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  1. Book ; Online: Streamlining models with explanations in the learning loop

    Lomuscio, Francesco / Bajardi, Paolo / Perotti, Alan / Amparore, Elvio G.

    2023  

    Abstract: Several explainable AI methods allow a Machine Learning user to get insights on the classification process of a black-box model in the form of local linear explanations. With such information, the user can judge which features are locally relevant for ... ...

    Abstract Several explainable AI methods allow a Machine Learning user to get insights on the classification process of a black-box model in the form of local linear explanations. With such information, the user can judge which features are locally relevant for the classification outcome, and get an understanding of how the model reasons. Standard supervised learning processes are purely driven by the original features and target labels, without any feedback loop informed by the local relevance of the features identified by the post-hoc explanations. In this paper, we exploit this newly obtained information to design a feature engineering phase, where we combine explanations with feature values. To do so, we develop two different strategies, named Iterative Dataset Weighting and Targeted Replacement Values, which generate streamlined models that better mimic the explanation process presented to the user. We show how these streamlined models compare to the original black-box classifiers, in terms of accuracy and compactness of the newly produced explanations.

    Comment: 16 pages, 10 figures, available repository
    Keywords Computer Science - Machine Learning ; 68T05 ; I.2.6
    Subject code 006
    Publishing date 2023-02-15
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: GRAPHSHAP

    Perotti, Alan / Bajardi, Paolo / Bonchi, Francesco / Panisson, André

    Explaining Identity-Aware Graph Classifiers Through the Language of Motifs

    2022  

    Abstract: Most methods for explaining black-box classifiers (e.g. on tabular data, images, or time series) rely on measuring the impact that removing/perturbing features has on the model output. This forces the explanation language to match the classifier's ... ...

    Abstract Most methods for explaining black-box classifiers (e.g. on tabular data, images, or time series) rely on measuring the impact that removing/perturbing features has on the model output. This forces the explanation language to match the classifier's feature space. However, when dealing with graph data, in which the basic features correspond to the edges describing the graph structure, this matching between features space and explanation language might not be appropriate. Decoupling the feature space (edges) from a desired high-level explanation language (such as motifs) is thus a major challenge towards developing actionable explanations for graph classification tasks. In this paper we introduce GRAPHSHAP, a Shapley-based approach able to provide motif-based explanations for identity-aware graph classifiers, assuming no knowledge whatsoever about the model or its training data: the only requirement is that the classifier can be queried as a black-box at will. For the sake of computational efficiency we explore a progressive approximation strategy and show how a simple kernel can efficiently approximate explanation scores, thus allowing GRAPHSHAP to scale on scenarios with a large explanation space (i.e. large number of motifs). We showcase GRAPHSHAP on a real-world brain-network dataset consisting of patients affected by Autism Spectrum Disorder and a control group. Our experiments highlight how the classification provided by a black-box model can be effectively explained by few connectomics patterns.

    Comment: Accepted by International Joint Conference on Neural Networks 2023 (IJCNN)
    Keywords Computer Science - Machine Learning ; Computer Science - Artificial Intelligence
    Subject code 004
    Publishing date 2022-02-17
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Multiscale Non-stationary Causal Structure Learning from Time Series Data

    D'Acunto, Gabriele / Morales, Gianmarco De Francisci / Bajardi, Paolo / Bonchi, Francesco

    2022  

    Abstract: This paper introduces a new type of causal structure, namely multiscale non-stationary directed acyclic graph (MN-DAG), that generalizes DAGs to the time-frequency domain. Our contribution is twofold. First, by leveraging results from spectral and ... ...

