News

2023

August 2023. Welcome to Mostafa! He joined our group as a PhD student. He works on analyzing single cell sequencing data and images.

August 2023. Congratulations to Masum! his paper titled “A Scaled Denoising Attention-based Transformer for Breast Cancer Detection and Classification,” is accepted for presentation at the MICCAI 2023,  14th workshop on Machine Learning in Medical Imaging (MLMI 2023).

July 2023. Congratulations to Sahand and Jun! Their paper titled “3D Biological/Biomedical Image Registration with enhanced Feature Extraction and Outlier Detection” is accepted for presentation At 2023 ACM-BCB conference.

July 2023. Congratulations to Bingjun! His abstract titled “Contrastive Learning in Single-cell Multiomics Clustering,” is accepted at the 2023 ACM-BCB conference as poster presentation.

June 2023. Masum join our group for his PhD study. He is  working on analyzing biomedical images. Welcome Masum!

May 2023. Congratulations to Josue! his paper titled ” Addressing Vulnerability in Medical Deep Learning through Robust Training,” is accepted for presentation at the 2023 IEEE Conference on Artificial Intelligence (CAI).

May 2023. Congratulations  to Jun, Bingjun and  Josue!  Jun received the Taylor L. Booth Graduate Fellowship (2023) that is the highest honor for doctoral students and  Bingjun and Josue received Predoctoral Fellowship for outstanding scholars and research accomplishment.

April 2023. Congratulation to Jun! she defended her PhD thesis! Well done Jun! We will miss her! She will join University of Cincinnati as an Assistant professor.

January 2023. Welcome to Sahand and Afsana! They joined our research group as PhD student. Sahand works on analyzing multiplex Brian microscopy images and Afsana works on analyzing 2D and 3D images.

2022

December 2022. Congratulations to Jun! Her abstract titled  “Unsupervised feature correlation network for localizing breast cancer using history of mammograms,” was accepted for poster presentation for the Medical Imaging meets NeurIPS workshop, at the NeurIP 2022 conference (https://nips.cc/media/PosterPDFs/NeurIPS%202022/63501.png?t=1668797609.0550115).

June 2022. Congratulations to Jun and Tianyu! Their paper titled “Applying Graph Convolution Neural Network in Digital Breast Tomosynthesis for Cancer Classification,” was accepted for presentation  in the ACM BCB 2021 conference.
June 2022. Congratulations to Jun and Bingjun! Their paper titled “Semi-supervised classification of disease prognosis using CR images with clinical data structured graph,” was accepted for presentation  in the ACM BCB 2021 conference.
May 2022. Congratulations  to Bingjun and Jun!  They received Predoctoral Fellowship for outstanding scholars and research accomplishment.  

March 2022. Congratulations to  Jun and Tianyu! Their paper titled “Feature fusion Siamese network for breast cancer detection comparing current and prior mammograms” is published in the Medical Physics journal  (https://doi.org/10.1002/mp.15598).

March 2022. Our book chapter titled “Identification of Copy Number Alterations from Next-Generation Sequencing Data” as part of the Computational Methods for Precision Oncology book (https://doi.org/10.1007/978-3-030-91836-1_4) is published.

2021

December 2021. Congratulations to  Tianyu and Jun! Their paper entitled “Single-cell classification using graph convolutional networks,” was published in the BMC bioinformatics journal.
October 2021. Congratulations to Bingjun and Tianyu! Their paper titled “Single-cell RNA sequencing data clustering using graph convolutional networks,” was accepted for presentation at the 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

August 2021. Congratulations to  Tianyu! She defended her PhD. Currently she is a Research Scientist at Meta! 

June 2021. Congratulations to Bingjun and Tianyu! their paper titled “Cancer Molecular Subtype Classification by Graph Convolutional Networks on Multi-omics Data” was accepted for publication in the ACM BCB 2021 conference.

May 2021. Congratulations  to Tianyu and Jun!  Tianyu received the Taylor L. Booth Graduate Fellowship (2019) that is the highest honor for doctoral students and  Jun received Predoctoral Fellowship for outstanding scholars and research. accomplishment.  

March 2021. Congratulations to Jun! Her paper titled “Applying deep learning in digital breast tomosynthesis for automatic breast cancer detection: A review” was published in the Medical Image Analysis Journal (https://doi.org/10.1016/j.media.2021.102049). 

 

2020

September 2020. Congratulations to Fatima! She defended her PhD. She will join Harvard School of Public Health as a postdoctoral fellow.

August 2020. Welcome Bingjun Li! He joined our team. He is  working on integrating multi comics data employing statistical deep learning models. 

