A Model of Colonic Crypts using SBML Spatial

The Spatial Processes package enables an explicit definition of a spatial environment on top of the normal dynamic modeling SBML capabilities. The possibility of an explicit representation of spatial dynamics increases the representation power of SBML. In this work we used those new SBML features to define an extensive model of colonic crypts composed of the main cellular types (from stem cells to fully differentiated cells), alongside their spatial dynamics.Comment: In Proceedings Wivace 2013, arXiv:1309.712

Modeling cumulative biological phenomena with Suppes-Bayes Causal Networks

Several diseases related to cell proliferation are characterized by the accumulation of somatic DNA changes, with respect to wildtype conditions. Cancer and HIV are two common examples of such diseases, where the mutational load in the cancerous/viral population increases over time. In these cases, selective pressures are often observed along with competition, cooperation and parasitism among distinct cellular clones. Recently, we presented a mathematical framework to model these phenomena, based on a combination of Bayesian inference and Suppes' theory of probabilistic causation, depicted in graphical structures dubbed Suppes-Bayes Causal Networks (SBCNs). SBCNs are generative probabilistic graphical models that recapitulate the potential ordering of accumulation of such DNA changes during the progression of the disease. Such models can be inferred from data by exploiting likelihood-based model-selection strategies with regularization. In this paper we discuss the theoretical foundations of our approach and we investigate in depth the influence on the model-selection task of: (i) the poset based on Suppes' theory and (ii) different regularization strategies. Furthermore, we provide an example of application of our framework to HIV genetic data highlighting the valuable insights provided by the inferred

Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena

Structural learning of Bayesian Networks (BNs) is a NP-hard problem, which is further complicated by many theoretical issues, such as the I-equivalence among different structures. In this work, we focus on a specific subclass of BNs, named Suppes-Bayes Causal Networks (SBCNs), which include specific structural constraints based on Suppes' probabilistic causation to efficiently model cumulative phenomena. Here we compare the performance, via extensive simulations, of various state-of-the-art search strategies, such as local search techniques and Genetic Algorithms, as well as of distinct regularization methods. The assessment is performed on a large number of simulated datasets from topologies with distinct levels of complexity, various sample size and different rates of errors in the data. Among the main results, we show that the introduction of Suppes' constraints dramatically improve the inference accuracy, by reducing the solution space and providing a temporal ordering on the variables. We also report on trade-offs among different search techniques that can be efficiently employed in distinct experimental settings. This manuscript is an extended version of the paper "Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena" presented at the 2018 International Conference on Computational Science

L’homme-chien ou la fraternité du désespoir

Sony Labou Tansi et Bernard-Marie Koltès, le premier originaire d’un Sud appauvri et négligé, le second natif d’un Nord tout-puissant et altier, ont chacun à leur manière témoigné de leur siècle à travers, entre autres, l’écriture théâtrale. Si ces deux écrivains ne se sont jamais rencontrés, le regard, très critique, qu’ils ont porté sur leurs contemporains a montré que l’Histoire n’a jamais tourné au profit de l’être humain. L’Afrique est au coeur de leur oeuvre; elle en est le creuset poétique. Il sera question ici de tenter un rapprochement des pièces Je soussigné cardiaque, de Labou Tansi, et Roberto Zucco, de Koltès, à travers, entre autres, la figure du chien, de l’homme-chien, récurrente dans leurs oeuvres.Sony Labou Tansi comes from the poor and neglected South; Bernard-Marie Koltès was born in the almighty and haughty North: each in his own way, through his writings, especially his plays, is a witness for the twentieth century. These two writers never met; however, their critical view of their contemporaries shows that History has never profited mankind. For both, Africa is at the heart of their writings, it is their poetical crucible of sorts. This article attempts to find connections between Je soussigné cardiaque, by Labou Tansi, and Roberto Zucco, by Koltès, using, among other things, the figure of the dog, the man-dog, which is recurrent in these plays

