Seppo Virtanen

Aisvarya Adeseye, Jouni Isoaho, Seppo Virtanen et al.

Qualitative research often contains personal, contextual, and organizational details that pose privacy risks if not handled appropriately. Manual anonymization is time-consuming, inconsistent, and frequently omits critical identifiers. Existing automated tools tend to rely on pattern matching or fixed rules, which fail to capture context and may alter the meaning of the data. This study uses local LLMs to build a reliable, repeatable, and context-aware anonymization process for detecting and anonymizing sensitive data in qualitative transcripts. We introduce a Structured Framework for Adaptive Anonymizer (SFAA) that includes three steps: detection, classification, and adaptive anonymization. The SFAA incorporates four anonymization strategies: rule-based substitution, context-aware rewriting, generalization, and suppression. These strategies are applied based on the identifier type and the risk level. The identifiers handled by the SFAA are guided by major international privacy and research ethics standards, including the GDPR, HIPAA, and OECD guidelines. This study followed a dual-method evaluation that combined manual and LLM-assisted processing. Two case studies were used to support the evaluation. The first includes 82 face-to-face interviews on gamification in organizations. The second involves 93 machine-led interviews using an AI-powered interviewer to test LLM awareness and workplace privacy. Two local models, LLaMA and Phi were used to evaluate the performance of the proposed framework. The results indicate that the LLMs found more sensitive data than a human reviewer. Phi outperformed LLaMA in finding sensitive data, but made slightly more errors. Phi was able to find over 91% of the sensitive data and 94.8% kept the same sentiment as the original text, which means it was very accurate, hence, it does not affect the analysis of the qualitative data.

Seppo Virtanen, Homayun Afrabandpey, Samuel Kaski

A main goal of data visualization is to find, from among all the available alternatives, mappings to the 2D/3D display which are relevant to the user. Assuming user interaction data, or other auxiliary data about the items or their relationships, the goal is to identify which aspects in the primary data support the userś input and, equally importantly, which aspects of the userś potentially noisy input have support in the primary data. For solving the problem, we introduce a multi-view embedding in which a latent factorization identifies which aspects in the two data views (primary data and user data) are related and which are specific to only one of them. The factorization is a generative model in which the display is parameterized as a part of the factorization and the other factors explain away the aspects not expressible in a two-dimensional display. Functioning of the model is demonstrated on several data sets.

Suleiman A Khan, Seppo Virtanen, Olli P Kallioniemi et al.

Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for integrated analyses of a large number of chemical features of drugs against the corresponding genome-wide responses of multiple cell models. Results: In this paper, we present the first comprehensive multi-set analysis on how the chemical structure of drugs impacts on ge-nome-wide gene expression across several cancer cell lines (CMap database). The task is formulated as searching for drug response components across multiple cancers to reveal shared effects of drugs and the chemical features that may be responsible. The com-ponents can be computed with an extension of a very recent ap-proach called Group Factor Analysis (GFA). We identify 11 compo-nents that link the structural descriptors of drugs with specific gene expression responses observed in the three cell lines, and identify structural groups that may be responsible for the responses. Our method quantitatively outperforms the limited earlier studies on CMap and identifies both the previously reported associations and several interesting novel findings, by taking into account multiple cell lines and advanced 3D structural descriptors. The novel observations include: previously unknown similarities in the effects induced by 15-delta prostaglandin J2 and HSP90 inhibitors, which are linked to the 3D descriptors of the drugs; and the induction by simvastatin of leukemia-specific anti-inflammatory response, resem-bling the effects of corticosteroids.

Seppo Virtanen, Yangqing Jia, Arto Klami et al.

Multi-modal data collections, such as corpora of paired images and text snippets, require analysis methods beyond single-view component and topic models. For continuous observations the current dominant approach is based on extensions of canonical correlation analysis, factorizing the variation into components shared by the different modalities and those private to each of them. For count data, multiple variants of topic models attempting to tie the modalities together have been presented. All of these, however, lack the ability to learn components private to one modality, and consequently will try to force dependencies even between minimally correlating modalities. In this work we combine the two approaches by presenting a novel HDP-based topic model that automatically learns both shared and private topics. The model is shown to be especially useful for querying the contents of one domain given samples of the other.

Arto Klami, Seppo Virtanen, Samuel Kaski

Exponential family extensions of principal component analysis (EPCA) have received a considerable amount of attention in recent years, demonstrating the growing need for basic modeling tools that do not assume the squared loss or Gaussian distribution. We extend the EPCA model toolbox by presenting the first exponential family multi-view learning methods of the partial least squares and canonical correlation analysis, based on a unified representation of EPCA as matrix factorization of the natural parameters of exponential family. The models are based on a new family of priors that are generally usable for all such factorizations. We also introduce new inference strategies, and demonstrate how the methods outperform earlier ones when the Gaussianity assumption does not hold.