Hi, my name is Jonathan Borg
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Hi there, I'm Jonathan! A curious person by nature, driven to leave an impact that matters.

I have recently graduated from TU Delft, specialising in Artificial Intelligence, and I am excited to rejoin the workforce. My work experience shows that I take responsibility, work well in team and individual settings, and manage my time efficiently. Throughout my studies and previous work experience, I have developed a strong interest in Data Science and Machine Learning.

When unwinding, you can usually find me playing basketball with friends or trying to capture the world's beauty through my camera. If you want to learn more, please read ahead or get in contact.

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Project Spotlight


Master Thesis

My thesis, "Representations of DNA Sequence Context and Mutational Spectra for Prediction of Repair Deficiencies," was the culmination of the master study.

In the study, we researched the problem of predicting Non-Homologous End Joining (NHEJ) repair deficiencies. We evaluated how accurately we could predict NHEJ repair deficiency using only the mutational outcome frequencies. Afterwards, we examined how combining mutational spectra with representations of the sequence surrounding the break site could improve the prediction of NHEJ repair deficiency.

Python pandas NumPy SciPy scikit-learn Plotly BERT

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A reproduction study: inDelphi

Considering template-free applications, it is crucial to predict the resulting repair outcome after a CRISPR-Cas9-induced double-strand break (DSB). To predict Cas9 repair outcomes, researchers from MIT created inDelphi, a machine learning algorithm that predicts the identities and frequencies of repair indels forming after a Cas9-induced DSB. Receiving as input a local (e.g., 60-base-pair long) DNA sequence and its cut site due to a Cas9 guide RNA (gRNA), inDelphi predicts the frequencies and identities of 1- to 60-base-pair deletions and 1-base-pair (1-bp) insertions occurring at that site.

Python pandas NumPy SciPy scikit-learn Matplotlib Neural Networks

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Professional Timeline


2021-2023

Delft, Netherlands

Master of Science - Computer Science

Delft University of Technology (TU Delft)

Artificial Intelligence Track - Bioinformatics Specialisation
- Using Data Science concepts in different areas of study.
- Creating AI Models to tackle different prediction problems.
- Visualising and presenting results to people from different backgrounds.

Python Pandas Plotly PyTorch

2018-2021

Qormi, Malta

Software Developer

Deloitte Digital

- Creating Robotic Process Automation and AI Technologies.
- Meeting clients to gather business & technical requirements.
- Creating REST APIs for cross-component interaction.
- Setting up CI/CD processes for multiple projects.

C# Python MSSQL VB.NET

2016-2018

Marsa, Malta

Software Developer

KPMG Crimsonwing

- Creating a tailor-made Sales Force Automation Application.
- Building solutions for specific client modifications.
- Maintaining pre-existing client software systems.
- Modifying Microsoft Dynamics GP applications.

C# VB.NET MSSQL X++

2014-2017

Msida, Malta

Bachelor of Science - Computing Science

University of Malta

- Learning the fundamentals of Computer Science.
- Studying different areas such as AI, Security and Vision
- Solving different problems using Computer Science concepts.
- Participated in the Erasmus+ Student Exchange Programme (University of Essex)

C++ Java C PostgreSQL

Blog Posts


A reproducibility study: SwinIR

We looked into SwinIR: Image Restoration Using Swin Transformer, a model for image restoration based on the Swin Transformer. Their model combines a traditional Convolutional approach with Swin Transformer layers, which is a residual transformer approach to image processing.

The contribution of this blog post is twofold. First of all, we explained the technical details of the SwinIR paper in our own words, providing ample detail to understand the authors’ contribution and algorithm. Secondly, we explored modifying the architecture used in the paper to allow it to run using reduced resources, 1 RTX 3070 instead of the 8 RTX 2080TIs used in the paper. Our primary focus is to investigate whether the model could be reduced and achieve results comparable to the original model.

Python PyTorch scikit-learn Matplotlib Transformers

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Animated Face Creation using Generative Adversarial Networks

We created a Generative Adversarial Network (GAN) capable of generating animated faces based on the data set provided during training (specific to a particular drawing style — cartoon or anime).

GANs are composed of two primary components: The generator, a neural network tasked with generating images appearing to be as ‘real’ as possible. The discriminator is another neural network that determines if the supplied image is real or fake (i.e., generated by the other network). These two networks compete against each other to form a zero-sum game, where one agent’s gain is another agent’s loss.

Following the advancements of GANs in several fields, we decided to implement a model capable of generating animated faces. Apart from the model generation, ample tests, such as different model architectures and different datasets with diverse animation styles, were conducted to develop a robust and stable model.

Python PyTorch NumPy SciPy Matplotlib GAN

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