We use distributed computing tools to provide a new perspective on the behavior of cooperative biological ensembles. We introduce the Ants Nearby Treasure Search (ANTS) problem, a generalization of the classical cow-path problem [10, 20, 41, 42], which is relevant for collective foraging in animal groups. In the ANTS problem, k identical (probabilistic) agents, initially placed at some central location, collectively search for a treasure in the two-dimensional plane. The treasure is placed at a target location by an adversary and the goal is to find it as fast as possible as a function of both k and D, where D is the distance between the central location and the target. This is biologically motivated by cooperative, central place foraging, such as performed by ants around their nest. In this type of search there is a strong preference to locate nearby food sources before those that are further away. We focus on trying to find what can be achieved if communication is limited or altogether absent. Indeed, to avoid overlaps agents must be highly dispersed making communication difficult. Furthermore, if the agents do not commence the search in synchrony, then even initial communication is problematic. This holds, in particular, with respect to the question of whether the agents can communicate and conclude their total number, k. It turns out that the knowledge of k by the individual agents is crucial for performance. Indeed, it is a straightforward observation that the time required for finding the treasure is Ω(D + D2 k), and we show in this paper that this bound can be matched if the agents have knowledge of k up to some constant approximation. We present a tight bound for the competitive penalty that must be paid, in the running time, if the agents have no information about k. Specifically, this bound is slightly more than logarithmic in the number of agents. In addition, we give a lower bound for the setting in which the agents are given some estimation of k. Informally, our results imply that the agents can potentially perform well without any knowledge of their total number k, however, to further improve, they must use some information regarding k. Finally, we propose a uniform algorithm that is both efficient and extremely simple, suggesting its relevance for actual biological scenarios.
Our work falls within the scope of natural algorithms, a recent attempt to investigate biological phenomena from an algorithmic perspective @cite_1 @cite_51 @cite_5 .
@cite_51 @cite_5 @cite_1
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Computational systems biology unifies the mechanistic approach of systems biology with the data-driven approach of computational biology. Computational systems biology aims to develop algorithms that uncover the structure and parameterization of the underlying mechanistic model--in other words, to answer specific questions about the underlying mechanisms of a biological system--in a process that can be thought of as learning or inference. This volume offers state-of-the-art perspectives from computational biology, statistics, modeling, and machine learning on new methodologies for learning and inference in biological networks.The chapters offer practical approaches to biological inference problems ranging from genome-wide inference of genetic regulation to pathway-specific studies. Both deterministic models (based on ordinary differential equations) and stochastic models (which anticipate the increasing availability of data from small populations of cells) are considered. Several chapters emphasize Bayesian inference, so the editors have included an introduction to the philosophy of the Bayesian approach and an overview of current work on Bayesian inference. Taken together, the methods discussed by the experts in Learning and Inference in Computational Systems Biology provide a foundation upon which the next decade of research in systems biology can be built. Florence d'Alch e-Buc, John Angus, Matthew J. Beal, Nicholas Brunel, Ben Calderhead, Pei Gao, Mark Girolami, Andrew Golightly, Dirk Husmeier, Johannes Jaeger, Neil D. Lawrence, Juan Li, Kuang Lin, Pedro Mendes, Nicholas A. M. Monk, Eric Mjolsness, Manfred Opper, Claudia Rangel, Magnus Rattray, Andreas Ruttor, Guido Sanguinetti, Michalis Titsias, Vladislav Vyshemirsky, David L. Wild, Darren Wilkinson, Guy Yosiphon While evolutionary computation and evolutionary robotics take inspiration from nature, they have long focused mainly on problems of performance optimization. Yet evolution in nature can be interpreted as more nuanced than a process of simple optimization. In particular, natural evolution is a divergent search that optimizes locally within each niche as it simultaneously diversifies. This tendency to discover both quality and diversity at the same time differs from many of the conventional algorithms of machine learning, and also thereby suggests a different foundation for inferring the approach of greatest potential for evolutionary algorithms. In fact, several recent evolutionary algorithms called quality diversity (QD) algorithms(e.g. novelty search with local competition and MAP-Elites) have drawn inspiration from this more nuanced view, aiming to fill a space of possibilities with the best possible example of each type of achievable behavior. The result is a new class of algorithms that return an archive of diverse, high-quality behaviors in a single run. The aim in this paper is to study the application of QD algorithms in challenging environments (in particular complex mazes) to establish their best practices for ambitious domains in the future. In addition to providing insight into cases when QD succeeds and fails, a new approach is investigated that hybridizes multiple views of behaviors (called behavior characterizations) in the same run, which succeeds in overcoming some of the challenges associated with searching for QD with respect to a behavior characterization that is not necessarily sufficient for generating both quality and diversity at the same time. Biomedical Natural Language Processing (BioNLP) attempts to capture biomedical phenomena from texts by extracting relations between biomedical entities (i.e. proteins and genes). Traditionally, only binary relations have been extracted from large numbers of published papers. Recently, more complex relations (biomolecular events) have also been extracted. Such events may include several entities or other relations. To evaluate the performance of the text mining systems, several shared task challenges have been arranged for the BioNLP community. With a common and consistent task setting, the BioNLP'09 shared task evaluated complex biomolecular events such as binding and regulation.Finding these events automatically is important in order to improve biomedical event extraction systems. In the present paper, we propose an automatic event extraction system, which contains a model for complex events, by solving a classification problem with rich features. The main contributions of the present paper are: (1) the proposal of an effective bio-event detection method using machine learning, (2) provision of a high-performance event extraction system, and (3) the execution of a quantitative error analysis. The proposed complex (binding and regulation) event detector outperforms the best system from the BioNLP'09 shared task challenge. Objective: The amount of new discoveries (as published in the scientific literature) in the biomedical area is growing at an exponential rate. This growth makes it very difficult to filter the most relevant results, and thus the extraction of the core information becomes very expensive. Therefore, there is a growing interest in text processing approaches that can deliver selected information from scientific publications, which can limit the amount of human intervention normally needed to gather those results. Materials and methods: This paper presents and evaluates an approach aimed at automating the process of extracting functional relations (e.g. interactions between genes and proteins) from scientific literature in the biomedical domain. The approach, using a novel dependency-based parser, is based on a complete syntactic analysis of the corpus. Results: We have implemented a state-of-the-art text mining system for biomedical literature, based on a deep-linguistic, full-parsing approach. The results are validated on two different corpora: the manually annotated genomics information access (GENIA) corpus and the automatically annotated arabidopsis thaliana circadian rhythms (ATCR) corpus. Conclusion: We show how a deep-linguistic approach (contrary to common belief) can be used in a real world text mining application, offering high-precision relation extraction, while at the same time retaining a sufficient recall.