About me

Hello, this is Saem! I am currently working as a Lecturer at the Department of Computer Science & Engineering of Bangladesh University of Engineering & Technology. I completed my Bachelors degree from the same department this May, 2023. Currently I am aiming for a research oriented career in the field of Computational Biology and Deep Learning. My end goal is to have an impact on the education sector overall through my works.

During my bachelors degree, I explored different fields to find out my interest and knack for research. My undergraduate thesis was in Bioinformatics under the supervision of Dr. Md.Shamsuzzoha Bayzid on finding terraces in species tree estimation. I am currently conducting research in the field of bioinformatics phylogeny, specifically analyzing and inferring species and gene trees. My main objective is to enhance summary methods to gain a deeper comprehension of the evolutionary connections among biological entities.

Research Experience

Ongoing Projects

  1. Iterative ScribbleDom

    July 2023 - Present

    Bioinformatics

    Single Cell

    Deep Learning

    Supervisor: Dr. Mohammad Saifur Rahman

    Iteratively guiding the model to learn from the user's scribbles. We are currently preparing the final manuscript.

  2. Extension of PMAO using Evolutionary Algorithms

    December 2023 - Present

    Bioinformatics

    Phylogeny

    Multi Objective Optimization

    Supervisor: Dr. M. Sohel Rahman

    Using Multi-objective algorithms to extend the PMAO algorithm. We are currently preparing the final manuscript.

  3. STELAR: Beyond Rooted Gene Trees

    August 2023 - Present

    Bioinformatics

    Phylogeny

    Supervisor: Dr. Md. Shamsuzzoha Bayzid

    Extending the STELAR algorithm to handle unrooted gene trees.

Publications

  1. Terraces in species tree inference from gene trees

    [Paper Link]
    Journal: BMC Ecology and Evolution

    Bioinformatics

    Phylogeny

    Species Tree Estimation

    Summary Method

    Supervisor: Dr. Md. Shamsuzzoha Bayzid

    A terrace in a phylogenetic tree space is a region where all trees contain the same set of subtrees, due to certain patterns of missing data among the taxa sampled, resulting in an identical optimality score for a given data set. This was first investigated in the context of phylogenetic tree estimation from sequence alignments using maximum likelihood (ML) and maximum parsimony (MP). It was later extended to the species tree inference problem from a collection of gene trees, where a set of equally optimal species trees was referred to as a “pseudo” species tree terrace which does not consider the topological proximity of the trees in terms of the induced subtrees resulting from certain patterns of missing data. In this study, we mathematically characterize species tree terraces and investigate the mathematical properties and conditions that lead multiple species trees to induce/display an identical set of locus-specific subtrees owing to missing data. We report that species tree terraces are agnostic to gene tree heterogeneity. Therefore, we introduce and characterize a special type of gene tree topology-aware terrace which we call “peak terrace”. Moreover, we empirically investigated various challenges and opportunities related to species tree terraces through extensive empirical studies using simulated and real biological data. We demonstrate the prevalence of species tree terraces and the resulting ambiguity created for tree search algorithms. Remarkably, our findings indicate that the identification of terraces could potentially lead to advances that enhance the accuracy of summary methods and provide reasonably accurate branch support.

Resume

Education

  1. MSc, Computer Science & Engineering

    Bangladesh University of Engineering & Technology (BUET)

    July 2023 - Present

    CGPA : 4.00
    Registered Courses : Computational Proteomics, Evolutionary Algorithms, Meta-Heuristics, Distributed Computing Systems, Programming Languages and Systems

  2. BSc, Computer Science & Engineering

    Bangladesh University of Engineering & Technology (BUET)

    March 2018 - May 2023

    CGPA : 3.96
    Rank : 3/129
    Notable Courses : Machine Learning, Simulation & Modelling, Computer Graphics, Software Engineering, Computer Security, Computer Networking, Artificial Intelligence, Operating System, Compiler, Bioinformatics, Computer Architecture, Microprocessor Microcontroller & Embedded Systems

  3. Higher Secondary Certificate

    Dhaka City College

    2015 - 2017

    GPA : 5.00

  4. Secondary School Certificate

    Muradnagar D.R. Govt. High School, Cumilla

    2013 - 2015

    GPA : 5.00

Experience

  1. Lecturer

    Department of Computer Science & Engineering, BUET October 2023 - Present

    • Term: January 2024

      • Course Instructor @ Computer Architecture (CSE 209)
      • Course Instructor @ Computer Architecture Sessional (CSE 210)
      • Course Instructor @ Simulation and Modeling Sessional (CSE 412)
      • Course Instructor @ Object Oriented Programming Language Sessional (CSE 108)
      • Course Instructor @ Technical Writing and Presentation (CSE 200)
      • Course Instructor @ Structured Programming Language Sessional (CSE 102)

    • Term: July 2023

      • Course Instructor @ Computer Architecture (CSE 305)
      • Course Instructor @ Computer Architecture Sessional (CSE 306)
      • Course Instructor @ Digital Logic Design Sessional (CSE 206)
      • Course Instructor @ Computer Programming Sessional (CSE 282)
      • Course Instructor @ Structured Programming Language Sessional (CSE 102)

  2. Adjunct Lecturer

    Department of Computer Science & Engineering, BUET June 2023 - October 2023

    • Term: January 2023

      • Course Instructor @ Data Structures and Algorithms I Sessional (CSE 106)
      • Course Instructor @ Object Oriented Programming Language Sessional (CSE 108)
      • Course Instructor @ Database Sessional (CSE 216)
      • Course Instructor @ Computer Security Sessional (CSE 406)
      • Course Instructor @ Software Development Sessional (CSE 408)

