Mass data exploration in oncology: an information synthesis approach.

New technologies and equipment allow for mass treatment of samples and research teams share acquired data on an always larger scale. In this context scientists are facing a major data exploitation problem. More precisely, using these data sets through data mining tools or introducing them in a classical experimental approach require a preliminary understanding of the information space, in order to direct the process. But acquiring this grasp on the data is a complex activity, which is seldom supported by current software tools. The goal of this paper is to introduce a solution to this scientific data grasp problem. Illustrated in the Tissue MicroArrays application domain, the proposal is based on the synthesis notion, which is inspired by Information Retrieval paradigms. The envisioned synthesis model gives a central role to the study the researcher wants to conduct, through the task notion. It allows for the implementation of a task-oriented Information Retrieval prototype system. Cases studies and user studies were used to validate this prototype system. It opens interesting prospects for the extension of the model or extensions towards other application domains.

Distributed local MRF models for tissue and structure brain segmentation.

Accurate tissue and structure segmentation of magnetic resonance (MR) brain scans is critical in several applications. In most approaches this task is handled through two sequential steps. We propose to carry out cooperatively both tissue and subcortical structure segmentation by distributing a set of local and cooperative Markov random field (MRF) models Tissue segmentation is performed by partitioning the volume into subvolumes where local MRFs are estimated in cooperation with their neighbors to ensure consistency. Local estimation fits precisely to the local intensity distribution and thus handles nonuniformity of intensity without any bias field modelization. Similarly, subcortical structure segmentation is performed via local MRF models that integrate localization constraints provided by a priori fuzzy description of brain anatomy. Subcortical structure segmentation is not reduced to a subsequent processing step but joined with tissue segmentation: the two procedures cooperate to gradually and conjointly improve model accuracy. We propose a framework to implement this distributed modeling integrating cooperation, coordination, and local model checking in an efficient way. Its evaluation was performed using both phantoms and real 3 T brain scans, showing good results and in particular robustness to nonuniformity and noise with a low computational cost. This original combination of local MRF models, including anatomical knowledge, appears as a powerful and promising approach for MR brain scan segmentation.

Agentification of Markov model-based segmentation: application to magnetic resonance brain scans.

OBJECTIVE: Markov random field (MRF) models have been traditionally applied to the task of robust-to-noise image segmentation. Most approaches estimate MRF parameters on the whole image via a global expectation-maximization (EM) procedure. The resulting estimated parameters are likely to be uncharacteristic of local image features. Instead, we propose to distribute a set of local MRF models within a multiagent framework. MATERIALS AND METHODS: Local segmentation agents estimate local MRF models via local EM procedures and cooperate to ensure a global consistency of local models. We demonstrate different types of cooperations between agents that lead to additional levels of regularization compared to the standard label regularization provided by MRF. Embedding Markovian EM procedures into a multiagent paradigm shows interesting properties that are illustrated on magnetic resonance (MR) brain scan segmentation. RESULTS: A cooperative tissue and subcortical structure segmentation approach is designed with such a framework, where both models mutually improve. Several experiments are reported and illustrate the working of Markovian EM agents. The evaluation of MR brain scan segmentation was performed using both phantoms and real 3T brain scans. It showed a robustness to intensity non-uniformity and noise, together with a low computational time. CONCLUSION: Based on these experiments MRF agent-based approach appears to be a very promising new tool for complex image segmentation.

Knowledge construction from time series data using a collaborative exploration system.

This paper deals with the exploration of biomedical multivariate time series to construct typical parameter evolution or scenarios. This task is known to be difficult: the temporal and multivariate nature of the data at hand and the context-sensitive aspect of data interpretation hamper the formulation of a priori knowledge about the kind of patterns that can be detected as well as their interrelations. This paper proposes a new way to tackle this problem based on a human-computer collaborative approach involving specific annotations. Three grounding principles, namely autonomy, adaptability and emergence, support the co-construction of successive abstraction levels for data interpretation. An agent-based design is proposed to support these principles. Preliminary results in a clinical context are presented to support our proposal. A comparison with two well-known time series exploration tools is furthermore performed.

Learning recurrent behaviors from heterogeneous multivariate time-series.

OBJECTIVE: For the last years, time-series mining has become a challenging issue for researchers. An important application lies in most monitoring purposes, which require analyzing large sets of time-series for learning usual patterns. Any deviation from this learned profile is then considered as an unexpected situation. Moreover, complex applications may involve the temporal study of several heterogeneous parameters. In that paper, we propose a method for mining heterogeneous multivariate time-series for learning meaningful patterns. METHODS: The proposed approach allows for mixed time-series - containing both pattern and non-pattern data - such as for imprecise matches, outliers, stretching and global translating of patterns instances in time. RESULTS: We present the results of our approach on synthetic data generated in the context of monitoring a person at home, as well as early results on few real sequences. The purpose is to build a behavioral profile of a person in their daily activities by analyzing the time variations of several quantitative or qualitative parameters recorded through a provision of sensors. CONCLUSIONS: The results are very promising. They also highlight the difficulty of tuning the parameters of the method.

Automated segmentation of human brain MR images using a multi-agent approach.

Image interpretation consists in finding a correspondence between radiometric information and symbolic labeling with respect to specific spatial constraints. It is intrinsically a distributed process in terms of goals to be reached, zones in the image to be processed and methods to be applied. To cope the the difficulty inherent in this process, several information processing steps are required to gradually extract information. In this paper we advocate the use of situated cooperative agents as a framework for managing such steps. Dedicated agent behaviors are dynamically adapted depending on their position in the image, of their topographic relationships and of the radiometric information available. The information collected by the agents is gathered, shared via qualitative maps, or used as soon as available by acquaintances. Incremental refinement of interpretation is obtained through a coarse to fine strategy. Our work is essentially focused on radiometry-based tissue interpretation where knowledge is introduced or extracted at several levels to estimate models for tissue-intensity distribution and to cope with noise, intensity non-uniformity and partial volume effect. Several experiments on phantom and real images were performed. A complete volume can be segmented in less than 5 min with about 0.84% accuracy of the segmented reference. Comparison with other techniques demonstrates the potential interest of our approach for magnetic resonance imaging (MRI) brain scan interpretation.

A knowledge-driven agent-centred framework for data mining in EMG.

In this paper, we present a multi-agent framework for data mining in electromyography. This application, based on a web interface, provides a set of functionalities allowing to manipulate 1000 medical cases and more than 25,000 neurological tests stored in a medical database. The aim is to extract medical information using data mining algorithms and to supply a knowledge base with pertinent information. The multi-agent platform gives the possibility to distribute the data management process between several autonomous entities. This framework provides a parallel and flexible data manipulation.