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2023
Journal article
Open Access
Raman spectroscopy and topological machine learning for cancer grading
Conti F., D'Acunto M., Caudai C., Colantonio C., Gaeta R., Moroni D., Pascali M. A.
In the last decade, Raman Spectroscopy is establishing itself as a highly promising technique for the classification of tumour tissues as it allows to obtain the biochemical maps of the tissues under investigation, making it possible to observe changes among different tissues in terms of biochemical constituents (proteins, lipid structures, DNA, vitamins, and so on). In this paper, we aim to show that techniques emerging from the cross-fertilization of persistent homology and machine learning can support the classification of Raman spectra extracted from cancerous tissues for tumour grading. In more detail, topological features of Raman spectra and machine learning classifiers are trained in combination as an automatic classification pipeline in order to select the best-performing pair. The case study is the grading of chondrosarcoma in four classes: cross and leave-one-patient-out validations have been used to assess the classification accuracy of the method. The binary classification achieves a validation accuracy of 81% and a test accuracy of 90%. Moreover, the test dataset has been collected at a different time and with different equipment. Such results are achieved by a support vector classifier trained with the Betti Curve representation of the topological features extracted from the Raman spectra, and are excellent compared with the existing literature. The added value of such results is that the model for the prediction of the chondrosarcoma grading could easily be implemented in clinical practice, possibly integrated into the acquisition system.Source: Scientific reports (Nature Publishing Group) 13 (2023). doi:10.1038/s41598-023-34457-5
DOI: 10.1038/s41598-023-34457-5
Metrics:
Conti F., D'Acunto M., Caudai C., Colantonio C., Gaeta R., Moroni D., Pascali M. A.
In the last decade, Raman Spectroscopy is establishing itself as a highly promising technique for the classification of tumour tissues as it allows to obtain the biochemical maps of the tissues under investigation, making it possible to observe changes among different tissues in terms of biochemical constituents (proteins, lipid structures, DNA, vitamins, and so on). In this paper, we aim to show that techniques emerging from the cross-fertilization of persistent homology and machine learning can support the classification of Raman spectra extracted from cancerous tissues for tumour grading. In more detail, topological features of Raman spectra and machine learning classifiers are trained in combination as an automatic classification pipeline in order to select the best-performing pair. The case study is the grading of chondrosarcoma in four classes: cross and leave-one-patient-out validations have been used to assess the classification accuracy of the method. The binary classification achieves a validation accuracy of 81% and a test accuracy of 90%. Moreover, the test dataset has been collected at a different time and with different equipment. Such results are achieved by a support vector classifier trained with the Betti Curve representation of the topological features extracted from the Raman spectra, and are excellent compared with the existing literature. The added value of such results is that the model for the prediction of the chondrosarcoma grading could easily be implemented in clinical practice, possibly integrated into the acquisition system.Source: Scientific reports (Nature Publishing Group) 13 (2023). doi:10.1038/s41598-023-34457-5
DOI: 10.1038/s41598-023-34457-5
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ISTI Repository 
| www.nature.com | CNR ExploRA
2023
Conference article
Open Access
Analysis of sea surface temperature maps via topological machine learning
Conti F., Papini O., Moroni D., Pieri G., Reggiannini M., Pascali M. A.
Computational methods to leverage topological features occurring in signals and images are currently one of the most innovative trends in applied mathematics. In this paper a pipeline of topological machine learning is applied to the challenging task of classifying four specific marine mesoscale patterns from remote sensing data, i.e., Sea Surface Temperature maps of the southwestern region of the Iberian Peninsula. Our preliminary study achieves an accuracy of 56% in the 4-label classification. Such results are encouraging, especially considering that the data are affected by noise and that there are low-quality/missing data. Also, the paper devises directions for future improvements.Source: ITNT 2023 - IX International Conference on Information Technology and Nanotechnology, Samara, Russia, 17-21/04/2023
DOI: 10.1109/itnt57377.2023.10139044
Project(s): NAUTILOS
Metrics:
Conti F., Papini O., Moroni D., Pieri G., Reggiannini M., Pascali M. A.