    Abstract This paper introduces a new type of causal structure, namely multiscale non-stationary directed acyclic graph (MN-DAG), that generalizes DAGs to the time-frequency domain. Our contribution is twofold. First, by leveraging results from spectral and causality theories, we expose a novel probabilistic generative model, which allows to sample an MN-DAG according to user-specified priors concerning the time-dependence and multiscale properties of the causal graph. Second, we devise a Bayesian method for the estimation of MN-DAGs, by means of stochastic variational inference (SVI), called Multiscale Non-Stationary Causal Structure Learner (MN-CASTLE). In addition to direct observations, MN-CASTLE exploits information from the decomposition of the total power spectrum of time series over different time resolutions. In our experiments, we first use the proposed model to generate synthetic data according to a latent MN-DAG, showing that the data generated reproduces well-known features of time series in different domains. Then we compare our learning method MN-CASTLE against baseline models on synthetic data generated with different multiscale and non-stationary settings, confirming the good performance of MN-CASTLE. Finally, we show some insights derived from the application of MN-CASTLE to study the causal structure of 7 global equity markets during the Covid-19 pandemic.
    Keywords Computer Science - Machine Learning ; Statistics - Methodology ; Statistics - Machine Learning
    Subject code 006
    Publishing date 2022-08-31
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: DNA Mutations via Chern-Simons Currents.

    Bajardi, Francesco / Altucci, Lucia / Benedetti, Rosaria / Capozziello, Salvatore / Sorbo, Maria Rosaria Del / Franci, Gianluigi / Altucci, Carlo

    European physical journal plus

    2021  Volume 136, Issue 10, Page(s) 1080

    Abstract: We test the validity of a possible schematization of DNA structure and dynamics based on the Chern-Simons theory, that is a topological field theory mostly considered in the context of effective gravity theories. By means of the expectation value of the ... ...

    Abstract We test the validity of a possible schematization of DNA structure and dynamics based on the Chern-Simons theory, that is a topological field theory mostly considered in the context of effective gravity theories. By means of the expectation value of the Wilson Loop, derived from this analogue gravity approach, we find the point-like curvature of genomic strings in KRAS human gene and COVID-19 sequences, correlating this curvature with the genetic mutations. The point-like curvature profile, obtained by means of the Chern-Simons currents, can be used to infer the position of the given mutations within the genetic string. Generally, mutations take place in the highest Chern-Simons current gradient locations and subsequent mutated sequences appear to have a smoother curvature than the initial ones, in agreement with a free energy minimization argument.
    Language English
    Publishing date 2021-10-28
    Publishing country Germany
    Document type Journal Article
    ISSN 2190-5444
    ISSN (online) 2190-5444
    DOI 10.1140/epjp/s13360-021-01960-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Exploring the Photodynamic Properties of Two Antiproliferative Benzodiazopyrrole Derivatives.

    Imperatore, Concetta / Valadan, Mohammadhassan / Tartaglione, Luciana / Persico, Marco / Ramunno, Anna / Menna, Marialuisa / Casertano, Marcello / Dell'Aversano, Carmela / Singh, Manjot / d'Aulisio Garigliota, Maria Luisa / Bajardi, Francesco / Morelli, Elena / Fattorusso, Caterina / Altucci, Carlo / Varra, Michela

    International journal of molecular sciences

    2020  Volume 21, Issue 4

    Abstract: The identification of molecules whose biological activity can be properly modulated by light is a promising therapeutic approach aimed to improve drug selectivity and efficacy on the molecular target and to limit the side effects compared to traditional ... ...

    Abstract The identification of molecules whose biological activity can be properly modulated by light is a promising therapeutic approach aimed to improve drug selectivity and efficacy on the molecular target and to limit the side effects compared to traditional drugs. Recently, two photo-switchable diastereomeric benzodiazopyrrole derivatives
    MeSH term(s) Cell Proliferation/drug effects ; Chromatography, Liquid ; Colorectal Neoplasms/pathology ; Colorectal Neoplasms/therapy ; Diazonium Compounds/chemistry ; Diazonium Compounds/pharmacology ; HCT116 Cells ; Humans ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Photochemotherapy ; Pyrroles/chemistry ; Pyrroles/pharmacology
    Chemical Substances Diazonium Compounds ; Pyrroles
    Language English
    Publishing date 2020-02-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms21041246
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Combating Actions of Green 2D-Materials on Gram Positive and Negative Bacteria and Enveloped Viruses.

