderboard submissions (KGI + Re2G models).

Re2G: Retrieve, Rerank, Generate

Robust Retrieval Augmented Generation for Zero-shot Slot Filling

KGI: An Integrated Framework for Knowledge Intensive Language Tasks

Zero-shot Slot Filling with DPR and RAG


Python port of B. Kelly's LINMIX_ERR IDL package

Compact Disks in a High-resolution ALMA Survey of Dust Structures in the Taurus Molecular Cloud

Evidence for a correlation between mass accretion rates onto young stars and the mass of their protoplanetary disks

Spectral Properties of Quasars from Sloan Digital Sky Survey Data Release 14: The Catalog

CHAOS. III. GAS-PHASE ABUNDANCES IN NGC 5457

Physical properties of dusty protoplanetary disks in Lupus: evidence for viscous evolution?

The ALPINE-ALMA [C II] survey No or weak evolution in the [C II]-SFR relation over the last 13 Gyr

Scaling Relations Associated with Millimeter Continuum Sizes in Protoplanetary Disks

An ALMA Survey of CO Isotopologue Emission from Protoplanetary Disks in Chamaeleon I

CHAOS IV: Gas-phase Abundance Trends from the First Four CHAOS Galaxies

First Results from SMAUG: Characterization of Multiphase Galactic Outflows from a Suite of Local Star-forming Galactic Disk Simulations


Collection of public available person re-identification datasets

Deep Learning for Person Re-identification: A Survey and Outlook

Torchreid: A Library for Deep Learning Person Re-Identification in Pytorch

Dual Branch Attention Network for Person Re-Identification


An open science effort to benchmark legal reasoning in foundation models

On the Opportunities and Risks of Foundation Models

LegalBench: A Collaboratively Built Benchmark for Measuring Legal Reasoning in Large Language Models

LegalBench: Prototyping a Collaborative Benchmark for Legal Reasoning

Learning to Generate Instruction Tuning Datasets for Zero-Shot Task Adaptation

Caveat Lector: Large Language Models in Legal Practice

Chain of Logic: Rule-Based Reasoning with Large Language Models


Magic-BLAST, an accurate RNA-seq aligner for long and short reads

Technology dictates algorithms: Recent developments in read alignment

Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads


Recipes to train reward model for RLHF.

RAFT: Reward rAnked FineTuning for Generative Foundation Model Alignment

Gibbs Sampling from Human Feedback: A Provable KL- constrained Framework for RLHF

Interpretable Preferences via Multi-Objective Reward Modeling and
  Mixture-of-Experts

RLHF Workflow: From Reward Modeling to Online RLHF

Online Iterative Reinforcement Learning from Human Feedback with General Preference Model

OffsetBias: Leveraging Debiased Data for Tuning Evaluators

Uncertainty-aware Reward Model: Teaching Reward Models to Know What is Unknown


The RNA-binding protein AKAP8 suppresses tumor metastasis by antagonizing EMT-associated alternative splicing

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

Gain-of-function mutation of microRNA-140 in human skeletal dysplasia

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

clipplotr - a comparative visualisation and analysis tool for CLIP data

RNA-binding protein MEX3A controls G1/S transition via regulating the RB/E2F pathway in clear cell renal cell carcinoma

KHSRP combines transcriptional and posttranscriptional mechanisms to regulate monocytic differentiation

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma


CURL: Contrastive Unsupervised Representation Learning for Sample-Efficient Reinforcement Learning

CURL: Contrastive Unsupervised Representations for Reinforcement Learning

Debiased Contrastive Learning

SoftGym: Benchmarking Deep Reinforcement Learning for Deformable Object Manipulation

Masked Contrastive Representation Learning for Reinforcement Learning

PlayVirtual: Augmenting Cycle-Consistent Virtual Trajectories for Reinforcement Learning

Value Function Spaces: Skill-Centric State Abstractions for Long-Horizon Reasoning

Learning Representations for Pixel-based Control: What Matters and Why?

