Aristotle’s modal syllogistic and first-order modal logic

In Prior Analytics 1.1–22, Aristotle develops his proof system of non-modal and modal propositions. This system is given in the language of propositions, and Aristotle is concerned with establishing some properties and relations that the expressions of this language enjoy. However, modern scholarship has found some of his results inconsistent with positions defended elsewhere. The set of rules of inference of this system has also caused perplexity: there does not seem to be a single interpretation that validates all the rules which Aristotle is explicitly committed to using in his proofs. Some commentators have argued that these and other problems cannot be successfully addressed from the viewpoint of the traditional, ‘first-order’ interpretation of Aristotle’s syllogistic, whereby propositions are taken to involve quantification over individuals only. Accordingly, this interpretation not only is inadequate for formal analysis, but also stems from a misunderstanding of Aristotle’s ideas about quantification. On the contrary, in this study I purport to vindicate the adequacy and plausibility of the first-order interpretation. Together with some assumptions about the language of propositions and an appropriate regimentation, the first-order interpretation yields promising solutions to many of the problems raised by the modal syllogistic. Thus, I present a reconstruction of the language of propositions and a formal interpretation thereof which will prove respectful and responsive to most of the views endorsed by Aristotle in the ‘modal’ chapters of the Analytics.

Development of machine learning methods for multi-modal biomarkers detection and integration

In medicine, innovation depends on a better knowledge of the human body mechanism, which represents a complex system of multi-scale constituents. Unraveling the complexity underneath diseases proves to be challenging. A deep understanding of the inner workings comes with dealing with many heterogeneous information. Exploring the molecular status and the organization of genes, proteins, metabolites provides insights on what is driving a disease, from aggressiveness to curability. Molecular constituents, however, are only the building blocks of the human body and cannot currently tell the whole story of diseases. This is why nowadays attention is growing towards the contemporary exploitation of multi-scale information. Holistic methods are then drawing interest to address the problem of integrating heterogeneous data. The heterogeneity may derive from the diversity across data types and from the diversity within diseases. Here, four studies conducted data integration using customly designed workflows that implement novel methods and views to tackle the heterogeneous characterization of diseases. The first study devoted to determine shared gene regulatory signatures for onco-hematology and it showed partial co-regulation across blood-related diseases. The second study focused on Acute Myeloid Leukemia and refined the unsupervised integration of genomic alterations, which turned out to better resemble clinical practice. In the third study, network integration for artherosclerosis demonstrated, as a proof of concept, the impact of network intelligibility when it comes to model heterogeneous data, which showed to accelerate the identification of new potential pharmaceutical targets. Lastly, the fourth study introduced a new method to integrate multiple data types in a unique latent heterogeneous-representation that facilitated the selection of important data types to predict the tumour stage of invasive ductal carcinoma. The results of these four studies laid the groundwork to ease the detection of new biomarkers ultimately beneficial to medical practice and to the ever-growing field of Personalized Medicine.

Non-normal modal logics, quantification, and deontic dilemmas. A study in multi-relational semantics

This dissertation is devoted to the study of non-normal (modal) systems for deontic logics, both on the propositional level, and on the first order one. In particular we developed our study the Multi-relational setting that generalises standard Kripke Semantics. We present new completeness results concerning the semantic setting of several systems which are able to handle normative dilemmas and conflicts. Although primarily driven by issues related to the legal and moral field, these results are also relevant for the more theoretical field of Modal Logic itself, as we propose a syntactical, and semantic study of intermediate systems between the classical propositional calculus CPC and the minimal normal modal logic K.

Valutazione dell'efficacia delle procedure di Pushover convenzionali, modali ed adattive applicate a telai piani in c.a. regolari ed irregolari in elevazione.

