Mostofa Rafid Uddin

Computational Biology Researcher | Educator | Tech Geek

I am a graduate student in the Joint Carnegie Mellon University- University of Pittsburgh Computational Biology (CPCB) Ph.D. program. Prior to this, I received my B.Sc.Engg. in Computer Science and Engineering from Bangladesh University of Engineering and Technology(BUET) and later worked as a lecturer in Department of CSE, East West University, Dhaka . I completed my undergrad thesis under the supervision of Dr. Md. Shamsuzzoha Bayzid. My research interest lies broadly in application of machine learning in computational biology and bioinformatics. More specifically, I like to map the problems in computational biology to popular machine learning problems and come up with new efficient algorithms.
Previously, I have worked on structural bioinformatics, specifically, protein folding. Recently, I am fascinated by spatial biology, and exploring the computational challenges in this field. I am also working in a collaborative project of spatial pattern mining from mIHC imaging data of breast cancer tumors with Osmanbeyoglu Lab, and Vignali and Oesterreich Labs.

Apart from academic activities, I like to travel-meet different types of people and taste different types of foods. In my free times, I like to make outings with my friends and family.


Research

SAINT : Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction

Co-authors: Sazan Mahbub, Dr. Md Saifur Rahman, Dr. Md Shamsuzzoha Bayzid

In this work, we present SAINT, a highly accurate and fast method for protein Q8 structure prediction, which incorporates self-attention mechanism (a concept from natural language processing) with the Deep Inception-Inside-Inception (Deep3I) network in order to effectively capture both the short-range and long-range dependencies among the amino acid residues. SAINT offers a more interpretable framework than the typical black-box deep neural network methods. We report, on an extensive evaluation study, the performance of SAINT in comparison with the existing best methods on a collection of recent benchmark dataset, namely TEST2016, TEST2018, CASP12 and CASP13. We have made SAINT freely available at this link.

Status: Published at Bioinformatics, Oxford University Press. [Link] Preprint available at biorxiv.

eMED-DNA: An in silico operating system for clinical medical data storage within the human genome

Co-authors : Kowshika Sarker, Md Jakaria, Trisha Das, Md. Mohaiminul Islam, Dr. Rameen Shakur, Dr. Md Shamsuzzoha Bayzid

The propitious developments in molecular biology and next generation sequencing have enabled the possibility for DNA storage technologies. However, the full application and power of our genomic revolution have not been fully utilized in clinical medicine given a lack of transition from research to real world clinical practice. This has identified an increasing need for an operating system which allows for the transition from research to clinical use. We present eMED-DNA, an in silico operating system for archiving and managing all forms of electronic health records (EHRs) within one’s own copy of the sequenced genome to aid in the application and integration of genomic medicine within real world clinical practice. We incorporated an efficient and sophisticated in-DNA file management system for the lossless management of EHRs within a genome. This represents the first in silico integrative system which would bring closer the utopian ideal for integrating genotypic data with phenotypic clinical data for future medical practice.

Status: Under review. Preprint available at biorxiv.
Patent: UK Patent Application No. 1901754.0. Patent Pending.

Teaching Experiences

Fall 2020

  • CSE498 Social and Professional Issues in Computing
  • CSE207 Data Structures
September 2020 - December 2020

Summer 2020

  • CSE498 Social and Professional Issues in Computing
  • CSE207 Data Structures
  • CSE350 Data Communications
July 2020 - September 2020

Spring 2020

  • CSE498 Social and Professional Issues in Computing
  • CSE103 Structured Programming
  • CSE350 Data Communications
Janurary 2020 - May 2020

Fall 2019

  • CSE103 Structured Programming
  • CSE350 Data Communications
  • CSE101 Computer Fundamentals
September 2019 - December 2019

Summer 2019

  • CSE106 Discrete Mathematics
  • CSE103 Structured Programming
  • CSE350 Data Communications
May 2019 - August 2019

Spring 2019

  • CSE103 Structured Programming
  • CSE101 Computer Fundamentals
January 2019 - April 2019

YSIBangla Online Tutor

  • Machine Learning
November 2018-December 2018

Awards & Honors

  • Deans List Award and University Merit Scholarship
  • 1st Place - Poster Presentation, International Conference on Networking, Systems and Security (4th NSysS 2017) pdf
  • 1st Place - Hackathon for environmental migrants in Bangladesh arranged by Wageningen University, Netherlands. report
  • 2nd Place - Bracathon 2017 by BRAC
  • 3rd Place - National Hackathon 2016 by ICT Division.
  • 3rd Place - BUET Website Design Competition by IICT, BUET

Activities & Workshop

Notable Projects

Pytorch Autograd Implementation of OpenMM local energy minimizer

Tools : Pytorch, OpenMM

In this project, we implemented the openmm local energy minimizer (that is used to minimize the free energy of protein in protein dynamics) using pytorch. We extended the autograd mechanics of pytorch for a custom backpropagation where in the forward pass the energy is calculated and in the backward pass, each atom's coordinate is updated according to the energy gradients. This work was done under supervision of Prof. David Koes.

Project is available here.

Bangla to English Machine Translation Using Seq2seq Model with Attention Mechanism

Tools : Keras library (Tensorflow Backend), Python

In this term project, we did an experiment on Neural Machine Translation(NMT) for Bangla to English Translation. We used a moderate size dataset containing 4379 sentence translations from English to Bangla. We used seq2seq encoder-decoder model containing Word2Vec and LSTMs with and without attention for small epochs. With finely tuned hyperparameters, we observed that using Bahdanau's attention with the vanilla encoder-decoder model improves the BLEU score for Bangla to English translation.

Project is available here.

Posture Corrector using Arduino

Tools : Arduino, Android, Bluetooth Module

In this work, we developed a posture corrector android application that can detect unusual bending of the user. The application is connected with a wearable device containing Arduino and flex sensor. A user wearing a dress containing the device gets a notification in his application if he bends in a way that is harmful to his posture. Later a small physical motor was also introduced with the device that will force the user to correct his posture in case he doesn't has his phone nearby. However, the work was done for term project purpose and not commercially deployable.

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BD-Tourists : A cross platform application designed for travelers inside Bangladesh

Tools : AngularJS, Django

In this term project, a cross-platform application was developed for travelers inside Bangladesh. Using the app, anyone can easily find the popular tourist places in Bangladesh, see user reviews and available accommodations nearby the place, view the places with high risks and get suggestions on how to avoid them. The project was deployed using AngularJs framework Ionic for frontend and a Python Django server for backend; the communication between frontend and backend was established using a REST API.

Project code is available here.

GlowHockey using ATMega32

Tools : ATMega32

In this term project, an android game named glowhockey was deployed in a board containing 4 LED matrices. The gamers could use the gyro sensor in their hands to move the glowing hockey sticks in the board. The sensors and LED matrix were governed by an ATMega32 microprocessor which was programmed in C.

FoodiesDhaka : A Restaurant Rating Application

Tools : Java, MySQL

In this sophomore project, an application named FoodiesDhaka was developed using JavaFX and MySQL. In this application, the app users are provided with a choice of restaurants according to different areas in Dhaka city and they can see the user reviews and ratings for the restaurants. They can also suggest adding new restaurants in the list that can be further reviewed and checked by the admin side. The communication is done using Java Networking. However, the whole project was done in the localhost for term project purpose and is not deployable commercially.

Project code is available here.


Contact


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