Improving Computational Efficiency in Visual Reinforcement Learning via Stored Embeddings

Frustratingly Easy Regularization on Representation Can Boost Deep Reinforcement Learning

Intrinsically Motivated Self-supervised Learning in Reinforcement Learning


Udacity Self-Driving Car Engineer Nanodegree projects.

Paracosm: A Language and Tool for Testing Autonomous Driving Systems

VERIFAI: A Toolkit for the Design and Analysis of Artificial Intelligence-Based Systems

Implementation of NAO Robot Maze Navigation Based on Computer Vision and Collaborative Learning

A pipeline framework for robot maze navigation using computer vision, path planning and communication protocols

International Conference on Developments in eSystems Engineering


Proper implementation of ResNet-s for CIFAR10/100 in pytorch that matches description of the original paper.

Deep Residual Learning for Image Recognition

R-Drop: Regularized Dropout for Neural Networks

Functional Adversarial Attacks

Decoupled Contrastive Learning

Convolutional Dynamic Alignment Networks for Interpretable Classifications

Understanding AdamW through Proximal Methods and Scale-Freeness

QuPeD: Quantized Personalization via Distillation with Applications to Federated Learning

Initialization and Regularization of Factorized Neural Layers

DeepView: Visualizing Classification Boundaries of Deep Neural Networks as Scatter Plots Using Discriminative Dimensionality Reduction

Rare Gems: Finding Lottery Tickets at Initialization


code to run sei and obtain sei and sequence class predictions

A sequence-based global map of regulatory activity for deciphering human genetics

Hypothyroidism and rheumatoid arthritis: a two-sample Mendelian randomization study

Identification and Interpretation of eQTL and eGenes for Hodgkin Lymphoma Susceptibility

Sei framework resources (hg19 and hg38 FASTA files)

Current genomic deep learning models display decreased performance in cell type-specific accessible regions


Contriever: Unsupervised Dense Information Retrieval with Contrastive Learning

Generate rather than Retrieve: Large Language Models are Strong Context Generators

Scaling Retrieval-Based Language Models with a Trillion-Token Datastore

Knowledge Pursuit Prompting for Zero-Shot Multimodal Synthesis

Retrieve What You Need: A Mutual Learning Framework for Open-domain Question Answering

Transactions of the Association for Computational Linguistics

Beyond Surface Similarity: Detecting Subtle Semantic Shifts in Financial Narratives

Evaluating Dense Passage Retrieval using Transformers

Neural Locality Sensitive Hashing for Entity Blocking

Pre-trained Language Models for Entity Blocking: A Reproducibility Study

North American Chapter of the Association for Computational Linguistics


Pipeline to generate the Standardized Project Gutenberg Corpus

A standardized Project Gutenberg corpus for statistical analysis of natural language and quantitative linguistics

Can Pre-trained Language Models Interpret Similes as Smart as Human?

Quantifying the Dissimilarity of Texts


Open source library for Single Object Tracking in point clouds.

P2B: Point-to-Box Network for 3D Object Tracking in Point Clouds

Box-Aware Feature Enhancement for Single Object Tracking on Point Clouds

Beyond 3D Siamese Tracking: A Motion-Centric Paradigm for 3D Single Object Tracking in Point Clouds

STTracker: Spatio-Temporal Tracker for 3D Single Object Tracking

GLT-T++: Global-Local Transformer for 3D Siamese Tracking with Ranking Loss

An Effective Motion-Centric Paradigm for 3D Single Object Tracking in Point Clouds


Robust evasion attacks against neural network to find adversarial examples

Towards Evaluating the Robustness of Neural Networks

ZOO: Zeroth Order Optimization based Black-box Attacks to Deep Neural
  Networks without Training Substitute Models

Proceedings of the 10th ACM Workshop on Artificial Intelligence and Security

Decision-Based Adversarial Attacks: Reliable Attacks Against Black-Box Machine Learning Models

Gradient Descent Maximizes the Margin of Homogeneous Neural Networks

Detecting Adversarial Image Examples in Deep Neural Networks with Adaptive Noise Reduction

IEEE Transactions on Dependable and Secure Computing

Zeroth-Order Stochastic Variance Reduction for Nonconvex Optimization

Adversarial Examples, Uncertainty, and Transfer Testing Robustness in Gaussian Process Hybrid Deep Networks

