arXiv subjects

Emanuela Merelli

Publications and source records attributed to Emanuela Merelli.

At least 19 recordsLinked to original sources

arXiv2025

Space of Data through the Lens of Multilevel Graph

This work seeks to tackle the inherent complexity of dataspaces by introducing a novel data structure that can represent datasets across multiple levels of abstraction, ranging from local to global. We propose the concept of a multilevel graph, which is equipped with two fundamental operations: contraction and expansion of its topology. This multilevel graph is specifically designed to fulfil the requirements for incremental abstraction and flexibility, as outlined in existing definitions of dataspaces. Furthermore, we provide a comprehensive suite of methods for manipulating this graph structure, establishing a robust framework for data analysis. While its effectiveness has been empirically validated for unstructured data, its application to structured data is also inherently viable. Preliminary results are presented through a real-world scenario based on a collection of dream reports.

cs.DS↗

arXiv2024

Factorizing the Brauer monoid in polynomial time

Finding a minimal factorization for a generic semigroup can be done by using the Froidure-Pin Algorithm, which is not feasible for semigroups of large sizes. On the other hand, if we restrict our attention to just a particular semigroup, we could leverage its structure to obtain a much faster algorithm. In particular, $\mathcal{O}(N^2)$ algorithms are known for factorizing the Symmetric group $S_N$ and the Temperley-Lieb monoid $\mathcal{T}\mathcal{L}_N$, but none for their superset the Brauer monoid $\mathcal{B}_{N}$. In this paper we hence propose a $\mathcal{O}(N^4)$ factorization algorithm for $\mathcal{B}_{N}$. At each iteration, the algorithm rewrites the input $X \in \mathcal{B}_{N}$ as $X = X' \circ p_i$ such that $\ell(X') = \ell(X) - 1$, where $p_i$ is a factor for $X$ and $\ell$ is a length function that returns the minimal number of factors needed to generate $X$.

math.RA↗

arXiv2021

Automaton of molecular perceptions in biochemical reactions

Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based representation of the behaviour of biomolecules in living cells. Our approach considers the capability of a molecule to perceive its surroundings a key property of bimolecular interactions, which we investigate from a theoretical perspective. Graph-based reaction systems are then leveraged to abstract enzyme regulation as a result of the influence exerted by the environment on a catalysed reaction. By combining these methods, we aim at overcoming some limitations of current kinetic models, which do not take into account local molecular interactions and the way they are affected by the reaction environment.

cs.CE↗

arXiv2019

Topological Run-time Monitoring for Complex Systems

In this paper we introduce a new data-driven run-time monitoring system for analysing the behaviour of time evolving complex systems. The monitor controls the evolution of the whole system but it is mined from the data produced by its single interacting components. Relevant behavioural changes happening at the component level and that are responsible for global system evolution are captured by the monitor. Topological Data Analysis is used for shaping and analysing the data for mining an automaton mimicking the global system dynamics, the so-called Persistent Entropy Automaton (PEA). A slight augmented PEA, the monitor, can be used to run current or past executions of the system to mine temporal invariants, for instance through statistical reasoning. Such invariants can be formulated as properties of a temporal logic, e.g. bounded LTL, that can be run-time model-checked. We have performed a feasibility assessment of the PEA and the associated monitoring system by analysing a simulated biological complex system, namely the human immune system. The application of the monitor to simulated traces reveals temporal properties that should be satisfied in order to reach immunization memory.

cs.LO↗

arXiv2019

Topological Interpretation of Interactive Computation

It is a great pleasure to write this tribute in honor of Scott A. Smolka on his 65th birthday. We revisit Goldin, Smolka hypothesis that persistent Turing machine (PTM) can capture the intuitive notion of sequential interaction computation. We propose a topological setting to model the abstract concept of environment. We use it to define a notion of a topological Turing machine (TTM) as a universal model for interactive computation and possible model for concurrent computation.

cs.LO↗

arXiv2016

A Graph Grammar for Modelling RNA Folding

We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour resembles the one of a self-adaptive system. Each RNA configuration is a graph and the evolution of configurations is constrained by precise rules that can be described by a graph grammar.

cs.FL↗

arXiv2016

Topological classifier for detecting the emergence of epileptic seizures

In this work we study how to apply topological data analysis to create a method suitable to classify EEGs of patients affected by epilepsy. The topological space constructed from the collection of EEGs signals is analyzed by Persistent Entropy acting as a global topological feature for discriminating between healthy and epileptic signals. The Physionet data-set has been used for testing the classifier.

q-bio.NC↗

arXiv2015

A new topological entropy-based approach for measuring similarities among piecewise linear functions

In this paper we present a novel methodology based on a topological entropy, the so-called persistent entropy, for addressing the comparison between discrete piecewise linear functions. The comparison is certified by the stability theorem for persistent entropy. The theorem is used in the implementation of a new algorithm. The algorithm transforms a discrete piecewise linear function into a filtered simplicial complex that is analyzed with persistent homology and persistent entropy. Persistent entropy is used as discriminant feature for solving the supervised classification problem of real long length noisy signals of DC electrical motors. The quality of classification is stated in terms of the area under receiver operating characteristic curve (AUC=94.52%).