July 2020. Congratulations to Fatima! Her paper on employing deep learning for  pancancer molecular subtype classification using histopathological images and RNAseq data has been accepted in the ACM-BCB 2020 conference.

May 2020. Congratulations to Fatima and Tianyu! They received Predoctoral Fellowship for outstanding scholars and research accomplishment.  

February 2020. Congratulations to Tianyu! She defended her PhD proposal. The title of her PhD thesis is Computational Methods for Single-cell RNA Sequencing Data Analysis.

January 2020. Congratulations to Dina! She defended her PhD. She is my first PhD graduate.

2019

December  2019. Congratulations to Fatima! she defended her PhD proposal. The title of her PhD thesis is “Developing Novel Copy Number Variation Detection Methods using Emerging Sequencing Data.”

November 2019. Tianyu presented her research on imputation methods for single cell RNA sequencing data, titled : Single-cell RNAseq Imputation Based on Matrix Completion with Side Information, at IEEE BIBM conference. I also presented our recent research on developing computational methods for analyzing single cell sequencing data as an invited talk at the IEEE BIBM conference.

September 2019. Welcome June Bai! She joined our team, working on deep learning models for biomedical image analysis and genomic data analysis.

August 2019. Congratulations to Tom! He graduated in May and joined Broad institute as a computational biologist.

June 2019. Congratulations to Dina! She defended her PhD proposal. The title of her thesis is “Deep Learning Systems for Automated Lesion Detection, Segmentation, and Classification in Mammography.”

June 2019. Congratulations to Dina and Fatima! Dina paper on residual deep learning for mass segmentation and classification in mammogram images is accepted for oral presentation at ACM-BCB 2019 conference (doi>10.1145/3307339.3342157). Fatima paper on CNV detection using Taut String is also accepted for oral presentation at the ACM-BCB 2019 conference (doi>10.1145/3307339.3342181).

May 2019. Congratulations to Dina, Fatima and Tianyu! Dina and Tianyu received Predoctoral Fellowship for outstanding scholars and research accomplishment. Fatima received Predoctoral Price for Research Excellent award for outstanding research accomplishment.  

 

January 2019. Congratulations to Tianyu! her paper on comparative analysis of differential gene expression analysis tools for single cell sequencing data is published in BMC Bioinformatics (https://doi.org/10.1186/s12859-019-2599-6).

2018

December 2018.  We organized a workshop on  Applications of Machine Learning and Signal Processing in Biomedical Informatics and Computational Genomics at IEEE BIBM 2018 conference.

October 2018. Congratulation to Dina! Her paper is accepted for oral presentation at the ICCABS2018 conference. 

October 2018. We presented our research at the Research Connections event to first year and second year students.

 

August 2018. Tianyu’s paper in Methods on single cell differential expression analysis has been published. (https://doi.org/10.1016/j.ymeth.2018.04.017).

June 2018. Congratulations to Tianyu! Her paper on clustering single cell data is accepted for oral presentation at the ACM-BCB 2018 conference (doi.org/10.1145/3233547.3233590). 

July 2018. We presented our research to high school and middle school girls who were interested in coding.

 

May 2018. We mentored an undergraduate student from the Uconn McNair Scholars Program in our lab.

April 2018. Congratulations to Tianyu! Her paper on a new method for differential analysis of single cell RNA-seq data is accepted for publication in Methods.

April 2018. Congratulations to Fatima! Her paper on using total variation approach to reduce noise for CNV detection has been accepted for publication in BMC Bioinformatics(https://doi.org/10.1186/s12859-018-2332-x).

January 2018. Welcome Thomas Davis! He joined our team.

2017

December 2017. Congratulations to Dina! Her abstract is accepted for poster presentation at the International Symposium on Biomedical Imaging Conference (ISBI’18), 2018.

October 2017. Congratulations to Fatima and Tianyu! their papers are accepted for full paper oral presentation at IEEE BIM 2017 conference.

September 2017. We presented our research to young female students who were interested in computer science and engineering at the Uconn Women in Engineering Day event.

September 2017. Congratulation to Dina! Her paper is accepted for presentation at the ICCABS  2017 workshop.

August 2017. Congratulations to Fatima! She won the best poster award at the ACM-BCB 2017 conference.

 

June 2017. Congratulations to Fatima and Abdelrahman! Their abstracts are accepted for poster presentation in ACM-BCB 2017 conference.

June 2017. Congratulations to Fatima! Her paper on evaluating CNV detection tools is published in BMC Bioinformatics.

May 2017. Congratulations to Nick Monteleone! He is graduated.

2016

November 2016. Congratulations to Abdelrahman! He defended his Master’s.