Presentation
Machine learning (ML) is increasingly applied to a variety of biomedical fields with the aim of providing insight into complex patterns in the high-dimensional large-scale data. One such field is the study of Adaptive Immune Receptor Repertoires (AIRR), which records past and ongoing immune responses and might be used for diagnostic and therapeutic developments. However, the widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency and interoperability. The immuneML software platform addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem with standardized workflows.
To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. To demonstrate the applicability of the platform, we (1) reproduced a large-scale diagnostic study, (2) developed, integrated and applied a new deep learning method for immune receptor specificity prediction and (3) showcased a streamlined interpretability-focused benchmarking of AIRR ML.
Speaker
Milena Pavlovi? is a postdoctoral research fellow at the Department of Informatics working in machine learning, causal inference and their applications to biomedical domains. During her PhD, she developed the immuneML platform for machine learning analysis of adaptive immune receptor repertoires (AIRR), and examined how causal inference could improve generalization of biomarkers discovered by machine learning in the AIRR field.
Program
11:30 – Doors open and lunch is served
12:00 – "immuneML: Robust Workflows for Machine Learning Analyses in Biomedical Research" by Milena Pavlovic (Postdoctoral Fellow, Department of Informatics, UiO)
This event is open for all PhD candidates and postdocs. No registration needed.
About the seminar series
Once a month, dScience will invite you to join us for lunch, soft drinks and professional talks at the Science Library. In addition to these, we will serve lunch to PhD candidates in our lounge in Kristine Bonnevies hus every Thursday. Due to limited space (40 people), this will be first come, first served. See how to find us here (download).
Our lounge can also be booked by PhDs and Postdocs on a regular basis, whether it is for a meeting or just to hang out – we have fresh coffee all day long! Read more about the seminar series here.