cs.DM↗

arXiv2015

Topological characterization of S[B] systems: From data to models of complexity

In this paper we propose a methodology for deriving a model of a complex system by exploiting the information extracted from Topological Data Analysis. Central to our approach is the S[B] paradigm in which a complex system is represented by a two-level model. One level, the structural S one, is derived using the newly introduced quantitative concept of Persistent Entropy. The other level, the behavioral B one, is characterized by a network of interacting computational agents described by a Higher Dimensional Automaton. The methodology yields also a representation of the evolution of the derived two-level model as a Persistent Entropy Automaton. The presented methodology is applied to a real case study, the Idiotypic Network of the mammal immune system.

cs.ET↗

arXiv2014

Neural Hypernetwork Approach for Pulmonary Embolism diagnosis

This work introduces an integrative approach based on Q-analysis with machine learning. The new approach, called Neural Hypernetwork, has been applied to a case study of pulmonary embolism diagnosis. The objective of the application of neural hyper-network to pulmonary embolism (PE) is to improve diagnose for reducing the number of CT-angiography needed. Hypernetworks, based on topological simplicial complex, generalize the concept of two-relation to many-body relation. Furthermore, Hypernetworks provide a significant generalization of network theory, enabling the integration of relational structure, logic and analytic dynamics. Another important results is that Q-analysis stays close to the data, while other approaches manipulate data, projecting them into metric spaces or applying some filtering functions to highlight the intrinsic relations. A pulmonary embolism (PE) is a blockage of the main artery of the lung or one of its branches, frequently fatal. Our study uses data on 28 diagnostic features of 1,427 people considered to be at risk of PE. The resulting neural hypernetwork correctly recognized 94% of those developing a PE. This is better than previous results that have been obtained with other methods (statistical selection of features, partial least squares regression, topological data analysis in a metric space).

physics.med-ph↗

arXiv2014

Using Topological Data Analysis for diagnosis pulmonary embolism

Pulmonary Embolism (PE) is a common and potentially lethal condition. Most patients die within the first few hours from the event. Despite diagnostic advances, delays and underdiagnosis in PE are common.To increase the diagnostic performance in PE, current diagnostic work-up of patients with suspected acute pulmonary embolism usually starts with the assessment of clinical pretest probability using plasma d-Dimer measurement and clinical prediction rules. The most validated and widely used clinical decision rules are the Wells and Geneva Revised scores. We aimed to develop a new clinical prediction rule (CPR) for PE based on topological data analysis and artificial neural network. Filter or wrapper methods for features reduction cannot be applied to our dataset: the application of these algorithms can only be performed on datasets without missing data. Instead, we applied Topological data analysis (TDA) to overcome the hurdle of processing datasets with null values missing data. A topological network was developed using the Iris software (Ayasdi, Inc., Palo Alto). The PE patient topology identified two ares in the pathological group and hence two distinct clusters of PE patient populations. Additionally, the topological netowrk detected several sub-groups among healthy patients that likely are affected with non-PE diseases. TDA was further utilized to identify key features which are best associated as diagnostic factors for PE and used this information to define the input space for a back-propagation artificial neural network (BP-ANN). It is shown that the area under curve (AUC) of BP-ANN is greater than the AUCs of the scores (Wells and revised Geneva) used among physicians. The results demonstrate topological data analysis and the BP-ANN, when used in combination, can produce better predictive models than Wells or revised Geneva scores system for the analyzed cohort

physics.med-ph↗

arXiv2014

Adaptability Checking in Multi-Level Complex Systems

A hierarchical model for multi-level adaptive systems is built on two basic levels: a lower behavioural level B accounting for the actual behaviour of the system and an upper structural level S describing the adaptation dynamics of the system. The behavioural level is modelled as a state machine and the structural level as a higher-order system whose states have associated logical formulas (constraints) over observables of the behavioural level. S is used to capture the global and stable features of B, by a defining set of allowed behaviours. The adaptation semantics is such that the upper S level imposes constraints on the lower B level, which has to adapt whenever it no longer can satisfy them. In this context, we introduce weak and strong adaptabil- ity, i.e. the ability of a system to adapt for some evolution paths or for all possible evolutions, respectively. We provide a relational characterisation for these two notions and we show that adaptability checking, i.e. deciding if a system is weak or strong adaptable, can be reduced to a CTL model checking problem. We apply the model and the theoretical results to the case study of motion control of autonomous transport vehicles.

cs.SE↗

arXiv2013

A multi-level model for self-adaptive systems

This work introduces a general multi-level model for self-adaptive systems. A self-adaptive system is seen as composed by two levels: the lower level describing the actual behaviour of the system and the upper level accounting for the dynamically changing environmental constraints on the system. In order to keep our description as general as possible, the lower level is modelled as a state machine and the upper level as a second-order state machine whose states have associated formulas over observable variables of the lower level. Thus, each state of the second-order machine identifies the set of lower-level states satisfying the constraints. Adaptation is triggered when a second-order transition is performed; this means that the current system no longer can satisfy the current high-level constraints and, thus, it has to adapt its behaviour by reaching a state that meets the new constraints. The semantics of the multi-level system is given by a flattened transition system that can be statically checked in order to prove the correctness of the adaptation model. To this aim we formalize two concepts of weak and strong adaptability providing both a relational and a logical characterization. We report that this work gives a formal computational characterization of multi-level self-adaptive systems, evidencing the important role that (theoretical) computer science could play in the emerging science of complex systems.