The research performed during the PhD and presented in this thesis, allowed to make judgments on pushover analysis method about its application in evaluating the correct structural seismic response. In this sense, the extensive critical review of existing pushover procedures (illustrated in chapter 1) outlined their major issues related to assumptions and to hypothesis made in the application of the method. Therefore, with the purpose of evaluate the effectiveness of pushover procedures, a wide numerical investigation have been performed. In particular the attention has been focused on the structural irregularity on elevation, on the choice of the load vector and on its updating criteria. In the study eight pushover procedures have been considered, of which four are conventional type, one is multi-modal, and three are adaptive. The evaluation of their effectiveness in the identification of the correct dynamic structural response, has been done by performing several dynamic and static non-linear analysis on eight RC frames, characterized by different proprieties in terms of regularity in elevation. The comparisons of static and dynamic results have then permitted to evaluate the examined pushover procedures and to identify the expected margin of error by using each of them. Both on base shear-top displacement curves and on considered storey parameters, the best agreement with the dynamic response has been noticed on Multi-Modal Pushover procedure. Therefore the attention has been focused on Displacement-based Adative Pushover, coming to define for it an improvement strategy, and on modal combination rules, advancing an innovative method based on a quadratic combination of the modal shapes (QMC). This latter has been implemented in a conventional pushover procedure, whose results have been compared with those obtained by other multi-modal procedures. The development of research on pushover analysis is very important because the objective is to come to the definition of a simple, effective and reliable analysis method, indispensable tool in the seismic evaluation of new or existing structures.

Reconstructive Microsurgery and Tissue Engineering in Musculo-Skeletal Oncology - Innovative Techniques

Tumors involving bone and soft tissues are extremely challenging situations. With the recent advances of multi-modal treatment, not only the type of surgery has moved from amputation to limb-sparing procedures, but also the survivorship has improved considerably and reconstructive techniques have the goal to allow a considerably higher quality of life. In bone reconstruction, tissue engineering strategies are the main area of research. Re-vascularization and re-vitalisation of a massive allograft would considerably improve the outcome of biological reconstructions. Using a rabbit animal model, in this study we showed that, by implanting a vascular pedicle inside a weight bearing massive cortical allograft, the bone regeneration inside the allograft was higher compared to the non-vascularized implants, given the patency of the vascular pedicle. Improvement in the animal model and the addition of Stem Cells and Growth factors will allow a further improvement in the results. In soft tissue tumors, free and pedicled flaps have been proven to be of great help as reconstruction strategies. In this study we analyzed the functional and overall outcome of 14 patients who received a re-innervated vascularized flap. We have demonstrated that the use of the innovative technique of motor re-innervated muscular flaps is effective when the resection involves important functional compartments of the upper or lower limb, with no increase of post-operative complications. Although there was no direct comparison between this type of reconstruction and the standard non-innervated reconstruction, we underlined the remarkable high overall functional scores and patient satisfaction following this procedure.

Coupling instrumentation and methodology in the search for traces of life on the early Earth and Mars

Evaluating the nature of the earliest, often controversial, traces of life in the geological record (dating to the Palaeoarchaean, up to ~3.5 billion years before the present) is of fundamental relevance for placing constraints on the potential that life emerged on Mars at approximately the same time (the Noachian period). In their earliest histories, the two planets shared many palaeoenvironmental similarities, before the surface of Mars rapidly became inhospitable to life as we know it. Multi-scalar, multi-modal analyses of fossiliferous rocks from the Barberton greenstone belt of South Africa and the East Pilbara terrane of Western Australia are a window onto primitive prokaryotic ecoystems. Complementary petrographic, morphological, (bio)geochemical and nanostructural analyses of chert horizons and the carbonaceous material within using a wide range of techniques – including optical microscopy, SEM-EDS, Raman spectroscopy, PIXE, µCT, laser ablation ICP-MS, high-resolution TEM-based analytical techniques and secondary ion mass spectrometry – can characterise, at scales from macroscopic to nanoscopic, the fossilised biomes of the earliest Earth. These approaches enable the definition of the palaeoenvironments, and potentially metabolic networks, preserved in ancient rocks. Modifying these protocols is necessary for Martian exploration using rovers, since the range and power of space instrumentation is significantly reduced relative to terrestrial laboratories. Understanding the crucial observations possible using highly complementary rover-based payloads is therefore critical in scientific protocols aiming to detect traces of life on Mars.

