Context-aware visual exploration of molecular databases

Facilitating the visual exploration of scientific data has received increasing attention in the past decade or so. Especially in life science related application areas the amount of available data has grown at a breath taking pace. In this paper we describe an approach that allows for visual inspection of large collections of molecular compounds. In contrast to classical visualizations of such spaces we incorporate a specific focus of analysis, for example the outcome of a biological experiment such as high throughout screening results. The presented method uses this experimental data to select molecular fragments of the underlying molecules that have interesting properties and uses the resulting space to generate a two dimensional map based on a singular value decomposition algorithm and a self organizing map. Experiments on real datasets show that the resulting visual landscape groups molecules of similar chemical properties in densely connected regions

Fast training of self organizing maps for the visual exploration of molecular compounds

Visual exploration of scientific data in life science area is a growing research field due to the large amount of available data. The Kohonen’s Self Organizing Map (SOM) is a widely used tool for visualization of multidimensional data. In this paper we present a fast learning algorithm for SOMs that uses a simulated annealing method to adapt the learning parameters. The algorithm has been adopted in a data analysis framework for the generation of similarity maps. Such maps provide an effective tool for the visual exploration of large and multi-dimensional input spaces. The approach has been applied to data generated during the High Throughput Screening of molecular compounds; the generated maps allow a visual exploration of molecules with similar topological properties. The experimental analysis on real world data from the National Cancer Institute shows the speed up of the proposed SOM training process in comparison to a traditional approach. The resulting visual landscape groups molecules with similar chemical properties in densely connected regions

Curbing domestic violence: instantiating C-K theory with formal concept analysis and emergent self organizing maps.

In this paper we propose a human-centered process for knowledge discovery from unstructured text that makes use of Formal Concept Analysis and Emergent Self Organizing Maps. The knowledge discovery process is conceptualized and interpreted as successive iterations through the Concept-Knowledge (C-K) theory design square. To illustrate its effectiveness, we report on a real-life case study of using the process at the Amsterdam-Amstelland police in the Netherlands aimed at distilling concepts to identify domestic violence from the unstructured text in actual police reports. The case study allows us to show how the process was not only able to uncover the nature of a phenomenon such as domestic violence, but also enabled analysts to identify many types of anomalies in the practice of policing. We will illustrate how the insights obtained from this exercise resulted in major improvements in the management of domestic violence cases.Formal concept analysis; Emergent self organizing map; C-K theory; Text mining; Actionable knowledge discovery; Domestic violence;

Detecting domestic violence.

Over 90% of the case data from police inquiries is stored as unstructured text in police databases. We use the combination of Formal Concept Analysis and Emergent Self Organizing Maps for exploring a dataset of unstructured police reports out of the Amsterdam-Amstelland police region in the Netherlands. In this paper, we specifically aim at making the reader familiar with how we used these two tools for browsing the dataset and how we discovered useful patterns for labelling cases as domestic or as non-domestic violence.Formal concept analysis (FCA); Emergent SOM; Domestic violence; Knowledge discovery in databases; Text mining; Exploratory data analysis;

A case of using formal concept analysis in combination with emergent self organizing maps for detecting domestic violence.

In this paper, we propose a framework for iterative knowledge discovery from unstructured text using Formal Concept Analysis and Emergent Self Organizing Maps. We apply the framework to a real life case study using data from the Amsterdam-Amstelland police. The case zooms in on the problem of distilling concepts for domestic violence from the unstructured text in police reports. Our human-centered framework facilitates the exploration of the data and allows for an efficient incorporation of prior expert knowledge to steer the discovery process. This exploration resulted in the discovery of faulty case labellings, common classification errors made by police officers, confusing situations, missing values in police reports, etc. The framework was also used for iteratively expanding a domain-specific thesaurus. Furthermore, we showed how the presented method was used to develop a highly accurate and comprehensible classification model that automatically assigns a domestic or non-domestic violence label to police reports.Formal concept analysis; Emergent self organizing map; Text mining; Actionable knowledge discovery; Domestic violence;

Concept discovery innovations in law enforcement: a perspective.

In the past decades, the amount of information available to law enforcement agencies has increased significantly. Most of this information is in textual form, however analyses have mainly focused on the structured data. In this paper, we give an overview of the concept discovery projects at the Amsterdam-Amstelland police where Formal Concept Analysis (FCA) is being used as text mining instrument. FCA is combined with statistical techniques such as Hidden Markov Models (HMM) and Emergent Self Organizing Maps (ESOM). The combination of this concept discovery and refinement technique with statistical techniques for analyzing high-dimensional data not only resulted in new insights but often in actual improvements of the investigation procedures.Formal concept analysis; Intelligence led policing; Knowledge discovery;

ANTIDS: Self-Organized Ant-based Clustering Model for Intrusion Detection System

Security of computers and the networks that connect them is increasingly becoming of great significance. Computer security is defined as the protection of computing systems against threats to confidentiality, integrity, and availability. There are two types of intruders: the external intruders who are unauthorized users of the machines they attack, and internal intruders, who have permission to access the system with some restrictions. Due to the fact that it is more and more improbable to a system administrator to recognize and manually intervene to stop an attack, there is an increasing recognition that ID systems should have a lot to earn on following its basic principles on the behavior of complex natural systems, namely in what refers to self-organization, allowing for a real distributed and collective perception of this phenomena. With that aim in mind, the present work presents a self-organized ant colony based intrusion detection system (ANTIDS) to detect intrusions in a network infrastructure. The performance is compared among conventional soft computing paradigms like Decision Trees, Support Vector Machines and Linear Genetic Programming to model fast, online and efficient intrusion detection systems.Comment: 13 pages, 3 figures, Swarm Intelligence and Patterns (SIP)- special track at WSTST 2005, Muroran, JAPA