Computational methods to leverage topological features occurring in signals and images are currently one of the most innovative trends in applied mathematics. In this paper a pipeline of topological machine learning is applied to the challenging task of classifying four specific marine mesoscale patterns from remote sensing data, i.e., Sea Surface Temperature maps of the southwestern region of the Iberian Peninsula. Our preliminary study achieves an accuracy of 56% in the 4-label classification. Such results are encouraging, especially considering that the data are affected by noise and that there are low-quality/missing data. Also, the paper devises directions for future improvements.Source: ITNT 2023 - IX International Conference on Information Technology and Nanotechnology, Samara, Russia, 17-21/04/2023
DOI: 10.1109/itnt57377.2023.10139044
Project(s): NAUTILOS
Metrics:
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ISTI Repository | ieeexplore.ieee.org 
| CNR ExploRA
2023
Report
Open Access
Alzheimer disease detection from Raman spectroscopy of the cerebrospinal fluid via topological machine learning
Conti F., Banchelli M., Bessi V., Cecchi C., Chiti F., Colantonio S., D'Andrea C., De Angelis M., Moroni D., Nacmias B., Pascali M. A., Sorbi S., Matteini P.
The cerebrospinal fluid (CSF) of 19 subjects who received a clinical diagnosis of Alzheimer's disease (AD) as well as of 5 pathological controls have been collected and analysed by Raman spectroscopy (RS). We investigated whether the raw and preprocessed Raman spectra could be used to distinguish AD from controls. First, we applied standard Machine Learning (ML) methods obtaining unsatisfactory results. Then, we applied ML to a set of topological descriptors extracted from raw spectra, achieving a very good classification accuracy (> 87%). Although our results are preliminary, they indicate that RS and topological analysis together may provide an effective combination to confirm or disprove a clinical diagnosis of AD. The next steps will include enlarging the dataset of CSF samples to validate the proposed method better and, possibly, to understand if topological data analysis could support the characterization of AD subtypes.Source: ISTI Working paper, 2309.03664, pp.1–7, 2023
Conti F., Banchelli M., Bessi V., Cecchi C., Chiti F., Colantonio S., D'Andrea C., De Angelis M., Moroni D., Nacmias B., Pascali M. A., Sorbi S., Matteini P.
The cerebrospinal fluid (CSF) of 19 subjects who received a clinical diagnosis of Alzheimer's disease (AD) as well as of 5 pathological controls have been collected and analysed by Raman spectroscopy (RS). We investigated whether the raw and preprocessed Raman spectra could be used to distinguish AD from controls. First, we applied standard Machine Learning (ML) methods obtaining unsatisfactory results. Then, we applied ML to a set of topological descriptors extracted from raw spectra, achieving a very good classification accuracy (> 87%). Although our results are preliminary, they indicate that RS and topological analysis together may provide an effective combination to confirm or disprove a clinical diagnosis of AD. The next steps will include enlarging the dataset of CSF samples to validate the proposed method better and, possibly, to understand if topological data analysis could support the characterization of AD subtypes.Source: ISTI Working paper, 2309.03664, pp.1–7, 2023
See at:
arxiv.org | CNR ExploRA
2023
Journal article
Open Access
Alzheimer disease detection from Raman spectroscopy of the cerebrospinal fluid via topological machine learning
Conti F., Banchelli M., Bessi V., Cecchi C., Chiti F., Colantonio S., D'Andrea C., De Angelis M., Moroni D., Nacmias B., Pascali M. A., Sorbi S., Matteini P.
The cerebrospinal fluid (CSF) of 19 subjects who received a clinical diagnosis of Alzheimer's disease (AD) as well as of 5 pathological controls was collected and analyzed by Raman spectroscopy (RS). We investigated whether the raw and preprocessed Raman spectra could be used to distinguish AD from controls. First, we applied standard Machine Learning (ML) methods obtaining unsatisfactory results. Then, we applied ML to a set of topological descriptors extracted from raw spectra, achieving a very good classification accuracy (>87%). Although our results are preliminary, they indicate that RS and topological analysis may provide an effective combination to confirm or disprove a clinical diagnosis of AD. The next steps include enlarging the dataset of CSF samples to validate the proposed method better and, possibly, to investigate whether topological data analysis could support the characterization of AD subtypes.Source: Engineering proceedings (Basel) 51 (2023). doi:10.3390/engproc2023051014
DOI: 10.3390/engproc2023051014
Metrics:
Conti F., Banchelli M., Bessi V., Cecchi C., Chiti F., Colantonio S., D'Andrea C., De Angelis M., Moroni D., Nacmias B., Pascali M. A., Sorbi S., Matteini P.
