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Dipartimento di Ingegneria "Enzo Ferrari"

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2024 - Enhancing Patch-Based Learning for the Segmentation of the Mandibular Canal [Articolo su rivista]
Lumetti, Luca; Pipoli, Vittorio; Bolelli, Federico; Ficarra, Elisa; Grana, Costantino

Segmentation of the Inferior Alveolar Canal (IAC) is a critical aspect of dentistry and maxillofacial imaging, garnering considerable attention in recent research endeavors. Deep learning techniques have shown promising results in this domain, yet their efficacy is still significantly hindered by the limited availability of 3D maxillofacial datasets. An inherent challenge is posed by the size of input volumes, which necessitates a patch-based processing approach that compromises the neural network performance due to the absence of global contextual information. This study introduces a novel approach that harnesses the spatial information within the extracted patches and incorporates it into a Transformer architecture, thereby enhancing the segmentation process through the use of prior knowledge about the patch location. Our method significantly improves the Dice score by a factor of 4 points, with respect to the previous work proposed by Cipriano et al., while also reducing the training steps required by the entire pipeline. By integrating spatial information and leveraging the power of Transformer architectures, this research not only advances the accuracy of IAC segmentation, but also streamlines the training process, offering a promising direction for improving dental and maxillofacial image analysis.

2024 - High-level Biomedical Data Integration in a Semantic Knowledge Graph with OncodashKB for finding Personalized Actionable Drugs in Ovarian Cancer [Abstract in Atti di Convegno]
Dreo, Johann; Lobentanzer, Sebastian; Gaydukova, Ekaterina; Baric, Marko; Maarala, Ilari; Muranen, Taru; Oikkonen, Jaana; Bolelli, Federico; Pipoli, Vittorio; Isoviita, Veli-Matti; Hynninen, Johanna; Schwikowski, Benno

Background: The growing amount of biomedical knowledge about cancer in combination with genome-scale patient profiling data offers unprecedented opportunities for personalized oncology. However, the large amounts of knowledge and data require scalable approaches to providing actionable information to support clinicians in decision-making [1]. Objective: To develop software and methods that integrate all relevant clinical and genomic data about patients and that enable the discovery of optimal personalized treatment options, together with the supporting literature knowledge and data. Methods: We exploit a Semantic Knowledge Graph (SKG), a type of database that represents medical data in the form of objects and relationships, linking previously unconnected information across several cancer databases. To build up this SKG (OncodashKB), we use the BioCypher library [2]. We then integrate clinical data from patients with high-grade serous ovarian cancer, including information on genome changes collected as part of the DECIDER project ( The SKG can then be queried to gather evidence paths linking patient-specific alterations to actionable drugs. Results: Our approach provides a fully automated, systematic, and reproducible data integration workflow, along with the use of existing expert-made ontologies to provide interoperability and semantic descriptions. The integrated data is assessed by experts on molecular tumor boards and allows for the exploration of relevant clinical and genomic patient data in a visually accessible format, designed for ease of interpretation by clinicians. Importantly, we expect the system to reveal unexpected evidence paths between patient sequencing data and optimal treatment options based on biomedical knowledge described in the literature and confirmed by high-level evidence. Conclusion: Decision support systems using graph databases emerge as valuable tools by revealing new connections between various patient data and treatment options shown in an easy-to-understand format. References: [1] Reisle, C., Williamson, L.M., Pleasance, E. et al. A platform for oncogenomic reporting and interpretation. Nat Commun 13, 756 (2022). [2] Lobentanzer, S., Aloy, P., Baumbach, J. et al. Democratizing knowledge representation with BioCypher. Nat Biotechnol 41, 1056–1059 (2023).

2023 - Annotating the Inferior Alveolar Canal: the Ultimate Tool [Relazione in Atti di Convegno]
Lumetti, Luca; Pipoli, Vittorio; Bolelli, Federico; Grana, Costantino

The Inferior Alveolar Nerve (IAN) is of main interest in the maxillofacial field, as an accurate localization of such nerve reduces the risks of injury during surgical procedures. Although recent literature has focused on developing novel deep learning techniques to produce accurate segmentation masks of the canal containing the IAN, there are still strong limitations due to the scarce amount of publicly available 3D maxillofacial datasets. In this paper, we present an improved version of a previously released tool, IACAT (Inferior Alveolar Canal Annotation Tool), today used by medical experts to produce 3D ground truth annotation. In addition, we release a new dataset, ToothFairy, which is part of the homonymous MICCAI2023 challenge hosted by the Grand-Challenge platform, as an extension of the previously released Maxillo dataset, which was the only publicly available. With ToothFairy, the number of annotations has been increased as well as the quality of existing data.

2022 - Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers [Articolo su rivista]
Pipoli, Vittorio; Cappelli, Mattia; Palladini, Alessandro; Peluso, Carlo; Lovino, Marta; Ficarra, Elisa

Background and objectives: In the latest years, the prediction of gene expression levels has been crucial due to its potential applications in the clinics. In this context, Xpresso and others methods based on Convolutional Neural Networks and Transformers were firstly proposed to this aim. However, all these methods embed data with a standard one-hot encoding algorithm, resulting in impressively sparse matrices. In addition, post-transcriptional regulation processes, which are of uttermost importance in the gene expression process, are not considered in the model.Methods: This paper presents Transformer DeepLncLoc, a novel method to predict the abundance of the mRNA (i.e., gene expression levels) by processing gene promoter sequences, managing the problem as a regression task. The model exploits a transformer-based architecture, introducing the DeepLncLoc method to perform the data embedding. Since DeepLncloc is based on word2vec algorithm, it avoids the sparse matrices problem.Results: Post-transcriptional information related to mRNA stability and transcription factors is included in the model, leading to significantly improved performances compared to the state-of-the-art works. Transformer DeepLncLoc reached 0.76 of R-2 evaluation metric compared to 0.74 of Xpresso.Conclusion: The Multi-Headed Attention mechanisms which characterizes the transformer methodology is suitable for modeling the interactions between DNA's locations, overcoming the recurrent models. Finally, the integration of the transcription factors data in the pipeline leads to impressive gains in predictive power. (C) 2022 Elsevier B.V. All rights reserved.