scholarly journals Text Mining for Building Biomedical Networks Using Cancer as a Case Study

Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1430
Author(s):  
Sofia I. R. Conceição ◽  
Francisco M. Couto
Keyword(s):  
Text Mining ◽  
Biological Networks ◽  
Scientific Literature ◽  
Real Life ◽  
Relation Extraction ◽  
Cancer Disease ◽  
Network Building ◽  
Automatic Information ◽  
Notable Increase

In the assembly of biological networks it is important to provide reliable interactions in an effort to have the most possible accurate representation of real-life systems. Commonly, the data used to build a network comes from diverse high-throughput essays, however most of the interaction data is available through scientific literature. This has become a challenge with the notable increase in scientific literature being published, as it is hard for human curators to track all recent discoveries without using efficient tools to help them identify these interactions in an automatic way. This can be surpassed by using text mining approaches which are capable of extracting knowledge from scientific documents. One of the most important tasks in text mining for biological network building is relation extraction, which identifies relations between the entities of interest. Many interaction databases already use text mining systems, and the development of these tools will lead to more reliable networks, as well as the possibility to personalize the networks by selecting the desired relations. This review will focus on different approaches of automatic information extraction from biomedical text that can be used to enhance existing networks or create new ones, such as deep learning state-of-the-art approaches, focusing on cancer disease as a case-study.

scholarly journals Extracting kinetic information from literature with KineticRE

2015 ◽  
Vol 12 (4) ◽  
pp. 56-68
Author(s):  
Ana Alão Freitas ◽  
Hugo Costa ◽  
Isabel Rocha
Keyword(s):  
Text Mining ◽  
Metabolic Networks ◽  
Scientific Literature ◽  
Kluyveromyces Lactis ◽  
Relevant Information ◽  
Text Documents ◽  
Kinetic Information ◽  
Mining Tool ◽  
Text Mining Tool

Summary To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

A Potential Case of Inattentional Blindness in a Police-Pursuit Collision

2020 ◽  
Vol 64 (1) ◽  
pp. 536-540
Author(s):  
Jeffrey A. Martin
Keyword(s):  
Scientific Literature ◽  
Real Life ◽  
Inattentional Blindness ◽  
Potential Case ◽  
Perceptual Phenomenon

The perceptual phenomenon of “inattentional blindness” has been widely acknowledged in the scientific literature for 30 years. In addition to the laboratory-based examples, real-life examples appear in the literature. This paper provides a case study where a deputy sheriff’s patrol car collided with a fleeing motorcyclist – with unique circumstances – as recorded on in-car-camera (ICC) videos. Although the motorcyclist brought suit alleging the deputy intentionally collided with him, the deputy reported that he first noticed another deputy running after the motorcyclist prior to seeing the fleeing motorcyclist. However, the ICC video from the involved deputy’s patrol car strongly supports the motorcyclist was visible from the deputy’s perspective before the on-foot deputy appeared. The facts of this incident are compared to the widely accepted characteristics of inattentional blindness in exploring whether that perceptual phenomenon may have been at play in this case.

Contamination Lab of Turin (CLabTo)

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Eleonora FIORE ◽  
Giuliano SANSONE ◽  
Chiara Lorenza REMONDINO ◽  
Paolo Marco TAMBORRINI
Keyword(s):  
University Students ◽  
Single Case ◽  
Real Life ◽  
Learning By Doing ◽  
Assessment Data ◽  
Entrepreneurial Skills ◽  
Fields Of Study ◽  
Education Levels ◽  
Positive Effect

Interest in offering Entrepreneurship Education (EE) to all kinds of university students is increasing. Therefore, universities are increasing the number of entrepreneurship courses intended for students from different fields of study and with different education levels. Through a single case study of the Contamination Lab of Turin (CLabTo), we suggest how EE may be taught to all kinds of university students. We have combined design methods with EE to create a practical-oriented entrepreneurship course which allows students to work in transdisciplinary teams through a learning-by-doing approach on real-life projects. Professors from different departments have been included to create a multidisciplinary environment. We have drawn on programme assessment data, including pre- and post-surveys. Overall, we have found a positive effect of the programme on the students’ entrepreneurial skills. However, when the data was broken down according to the students’ fields of study and education levels, mixed results emerged.

Participation and spatial transformation in large housing estates in Poland. Case study of Ursynów Północny

2018 ◽  
Vol 60 (1) ◽  
pp. 55-65
Author(s):  
Krystyna Ilmurzyńska
Keyword(s):  
Basic Assumption ◽  
Real Life ◽  
Business Environment ◽  
Spatial Transformation ◽  
Reciprocal Relationships ◽  
Spatial Transformations ◽  
Large Housing Estates ◽  
Existing Housing ◽  
Housing Estates

Abstract This article investigates the suitability of traditional and participatory planning approaches in managing the process of spatial development of existing housing estates, based on the case study of Warsaw’s Ursynów Północny district. The basic assumption of the article is that due to lack of government schemes targeted at the restructuring of large housing estates, it is the business environment that drives spatial transformations and through that shapes the development of participation. Consequently the article focuses on the reciprocal relationships between spatial transformations and participatory practices. Analysis of Ursynów Północny against the background of other estates indicates that it presents more endangered qualities than issues to be tackled. Therefore the article focuses on the potential of the housing estate and good practices which can be tracked throughout its lifetime. The paper focuses furthermore on real-life processes, addressing the issue of privatisation, development pressure, formal planning procedures and participatory budgeting. In the conclusion it attempts to interpret the existing spatial structure of the estate as a potential framework for a participatory approach.