The cerebrospinal fluid (CSF) of 19 subjects who received a clinical diagnosis of Alzheimer's disease (AD) as well as of 5 pathological controls was collected and analyzed by Raman spectroscopy (RS). We investigated whether the raw and preprocessed Raman spectra could be used to distinguish AD from controls. First, we applied standard Machine Learning (ML) methods obtaining unsatisfactory results. Then, we applied ML to a set of topological descriptors extracted from raw spectra, achieving a very good classification accuracy (>87%). Although our results are preliminary, they indicate that RS and topological analysis may provide an effective combination to confirm or disprove a clinical diagnosis of AD. The next steps include enlarging the dataset of CSF samples to validate the proposed method better and, possibly, to investigate whether topological data analysis could support the characterization of AD subtypes.Source: Engineering proceedings (Basel) 51 (2023). doi:10.3390/engproc2023051014
DOI: 10.3390/engproc2023051014
Metrics:
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www.mdpi.com | CNR ExploRA
2022
Contribution to conference
Open Access
A topological pipeline for machine learning
Conti F.
The development of a topological pipeline for machine learning involves two crucial steps that strongly influence the performance of the pipeline. The first step is the choice of the filtration that associates a persistence diagram with digital data. The second step is the choice of the representation method for the persistence diagrams, which often relies on several parameters. In this work we develop a pipeline that associates persistence diagrams to digital data, via the most appropriate filtration for the type of data considered. Using a grid search approach, this pipeline determines optimal representation methods and parameters. We assess the performance of our pipeline, and in parallel we compare the different representation methods, on popular benchmark datasets. This work is a first step towards both an easy, ready to use, pipeline for data classification using persistent homology and machine learning, and to understand the theoretical reasons why, given a dataset and a task to be performed, a pair (filtration, topological representation) is better than another.Source: Bridging applied and quantitative topology, Online conference, 09-13/05/2022
Conti F.
The development of a topological pipeline for machine learning involves two crucial steps that strongly influence the performance of the pipeline. The first step is the choice of the filtration that associates a persistence diagram with digital data. The second step is the choice of the representation method for the persistence diagrams, which often relies on several parameters. In this work we develop a pipeline that associates persistence diagrams to digital data, via the most appropriate filtration for the type of data considered. Using a grid search approach, this pipeline determines optimal representation methods and parameters. We assess the performance of our pipeline, and in parallel we compare the different representation methods, on popular benchmark datasets. This work is a first step towards both an easy, ready to use, pipeline for data classification using persistent homology and machine learning, and to understand the theoretical reasons why, given a dataset and a task to be performed, a pair (filtration, topological representation) is better than another.Source: Bridging applied and quantitative topology, Online conference, 09-13/05/2022
See at:
ISTI Repository | sites.google.com | CNR ExploRA
2022
Journal article
Open Access
On the construction of group equivariant non-expansive operators via permutants and symmetric functions
Conti F., Frosini P., Quercioli N.
Group Equivariant Operators (GEOs) are a fundamental tool in the research on neural networks, since they make available a new kind of geometric knowledge engineering for deep learning, which can exploit symmetries in artificial intelligence and reduce the number of parameters required in the learning process. In this paper we introduce a new method to build non-linear GEOs and non-linear Group Equivariant Non-Expansive Operators (GENEOs), based on the concepts of symmetric function and permutant. This method is particularly interesting because of the good theoretical properties of GENEOs and the ease of use of permutants to build equivariant operators, compared to the direct use of the equivariance groups we are interested in. In our paper, we prove that the technique we propose works for any symmetric function, and benefits from the approximability of continuous symmetric functions by symmetric polynomials. A possible use in Topological Data Analysis of the GENEOs obtained by this new method is illustrated.Source: Frontiers in artificial intelligence 5 (2022). doi:10.3389/frai.2022.786091
DOI: 10.3389/frai.2022.786091
Metrics:
Conti F., Frosini P., Quercioli N.
Group Equivariant Operators (GEOs) are a fundamental tool in the research on neural networks, since they make available a new kind of geometric knowledge engineering for deep learning, which can exploit symmetries in artificial intelligence and reduce the number of parameters required in the learning process. In this paper we introduce a new method to build non-linear GEOs and non-linear Group Equivariant Non-Expansive Operators (GENEOs), based on the concepts of symmetric function and permutant. This method is particularly interesting because of the good theoretical properties of GENEOs and the ease of use of permutants to build equivariant operators, compared to the direct use of the equivariance groups we are interested in. In our paper, we prove that the technique we propose works for any symmetric function, and benefits from the approximability of continuous symmetric functions by symmetric polynomials. A possible use in Topological Data Analysis of the GENEOs obtained by this new method is illustrated.Source: Frontiers in artificial intelligence 5 (2022). doi:10.3389/frai.2022.786091
DOI: 10.3389/frai.2022.786091
Metrics:
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ISTI Repository | www.frontiersin.org | CNR ExploRA
2022
Journal article
Open Access
A topological machine learning pipeline for classification
Conti F., Moroni D., Pascali M. A.
