Nahin Khan

Education

2023-2025 ETH Zurich

• Masters of Science in Computational Biology and Bioinformatics
• Relevant Courses:
  • Big Data, Probabilistic Artificial Intelligence, Applications of Deep Learning on Graphs, Computational Biology

2016-2021 Carnegie Mellon University

• Bachelors of Science in Computer Science
• Bachelors of Science in Biological Sciences
• GPA: 3.94
• Dean’s List High Honors: Fall 2016 - Spring 2021
• Relevant Courses:
  • Computer Networks, Computer Security, Natural Language Processing, Complexity Theory, Machine Learning (Coursera), Graph Theory
  • Molecular Biology, Immunology, Cell Biology

Work Experience

Jan 2022 - Aug 2023 Research Assistant, Qatar Computing Research Institute

• Contributed to bioinformatics-related projects
• Conducted literature search to familiarize myself with current state of research
• Implemented methods and created pipelines to analyze data and gain biological insights
• Automated processes using Makefiles and common command-line tools (awk, sed, xargs, etc)
• Trained CNN and BERT models to predict protein binding strength using Tensorflow and Hugging Face
• Wrote and submitted papers for publishing with various teams

Oct 2021 - Jan 2022 Full Stack Developer, sKora

• Set up development, staging, and production environments for product development on Linode
• Set up CI/CD pipelines for automated tests and deployments to Kubernetes clusters using GitHub Actions
• Implemented backend API using FastAPI and frontend using ReactJS
• Performed code reviews and gave feedback to team members

Dec 2020 - Jan 2021 Backend Engineer, sKora, Intern

• Scraped millions of records from a football transfer market website
• Populated internal databases after cleaning the data using MySQL-Python integrations

Aug - Dec 2019 Parallel Data Structures and Algorithms Teaching Assistant, CMU Pittsburgh

• Led weekly 50-minute recitation sessions to teach key concepts to students in SML
• Led review sessions to help prepare 250+ students for midterms and exams

Jan - May 2020 Ballroom Dancing Instructor, Carnegie Mellon University Qatar

• Co-instructed a Student-led Course (StuCo) designed to be an introduction to ballroom dancing
• Taught cha cha, waltz, foxtrot, tango, salsa and more

Skills

Coding

• Python, C, Bash, JavaScript, SML, HTML, CSS, Matlab, R, x86 Assembly

Technologies / Environment

• Kubernetes, Docker, GitHub Actions, Django, FastAPI, MySQL, Nginx, ReactJS, Linux

Machine Learning

• Pytorch, Pytorch Geometric, Tensorflow, Keras, CNNs, GNNs, VAEs, Transformers, BERT models

Open Source Contributions

May 2023 CMplot

• R package that allows users to generate various genomic plots
• Enhanced a particular type of plot by adding the option to view multiple x-axes

Apr 2023 langchain

• Enhanced the documentation by fixing typos

Apr 2023 alpaca.cpp

• Fixed a bug that could result in a segfault error to occur on some architectures

May 2022 Tensorflow

• Corrected the tutorial’s explanation for what the attention values mean in a transformer

Mar 2022 Mephisto

• Corrected quoting issues in part of the documentation explaining how to launch via Docker

Mar 2022 atomium

• A Python package useful for parsing PDB (3D molecular) files and manipulating 3D structural data
• Added a feature that allows the user to see the origin (organism) of each protein chain in the PDB file
• For example, an antibody-related PDB file often has human / mouse chains and viral chains together, which this PR makes viewable programmatically

Feb 2022 cs228-notes

• Corrected a slight error on course notes for Probabilistic Graphical Models (Stanford CS228)

Aug 2021 nginx-proxy

• Fixed a typo in the documentation

Aug 2021 ukemi

• Fixed a typo in the docs

Aug 2021 bedtools2

• Fixed a typo in the docs

Jul 2021 Docker Docs

• Fixed an error in the layout of the documentation
• Fixed grammatical errors in other parts of the docs as well

Jul 2021 celery

• Fixed doc grammar

June 2021 Python Packaging User Guide (pypa)

• Fixed a typo in the docs

May 2021 Missing Semester

• A useful resource for people to learn tools that are helpful for everyday use of computers (for people in CS-related fields)
• Improved the clarity for one part of the notes that explained input / output streams in shell programs

May 2021 TLDR

• Useful tool for looking up cheatsheets for console commands
• Added a page that explained how “bfg”, a tool for removing large files or passwords from Git history, works

Awards and Honors

Oct 2019 Andrew Carnegie Scholar and Qatar Campus Scholar, Awardee

• Selected for showing high standards of academic excellence and leadership in the community

May 2019 Fifth Year Scholar, Awardee

• CMU program that sponsors a student to study for an extra year after graduating

