Student: “Eirini Baltzi”
Program: “Data Science and Information Technologies”
Title: “Transformer-Based Modeling of Irregular Clinical Time Series: Bi-Axial Attention and Temporal Encoding”
Abstract:
In this work, we study transformer-based modeling of irregular clinical time series derived from Electronic Health Records, with particular focus on the Bi-Axial Transformer (BAT) architecture. Clinical prediction from EHR data remains challenging due to irregular sampling, sparse observations, informative missingness and the coexistence of dynamic and static patient information. Within this setting, our goal is to first, reproduce the BAT architecture and verify that the reconstructed implementation is consistent with the original pa- per and second, to investigate a modification of its temporal encoding mechanism through Rotary Positional Encoding (RoPE). The experimental evaluation is conducted on three clinical benchmarks: PhysioNet 2019 for sepsis prediction, PhysioNet 2012 for in-hospital mortality prediction, and MIMIC-III, where additional experiments are performed under a separate preprocessing pipeline. In addition to the reproduced BAT and the proposed BAT-RoPE variant, two baseline models are considered, namely GRU-D and a standard Transformer. The results show that BAT is a strong and competitive architecture across both datasets. The original BAT achieves the best AUPRC on PhysioNet 2019, while BAT-RoPE performs best on PhysioNet 2012. Additional attention and ablation analyses suggest that BAT captures structured temporal and inter-variable relationships and relies primarily on the dynamic clinical time series, while focal loss does not provide a consistent improvement.

Date-Time: 2/7/2026 – 11:00 AM
Examination Committee:
Associate Professor Aggelos Pikrakis, University of Piraeus
Dr. Kosmas Kritsis, ILSP/Athena Research Center
Dr. Vassilis Psomas, Czech Technical University, Prague

Msc Thesis Presentation
Thursday, July 2 · 11:00am – 12:00pm
Time zone: Europe/Athens
Webex joining info
Video call link: https://unipi.webex.com/meet/webex-host2