OxML Report Day4 πŸ“œ

The report of all talks during the fourth day of OxML Health 2023 where I’ve been on behalf of Appsilon..

This day talks were on:

  1. Insightful Lecture on ML for Mental Health - Munmun De Chodhury
  2. Drug Discovery with ML - Ravi Patel
  3. How to make sure the Market wants your solution - Reza Khorshidi
Read more β†’

OxML Report Day3 πŸ“œ

The report of all talks during the third day of OxML Health 2023 where I’ve been on behalf of Appsilon..

This day talks were on:

  1. Introduction to Neural Networks - Gitta Kutyniok
  2. Medical Expert’s View on Impactful and Responsible ML in Health with EHR - Kazem Rahimi
  3. Chaotic Lecture on Graphs and ML - Pietro LiΓ²
Read more β†’

OxML Report Day2 πŸ“œ

The report of all talks during the second day of OxML Health 2023 where I’ve been on behalf of Appsilon..

This day talks were on:

  1. The State of Computer Vision and Many CV Experiments - Cristian Rupprecht
  2. ML Challenges in Oncology and Multi-omics data - Mireira Crispin
  3. What is a Multimodality and How To Work With It? - Louis-Philippe (LP) Morency
Read more β†’

OxML Report Day 1 πŸ“œ

The report of all talks during the first day of OxML Health 2023 where I’ve been on behalf of Appsilon.

This day talks were on:

  1. Casual Inference - Cheng Zhang
  2. Computer Vision in medicine - Jorge Cardoso
  3. Knowledge Representation - Ali Eslami
Read more β†’

OxML Health 2023 - Summary πŸŒπŸ“šβ€οΈβ€πŸ©Ή

Long time no see ^^ Today, I’d like to share my experience from OxML Health Summer School that I attended in person this year on behalf of Appsilon.

Read more β†’

Detecting Antarctic Shag Nests πŸ§πŸ»β€β„οΈπŸ‡¦πŸ‡Ά

It’s always nice if you can use your technical skills for something good for our planet. I have this opportunity during work at Appsilon where from time to time we work on Data4Good projects. One such project was copepods/plankton project where I was doing segmentation of the oil sac in the Arctic plankton. This time I’d like to share something from the other pole of the globe.

Currently we work on detecting the Antarctic shags nests on the Antarctic islands. Together with JΔ™drzej ŚwieΕΌewski and Joanna Kaleta we were cooperating with researchers from IBB PAS on this task. Checkout the engagement summary blog post on the Appsilon blog.

Read more β†’

Jupyter Notebooks and Quarto πŸ““πŸ“ƒ

What if you just don’t like rmd/qmd format anymore? You love jupyter notebooks and that’s your way of working (that’s me). Still, you must generate report from time to time. Fortunately quarto solves this problem brilliantly!

The reports look beautifully. Not only htmls what we might expect, but pdfs as well!

I wrote a post for Appsilon that has been published on medium regarding this topic. Be sure to check it out, it was a real game-changer for me!

Read more β†’

Quarto, Python, and VSCode πŸ“ƒπŸ

Working with quarto files in RStudio is probably the suggested way. However, you may prefer to use VS Code. Especially if you work mainly in python. It’s not a problem by any means!

I wrote a post on medium on working with quarto in VS Code on python files.

Read more β†’

PyTorch Serialization πŸ“¦βš™οΈ

One thing is to train the model, but another is to serve it. In between those two phases, model serialization and deserialization occurs. In simpler words it’s just model saving and loading. It’s important because different methods result in different:

  1. Inference speed
  2. Model size
  3. Python environment size

If you are curious what are the ways to serialize model in PyTorch and how they compare, checkout my new post on Appsilon blog.

Read more β†’

DaftAcademy Course Finished 🐍🏁

I’d like to inform that the course has finished and the total of 56 people received a graduation certificate (which required passing homeworks for over 70%), congratulations! πŸŽ‰ It was a great experience and I’m happy that I was able to teach so many young students!