A game-based approximate verification of deep neural networks with provable guarantees

Subspace Attack: Exploiting Promising Subspaces for Query-Efficient Black-box Attacks

Improved Zeroth-Order Variance Reduced Algorithms and Analysis for Nonconvex Optimization


Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

Domain-Adversarial Training of Neural Networks

Improving performance of deep learning models with axiomatic attribution priors and expected gradients

Semisupervised adversarial neural networks for single-cell classification

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

基因组蛋白质组与生物信息学报


Available documentation and binaries

Towards Touch-to-Access Device Authentication Using Induced Body Electric Potentials

MOBICOM'19: PROCEEDINGS OF THE 25TH ANNUAL INTERNATIONAL CONFERENCE ON MOBILE COMPUTING AND NETWORKING

Path Loss Determination Using Linear and Cubic Regression Inside a Classic Tomato Greenhouse

International journal of environmental research and public health

Battery draining attacks against edge computing nodes in IoT networks

HARE: Supporting efficient uplink multi-hop communications in self-organizing LPWANs

A Versatile Out-of-Band Software-Defined Networking Solution for the Internet of Things

Collision-Free Advertisement Scheduling for IEEE 802.15.4-TSCH Networks

Empirical Model of Radio Wave Propagation in the Presence of Vegetation inside Greenhouses Using Regularized Regressions

Design of an Electrically Small, Planar Quasi-Isotropic Antenna for Enhancement of Wireless Link Reliability under NLOS Channels

Towards Energy Efficient LPWANs through Learning-based Multi-hop Routing

Addressing the Security Gap in IoT: Towards an IoT Cyber Range


Venn Diagram by ggplot2, with really easy-to-use API.

Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline

Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions

Early and late genome-wide gastric epithelial transcriptome response during infection with the human carcinogen Helicobacterpylori.

miRNA signatures underlie chemoresistance in the gemcitabine-resistant pancreatic ductal adenocarcinoma cell line MIA PaCa-2 GR

Serotype-dependent adhesion of Shiga toxin-producing Escherichia coli to bovine milk fat globule membrane proteins


State-of-the-art deep learning model for analyzing sentiment, emotion, sarcasm etc.

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

Empirical Methods in Natural Language Processing

A Survey on Text Classification: From Shallow to Deep Learning

CARER: Contextualized Affect Representations for Emotion Recognition

SEntiMoji: an emoji-powered learning approach for sentiment analysis in software engineering

TRAC-1 Shared Task on Aggression Identification: IIT(ISM)@COLING’18

International Conference on Computational Linguistics

A Comprehensive Analysis of Preprocessing for Word Representation Learning in Affective Tasks

Meeting of the Association for Computational Linguistics

NLPRL-IITBHU at SemEval-2018 Task 3: Combining Linguistic Features and Emoji pre-trained CNN for Irony Detection in Tweets

Irony Detection in Persian Language: A Transfer Learning Approach Using Emoji Prediction

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

Shaping the Narrative Arc: An Information-Theoretic Approach to Collaborative Dialogue

Predicting Suicide Risk from Online Postings in Reddit The UGent-IDLab submission to the CLPysch 2019 Shared Task A


Implementation of Attention-based Deep Multiple Instance Learning in PyTorch

Cancer Diagnosis Using Deep Learning: A Bibliographic Review

FLamby: Datasets and Benchmarks for Cross-Silo Federated Learning in Realistic Healthcare Settings

Breast Cancer Dataset, Classification and Detection Using Deep Learning

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data

Interpretable and Interactive Deep Multiple Instance Learning for Dental Caries Classification in Bitewing X-rays


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

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

Reconstructing the Deep Population History of Central and South America

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

Insights into the Host-Pathogen Interaction Pathways through RNA-Seq Analysis of Lens culinaris Medik. in Response to Rhizoctonia bataticola Infection

Direct Antiviral Treatments for Hepatitis C Virus Have Off-Target Effects of Oncologic Relevance in Hepatocellular Carcinoma

