1,050,769 research outputs found

    Towards a Protein-Protein Interaction information extraction system: recognizing named entities

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    [EN] The majority of biological functions of any living being are related to Protein Protein Interactions (PPI). PPI discoveries are reported in form of research publications whose volume grows day after day. Consequently, automatic PPI information extraction systems are a pressing need for biologists. In this paper we are mainly concerned with the named entity detection module of PPIES (the PPI information extraction system we are implementing) which recognizes twelve entity types relevant in PPI context. It is composed of two sub-modules: a dictionary look-up with extensive normalization and acronym detection, and a Conditional Random Field classifier. The dictionary look-up module has been tested with Interaction Method Task (IMT), and it improves by approximately 10% the current solutions that do not use Machine Learning (ML). The second module has been used to create a classifier using the Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA 04) data set. It does not use any external resources, or complex or ad hoc post-processing, and obtains 77.25%, 75.04% and 76.13 for precision, recall, and F1-measure, respectively, improving all previous results obtained for this data set.This work has been funded by MICINN, Spain, as part of the "Juan de la Cierva" Program and the Project DIANA-Applications (TIN2012-38603-C02-01), as well as the by the European Commission as part of the WIQ-EI IRSES Project (Grant No. 269180) within the FP 7 Marie Curie People Framework.Danger Mercaderes, RM.; Pla SantamarĂ­a, F.; Molina Marco, A.; Rosso, P. (2014). Towards a Protein-Protein Interaction information extraction system: recognizing named entities. Knowledge-Based Systems. 57:104-118. https://doi.org/10.1016/j.knosys.2013.12.010S1041185

    From creation to consolidation: a novel framework for memory processing

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    Long after playing squash, your brain continues to process the events that occurred during the game, thereby improving your game, and more generally, enhancing adaptive behavior. Understanding these mysterious processes may require novel theories

    Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity.

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    A crisis continues to brew within the pharmaceutical research and development (R&D) enterprise: productivity continues declining as costs rise, despite ongoing, often dramatic scientific and technical advances. To reverse this trend, we offer various suggestions for both the expansion and broader adoption of modeling and simulation (M&S) methods. We suggest strategies and scenarios intended to enable new M&S use cases that directly engage R&D knowledge generation and build actionable mechanistic insight, thereby opening the door to enhanced productivity. What M&S requirements must be satisfied to access and open the door, and begin reversing the productivity decline? Can current methods and tools fulfill the requirements, or are new methods necessary? We draw on the relevant, recent literature to provide and explore answers. In so doing, we identify essential, key roles for agent-based and other methods. We assemble a list of requirements necessary for M&S to meet the diverse needs distilled from a collection of research, review, and opinion articles. We argue that to realize its full potential, M&S should be actualized within a larger information technology framework--a dynamic knowledge repository--wherein models of various types execute, evolve, and increase in accuracy over time. We offer some details of the issues that must be addressed for such a repository to accrue the capabilities needed to reverse the productivity decline

    Quantitative Verification: Formal Guarantees for Timeliness, Reliability and Performance

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    Computerised systems appear in almost all aspects of our daily lives, often in safety-critical scenarios such as embedded control systems in cars and aircraft or medical devices such as pacemakers and sensors. We are thus increasingly reliant on these systems working correctly, despite often operating in unpredictable or unreliable environments. Designers of such devices need ways to guarantee that they will operate in a reliable and efficient manner. Quantitative verification is a technique for analysing quantitative aspects of a system's design, such as timeliness, reliability or performance. It applies formal methods, based on a rigorous analysis of a mathematical model of the system, to automatically prove certain precisely specified properties, e.g. ``the airbag will always deploy within 20 milliseconds after a crash'' or ``the probability of both sensors failing simultaneously is less than 0.001''. The ability to formally guarantee quantitative properties of this kind is beneficial across a wide range of application domains. For example, in safety-critical systems, it may be essential to establish credible bounds on the probability with which certain failures or combinations of failures can occur. In embedded control systems, it is often important to comply with strict constraints on timing or resources. More generally, being able to derive guarantees on precisely specified levels of performance or efficiency is a valuable tool in the design of, for example, wireless networking protocols, robotic systems or power management algorithms, to name but a few. This report gives a short introduction to quantitative verification, focusing in particular on a widely used technique called model checking, and its generalisation to the analysis of quantitative aspects of a system such as timing, probabilistic behaviour or resource usage. The intended audience is industrial designers and developers of systems such as those highlighted above who could benefit from the application of quantitative verification,but lack expertise in formal verification or modelling

    Formal vs self-organised knowledge systems: a network approach

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    In this work we consider the topological analysis of symbolic formal systems in the framework of network theory. In particular we analyse the network extracted by Principia Mathematica of B. Russell and A.N. Whitehead, where the vertices are the statements and two statements are connected with a directed link if one statement is used to demonstrate the other one. We compare the obtained network with other directed acyclic graphs, such as a scientific citation network and a stochastic model. We also introduce a novel topological ordering for directed acyclic graphs and we discuss its properties in respect to the classical one. The main result is the observation that formal systems of knowledge topologically behave similarly to self-organised systems.Comment: research pape

    Splitting hybrid Make-To-Order and Make-To-Stock demand profiles

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    In this paper a demand time series is analysed to support Make-To-Stock (MTS) and Make-To-Order (MTO) production decisions. Using a purely MTS production strategy based on the given demand can lead to unnecessarily high inventory levels thus it is necessary to identify likely MTO episodes. This research proposes a novel outlier detection algorithm based on special density measures. We divide the time series' histogram into three clusters. One with frequent-low volume covers MTS items whilst a second accounts for high volumes which is dedicated to MTO items. The third cluster resides between the previous two with its elements being assigned to either the MTO or MTS class. The algorithm can be applied to a variety of time series such as stationary and non-stationary ones. We use empirical data from manufacturing to study the extent of inventory savings. The percentage of MTO items is reflected in the inventory savings which were shown to be an average of 18.1%.Comment: demand analysis; time series; outlier detection; production strategy; Make-To-Order(MTO); Make-To-Stock(MTS); 15 pages, 9 figure
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