An exploration of the food semiosphere in Alto Adige

openThis study aims to provide a partial unveiling of the symbolic dimension of food in Italy’s Alto Adige (German: Südtirol. English: South Tyrol), through research conducted within the valleys of Val Badia, Val Marebbe and Val Pusteria. This unveiling occurred through the understanding of the meanings conveyed by selected restaurants and food stores, each of which contained unique local elements. The identification of the signs within the messages is carried out by the author throughout their food experiences in the area.The study was conducted taking as a lens the notion of semiosphere proposed by Juri Lotman (1990), combined with the qualitative research approach of thick description (Geertz, 1973) applied to the culture’s interpretation. The study adapts the step-by-step semiotic methodology proposed by Mingers and Willcocks (2017), which integrates the communication model proposed by Jakobson (1960) and the life-world developed by Habermas (1987). These worlds fit within the semiosphere space and building relations of sociomateirlaity, sociation and embodiment. The application of such an integrative approach allows to state that part of the food semiosphere in the studied area is rooted in sustainability, cultural hybridization and identity's preservation, which constitute key elements in the development of current food experiences today. Elements that before made part of the context have become part of the text, this last understood as a mechanism which triggers signification (Lotman, 1990). The nucleo of the semiosphere in South Tyrol is characterised by the mountain and Ladin cuisines and their influences. This study demonstrates that the application of the food semiosphere model to the food culture in South Tyrol is particularly insightful due to the geographical, historical, economic, social and cultural processes the region has undergone through time and that have made up its identity. Further research on the semiosphere is suggested for this region and related areas.This study aims to provide a partial unveiling of the symbolic dimension of food in Italy’s Alto Adige (German: Südtirol. English: South Tyrol), through research conducted within the valleys of Val Badia, Val Marebbe and Val Pusteria. This unveiling occurred through the understanding of the meanings conveyed by selected restaurants and food stores, each of which contained unique local elements. The identification of the signs within the messages is carried out by the author throughout their food experiences in the area.The study was conducted taking as a lens the notion of semiosphere proposed by Juri Lotman (1990), combined with the qualitative research approach of thick description (Geertz, 1973) applied to the culture’s interpretation. The study adapts the step-by-step semiotic methodology proposed by Mingers and Willcocks (2017), which integrates the communication model proposed by Jakobson (1960) and the life-world developed by Habermas (1987). These worlds fit within the semiosphere space and building relations of sociomateirlaity, sociation and embodiment. The application of such an integrative approach allows to state that part of the food semiosphere in the studied area is rooted in sustainability, cultural hybridization and identity's preservation, which constitute key elements in the development of current food experiences today. Elements that before made part of the context have become part of the text, this last understood as a mechanism which triggers signification (Lotman, 1990). The nucleo of the semiosphere in South Tyrol is characterised by the mountain and Ladin cuisines and their influences. This study demonstrates that the application of the food semiosphere model to the food culture in South Tyrol is particularly insightful due to the geographical, historical, economic, social and cultural processes the region has undergone through time and that have made up its identity. Further research on the semiosphere is suggested for this region and related areas

Parallel Implementation of Efficient Search Schemes for the Inference of Cancer Progression Models

The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model the order of accumulation of such mutations during the progression, which eventually leads to the disease, by means of probabilistic graphic models, i.e., Bayesian Networks (BNs). We investigate how to perform the task of learning the structure of such BNs, according to experimental evidence, adopting a global optimization meta-heuristics. In particular, in this work we rely on Genetic Algorithms, and to strongly reduce the execution time of the inference -- which can also involve multiple repetitions to collect statistically significant assessments of the data -- we distribute the calculations using both multi-threading and a multi-node architecture. The results show that our approach is characterized by good accuracy and specificity; we also demonstrate its feasibility, thanks to a 84x reduction of the overall execution time with respect to a traditional sequential implementation