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.

Ilenia Carboni, Elia Cereda, Lorenzo Lamberti et al.

Sub-30g nano-sized aerial robots can leverage their agility and form factor to autonomously explore cluttered and narrow environments, like in industrial inspection and search and rescue missions. However, the price for their tiny size is a strong limit in their resources, i.e., sub-100 mW microcontroller units (MCUs) delivering $\sim$100 GOps/s at best, and memory budgets well below 100 MB. Despite these strict constraints, we aim to enable complex vision-based tasks aboard nano-drones, such as dense 3D scene reconstruction: a key robotic task underlying fundamental capabilities like spatial awareness and motion planning. Top-performing 3D reconstruction methods leverage neural radiance fields (NeRF) models, which require GBs of memory and massive computation, usually delivered by high-end GPUs consuming 100s of Watts. Our work introduces Tiny-DroNeRF, a lightweight NeRF model, based on Instant-NGP, and optimized for running on a GAP9 ultra-low-power (ULP) MCU aboard our nano-drones. Then, we further empower our Tiny-DroNeRF by leveraging a collaborative federated learning scheme, which distributes the model training among multiple nano-drones. Our experimental results show a 96% reduction in Tiny-DroNeRF's memory footprint compared to Instant-NGP, with only a 5.7 dB drop in reconstruction accuracy. Finally, our federated learning scheme allows Tiny-DroNeRF to train with an amount of data otherwise impossible to keep in a single drone's memory, increasing the overall reconstruction accuracy. Ultimately, our work combines, for the first time, NeRF training on an ULP MCU with federated learning on nano-drones.

Daniele Malpetti, Marco Scutari, Francesco Gualdi et al.

Federated learning leverages data across institutions to improve clinical discovery while complying with data-sharing restrictions and protecting patient privacy. This paper provides a gentle introduction to this approach in bioinformatics, and is the first to review key applications in proteomics, genome-wide association studies (GWAS), single-cell and multi-omics studies in their legal as well as methodological and infrastructural challenges. As the evolution of biobanks in genetics and systems biology has proved, accessing more extensive and varied data pools leads to a faster and more robust exploration and translation of results. More widespread use of federated learning may have a similar impact in bioinformatics, allowing academic and clinical institutions to access many combinations of genotypic, phenotypic and environmental information that are undercovered or not included in existing biobanks.