Daniele Malpetti

Daniele Malpetti, Christian Berchtold, Francesco Gualdi et al.

In transcriptomics, gene-set-aware factorization methods such as the Pathway Level Information Extractor (PLIER) are most effective when trained on large, heterogeneous expression compendia. Yet, many clinically relevant cohorts cannot be pooled into a single dataset due to privacy and governance constraints. We present FPLIER, a federated extension of PLIER that enables distributed training across multiple data holders while incorporating publicly available datasets. Through secure aggregation, FPLIER produces training updates algebraically equivalent to those of a centralized pooled-data approach while keeping expression data local. We evaluate FPLIER across multiple scenarios in two simulated consortia (from the K-CLIER and MultiPLIER studies) and demonstrate stable convergence. We further conduct a systematic analysis of membership inference attacks targeting both intermediate training statistics and the released model. Our results show that privacy risk is governed by the rank of the training expression matrix. Incorporating public data or reducing data dimensionality increases this rank, moving the system toward a full-rank regime in which training and non-training samples become indistinguishable to the attacker, and membership-inference performance approaches random guessing.

Daniele Malpetti, Laura Azzimonti

We present a novel strategy for detecting global outliers in a federated learning setting, targeting in particular cross-silo scenarios. Our approach involves the use of two servers and the transmission of masked local data from clients to one of the servers. The masking of the data prevents the disclosure of sensitive information while still permitting the identification of outliers. Moreover, to further safeguard privacy, a permutation mechanism is implemented so that the server does not know which client owns any masked data point. The server performs outlier detection on the masked data, using either Isolation Forest or its extended version, and then communicates outlier information back to the clients, allowing them to identify and remove outliers in their local datasets before starting any subsequent federated model training. This approach provides comparable results to a centralized execution of Isolation Forest algorithms on plain data.

Claudio Bonesana, Daniele Malpetti, Sandra Mitrović et al.

We present Flotta, a Federated Learning framework designed to train machine learning models on sensitive data distributed across a multi-party consortium conducting research in contexts requiring high levels of security, such as the biomedical field. Flotta is a Python package, inspired in several aspects by Apache Spark, which provides both flexibility and security and allows conducting research using solely machines internal to the consortium. In this paper, we describe the main components of the framework together with a practical use case to illustrate the framework's capabilities and highlight its security, flexibility and user-friendliness.