Mapache: a flexible pipeline to map ancient DNA

Genome-wide identification, characterization, and functional analysis of lncRNAs in Hevea brasiliensis

Identification of an Actionable Mutation of KIT in a Case of Extraskeletal Myxoid Chondrosarcoma

International journal of molecular sciences

Molecular Signature of Biological Aggressiveness in Clear Cell Sarcoma of the Kidney (CCSK)

Mechanisms of resistance to a PI3K inhibitor in gastrointestinal stromal tumors: an omic approach to identify novel druggable targets

DOAJ (DOAJ: Directory of Open Access Journals)


Deep Learning for Time Series Classification

Deep learning for time series classification: a review

Unsupervised Scalable Representation Learning for Multivariate Time Series

Interpretable Time Series Classification using Linear Models and Multi-resolution Multi-domain Symbolic Representations

Time Series Extrinsic Regression

Can We Ditch Feature Engineering? End-to-End Deep Learning for Affect Recognition from Physiological Sensor Data

Automatic Classification of Plasma Regions in Near-Earth Space With Supervised Machine Learning: Application to Magnetospheric Multi Scale 2016–2019 Observations

Frontiers in Astronomy and Space Sciences

Monash University, UEA, UCR Time Series Regression Archive

Monash University, UEA, UCR Time Series Extrinsic Regression Archive

Detection of Unilateral Arm Paresis after Stroke by Wearable Accelerometers and Machine Learning


Temporal Graph Benchmark project repo

Temporal Graph Benchmark for Machine Learning on Temporal Graphs

An Empirical Evaluation of Temporal Graph Benchmark

A survey of dynamic graph neural networks


Real or Fake Text? Evaluation criteria for human-written and computer-generated text through the gamification of annotation. Published in EMNLP 2020.

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

Automatic Detection of Generated Text is Easiest when Humans are Fooled

RoFT: A Tool for Evaluating Human Detection of Machine-Generated Text


Different implementations of "Weighted Prediction Error" for speech dereverberation

An Investigation into the Effectiveness of Enhancement in ASR Training and Test for CHiME-5 Dinner Party Transcription

STC Speaker Recognition Systems for the VOiCES From a Distance Challenge

End-to-End Far-Field Speech Recognition with Unified Dereverberation and Beamforming

Unsupervised training of neural mask-based beamforming

Acoustic Modeling for Overlapping Speech Recognition: Jhu Chime-5 Challenge System

Speech Enhancement with Wide Residual Networks in Reverberant Environments


Bridging the gap between observation and theory

Hoki: Making BPASS accessible through Python

The DUVET Survey: Direct T  e -based Metallicity Mapping of Metal-enriched Outflows and Metal-poor Inflows in Markarian 1486

Progenitor, environment, and modelling of the interacting transient AT 2016jbu (Gaia16cfr)

Monthly notices of the Royal Astronomical Society

A systematic ageing method I: H ii regions D118 and D119 in NGC 300

Monthly Notices of the Royal Astronomical Society

End-to-end study of the host galaxy and genealogy of the first binary neutron star merger


SPlisHSPlasH is an open-source library for the physically-based simulation of fluids.

Lagrangian neural style transfer for fluids

Numerical Study on the Hydrodynamic Characteristics of a Double-Row Floating Breakwater Composed of a Pontoon and an Airbag

Journal of Marine Science and Engineering

A Contact Proxy Splitting Method for Lagrangian Solid-Fluid Coupling

Accelerating Surface Tension Calculation in SPH via Particle Classification & Monte Carlo Integration

A Variational Staggered Particle Framework for Incompressible Free-Surface Flows

Latent Intuitive Physics: Learning to Transfer Hidden Physics from A 3D
  Video


A Mechanical Turk Interface (amti)

GENIE: Toward Reproducible and Standardized Human Evaluation for Text Generation

Easy, Reproducible and Quality-Controlled Data Collection with CROWDAQ

EasyTurk: A User-Friendly Interface for High-Quality Linguistic Annotation with Amazon Mechanical Turk