    Singh, Manjot / Zannella, Carla / Folliero, Veronica / Di Girolamo, Rocco / Bajardi, Francesco / Chianese, Annalisa / Altucci, Lucia / Damasco, Achille / Del Sorbo, Maria Rosaria / Imperatore, Concetta / Rossi, Manuela / Valadan, Mohammadhassan / Varra, Michela / Vergara, Alessandro / Franci, Guanluigi / Galdiero, Massimiliano / Altucci, Carlo

    Frontiers in bioengineering and biotechnology

    2020  Volume 8, Page(s) 569967

    Abstract: Interactions of novel bi-dimensional nanomaterials and live matter such as bacteria and viruses represent an extremely hot topic due to the unique properties of the innovative nanomaterials, capable in some cases to exhibit bactericide and antiviral ... ...

    Abstract Interactions of novel bi-dimensional nanomaterials and live matter such as bacteria and viruses represent an extremely hot topic due to the unique properties of the innovative nanomaterials, capable in some cases to exhibit bactericide and antiviral actions. The interactions between bacteria and viruses and two dimensional nanosheets are here investigated. We extensively studied the interaction between a gram-negative bacterium,
    Language English
    Publishing date 2020-09-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2719493-0
    ISSN 2296-4185
    ISSN 2296-4185
    DOI 10.3389/fbioe.2020.569967
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Position Paper on Young Vascular Surgeons Training of the Mediterranean Federation for the Advancing of Vascular Surgery (MeFAVS): State of the Art and Perspectives.

    Bracale, Umberto Marcello / Ammollo, Raffaele Pio / Hussein, Emad A / Hoballah, Jamal J / Taurino, Maurizio / Saleem, Ben R / Setacci, Carlo / Pecoraro, Felice / Serra, Raffaele / Bracale, Giancarlo / Panagrosso, Marco / Peluso, Antonio / Petrone, Anna / Maisto, Marianna / Del Guercio, Luca / Dinoto, Ettore / Bajardi, Guido / Bouayed, Mohamed N / Zeebregts, Clark J /
    Pulli, Raffaele / Pane, Bianca / Pratesi, Giovanni / Castelli, Patrizio / Setacci, Francesco / Gargiulo, Mauro / Stella, Andrea / Illario, Maddalena / De Luca, Vincenzo / Verhoeven, Eric L G / Riambau, Vincent / Saratzis, Nikolaos / Cvjetko, Ivan / Resch, Timothy / Fernandes E Fernandes, José / Chiche, Laurent / Goeau-Brissonniere, Olivier

    Annals of vascular surgery

    2021  Volume 77, Page(s) e7–e13

    Abstract: The Mediterranean Federation for the Advancing of Vascular Surgery (MeFAVS) was founded in 2018, with the aim to promote cooperation among vascular professionals within Mediterranean countries. Due to its prominent social and economic impact on national ... ...

    Abstract The Mediterranean Federation for the Advancing of Vascular Surgery (MeFAVS) was founded in 2018, with the aim to promote cooperation among vascular professionals within Mediterranean countries. Due to its prominent social and economic impact on national health systems, diabetic peripheral artery was selected as the very first topic to be investigated by the federation. In this second paper, different experiences from delegates of participating countries were shared to define common strategies to harmonize, standardize, and optimize education and training in the Vascular Surgery specialty.
    MeSH term(s) Clinical Competence ; Curriculum ; Diabetic Angiopathies/diagnosis ; Diabetic Angiopathies/epidemiology ; Diabetic Angiopathies/surgery ; Education, Medical, Graduate ; Humans ; Internship and Residency ; Learning Curve ; Mediterranean Region/epidemiology ; Peripheral Arterial Disease/diagnosis ; Peripheral Arterial Disease/epidemiology ; Peripheral Arterial Disease/surgery ; Program Evaluation ; Specialization ; Surgeons/education ; Vascular Surgical Procedures/education
    Language English
    Publishing date 2021-08-25
    Publishing country Netherlands
    Document type Letter
    ZDB-ID 1027366-9
    ISSN 1615-5947 ; 0890-5096
    ISSN (online) 1615-5947
    ISSN 0890-5096
    DOI 10.1016/j.avsg.2021.08.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Book ; Online: Different approaches to unveil biomolecule configurations and their mutual interactions

