How to Color a French Flag--Biologically Inspired Algorithms for Scale-Invariant Patterning

In the French flag problem, initially uncolored cells on a grid must differentiate to become blue, white or red. The goal is for the cells to color the grid as a French flag, i.e., a three-colored triband, in a distributed manner. To solve a generalized version of the problem in a distributed computational setting, we consider two models: a biologically-inspired version that relies on morphogens (diffusing proteins acting as chemical signals) and a more abstract version based on reliable message passing between cellular agents. Much of developmental biology research has focused on concentration-based approaches using morphogens, since morphogen gradients are thought to be an underlying mechanism in tissue patterning. We show that both our model types easily achieve a French ribbon - a French flag in the 1D case. However, extending the ribbon to the 2D flag in the concentration model is somewhat difficult unless each agent has additional positional information. Assuming that cells are are identical, it is impossible to achieve a French flag or even a close approximation. In contrast, using a message-based approach in the 2D case only requires assuming that agents can be represented as constant size state machines. We hope that our insights may lay some groundwork for what kind of message passing abstractions or guarantees, if any, may be useful in analogy to cells communicating at long and short distances to solve patterning problems. In addition, we hope that our models and findings may be of interest in the design of nano-robots

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

Application of Common Sense Computing for the Development of a Novel Knowledge-Based Opinion Mining Engine

The ways people express their opinions and sentiments have radically changed in the past few years thanks to the advent of social networks, web communities, blogs, wikis and other online collaborative media. The distillation of knowledge from this huge amount of unstructured information can be a key factor for marketers who want to create an image or identity in the minds of their customers for their product, brand, or organisation. These online social data, however, remain hardly accessible to computers, as they are specifically meant for human consumption. The automatic analysis of online opinions, in fact, involves a deep understanding of natural language text by machines, from which we are still very far. Hitherto, online information retrieval has been mainly based on algorithms relying on the textual representation of web-pages. Such algorithms are very good at retrieving texts, splitting them into parts, checking the spelling and counting their words. But when it comes to interpreting sentences and extracting meaningful information, their capabilities are known to be very limited. Existing approaches to opinion mining and sentiment analysis, in particular, can be grouped into three main categories: keyword spotting, in which text is classified into categories based on the presence of fairly unambiguous affect words; lexical affinity, which assigns arbitrary words a probabilistic affinity for a particular emotion; statistical methods, which calculate the valence of affective keywords and word co-occurrence frequencies on the base of a large training corpus. Early works aimed to classify entire documents as containing overall positive or negative polarity, or rating scores of reviews. Such systems were mainly based on supervised approaches relying on manually labelled samples, such as movie or product reviews where the opinionist’s overall positive or negative attitude was explicitly indicated. However, opinions and sentiments do not occur only at document level, nor they are limited to a single valence or target. Contrary or complementary attitudes toward the same topic or multiple topics can be present across the span of a document. In more recent works, text analysis granularity has been taken down to segment and sentence level, e.g., by using presence of opinion-bearing lexical items (single words or n-grams) to detect subjective sentences, or by exploiting association rule mining for a feature-based analysis of product reviews. These approaches, however, are still far from being able to infer the cognitive and affective information associated with natural language as they mainly rely on knowledge bases that are still too limited to efficiently process text at sentence level. In this thesis, common sense computing techniques are further developed and applied to bridge the semantic gap between word-level natural language data and the concept-level opinions conveyed by these. In particular, the ensemble application of graph mining and multi-dimensionality reduction techniques on two common sense knowledge bases was exploited to develop a novel intelligent engine for open-domain opinion mining and sentiment analysis. The proposed approach, termed sentic computing, performs a clause-level semantic analysis of text, which allows the inference of both the conceptual and emotional information associated with natural language opinions and, hence, a more efficient passage from (unstructured) textual information to (structured) machine-processable data. The engine was tested on three different resources, namely a Twitter hashtag repository, a LiveJournal database and a PatientOpinion dataset, and its performance compared both with results obtained using standard sentiment analysis techniques and using different state-of-the-art knowledge bases such as Princeton’s WordNet, MIT’s ConceptNet and Microsoft’s Probase. Differently from most currently available opinion mining services, the developed engine does not base its analysis on a limited set of affect words and their co-occurrence frequencies, but rather on common sense concepts and the cognitive and affective valence conveyed by these. This allows the engine to be domain-independent and, hence, to be embedded in any opinion mining system for the development of intelligent applications in multiple fields such as Social Web, HCI and e-health. Looking ahead, the combined novel use of different knowledge bases and of common sense reasoning techniques for opinion mining proposed in this work, will, eventually, pave the way for development of more bio-inspired approaches to the design of natural language processing systems capable of handling knowledge, retrieving it when necessary, making analogies and learning from experience

Application of Common Sense Computing for the Development of a Novel Knowledge-Based Opinion Mining Engine

