Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information

BACKGROUND: The rapid publication of important research in the biomedical literature makes it increasingly difficult for researchers to keep current with significant work in their area of interest. RESULTS: This paper reports a scalable method for the discovery of protein-protein interactions in Medline abstracts, using a combination of text analytics, statistical and graphical analysis, and a set of easily implemented rules. Applying these techniques to 12,300 abstracts, a precision of 0.61 and a recall of 0.97 were obtained, (f = 0.74) and when allowing for two-hop and three-hop relations discovered by graphical analysis, the precision was 0.74 (f = 0.83). CONCLUSION: This combination of linguistic and statistical approaches appears to provide the highest precision and recall thus far reported in detecting protein-protein relations using text analytic approaches

Clique-Finding for Heterogeneity and Multidimensionality in Biomarker Epidemiology Research: The CHAMBER Algorithm

Commonly-occurring disease etiology may involve complex combinations of genes and exposures resulting in etiologic heterogeneity. We present a computational algorithm that employs clique-finding for heterogeneity and multidimensionality in biomedical and epidemiological research (the "CHAMBER" algorithm).This algorithm uses graph-building to (1) identify genetic variants that influence disease risk and (2) predict individuals at risk for disease based on inherited genotype. We use a set-covering algorithm to identify optimal cliques and a Boolean function that identifies etiologically heterogeneous groups of individuals. We evaluated this approach using simulated case-control genotype-disease associations involving two- and four-gene patterns. The CHAMBER algorithm correctly identified these simulated etiologies. We also used two population-based case-control studies of breast and endometrial cancer in African American and Caucasian women considering data on genotypes involved in steroid hormone metabolism. We identified novel patterns in both cancer sites that involved genes that sulfate or glucuronidate estrogens or catecholestrogens. These associations were consistent with the hypothesized biological functions of these genes. We also identified cliques representing the joint effect of multiple candidate genes in all groups, suggesting the existence of biologically plausible combinations of hormone metabolism genes in both breast and endometrial cancer in both races.The CHAMBER algorithm may have utility in exploring the multifactorial etiology and etiologic heterogeneity in complex disease

Telecommunications Network Design Algorithms

x, 368 tr. ; 23 cm

Telecommunications Network Design Algorithms

x, 368 tr. ; 21x30 cm

Telecomunications network design algorithms

xv, 368 p. : il.; 24 cm

Access rights analysis for Java

Java ™ 2 has a security architecture that protects systems from unauthorized access by mobile or statically configured code. The problem is in manually determining the set of security access rights required to execute a library or application. The commonly used strategy is to execute the code, note authorization failures, allocate additional access rights, and test again. This process iterates until the code successfully runs for the test cases in hand. Test cases usually do not cover all paths through the code, so failures can occur in deployed systems. Conversely, a broad set of access rights is allocated to the code to prevent authorization failures from occurring. However, this often leads to a violation of the “Principle of Least Privilege.” This paper presents a technique for computing the access rights requirements by using a context sensitive, flow sensitive, interprocedural data flow analysis. By using this analysis, we compute at each program point the set of access rights required by the code. We model features such as multi-threading, implicitly defined security policies, the semantics of the Permission.implies method and generation of a security policy description. We implemented the algorithms and present the results of our analysis on a set of programs. While the analysis techniques described in this paper are in the context of Java code, the basic techniques are applicable to access rights analysis issues in non-Java-based systems

Mobile Agents: Are they a good idea?

: Mobile agents are programs, typically written in a script language, which may be dispatched from a client computer and transported to a remote server computer for execution. Several authors have suggested that mobile agents offer an important new method of performing transactions and information retrieval in networks. Other writers have pointed out, however, that mobile agent introduce severe concerns for security. We consider the advantages offered by mobile agents and assess them against alternate methods of achieving the same function. We conclude that, while the individual advantages of agents do not represent an overwhelming motivation for their adoption, the creation of a pervasive agent framework facilitates a very large number of network services and applications. 1 March 28, 1995 1 This Research Report was de-classified from IBM Confidential on March 13, 1995. iv Mobile Agents Introduction The idea of performing client-server computing by the transmission of executable..