    Benedetti, Rosaria / Bajardi, Francesco / Capozziello, Salvatore / Carafa, Vincenzo / Conte, Mariarosaria / Del Sorbo, Maria Rosaria / Nebbioso, Angela / Singh, Manjot / Stunnenberg, Hendrik Gerard / Valadan, Mohammadhassan / Altucci, Lucia / Altucci, Carlo

    2020  

    Abstract: A novel technique was demonstrated that overcome important drawbacks to crosslink cells by irradiation with ultrashort UV laser pulses (L-crosslinking). To use this technique coupled to Chromatin ImmunoPrecipitation (ChIP) in a high throughput context, a ...

    Abstract A novel technique was demonstrated that overcome important drawbacks to crosslink cells by irradiation with ultrashort UV laser pulses (L-crosslinking). To use this technique coupled to Chromatin ImmunoPrecipitation (ChIP) in a high throughput context, a pre-screening fast method needs to be implemented to set up suitable irradiation conditions of the cell sample for efficient L-crosslinking with no final and long ChIP analysis. Here a fast method is reported where living human cells have been first transfected with a vector coding for Estrogen Receptor {\alpha} (ER{\alpha}), linked to Green Florescent protein (ER{\alpha}-GFP), so that the well-known interaction between the Estrogen Receptor Elements (ERE) region of the cell DNA and the ER{\alpha} protein can be detected by studying the fluorometric response of the irradiated cells. The damage induced to cells by UV irradiation is characterized by looking at DNA integrity, proteins stability and cellular viability. A second novel approach is presented to analyze or re-visit DNA and RNA sequences and their molecular configurations. This approach is based on methods derived from Chern-Simons super-gravity adapted to describe mutations in DNA/RNA strings, as well as interactions between nucleic acids. As a preliminary case we analyze the KRAS human gene sequence and some of its mutations. Interestingly, our model shows how the Chern-Simons current are capable to characterize the mutations within a sequence, in particular giving a quantitative indication of the mutation likelihood.

    Comment: 33 pages, 5 figures
    Keywords Quantitative Biology - Biomolecules
    Subject code 612
    Publishing date 2020-01-13
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Exploring the Photodynamic Properties of Two Antiproliferative Benzodiazopyrrole Derivatives

    Concetta Imperatore / Mohammadhassan Valadan / Luciana Tartaglione / Marco Persico / Anna Ramunno / Marialuisa Menna / Marcello Casertano / Carmela Dell’Aversano / Manjot Singh / Maria Luisa d’Aulisio Garigliota / Francesco Bajardi / Elena Morelli / Caterina Fattorusso / Carlo Altucci / Michela Varra

    International Journal of Molecular Sciences, Vol 21, Iss 4, p

    2020  Volume 1246

    Abstract: The identification of molecules whose biological activity can be properly modulated by light is a promising therapeutic approach aimed to improve drug selectivity and efficacy on the molecular target and to limit the side effects compared to traditional ... ...

    Abstract The identification of molecules whose biological activity can be properly modulated by light is a promising therapeutic approach aimed to improve drug selectivity and efficacy on the molecular target and to limit the side effects compared to traditional drugs. Recently, two photo-switchable diastereomeric benzodiazopyrrole derivatives 1RR and 1RS have been reported as microtubules targeting agents (MTAs) on human colorectal carcinoma p53 null cell line (HCT 116 p53-/-). Their IC 50 was enhanced upon Light Emitting Diode (LED) irradiation at 435 nm and was related to their cis form. Here we have investigated the photo-responsive behavior of the acid derivatives of 1RR and 1RS , namely, d 1RR and d 1RS , in phosphate buffer solutions at different pH. The comparison of the UV spectra, acquired before and after LED irradiation, indicated that the trans → cis conversion of d 1RR and d 1RS is affected by the degree of ionization. The apparent rate constants were calculated from the kinetic data by means of fast UV spectroscopy and the conformers of the putative ionic species present in solution (pH range: 5.7−8.0) were modelled. Taken together, our experimental and theoretical results suggest that the photo-conversions of trans d 1RR / d 1RS into the corresponding cis forms and the thermal decay of cis d 1RR / d 1RS are dependent on the presence of diazonium form of d 1RR / d 1RS . Finally, a photo-reaction was detected only for d 1RR after prolonged LED irradiation in acidic medium, and the resulting product was characterized by means of Liquid Chromatography coupled to High resolution Mass Spectrometry (LC-HRMS) and Nuclear Magnetic Resonance (NMR) spectroscopy.
    Keywords photoswitchable azoheteroarene ; diazo derivative ; cis - trans conversion ; fast uv spectroscopy ; lc-hrms ; conformational analysis ; dft optimization ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Model-based analysis of potassium removal during hemodialysis.

