Intelligent data analysis in biomedicine

A framework for intelligent Twitter data analysis with non-negative matrix factorization

Purpose

The purpose of this paper is to propose a framework for intelligent analysis of Twitter data. The purpose of the framework is to allow users to explore a collection of tweets by extracting topics with semantic relevance. In this way, it is possible to detect groups of tweets related to new technologies, events and other topics that are automatically discovered.

Design/methodology/approach

The framework is based on a three-stage process. The first stage is devoted to dataset creation by transforming a collection of tweets in a dataset according to the vector space model. The second stage, which is the core of the framework, is centered on the use of non-negative matrix factorizations (NMF) for extracting human-interpretable topics from tweets that are eventually clustered. The number of topics can be user-defined or can be discovered automatically by applying subtractive clustering as a preliminary step before factorization. Cluster analysis and word-cloud visualization are used in the last stage to enable intelligent data analysis.

Findings

The authors applied the framework to a case study of three collections of Italian tweets both with manual and automatic selection of the number of topics. Given the high sparsity of Twitter data, the authors also investigated the influence of different initializations mechanisms for NMF on the factorization results. Numerical comparisons confirm that NMF could be used for clustering as it is comparable to classical clustering techniques such as spherical k-means. Visual inspection of the word-clouds allowed a qualitative assessment of the results that confirmed the expected outcomes.

Originality/value

The proposed framework enables a collaborative approach between users and computers for an intelligent analysis of Twitter data. Users are faced with interpretable descriptions of tweet clusters, which can be interactively refined with few adjustable parameters. The resulting clusters can be used for intelligent selection of tweets, as well as for further analytics concerning the impact of products, events, etc. in the social network.

Optimal marker placement in hadrontherapy: intelligent optimization strategies with augmented Lagrangian pattern search

PURPOSE

In high precision photon radiotherapy and in hadrontherapy, it is crucial to minimize the occurrence of geometrical deviations with respect to the treatment plan in each treatment session. To this end, point-based infrared (IR) optical tracking for patient set-up quality assessment is performed. Such tracking depends on external fiducial points placement. The main purpose of our work is to propose a new algorithm based on simulated annealing and augmented Lagrangian pattern search (SAPS), which is able to take into account prior knowledge, such as spatial constraints, during the optimization process.

MATERIAL AND METHODS

The SAPS algorithm was tested on data related to head and neck and pelvic cancer patients, and that were fitted with external surface markers for IR optical tracking applied for patient set-up preliminary correction. The integrated algorithm was tested considering optimality measures obtained with Computed Tomography (CT) images (i.e. the ratio between the so-called target registration error and fiducial registration error, TRE/FRE) and assessing the marker spatial distribution. Comparison has been performed with randomly selected marker configuration and with the GETS algorithm (Genetic Evolutionary Taboo Search), also taking into account the presence of organs at risk.

RESULTS

The results obtained with SAPS highlight improvements with respect to the other approaches: (i) TRE/FRE ratio decreases; (ii) marker distribution satisfies both marker visibility and spatial constraints. We have also investigated how the TRE/FRE ratio is influenced by the number of markers, obtaining significant TRE/FRE reduction with respect to the random configurations, when a high number of markers is used.

CONCLUSIONS

The SAPS algorithm is a valuable strategy for fiducial configuration optimization in IR optical tracking applied for patient set-up error detection and correction in radiation therapy, showing that taking into account prior knowledge is valuable in this optimization process. Further work will be focused on the computational optimization of the SAPS algorithm toward fast point-of-care applications.

Data analysis and data mining: current issues in biomedical informatics

BACKGROUND

Medicine and biomedical sciences have become data-intensive fields, which, at the same time, enable the application of data-driven approaches and require sophisticated data analysis and data mining methods. Biomedical informatics provides a proper interdisciplinary context to integrate data and knowledge when processing available information, with the aim of giving effective decision-making support in clinics and translational research.

OBJECTIVES

To reflect on different perspectives related to the role of data analysis and data mining in biomedical informatics.

METHODS

On the occasion of the 50th year of Methods of Information in Medicine a symposium was organized, which reflected on opportunities, challenges and priorities of organizing, representing and analysing data, information and knowledge in biomedicine and health care. The contributions of experts with a variety of backgrounds in the area of biomedical data analysis have been collected as one outcome of this symposium, in order to provide a broad, though coherent, overview of some of the most interesting aspects of the field.

RESULTS

The paper presents sections on data accumulation and data-driven approaches in medical informatics, data and knowledge integration, statistical issues for the evaluation of data mining models, translational bioinformatics and bioinformatics aspects of genetic epidemiology.

CONCLUSIONS

Biomedical informatics represents a natural framework to properly and effectively apply data analysis and data mining methods in a decision-making context. In the future, it will be necessary to preserve the inclusive nature of the field and to foster an increasing sharing of data and methods between researchers.

The coming of age of artificial intelligence in medicine

This paper is based on a panel discussion held at the Artificial Intelligence in Medicine Europe (AIME) conference in Amsterdam, The Netherlands, in July 2007. It had been more than 15 years since Edward Shortliffe gave a talk at AIME in which he characterized artificial intelligence (AI) in medicine as being in its "adolescence" (Shortliffe EH. The adolescence of AI in medicine: will the field come of age in the '90s? Artificial Intelligence in Medicine 1993;5:93-106). In this article, the discussants reflect on medical AI research during the subsequent years and characterize the maturity and influence that has been achieved to date. Participants focus on their personal areas of expertise, ranging from clinical decision-making, reasoning under uncertainty, and knowledge representation to systems integration, translational bioinformatics, and cognitive issues in both the modeling of expertise and the creation of acceptable systems.