Interactions between normative systems and software cognitive agents. A formalization in temporal modal defeasible logic and its implementation

Sustainable computer systems require some flexibility to adapt to environmental unpredictable changes. A solution lies in autonomous software agents which can adapt autonomously to their environments. Though autonomy allows agents to decide which behavior to adopt, a disadvantage is a lack of control, and as a side effect even untrustworthiness: we want to keep some control over such autonomous agents. How to control autonomous agents while respecting their autonomy? A solution is to regulate agents’ behavior by norms. The normative paradigm makes it possible to control autonomous agents while respecting their autonomy, limiting untrustworthiness and augmenting system compliance. It can also facilitate the design of the system, for example, by regulating the coordination among agents. However, an autonomous agent will follow norms or violate them in some conditions. What are the conditions in which a norm is binding upon an agent? While autonomy is regarded as the driving force behind the normative paradigm, cognitive agents provide a basis for modeling the bindingness of norms. In order to cope with the complexity of the modeling of cognitive agents and normative bindingness, we adopt an intentional stance. Since agents are embedded into a dynamic environment, things may not pass at the same instant. Accordingly, our cognitive model is extended to account for some temporal aspects. Special attention is given to the temporal peculiarities of the legal domain such as, among others, the time in force and the time in efficacy of provisions. Some types of normative modifications are also discussed in the framework. It is noteworthy that our temporal account of legal reasoning is integrated to our commonsense temporal account of cognition. As our intention is to build sustainable reasoning systems running unpredictable environment, we adopt a declarative representation of knowledge. A declarative representation of norms will make it easier to update their system representation, thus facilitating system maintenance; and to improve system transparency, thus easing system governance. Since agents are bounded and are embedded into unpredictable environments, and since conflicts may appear amongst mental states and norms, agent reasoning has to be defeasible, i.e. new pieces of information can invalidate formerly derivable conclusions. In this dissertation, our model is formalized into a non-monotonic logic, namely into a temporal modal defeasible logic, in order to account for the interactions between normative systems and software cognitive agents.

Argumentation and artifacts for intelligent multi-agent systems

Reasoning under uncertainty is a human capacity that in software system is necessary and often hidden. Argumentation theory and logic make explicit non-monotonic information in order to enable automatic forms of reasoning under uncertainty. In human organization Distributed Cognition and Activity Theory explain how artifacts are fundamental in all cognitive process. Then, in this thesis we search to understand the use of cognitive artifacts in an new argumentation framework for an agent-based artificial society.

Specification and Verification of Declarative Open Interaction Models - A Logic-based framework

The advent of distributed and heterogeneous systems has laid the foundation for the birth of new architectural paradigms, in which many separated and autonomous entities collaborate and interact to the aim of achieving complex strategic goals, impossible to be accomplished on their own. A non exhaustive list of systems targeted by such paradigms includes Business Process Management, Clinical Guidelines and Careflow Protocols, Service-Oriented and Multi-Agent Systems. It is largely recognized that engineering these systems requires novel modeling techniques. In particular, many authors are claiming that an open, declarative perspective is needed to complement the closed, procedural nature of the state of the art specification languages. For example, the ConDec language has been recently proposed to target the declarative and open specification of Business Processes, overcoming the over-specification and over-constraining issues of classical procedural approaches. On the one hand, the success of such novel modeling languages strongly depends on their usability by non-IT savvy: they must provide an appealing, intuitive graphical front-end. On the other hand, they must be prone to verification, in order to guarantee the trustworthiness and reliability of the developed model, as well as to ensure that the actual executions of the system effectively comply with it. In this dissertation, we claim that Computational Logic is a suitable framework for dealing with the specification, verification, execution, monitoring and analysis of these systems. We propose to adopt an extended version of the ConDec language for specifying interaction models with a declarative, open flavor. We show how all the (extended) ConDec constructs can be automatically translated to the CLIMB Computational Logic-based language, and illustrate how its corresponding reasoning techniques can be successfully exploited to provide support and verification capabilities along the whole life cycle of the targeted systems.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.