Read more β†’

PyTorch-Lightning + Hydra to Boost Your PyTorch βš‘πŸ‰

When working with deep learning problems I usually use PyTorch. I like this framework as it gives me a lot of freedom and allows to write code in the pythonic way. Using bare pytorch unfortunately often means writing a lot of boilerplate code, which no-one like. Another problem that arises during longer and larger projects is experiments running and configuration maintenance. I tackle those two problems by using pytorch-lightning and Hydra.
Read more β†’

DaftAcademy Announcement πŸπŸ‘¨β€πŸ«

I’m happy to announce that I’ll create and teach the course Python LevelUP: Data Science by Appsilon in collaboration with DaftAcademy, part of DaftCode.

This will be a five-week course on the basics of Data Science in python. The course materials will be available on GitHub for free. Apart from teaching the classic stuff, I’ll try to show some of the newest and coolest libraries out there. Even if you already know most of this stuff, I really recommend to take a closer look on the unknown packages.

Read more β†’

Copepods Oil Sac πŸŒŠπŸ›’πŸ‘œ

Some time ago, I’ve worked on an oil sac (energy reservoir) detection in copepods (kind of zooplankton) for UniversitΓ© Laval. Apart from presenting the results on the ML4Plankton conference I’ve published a detailed blog post on the Appsilon blog that I strongly encourage you to read!

Read more β†’

Presentation at ML4Plankton Conference 🌊🐟

Recently I was working at work on detecting the oil sac in copepods. This is was a super cool problem in which we received data from professor FrΓ©dΓ©ric Maps from UniversitΓ© Laval. We together gave a talk on conference ML4Plankton that you can watch online! First Frederic gives some context on why this problem is important and later I explain methods used and problems you can find. Our talk is available online here:
Read more β†’

Streamlit Tutorial: How to Deploy Streamlit Apps on RStudio Connect πŸ’°

I wrote another post for Appsilon, this time about deploying streamlit applications on RStudio Connect infrastructure. This post might be totally useless for majority of audience, but a pure gold for a few πŸ’°. What is streamlit you can understand from my previous post. Having a running app in your browser is already cool, but how cool is it to deploy your app on the internet? If you need an enterprise solution for hosting dashboards in RShiny/streamlit, RSConnect is the way!
Read more β†’

Detecting Solar Panels from satellite images part 3 - PoC model deployment in streamlit 🎈

This one is short. :) Usually when we are doing ML experiments, training models, preparing EDA, we want to share the results with the World at some point. One of the quickest and easiest ways to do so in python, to create a simple webapp with results, is a super-cool library streamlit! If you thought building an app in flask is easy, you will be amazed by streamlit simplicity. Actually you do not have to create an ML related app, nobody checks that ;).
Read more β†’

Detecting Solar Panels from satellite images part 2 – machine learning in fastai πŸ€–

As mentioned a month ago, I write a series of posts on detecting solar panels from satellite images at my company, Appsilon. In this post I focus on using fastai python library to deliver a working ML model in few hours!

Read more β†’

Detecting Solar Panels from satellite images part 1 – data preparationπŸ›°οΈ

I’m writing a series of posts on detecting solar panels from satellite images at my company, Appsilon. To be honest, not from satellite images but from orthophotos. If you don’t know what are orthophotos, the good news is that the first post has been released recently!.

Read more β†’

ML Data Versioning With DVC: How to manage machine learning data πŸ—ƒ

Recently I wrote a post about DVC at my company’s, Appsilon blog. DVC is like a git, but for data, models and experiments. It also allows for creating an automated experiments pipelines. As a teaser I’ll just say that, having prepared scripts for model training and evaluating, when new data is added to the repo, the whole training is run automatically. Metrics are saved to appropriate files alongside with parameters, same with plots.
Read more β†’