Design process for serious activities inspired by play and games: a problem solving with a board game from disengamement and gamification processes (Preprint)

2020 ◽  
Author(s):  
Stéphane Goria ◽  
Louise Dupet ◽  
Maëva Négroni ◽  
Gabriel Sega ◽  
Philippe Arnoux ◽  
...  
Keyword(s):  
Cancer Detection ◽  
Serious Games ◽  
Diagnostic Method ◽  
Scientific Literature ◽  
Imaging Techniques ◽  
Point Of View ◽  
Board Game ◽  
Advantages And Disadvantages ◽  
Design Result

BACKGROUND most serious games and other game-based tools are designed as digital games or escape games. They are designed for learning or sometimes in the field of medicine as an aid to care. However, they can also be seen as an aid to research, in our case, to evaluate the advantages and disadvantages of imaging techniques for cancer detection. OBJECTIVE we present a case study of action research on the design of a serious board game intended to consider the advantages and weaknesses of a diagnostic method in a different ways. The goal was to better understand the principles of designing a tool using game or play. METHODS we explicitly implemented another process than gamification to develop a structure reminiscent of the game to highlight the strengths and weaknesses of different imaging techniques from the point of view of the respondents (in this case specialists not directly involved in the project). Based on this feedback and the scientific literature on this subject, we detail the main categories of games and games developed for serious use in order to understand their differences. Concerning the cancer research part to which game contributes, our method is based on questions asked to experts and practitioners of this specialty. RESULTS an expert point of view translation tool in the form of a game has been realized to apprehend a research in a different way. CONCLUSIONS we show with the help of a diagram, some possible design paths leading to this type of design result including two hidden dimensions to consider (the awareness of the game or play by the "player" and his role as a contributor or recipient).

Bleak Weather for Sun-Shine AG: A Case Study of Impairment of Assets

2014 ◽  
Vol 30 (2) ◽  
pp. 113-126 ◽  
Author(s):  
Dominic Detzen ◽  
Tobias Stork genannt Wersborg ◽  
Henning Zülch
Keyword(s):  
Real Life ◽  
Accounting Standards ◽  
Point Of View ◽  
Professional Judgment ◽  
Economic Point ◽  
Instructional Resource

ABSTRACT This case originates from a real-life business situation and illustrates the application of impairment tests in accordance with IFRS and U.S. GAAP. In the first part of the case study, students examine conceptual questions of impairment tests under IFRS and U.S. GAAP with respect to applicable accounting standards, definitions, value concepts, and frequency of application. In addition, the case encourages students to discuss the impairment regime from an economic point of view. The second part of the instructional resource continues to provide instructors with the flexibility of applying U.S. GAAP and/or IFRS when students are asked to test a long-lived asset for impairment and, if necessary, allocate any potential impairment. This latter part demonstrates that impairment tests require professional judgment that students are to exercise in the case.

Design and Real-life Deployment of a Smart Nanogrid: A Greek Case Study

2020 ◽  
Author(s):  
Apostolos C. Tsolakis ◽  
Angelina D. Bintoudi ◽  
Lampros Zyglakis ◽  
Stylianos Zikos ◽  
Christos Timplalexis ◽  
...  
Keyword(s):  
Real Life

scholarly journals Black-Box-Based Mathematical Modelling of Machine Intelligence Measuring

Mathematics ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 681
Author(s):  
László Barna Iantovics
Keyword(s):  
Problem Solving ◽  
Scientific Literature ◽  
Real Life ◽  
Intelligent Agent ◽  
Difficult Problem ◽  
Black Box ◽  
Machine Intelligence ◽  
Agent Based ◽  
Np Hard Problem ◽  
Box Method

Current machine intelligence metrics rely on a different philosophy, hindering their effective comparison. There is no standardization of what is machine intelligence and what should be measured to quantify it. In this study, we investigate the measurement of intelligence from the viewpoint of real-life difficult-problem-solving abilities, and we highlight the importance of being able to make accurate and robust comparisons between multiple cooperative multiagent systems (CMASs) using a novel metric. A recent metric presented in the scientific literature, called MetrIntPair, is capable of comparing the intelligence of only two CMASs at an application. In this paper, we propose a generalization of that metric called MetrIntPairII. MetrIntPairII is based on pairwise problem-solving intelligence comparisons (for the same problem, the problem-solving intelligence of the studied CMASs is evaluated experimentally in pairs). The pairwise intelligence comparison is proposed to decrease the necessary number of experimental intelligence measurements. MetrIntPairII has the same properties as MetrIntPair, with the main advantage that it can be applied to any number of CMASs conserving the accuracy of the comparison, while it exhibits enhanced robustness. An important property of the proposed metric is the universality, as it can be applied as a black-box method to intelligent agent-based systems (IABSs) generally, not depending on the aspect of IABS architecture. To demonstrate the effectiveness of the MetrIntPairII metric, we provide a representative experimental study, comparing the intelligence of several CMASs composed of agents specialized in solving an NP-hard problem.

scholarly journals Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Chris Bauer ◽  
Ralf Herwig ◽  
Matthias Lienhard ◽  
Paul Prasse ◽  
Tobias Scheffer ◽  
...  
Keyword(s):  
Text Mining ◽  
Knowledge Base ◽  
Survival Data ◽  
Scientific Literature ◽  
Entity Recognition ◽  
Literature Mining ◽  
Cancer Drugs ◽  
Classical Text ◽  
Anti Cancer ◽  
Cancer Types

Abstract Background There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. Methods In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. Results We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: https://knowledgebase.microdiscovery.de/heatmap. Conclusions Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.

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