    Ciandrini, Andrea / Severi, Stefano / Cavalcanti, Silvio / Fontanazzi, Francesco / Grandi, Fabio / Buemi, Michele / Mura, Carlo / Bajardi, Pietro / Badiali, Fabio / Santoro, Antonio

    Artificial organs

    2009  Volume 33, Issue 10, Page(s) 835–843

    Abstract: Potassium ion (K(+)) kinetics in intra- and extracellular compartments during dialysis was studied by means of a double-pool computer model, which included potassium-dependent active transport (Na-K-ATPase pump) in 38 patients undergoing chronic ... ...

    Abstract Potassium ion (K(+)) kinetics in intra- and extracellular compartments during dialysis was studied by means of a double-pool computer model, which included potassium-dependent active transport (Na-K-ATPase pump) in 38 patients undergoing chronic hemodialysis. Each patient was treated for 2 weeks with a constant K(+) dialysate concentration (K(+)(CONST) therapy) and afterward for 2 weeks with a time-varying (profiled) K(+) dialysate concentration (K(+)(PROF) therapy). The two therapies induced different levels of K(+) plasma concentration (K(+)(CONST): 3.71 +/- 0.88 mmol/L vs. K(+)(PROF): 3.97 +/- 0.64 mmol/L, time-averaged values, P < 0.01). The computer model was tuned to accurately fit plasmatic K(+) measured in the course and 1 h after K(+)(CONST) and K(+)(PROF) therapies and was then used to simulate the kinetics of intra- and extracellular K(+). Model-based analysis showed that almost all the K(+) removal in the first 90 min of dialysis was derived from the extracellular compartment. The different K(+) time course in the dialysate and the consequently different Na-K pump activity resulted in a different sharing of removed potassium mass at the end of dialysis: 56% +/- 17% from the extracellular compartment in K(+)(PROF) versus 41% +/- 14% in K(+)(CONST). At the end of both therapies, the K(+) distribution was largely unbalanced, and, in the next 3 h, K(+) continued to flow in the extracellular space (about 24 mmol). After rebalancing, about 80% of the K(+) mass that was removed derived from the intracellular compartment. In conclusion, the Na-K pump plays a major role in K(+) apportionment between extracellular and intracellular compartments, and potassium dialysate concentration strongly influences pump activity.
    MeSH term(s) Adult ; Aged ; Computer Simulation ; Diffusion ; Female ; Hemodialysis Solutions/chemistry ; Hemodialysis Solutions/metabolism ; Hemodialysis Solutions/therapeutic use ; Homeostasis ; Humans ; Italy ; Kidney Failure, Chronic/blood ; Kidney Failure, Chronic/therapy ; Kinetics ; Male ; Middle Aged ; Models, Biological ; Nonlinear Dynamics ; Potassium/blood ; Renal Dialysis ; Reproducibility of Results ; Sodium-Potassium-Exchanging ATPase/metabolism
    Chemical Substances Hemodialysis Solutions ; Sodium-Potassium-Exchanging ATPase (EC 3.6.3.9) ; Potassium (RWP5GA015D)
    Language English
    Publishing date 2009-10
    Publishing country United States
    Document type Journal Article ; Multicenter Study
    ZDB-ID 441812-8
    ISSN 1525-1594 ; 0160-564X
    ISSN (online) 1525-1594
    ISSN 0160-564X
    DOI 10.1111/j.1525-1594.2009.00806.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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