2017-2020 Qatar Foundation Scholarship, Recipient

• Competitive merit-based full scholarship given to students in Education City

Research Experience

Apr - Aug 2023 Genome-wide association study for ECG traits, QCRI

• Identified novel genetic regions that contribute to abnormal ECG patterns

Nov 2022 - Apr 2023 Improving Polygenic Risk Scores, QCRI

• Proposed methods for improving genetic risk scores when combining local population and published data

June - Nov 2022 Multiomics Project, Center for Precision Health and Medicine, QCRI

• Combined genomic and metabolomic data from 3000+ people with over 22,000 features
• Utilized multi-omic data to propose molecular mechanisms leading to coronary heart disease risk
• Proposed genetic and metabolomic risk factors to screen for coronary heart disease risk

Feb - Sept 2022 Antibody Project, Qatar Center for AI, Research Assistant

• Extracted binding strength data between antibody and antigen motif sequences using crystal structure data
• Trained machine learning models for predicting the strength of binding between antibodies and antigens

Jan - June 2020 Honors Thesis: A Bioinformatics Tool for Exploring RNA-Protein Interactions

• Developed a CLI tool that collects and visualizes RNA-Protein interactions (https://rnpfind.com)
• Developed features for studying correlation and overall-binding profiles of RNA binding proteins
• Utilized Django and Docker; run and managed on Linode hosts

April - Oct 2019 Genetically Engineered Machine Competition, Boston, Team Bioinformatician

• Built a machine capable of detecting recessive genetic disease in carriers in half an hour
• Collaborated with various international teams on molecular modelling of Cpf1, gRNA, and template DNA

June - Aug 2017 Woolford Lab, Mellon College of Science, Pittsburgh, USA, Research Intern

• Investigated the role of Drs1 in ribosome assembly
• Created spotting assays of mutagenized yeast strains and isolated preribosomes for protein analysis
• Constructed models of Drs1 function in assembly
• Presented results at Meeting of the Minds Conference (2018)

Aug - May 2017 Phage Genomics Research Course, Carnegie Mellon University

• Sequenced extracted DNA from isolated phages usign Ion Torrent machine to obtain DNA strand sequences
• Performed computational assembly and annotated the sequence DNA to generate a gene map

Projects

Dec 2023 Link Prediction on Knowledge Graphs

• Trained and evaluated an RGCN model on the FB15k-237 dataset
• Generated embedding representations for entities in a task-independent manner using contrastive learning
• Achieved mean reciprocal rank of 0.538

Dec 2023 Reinforcement Learning on a Pendulum

• Implemented an off-policy RL algorithm on the Pendulum environment
• Implemented soft actor critic (SAC) to directly predict Q-values and policy
• Used the modified variant which automatically sets the temperature

Nov 2023 Bayesian Optimization

• Optimized an unknown objective function that is costly time-wise to evaluate
• Addressed an unknown constraint function defining regions of unsafe evaluation
• Implemented a variant of the GP-UCB algorithm

Nov 2023 Approximate Bayesian Inference in Deep Neural Networks

• Implemented Stochastic Weight Averaging Gaussian (SWAG)
• Trained a deep CNN with posterior distribution estimates for parameters using SWAG
• Implemented histogram binning and temperature scaling to improve calibration

Oct 2023 Weather prediction with uncertainty estimates

• Used Gaussian Processor Regressors to estimate the weather based on location
• Improved efficiency by k-means clustering and learning multiple GPRs for each cluster
• Evaluated the model with an asymmetric cost to model realistic city requirements

Oct 2023 Custom Message Passing Layers in GNN

• Investigated the effects of breaking permutation invariance in a GNN message passing layer
• Concluded that some datasets benefit from breaking invariance due to hidden structures in node ordering

March 2021 Mini BitTorrent

• Wrote a peer-to-peer program for sharing files between multiple hosts in C
• Designed and implemented a TCP-like protocol for sharing chunks of data (over UDP)
• Implemented congestion control and the sliding window algorithm

Feb 2021 HTTP 1.1 Compliant Server

• Wrote an international standard (RFC2616) compliant web server in C, supporting GET, HEAD, and POST
• Integrated CGI support

May 2021 Question and Answer Model

• Wrote a program that generates questions from an article, and answers questions regarding the article
• Used word2vec word embeddings to find similarity between sentences in the article and the questions
• Utilized co-reference resolution to increase similarity matches

Nov 2020 Mailpile: Open-source Contribution

• Submitted a bugfix for an open-source mail client
• Fixed several issues by fixing the root cause of allowing duplicate email address registration
• Fixed both front-end and back-end

Oct 2020 Dynamic Memory Allocator

• Wrote a dynamic memory allocator (malloc) in C with high utilization (69%) and throughput (14k KOPS)
• Utilized a segregated free list and engineered a custom region for small-sized allocation requests

Nov 2020 Automated Theorem Prover

• Developed a prover of theorems in intuitionistic logic written in SML and Prolog

Nov 2016 Python Chess A.I.

• Developed a chess program with Artificial Intelligence in Python and shared online for a course
• Has been referenced by several repositories on GitHub and has attracted community attention