The ways people express their opinions and sentiments have radically changed in the past few years thanks to the advent of social networks, web communities, blogs, wikis and other online collaborative media. The distillation of knowledge from this huge amount of unstructured information can be a key factor for marketers who want to create an image or identity in the minds of their customers for their product, brand, or organisation. These online social data, however, remain hardly accessible to computers, as they are specifically meant for human consumption. The automatic analysis of online opinions, in fact, involves a deep understanding of natural language text by machines, from which we are still very far. Hitherto, online information retrieval has been mainly based on algorithms relying on the textual representation of web-pages. Such algorithms are very good at retrieving texts, splitting them into parts, checking the spelling and counting their words. But when it comes to interpreting sentences and extracting meaningful information, their capabilities are known to be very limited. Existing approaches to opinion mining and sentiment analysis, in particular, can be grouped into three main categories: keyword spotting, in which text is classified into categories based on the presence of fairly unambiguous affect words; lexical affinity, which assigns arbitrary words a probabilistic affinity for a particular emotion; statistical methods, which calculate the valence of affective keywords and word co-occurrence frequencies on the base of a large training corpus. Early works aimed to classify entire documents as containing overall positive or negative polarity, or rating scores of reviews. Such systems were mainly based on supervised approaches relying on manually labelled samples, such as movie or product reviews where the opinionist’s overall positive or negative attitude was explicitly indicated. However, opinions and sentiments do not occur only at document level, nor they are limited to a single valence or target. Contrary or complementary attitudes toward the same topic or multiple topics can be present across the span of a document. In more recent works, text analysis granularity has been taken down to segment and sentence level, e.g., by using presence of opinion-bearing lexical items (single words or n-grams) to detect subjective sentences, or by exploiting association rule mining for a feature-based analysis of product reviews. These approaches, however, are still far from being able to infer the cognitive and affective information associated with natural language as they mainly rely on knowledge bases that are still too limited to efficiently process text at sentence level. In this thesis, common sense computing techniques are further developed and applied to bridge the semantic gap between word-level natural language data and the concept-level opinions conveyed by these. In particular, the ensemble application of graph mining and multi-dimensionality reduction techniques on two common sense knowledge bases was exploited to develop a novel intelligent engine for open-domain opinion mining and sentiment analysis. The proposed approach, termed sentic computing, performs a clause-level semantic analysis of text, which allows the inference of both the conceptual and emotional information associated with natural language opinions and, hence, a more efficient passage from (unstructured) textual information to (structured) machine-processable data. The engine was tested on three different resources, namely a Twitter hashtag repository, a LiveJournal database and a PatientOpinion dataset, and its performance compared both with results obtained using standard sentiment analysis techniques and using different state-of-the-art knowledge bases such as Princeton’s WordNet, MIT’s ConceptNet and Microsoft’s Probase. Differently from most currently available opinion mining services, the developed engine does not base its analysis on a limited set of affect words and their co-occurrence frequencies, but rather on common sense concepts and the cognitive and affective valence conveyed by these. This allows the engine to be domain-independent and, hence, to be embedded in any opinion mining system for the development of intelligent applications in multiple fields such as Social Web, HCI and e-health. Looking ahead, the combined novel use of different knowledge bases and of common sense reasoning techniques for opinion mining proposed in this work, will, eventually, pave the way for development of more bio-inspired approaches to the design of natural language processing systems capable of handling knowledge, retrieving it when necessary, making analogies and learning from experience

Statistical mechanics of non equilibrium matter: from minimal models to morphogen gradients

Living systems are by definition far from thermodynamic equilibrium, a condition that can be maintained only at the cost of a continuous injection of energy at the microscale, e.g. via cellular metabolic processes, and dissipation into the surrounding environment. The absence of thermodynamic equilibrium, formalised in the breaking of the global detailed balance condition, allows for a wealth of exotic and often counterintuitive phenomena. Our understanding of the capabilities and limitations of living matter has been greatly informed by thermodynamic approaches, which have to be generalised with respect to their traditional counterparts in order to deal with systems subject to strong random fluctuations. The resulting toolkit of stochastic thermodynamics, in particular the concept of entropy production, gives us a quantitative handle on the degree of "non-equilibriumness" of such stochastic processes. Recently, stochastic thermodynamics has benefitted from cross-contamination with the field-theoretic literature and the techniques developed in the latter for the study of collective behaviour have opened the doors to the thermodynamic characterisation of increasingly complex systems. Starting from minimal mathematical models of single active particles and moving up across scales to the level of morphogenetic processes in real organisms (in particular, the formation of morphogen gradients), this thesis contributes to laying the foundations for a bridge between physical understanding and biological insight. While the focus is here on generic mechanisms and on the development of theoretical tools, the applicability to specific experimental scenarios will be pointed out where relevant.Open Acces

How to Color a French Flag: Biologically Inspired Algorithms for Scale-Invariant Patterning

© 2020, Springer Nature Switzerland AG. In the French flag problem, initially uncolored cells on a grid must differentiate to become blue, white or red. The goal is for the cells to color the grid as a French flag, i.e., a three-colored triband, in a distributed manner. To solve a generalized version of the problem in a distributed computational setting, we consider two models: a biologically-inspired version that relies on morphogens (diffusing proteins acting as chemical signals) and a more abstract version based on reliable message passing between cellular agents. Much of developmental biology research focuses on concentration-based approaches, since morphogen gradients are an underlying mechanism in tissue patterning. We show that both model types easily achieve a French ribbon - a French flag in the 1D case. However, extending the ribbon to the 2D flag in the concentration model is somewhat difficult unless each agent has additional positional information. Assuming that cells are identical, it is impossible to achieve a French flag or even a close approximation. In contrast, using a message-based approach in the 2D case only requires assuming that agents can be represented as logarithmic or constant size state machines. We hope that our insights may lay some groundwork for what kind of message passing abstractions or guarantees, if any, may be useful in analogy to cells communicating at long and short distances to solve patterning problems. We also hope our models and findings may be of interest in the design of nano-robots

Statistical Population Genomics

This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions