Francesco Archetti

Genetic programming for computational pharmacokinetics in drug discovery and development

The success of a drug treatment is strongly correlated with the ability of a molecule to reach its target in the patient’s organism without inducing toxic effects. Moreover the reduction of cost and time associated with drug discovery and development is becoming a crucial requirement for pharmaceutical industry. Therefore computational methods allowing reliable predictions of newly synthesized compounds properties are of outmost relevance. In this paper we discuss the role of genetic programming in predictive pharmacokinetics, considering the estimation of adsorption, distribution, metabolism, excretion and toxicity processes (ADMET) that a drug undergoes into the patient’s organism. We compare genetic programming with other well known machine learning techniques according to their ability to predict oral bioavailability (%F), median oral lethal dose (LD50) and plasma-protein binding levels (%PPB). Since these parameters respectively characterize the percentage of initial drug dose that effectively reaches the systemic blood circulation, the harmful effects and the distribution into the organism of a drug, they are essential for the selection of potentially good molecules. Our results suggest that genetic programming is a valuable technique for predicting pharmacokinetics parameters, both from the point of view of the accuracy and of the generalization ability.

Genetic programming for human oral bioavailability of drugs

Automatically assessing the value of bioavailability from the chemical structure of a molecule is a very important issue in biomedicine and pharmacology. In this paper, we present an empirical study of some well known Machine Learning techniques, including various versions of Genetic Programming, which have been trained to this aim using a dataset of molecules with known bioavailability. Genetic Programming has proven the most promising technique among the ones that have been considered both from the point of view of the accurateness of the solutions proposed, of the generalization capabilities and of the correlation between predicted data and correct ones. Our work represents a first answer to the demand for quantitative bioavailability estimation methods proposed in literature, since the previous contributions focus on the classification of molecules into classes with similar bioavailability.

A survey on the global optimization problem: General theory and computational approaches

Several different approaches have been suggested for the numerical solution of the global optimization problem: space covering methods, trajectory methods, random sampling, random search and methods based on a stochastic model of the objective function are considered in this paper and their relative computational effectiveness is discussed. A closer analysis is performed of random sampling methods along with cluster analysis of sampled data and of Bayesian nonparametric stopping rules.

An integrated communications framework for context aware continuous monitoring with body sensor networks

This paper deals with a wireless pervasive communication system to support advanced healthcare applications. The proposed system is based on an ad hoc interaction of mobile body sensor networks with independent wireless sensor networks already deployed within the environments in order to allow a continuous and context aware health monitoring for patients along their daily life scenarios with an unprecedented precision and flexibility of sensing. After an accurate protocol characterization, simulation results are provided, underlining remarkable performance with respect to existing solutions, for different mobility models and node density values.

A hierarchical document clustering environment based on the induced bisecting k-means

The steady increase of information on WWW, digital library, portal, database and local intranet, gave rise to the development of several methods to help user in Information Retrieval, information organization and browsing. Clustering algorithms are of crucial importance when there are no labels associated to textual information or documents. The aim of clustering algorithms, in the text mining domain, is to group documents concerning with the same topic into the same cluster, producing a flat or hierarchical structure of clusters. In this paper we present a Knowledge Discovery System for document processing and clustering. The clustering algorithm implemented in this system, called Induced Bisecting k-Means, outperforms the Standard Bisecting k-Means and is particularly suitable for on line applications when computational efficiency is a crucial aspect.

A probabilistic relational approach for web document clustering

The exponential growth of information available on the World Wide Web, and retrievable by search engines, has implied the necessity to develop efficient and effective methods for organizing relevant contents. In this field document clustering plays an important role and remains an interesting and challenging problem in the field of web computing. In this paper we present a document clustering method, which takes into account both contents information and hyperlink structure of web page collection, where a document is viewed as a set of semantic units. We exploit this representation to determine the strength of a relation between two linked pages and to define a relational clustering algorithm based on a probabilistic graph representation. The experimental results show that the proposed approach, called RED-clustering, outperforms two of the most well known clustering algorithm as k-Means and Expectation Maximization.

Emotional states in judicial courtrooms: An experimental investigation

Thanks to the recent progress in the judicial proceedings management, especially related to the introduction of audio/video recording facilities, the challenge of identification of emotional states can be tackled. Discovering affective states embedded into speech signals could help in semantic retrieval of multimedia clips, and therefore in a deep understanding of mechanisms behind courtroom debates and judges/jurors decision making processes. In this paper two main contributions are given: (1) the collection of real-world human emotions coming from courtroom audio recordings; (2) the investigation of a hierarchical classification system, based on a risk minimization method, able to recognize emotional states from speech signatures. The accuracy of the proposed classification approach - named Multilayer Support Vector Machines - has been evaluated by comparing its performance with traditional machine learning approaches, by using both benchmark datasets and real courtroom recordings. Results in recognition obtained by the proposed technique outperform the prediction power achieved by traditional approaches like SVM, k-Nearest Neighbors, Naive Bayes, Decision Trees and Bayesian Networks.

Audio-Based Emotion Recognition in Judicial Domain: A Multilayer Support Vector Machines Approach

Thanks to the recent progresses in judicial proceedings management, especially related to the introduction of audio/video recording systems, semantic retrieval is a key challenge. In this context emotion recognition engine, through the analysis of vocal signature of actors involved in judicial proceedings, could provide useful annotations for semantic retrieval of multimedia clips. With respect to the generation of semantic emotional tag in judicial domain, two main contributions are given: (1) the construction of an Italian emotional database for Italian proceedings annotation; (2) the investigation of a hierarchical classification system, based on risk minimization method, able to recognize emotional states from vocal signatures. In order to estimate the degree of affection we compared the proposed classification method with SVM, K-Nearest Neighbors and Naive Bayes, highlighting in terms of classification accuracy, the improvements given by a hierarchical learning approach.

IKNOS: inference and knowledge in networks of sensors

This paper presents a framework for managing data from sensor of poor quality, with the objective to reduce at the same time the communication load and hence energy consumption. Each node in a wireless sensor network maintains a simple local model of the data it is collecting and sends its parameters to a central location (sink), where it is executed the global monitoring. Local models are used to simulate sensors readings, minimising the need of communication with sensors and hence the consumption of their battery; they are updated locally, when sensor readings differ excessively from simulated data. At the sink the global model (a Bayesian Network) is learnt on the simulated data. It is used to identify and replace anomalous readings (outliers) that a sensor should have produced and to detect anomalies missed by any single node (when communication with a sensor is interrupted).

Enhancing web page classification through image-block importance analysis

We present a term weighting approach for improving web page classification, based on the assumption that the images of a web page are those elements which mainly attract the attention of the user. This assumption implies that the text contained in the visual block in which an image is located, called image-block, should contain significant information about the page contents. In this paper we propose a new metric, called the Inverse Term Importance Metric, aimed at assigning higher weights to important terms contained into important image-blocks identified by performing a visual layout analysis. We propose different methods to estimate the visual image-blocks importance, to smooth the term weight according to the importance of the blocks in which the term is located. The traditional TFxIDF model is modified accordingly and used in the classification task. The effectiveness of this new metric and the proposed block evaluation methods have been validated using different classification algorithms.