cs.LO↗

arXiv2012

Disease processes as hybrid dynamical systems

We investigate the use of hybrid techniques in complex processes of infectious diseases. Since predictive disease models in biomedicine require a multiscale approach for understanding the molecule-cell-tissue-organ-body interactions, heterogeneous methodologies are often employed for describing the different biological scales. Hybrid models provide effective means for complex disease modelling where the action and dosage of a drug or a therapy could be meaningfully investigated: the infection dynamics can be classically described in a continuous fashion, while the scheduling of multiple treatment discretely. We define an algebraic language for specifying general disease processes and multiple treatments, from which a semantics in terms of hybrid dynamical system can be derived. Then, the application of control-theoretic tools is proposed in order to compute the optimal scheduling of multiple therapies. The potentialities of our approach are shown in the case study of the SIR epidemic model and we discuss its applicability on osteomyelitis, a bacterial infection affecting the bone remodelling system in a specific and multiscale manner. We report that formal languages are helpful in giving a general homogeneous formulation for the different scales involved in a multiscale disease process; and that the combination of hybrid modelling and control theory provides solid grounds for computational medicine.

cs.LO↗

arXiv2011

Multiple verification in computational modeling of bone pathologies

We introduce a model checking approach to diagnose the emerging of bone pathologies. The implementation of a new model of bone remodeling in PRISM has led to an interesting characterization of osteoporosis as a defective bone remodeling dynamics with respect to other bone pathologies. Our approach allows to derive three types of model checking-based diagnostic estimators. The first diagnostic measure focuses on the level of bone mineral density, which is currently used in medical practice. In addition, we have introduced a novel diagnostic estimator which uses the full patient clinical record, here simulated using the modeling framework. This estimator detects rapid (months) negative changes in bone mineral density. Independently of the actual bone mineral density, when the decrease occurs rapidly it is important to alarm the patient and monitor him/her more closely to detect insurgence of other bone co-morbidities. A third estimator takes into account the variance of the bone density, which could address the investigation of metabolic syndromes, diabetes and cancer. Our implementation could make use of different logical combinations of these statistical estimators and could incorporate other biomarkers for other systemic co-morbidities (for example diabetes and thalassemia). We are delighted to report that the combination of stochastic modeling with formal methods motivate new diagnostic framework for complex pathologies. In particular our approach takes into consideration important properties of biosystems such as multiscale and self-adaptiveness. The multi-diagnosis could be further expanded, inching towards the complexity of human diseases. Finally, we briefly introduce self-adaptiveness in formal methods which is a key property in the regulative mechanisms of biological systems and well known in other mathematical and engineering areas.

cs.LO↗

arXiv2011

Multiscale Modelling: A Mobile Membrane Approach

Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different spatial and temporal scales. Although several ways to provide "multilayer" models have been proposed, only Complex Automata naturally embed spatial information and realize the multiscale approach with well-established inter-scale integration schemas. Recently, such approach has been restated in terms of Spatial P systems - a variant of P systems with a more geometric concept of space. In this work we discuss how mobile membranes, a variant of membrane systems inspired by the biological movements of endocytosis and exocytosis, can be efficaciously exploited to define a uniform multiscale coupling scheme relying only on the features of the formalism itself.

cs.FL↗

arXiv2010

Shape Calculus: Timed Operational Semantics and Well-formedness

The Shape Calculus is a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel that models naturally binding sites on the surface of shapes. Processes can represent molecules or other mobile objects and can be part of networks of processes that move simultaneously and interact in a given geometrical space. The calculus embeds collision detection and response, binding of compatible 3D processes and splitting of previously established bonds. In this work the full formal timed operational semantics of the calculus is provided, together with examples that illustrate the use of the calculus in a well-known biological scenario. Moreover, a result of well-formedness about the evolution of a given network of well-formed 3D processes is proved.

cs.PL↗

arXiv2010

Multiscale Bone Remodelling with Spatial P Systems

Many biological phenomena are inherently multiscale, i.e. they are characterized by interactions involving different spatial and temporal scales simultaneously. Though several approaches have been proposed to provide "multilayer" models, only Complex Automata, derived from Cellular Automata, naturally embed spatial information and realize multiscaling with well-established inter-scale integration schemas. Spatial P systems, a variant of P systems in which a more geometric concept of space has been added, have several characteristics in common with Cellular Automata. We propose such a formalism as a basis to rephrase the Complex Automata multiscaling approach and, in this perspective, provide a 2-scale Spatial P system describing bone remodelling. The proposed model not only results to be highly faithful and expressive in a multiscale scenario, but also highlights the need of a deep and formal expressiveness study involving Complex Automata, Spatial P systems and other promising multiscale approaches, such as our shape-based one already resulted to be highly faithful.

cs.CE↗