Projects by Year

Zhe’s PhD Defense - Toward Out-Of-Distribution Generalization Of Deep Learning Models

2 minute read

Ph.D. Dissertation Defense by Zhe Wang, Tues., 04/02/24, at 12:00PM (ET) Committee:

Arsh’s PhD Defense - Relational Structure Discovery for Deep Learning

1 minute read

Arshdeep Sekhon’s PhD Defense June 29, 2022.

JackL’s PhD Defense - Modeling interactions with Deep Learning

less than 1 minute read

Ph.D. Dissertation Defense by Jack Lanchantin Tuesday, July 20th, 2021 at 2:00 PM (ET), via Zoom. Committee: Vicente Ordóñez Román, Committee Chair, ...

DrQi’s tutorial talk on “Make Deep Learning Interpretable for Sequential Data Analysis in Biomedicine” (Including our work on DeepChrome - AttentiveChrome - GCNChrome - DeepMotif - DeepVHPPI - MotifTransformer)

less than 1 minute read

I gave a tutorial talk at UVA-VADC Seminar Series 2021 and at monthly NIH Data Science Showcase seminar.

ACM BCB - Transfer Learning for Predicting Virus-Host Protein Interactions for Novel Virus Sequences

2 minute read

Dr Qi’s Invited Talks on textattack

less than 1 minute read

On June 24th, 2021, I gave an invited talk at the Science Academy Machine Learning Summer School on “TextAttack: Generalizing Adversarial Examples to Natural...

CVPR - General Multi-label Image Classification with Transformers

1 minute read

Title: General Multi-label Image Classification with Transformers

AAAI - Curriculum Labeling- Self-paced Pseudo-Labeling for Semi-Supervised Learning

1 minute read

Title: Curriculum Labeling- Self-paced Pseudo-Labeling for Semi-Supervised Learning”

NeurIPS - Measuring Visual Generalization in Continuous Control from Pixels

less than 1 minute read

EMNLP - Benchmarking Search Algorithms for Generating NLP Adversarial Examples

1 minute read

Title: Searching for a Search Method: Benchmarking Search Algorithms for Generating NLP Adversarial Examples

EMNLP- On Quality of Generated Adversarial Examples and How to Set Attack Contraints

1 minute read

Title: Reevaluating Adversarial Examples in Natural Language

EMNLP - TextAttack- A Framework for Adversarial Attacks in Natural Language Processing

less than 1 minute read

Bioinformatics - Graph Convolutional Networks for Epigenetic State Prediction Using Both Sequence and 3D Genome Data

1 minute read

Bioinformatics - FastSK- Fast Sequence Analysis with Gapped String Kernels

1 minute read

DrQi’s tutorial talk about jointnets at UCLA computational genomics summer school 2019 for extracting connectomes from heterogeneous samples

less than 1 minute read

Here is the slide of my tutorial talk at UCLA computational genomics summer school 2019.

JointNets R package for Joint Network Estimation, Visualization, Simulation and Evaluation from Heterogeneous Samples

1 minute read

jointNets R package: a Suite of Fast and Scalable Tools for Learning Multiple Sparse Gaussian Graphical Models from Heterogeneous Data with Additional Knowle...

kDIFFNet - Adding Extra Knowledge in Scalable Learning of Sparse Differential Gaussian Graphical Models

1 minute read

Tool kDIFFNet: Adding Extra Knowledge in Scalable Learning of Sparse Differential Gaussian Graphical Models

Weilin’s PhD Defense - Improving Robustness of Machine Learning Models using Domain Knowledge

2 minute read

Ph.D. Dissertation Defense by Weilin Xu

DrQi’s Feature Squeezing- Invited Talk at GMU

less than 1 minute read

On April 23 2019, I gave an invited talk at the ARO Invitational Workshop on Foundations of Autonomous Adaptive Cyber Systems

ECML - Graph Neural Networks for Multi-Label Classification

1 minute read

DrQi’s Feature Squeezing- Invited Webinar Talk at I3P

less than 1 minute read

On December 21 @ 12noon, I gave a distinguished webinar talk in the Fall 2018 webinar series of the Institute for Information Infrastructure Protection (I3P)...

DrQi’s tutorial talk at UVA-CPHG seminar and healthDynamics workshop 2018 for Making Deep Learning Understandable for Genomics

less than 1 minute read

I gave a tutorial talk at UVA-CPHG Seminar Series 2018.

Bioinformatics - DeepDiff- Deep-learning for predicting Differential gene expression from histone modifications

1 minute read

Tool DeepDIff: DeepDiff: Deep-learning for predicting Differential gene expression from histone modifications

BCB- DrQ’s tutorial talk at ACM-BCB 2018 for Making Deep Learning Understandable for Genomics

less than 1 minute read

Here are the slides of tutorial talk I gave at ACM-BCB 2018.

A Series of Tutorials We wrote to explain the JointS GM tools we built for extracting connectomes from heterogeneous samples

less than 1 minute read

So far, we have released the following Tutorials:

Beilun’s PhD Defense - Fast and Scalable Joint Estimators for Learning Sparse Gaussian Graphical Models from Heterogeneous Data with Additional Knowledge

1 minute read

PhD Defense Presentation by Beilun Wang Friday, July 20, 2018 at 9:00 am in Rice 242 Committee Members: Mohammad Mahmoody (Chair), Yanjun Qi (Advisor), ...