  3. Course Instructor

    IAC, BUET November 2023 - Present

Highlighted Projects

  • Ray tracing

    Graphics

    OpenGL

    Implementation of Ray Tracing

    [Code]
    • 1. Implementation of ray tracing and illumination techniques using the Phong Lighting model
    • 2. Generation of realistic images of geometric shapes and a 2D plane
  • Design digest #80

    CNN

    Deep Learning

    Custom-Built CNN for Handwritten Bangla Character Recognition

    [Code] In this project, a Convolutional Neural Network (CNN) was built from scratch to recognize handwritten Bangla characters. The model architecture was designed to capture intricate features in Bangla script, tackling the unique challenges presented by its distinct and complex characters. The CNN model was trained on a dataset of Bangla handwritten characters, achieving robust accuracy in classification.

  • Design digest #79

    Academic

    OpenGL

    Computer Graphics Sessional

    [Code] Includes implementation of a raster based graphics pipeline and generation of different types of objects.

  • UI interactions of the week

    Software Development

    Travello

    Travelers can explore various locations on the website Travello. It will assist them in locating appropriate hotels, places to eat, and food in tourist areas

  • Best fonts every designer

    XV6

    Implementation of an Operating System

    [Code] Developed the paging framework, scheduling & memory management of xv6 operating system, as well as implementing many other functionalities of the operating system.

  • Best fonts every designer

    Flex

    YACC

    Compiler

    [Code] Implementation of symbol table in CPP, lexical analyzer in Flex, Syntax and Semantic Analyzer in Bison and generating intermediate assembly code as part of an academic assignment.

  • UI interactions of the week

    Database Project

    ESPN CRIC-INFO

    ESPN CRIC-INFO is a website that provides scorecards for various cricket events worldwide

  • Design digest #79

    Deep Learning

    NLP

    BERTSerini

    [Code]

    BERTSerini is an end-to-end question-answering system that integrates BERT with the open-source Anserini information retrieval toolkit

  • Design digest #79

    Networking

    NS3

    Implementation of TCPW-BR algorithm in NS3

    TCPW BR algorithm mainly works when any duplicate acknowledgement is received. When any duplicate acknowledgement is received, this algorithm checks the dupack count and the congestion level. Based on dupack count and congestion level, this algorithm multiplies the congestion window with the growth factor, P. This algorithm also does some modification in the congestion avoidance phase.

  • Best fonts every designer

    JavaFX

    Online Ticket Reservation System

    [Code] The Online Ticket Reservation System app allows you to book bus/train/movie tickets

Consultancy

Project

  1. Feasibility Study of Establishing Specialized Cyber Security Center

    Department of ICT, Peoples Republic of Bangladesh

    June 2024 - December 2024
  2. Member, Software Evaluation Team

    BUET Admission Test 2023-24

    March 2024 - May 2024
  3. Requirement Analysis of BIIS [Website Link]

    Bangladesh University of Engineering & Technology (BUET)

    November 2023 - November 2024
  4. Member, CSE Website Development [Website Link]

    CSE, Bangladesh University of Engineering & Technology (BUET)

    February 2024 - October 2024
  5. Member, Cloud Lab Setup at CSE, BUET

    CSE, Bangladesh University of Engineering & Technology (BUET)

    February 2024 - December 2024
  6. Roll-serial generation, Eligibility checking, Result processing, Report generation

    Nursing Admission Test 2023-24

    May 2024 - November 2024

Achievements

Honors & Awards

  • mobile app icon

    Dean's List

    Recipient of Dean’s List Scholarship for the year 2019, 2020, 2021, 2022 for academic excellence.

  • camera icon

    University Merit

    Recipient of University Merit Scholarship for the year 2019, 2020, 2021, 2022 for academic excellence.

  • Web development icon

    MTB Saifuddin A. Chowdhury Memorial Scholarship, 2021

    Recipient of the MTB Saifuddin A. Chowdhury Memorial Scholarship for outstanding academic performance in the second and third years of undergraduate studies.

Food for soul

Project 1

Lead, Routine Committee of CSE, BUET

Leading the routine committee of the CSE department at BUET since October 2023, I oversee the creation of all types of routines, including level-term, teacher, and sessional routines.

Project 2

Organizer, International Conference on Networking, Systems, and Security

Lead, Sponsor Committee, 11th NSysS 2024
Member, Sponsor Committee, 10th NSysS 2023
Organizer, Industy Session, 10th NSysS 2023
Organizer, Panel Discussion, 10th NSysS 2023
Member, Food Committee, 10th NSysS 2023

Project 2

Organizer, Energy Conference 2023

Member, Registration Committee, ENCON 2023
Member, Publication Committee, ENCON 2023

Convener, BUET CSE Fest 2024

As the convener for BUET CSE FEST 2024, I oversaw the entire program, acting as the coordinator between the CSE department and students, and supporting students in organizing the fest.

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Organizer, BUET CSE Fest 2022

A part of the organizing team of BUET CSE Fest 2022 which had several inter-university competitions such as hackathon, programming contest, deep learning competition, AI contest and several events such as cultural program, dance mob, treasure hunts, indoor and outdoor games.

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Project 2

Judge, Gamejam, BUET CSE FEST 2024

I served as a judge for the GameJam event at BUET CSE FEST 2024, which featured 50 teams competing under the theme "Heroes Never Die." Visit Gamejam page Visit Gamejam Submissions

Project 2

Class Representative, BUET CSE'17 Batch

I served as the class representative for the BUET CSE 17 batch during my final year of undergraduate studies.

Contact

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