In this work, we develop a pipeline that associates Persistence Diagrams to digital data via the most appropriate filtration for the type of data considered. Using a grid search approach, this pipeline determines optimal representation methods and parameters. The development of such a topological pipeline for Machine Learning involves two crucial steps that strongly affect its performance: firstly, digital data must be represented as an algebraic object with a proper associated filtration in order to compute its topological summary, the Persistence Diagram. Secondly, the persistence diagram must be transformed with suitable representation methods in order to be introduced in a Machine Learning algorithm. We assess the performance of our pipeline, and in parallel, we compare the different representation methods on popular benchmark datasets. This work is a first step toward both an easy and ready-to-use pipeline for data classification using persistent homology and Machine Learning, and to understand the theoretical reasons why, given a dataset and a task to be performed, a pair (filtration, topological representation) is better than another.Source: Mathematics 10 (2022). doi:10.3390/math10173086
DOI: 10.3390/math10173086
Metrics:
Conti F., Moroni D., Pascali M. A.
In this work, we develop a pipeline that associates Persistence Diagrams to digital data via the most appropriate filtration for the type of data considered. Using a grid search approach, this pipeline determines optimal representation methods and parameters. The development of such a topological pipeline for Machine Learning involves two crucial steps that strongly affect its performance: firstly, digital data must be represented as an algebraic object with a proper associated filtration in order to compute its topological summary, the Persistence Diagram. Secondly, the persistence diagram must be transformed with suitable representation methods in order to be introduced in a Machine Learning algorithm. We assess the performance of our pipeline, and in parallel, we compare the different representation methods on popular benchmark datasets. This work is a first step toward both an easy and ready-to-use pipeline for data classification using persistent homology and Machine Learning, and to understand the theoretical reasons why, given a dataset and a task to be performed, a pair (filtration, topological representation) is better than another.Source: Mathematics 10 (2022). doi:10.3390/math10173086
DOI: 10.3390/math10173086
Metrics:
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ISTI Repository | www.mdpi.com | CNR ExploRA
2022
Report
Open Access
SI-Lab annual research report 2021
Righi M., Leone G. R., Carboni A., Caudai C., Colantonio S., Kuruoglu E. E., Leporini B., Magrini M., Paradisi P., Pascali M. A., Pieri G., Reggiannini M., Salerno E., Scozzari A., Tonazzini A., Fusco G., Galesi G., Martinelli M., Pardini F., Tampucci M., Berti A., Bruno A., Buongiorno R., Carloni G., Conti F., Germanese D., Ignesti G., Matarese F., Omrani A., Pachetti E., Papini O., Benassi A., Bertini G., Coltelli P., Tarabella L., Straface S., Salvetti O., Moroni D.
The Signal & Images Laboratory is an interdisciplinary research group in computer vision, signal analysis, intelligent vision systems and multimedia data understanding. It is part of the Institute of Information Science and Technologies (ISTI) of the National Research Council of Italy (CNR). This report accounts for the research activities of the Signal and Images Laboratory of the Institute of Information Science and Technologies during the year 2021.Source: ISTI Annual reports, 2022
DOI: 10.32079/isti-ar-2022/003
Metrics:
Righi M., Leone G. R., Carboni A., Caudai C., Colantonio S., Kuruoglu E. E., Leporini B., Magrini M., Paradisi P., Pascali M. A., Pieri G., Reggiannini M., Salerno E., Scozzari A., Tonazzini A., Fusco G., Galesi G., Martinelli M., Pardini F., Tampucci M., Berti A., Bruno A., Buongiorno R., Carloni G., Conti F., Germanese D., Ignesti G., Matarese F., Omrani A., Pachetti E., Papini O., Benassi A., Bertini G., Coltelli P., Tarabella L., Straface S., Salvetti O., Moroni D.
The Signal & Images Laboratory is an interdisciplinary research group in computer vision, signal analysis, intelligent vision systems and multimedia data understanding. It is part of the Institute of Information Science and Technologies (ISTI) of the National Research Council of Italy (CNR). This report accounts for the research activities of the Signal and Images Laboratory of the Institute of Information Science and Technologies during the year 2021.Source: ISTI Annual reports, 2022
DOI: 10.32079/isti-ar-2022/003
Metrics:
See at:
ISTI Repository | CNR ExploRA