ICML - JEEK - Fast and Scalable Joint Estimator for Integrating Additional Knowledge in Learning Multiple Related Sparse Gaussian Graphical Models

3 minute read

Tool JEEK: A Fast and Scalable Joint Estimator for Integrating Additional Knowledge in Learning Multiple Related Sparse Gaussian Graphical Models

Rita’s PhD Defense - Fast and Interpretable Classification of Sequential Data in Biology

1 minute read

Ph.D. Dissertation Defense by Ritambhara Singh Monday, April 9, 2018 at 12:00PM in Rice 504.

DrQ Tutorial Talk about DeepChrome-AttentiveChrome-DeepMotif

less than 1 minute read

Here are the slides of lecture talks I gave at UCLA CGWI and NLM-CBB seminar about our deep learning tools: DeepChrome, AttentiveChrome and DeepMotif.

NDSS - Feature Squeezing- Detecting Adversarial Examples in Deep Neural Networks

1 minute read

Paper Arxiv

SPW - Blackbox Generation of Adversarial Text Sequences

1 minute read

EvadeML-Zoo Benchmarking and Visualization AE Tool is released

2 minute read

We are releasing EvadeML-Zoo: A Benchmarking and Visualization Tool for Adversarial Examples (with 8 pretrained deep models+ 9 state-of-art attacks).

Best Paper Award for Deep Motif Dashboard

less than 1 minute read

Jack’s DeepMotif paper (Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks ) have received the “best paper awar...

MLCB - Prototype Matching Networks for Large-Scale Multi-label Genomic Sequence Classification

1 minute read

AISTAT - DIFFEE to identify Sparse Changes in High-Dimensional Gaussian Graphical Model Structure

2 minute read

Tool DIFFEE: Fast and Scalable Learning of Sparse Changes in High-Dimensional Gaussian Graphical Model Structure

NeurIPS - W-SIMULE

1 minute read

Tool W-SIMULE: A Constrained, Weighted-L1 Minimization Approach for Joint Discovery of Heterogeneous Neural Connectivity Graphs with Additional Prior knowled...

VizSec17 - Adversarial-Playground Paper Appear @ VizSec17

1 minute read

NDSS- Feature Squeezing Mitigates and Detects Carlini-Wagner Adversarial Examples

less than 1 minute read

Paper Arxiv

NeurIPS - AttentiveChrome-Deep Attention Model to Understand Gene Regulation by Selective Attention on Chromatin

1 minute read

Tool AttentiveChrome: Attend and Predict: Using Deep Attention Model to Understand Gene Regulation by Selective Attention on Chromatin

ICLR - Memory Matching Networks for Genomic Sequence Classification

less than 1 minute read

PSB - Deep Motif Dashboard- Visualizing and Understanding Genomic Sequences Using Deep Neural Networks

1 minute read

Tool Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks

Bioinformatics - DeepChrome- deep-learning for predicting gene expression from histone modifications

1 minute read

Tool DeepChrome: deep-learning for predicting gene expression from histone modifications

VizSec - Adversarial-Playground- A Visualization Suite for Adversarial Sample Generation

less than 1 minute read

Paper Arxiv

ICLR- DeepCloak- Masking Deep Neural Network Models for Robustness against Adversarial Samples

less than 1 minute read

Paper ICLR17 Workshop

S&P -A Tool for Automatically Evading Classifiers for PDF Malware detection

1 minute read

ICLR - A Theoretical Framework for Robustness of (Deep) Classifiers Against Adversarial Samples

1 minute read

Paper ICLR17 workshop

ECML - GaKCo-SVM- a Fast GApped k-mer string Kernel using COunting

1 minute read

Tool GaKCo-SVM: a Fast GApped k-mer string Kernel using COunting

TCBB - TSK- Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction

1 minute read

Tool TSK: Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction

AISTAT - FASJEM R package is released!

1 minute read

Tool FASJEM: A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models

Journal Machine Learning - SIMULE R package is released!

2 minute read

Tool SIMULE: A constrained l1 minimization approach for estimating multiple Sparse Gaussian or Nonparanormal Graphical Models

AAAI - MUST-CNN- A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-based Protein Structure Prediction

less than 1 minute read

Tool MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-based Protein Structure Prediction

NeurIPS- Learning the Dependency Structure of Latent Factors

1 minute read

ICLR - Unsupervised Feature Learning by Deep Sparse Coding

less than 1 minute read

ECIR - Deep Learning for Character-based Information Extraction on Chinese and Protein Sequence

1 minute read

Title: Deep Learning for Character-based Information Extraction on Chinese and Protein Sequence

DrQ Talk in 2013 about our DeepLearning Works on Protein and BioNLP datasets

less than 1 minute read

Here are the slides of one lecture talk I gave at UVA CPHG Seminar Series in 2014 about our deep learning tools back then.

Plos- A unified multitask architecture for predicting local structural properties on proteins

1 minute read

Tool Multitask-ProteinTagging: A unified multitask architecture for predicting local protein properties

NeurIPS - A few other MRF tools we built

1 minute read

Paper1: Learning the Dependency Structure of Latent Factors Y. He, Y. Qi, K. Kavukcuoglu, H. Park (2012) NeurIPS PDF Talk: Slide

NeurIPS - Deep Metric Learning to Learn and to Use

4 minute read

Paper0: Learning to rank with (a lot of) word features

CIKM - Document classification with weighted supervised n-gram embedding

2 minute read

ECML - Systems and methods for semi-supervised relationship extraction

3 minute read

ICDM- Semi-Supervised Sequence Labeling with Self-Learned Feature

1 minute read

Bioinformatics - Semi-supervised multi-task learning Using BioText based Labels to Augument PPI Prediction

1 minute read