EACL 2021: THE 16TH CONFERENCE OF THE EUROPEAN CHAPTER OF THE ASSOCIATION FOR COMPUTATIONAL LINGUISTICS: PROCEEDINGS OF THE SYSTEM DEMONSTRATIONS


Universal Conceptual Cognitive Annotation (UCCA)

Simple and Effective Text Simplification Using Semantic and Neural Methods

SemEval-2019 Task 1: Cross-lingual Semantic Parsing with UCCA

Semantic Structural Decomposition for Neural Machine Translation

Joint Conference on Lexical and Computational Semantics

Cross-lingual Semantic Representation for NLP with UCCA

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


Twenty Years of Auxiliary-Field Quantum Monte Carlo in Quantum Chemistry: An Overview and Assessment on Main Group Chemistry and Bond-Breaking

ipie: A Python-based Auxiliary-Field Quantum Monte Carlo Program with Flexibility and Efficiency on CPUs and GPUs

Full Configuration Interaction Excited-State Energies in Large Active Spaces from Subspace Iteration with Repeated Random Sparsification

Scalable Ab Initio Electronic Structure Methods with Near Chemical
  Accuracy for Main Group Chemistry


Community dynamics metrics

codyn: An r package of community dynamics metrics

Deep Crustal Flow Within Postorogenic Metamorphic Core Complexes: Insights From the Southern Western Gneiss Region of Norway

Niche partitioning facilitates coexistence of closely related gut bacteria

Dynamic of Dominant Plant Communities in Kettle Holes (Northeast Germany) during a Five-Year Period of Extreme Weather Conditions


Normalizing flows in PyTorch

SBI -- A toolkit for simulation-based inference

Stochastic Normalizing Flows

Phase space sampling and inference from weighted events with autoregressive flows

Machine learning in solar physics

Full-shape analysis with simulation-based priors: Constraints on single field inflation from BOSS

Full-shape analysis with simulation-based priors: cosmological
  parameters and the structure growth anomaly

Lagrangian Flow Networks for Conservation Laws

Causal Inference with Cocycles

Systematic evaluation of generative machine learning capability to simulate distributions of observables at the large hadron collider


adaptive 1d numerical Gauss–Kronrod integration in Julia

Algorithms for the computation of the matrix logarithm based on the double exponential formula

Journal of Computational and Applied Mathematics

Modeling High-Frequency Backscattering from a Mesh of Curved Surfaces Using Kirchhoff Approximation

Journal of Theoretical and Computational Acoustics

Oscillations in a Becker-Döring model with injection and depletion

Learning Continuous Exponential Families Beyond Gaussian

Green's functions of and emission into discrete anisotropic and hyperbolic baths

Analysis of Bootstrap and Subsampling in High-dimensional Regularized
  Regression

Lattice Green's Functions for High Order Finite Difference Stencils

A Duet of Freeze-in and Freeze-out: Lepton-Flavored Dark Matter and Muon Colliders

Solving optimal control problems with non-smooth solutions using an integrated residual method and flexible mesh

A plausible link between dynamically unsettled molecular gas and the radio jet in NGC 6328


Python library and CLI tool to interface with Google Translate's text-to-speech API

Variational Reasoning for Question Answering with Knowledge Graph

Representations of language in a model of visually grounded speech signal

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

Encoding of phonology in a recurrent neural model of grounded speech

Conference on Computational Natural Language Learning

Visually Grounded Models of Spoken Language: A Survey of Datasets, Architectures and Evaluation Techniques

TIMIT-TTS: A Text-to-Speech Dataset for Multimodal Synthetic Media Detection

Using Spoken Word Posterior Features in Neural Machine Translation

International Workshop on Spoken Language Translation

ASDF: A Differential Testing Framework for Automatic Speech Recognition Systems

A Framework for Automatic Generation of Spoken Question-Answering Data

Findings of the Association for Computational Linguistics: EMNLP 2022

FunnyNet-W: Multimodal Learning of Funny Moments in Videos in the Wild

Synthesizing Speech Test Cases with Text-to-Speech? An Empirical Study on the False Alarms in Automated Speech Recognition Testing