Mikko Saukkoriipi

Mikko Saukkoriipi, Nicole Hernandez, Jaakko Sahlsten et al.

Clinicians often need to retrieve patient-specific information from electronic health records (EHRs), a task that is time-consuming and error-prone. We present a locally deployable Clinical Contextual Question Answering (CCQA) framework that answers clinical questions directly from EHRs without external data transfer. Open-source large language models (LLMs) ranging from 4B to 70B parameters were benchmarked under fully offline conditions using 1,664 expert-annotated question-answer pairs derived from records of 183 patients. The dataset consisted predominantly of Finnish clinical text. In free-text generation, Llama-3.1-70B achieved 95.3% accuracy and 97.3% consistency across semantically equivalent question variants, while the smaller Qwen3-30B-A3B-2507 model achieved comparable performance. In a multiple-choice setting, models showed similar accuracy but variable calibration. Low-precision quantization (4-bit and 8-bit) preserved predictive performance while reducing GPU memory requirements and improving deployment feasibility. Clinical evaluation identified clinically significant errors in 2.9% of outputs, and semantically equivalent questions occasionally yielded discordant responses, including instances where one formulation was correct and the other contained a clinically significant error (0.96% of cases). These findings demonstrate that locally hosted open-source LLMs can accurately retrieve patient-specific information from EHRs using natural-language queries, while highlighting the need for validation and human oversight in clinical deployment.

Mikko Saukkoriipi, Jaakko Sahlsten, Joel Jaskari et al.

The main treatment modality for oropharyngeal cancer (OPC) is radiotherapy, where accurate segmentation of the primary gross tumor volume (GTVp) is essential. However, accurate GTVp segmentation is challenging due to significant interobserver variability and the time-consuming nature of manual annotation, while fully automated methods can occasionally fail. An interactive deep learning (DL) model offers the advantage of automatic high-performance segmentation with the flexibility for user correction when necessary. In this study, we examine interactive DL for GTVp segmentation in OPC. We implement state-of-the-art algorithms and propose a novel two-stage Interactive Click Refinement (2S-ICR) framework. Using the 2021 HEad and neCK TumOR (HECKTOR) dataset for development and an external dataset from The University of Texas MD Anderson Cancer Center for evaluation, the 2S-ICR framework achieves a Dice similarity coefficient of 0.713 $\pm$ 0.152 without user interaction and 0.824 $\pm$ 0.099 after five interactions, outperforming existing methods in both cases.

Joel Jaskari, Chandreyee Roy, Fumiko Ogushi et al.

Graph neural networks (GNNs) have emerged as a state-of-the-art data-driven tool for modeling connectivity data of graph-structured complex networks and integrating information of their nodes and edges in space and time. However, as of yet, the analysis of social networks using the time series of people's mobile connectivity data has not been extensively investigated. In the present study, we investigate four snapshot - based temporal GNNs in predicting the phone call and SMS activity between users of a mobile communication network. In addition, we develop a simple non - GNN baseline model using recently proposed EdgeBank method. Our analysis shows that the ROLAND temporal GNN outperforms the baseline model in most cases, whereas the other three GNNs perform on average worse than the baseline. The results show that GNN based approaches hold promise in the analysis of temporal social networks through mobile connectivity data. However, due to the relatively small performance margin between ROLAND and the baseline model, further research is required on specialized GNN architectures for temporal social network analysis.