Author: Sander Timmer

PhD student in computational genetics at Cambridge University and EMBL-European Bioinformatics Institute
Reimagining leprosy elimination with AI analysis of a combination of skin lesion images with demographic and clinical data – The Lancet Regional Health – Americas

Reimagining leprosy elimination with AI analysis of a combination of skin lesion images with demographic and clinical data – The Lancet Regional Health – Americas

See the full paper here.

AI4Leprosy: A research project that aims to develop an AI-driven diagnosis assistant for leprosy, based on skin images and clinical data.

  • Dataset: The researchers collected 1229 skin images and 585 sets of metadata from 222 patients with leprosy or other dermatological conditions in a Brazilian leprosy referral center. The dataset is open-source and available for other researchers to use.
  • AI models: The researchers tested three AI models, using images and metadata both independently and in combination, to predict the probability of leprosy. They used convolutional neural networks (CNN) for image analysis and elastic-net logistic regression for metadata analysis.
  • Results: The best AI model achieved a high accuracy (90%) and area under curve (AUC) of 96.46% for leprosy diagnosis, using a combination of metadata and patient information. The most important clinical signs for leprosy were thermal sensitivity loss, nodules and papules, feet paresthesia, number of lesions and gender.
  • Implications: The AI model could be a useful tool to accelerate and improve leprosy diagnosis, especially in low-resource settings. The researchers plan to validate the model in larger and more diverse datasets, and to implement it in a smartphone app for frontline health workers.

Beyond building predictive models: TwinOps in biomanufacturing

Beyond building predictive models: TwinOps in biomanufacturing

On the wave of more and more manufacturers embracing the pervasive mission to build digital twins, also biopharmaceutical industry envisions a significant paradigm shift of digitalisation towards an intelligent factory where bioprocesses continuously learn from data to optimise and control productivity. While extensive efforts are made to build and combine the best mechanistic and data-driven models, there has not been a complete digital twin application in pharma. One of the main reasons is that production deployment becomes more complex regarding the possible impact such digital technologies could have on vaccine products and ultimately on patients. To address current technical challenges and fill regulatory gaps, this paper explores some best practices for TwinOps in biomanufacturing – from experiment to GxP validation – and discusses approaches to oversight and compliance that could work with these best practices towards building bioprocess digital twins at scale.

Please read our whole pre-print here: https://doi.org/10.36227/techrxiv.16478856.v1

Senior AI/ML engineer in Bengaluru, India at GSK

Senior AI/ML engineer in Bengaluru, India at GSK

I’m hiring a Senior AI/ML engineer in Bengaluru, India. You will work with the rest of our international team on delivering cutting edge AI/ML solutions to support our vaccines business. This is a great role to grow into a lead data scientist as well as developing your machine learning and modern DevOps skills.

https://gsk.wd5.myworkdayjobs.com/GSKCareers/job/India—Karnataka—Bengaluru/Senior-AIML-Engineer_272917

My next career step: GSK Vaccines

My next career step: GSK Vaccines

Weird day, after nearly 5yrs years at Microsoft I’ve handed in my badge and laptop. Very much excited about my next step that is even deeper into healthcare, but also sad leaving such a great company with amazing people behind. 

I cannot be more proud to join GSK as their new director of Analytics and AI. Their mantra feels like a homecoming: “We are a science-led global healthcare company with a special purpose: to help people do more, feel better, live longer.”

The economic case for clinical genomics

The economic case for clinical genomics

A great systematic review by Schwarze et.al. in Genetics in Medicine on the cost benefits of Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) in the clinical settings.

Main findings that interested me:

  • Doing molecular testing (using single-gene, panel testing, or microarrays) for genetic disorders only results in 50% molecular diagnosis. Many patients will still be going on extensive diagnostic testing to diagnose patients that is both slow and expensive.
  • Although the raw costs of sequencing are dropping in the clinical genetics setting the costs of both WGS and WES are stable and don’t decrease.
  • Diagnostic yield between WES and WGS varies a-lot. With for WES ranging 3 ~ 79% and for WGS 17 ~ 73%. Authors do note that in many of these cases in these studies the patients were hard to diagnose traditionally.