18235969
Learning Relations and Information Extraction Rules for Protein Annotation
Protein annotation is a task that describes protein X in terms of topic Y Until now, most of protein annotation work has been done manually by human annotators. However, as the number of biomedical papers grows ever rapidly, manual annotation becomes difficult, and there is increasing need to automate the protein annotation process. Recently, Information Extraction (IE) has been used to solve this problem. Typically, IE requires pre-defined relations and hand-crafted IE rules or annotated corpora, and these requirements are difficult to satisfy in real world domains such as the biomedical domain. In this paper, we describe an IE system which requires only sentences labeled relevant or not to a given topic by domain experts.
6458402
METIS: multiple extraction techniques for informative sentences
SUMMARY
METIS is a web-based integrated annotation tool. From single query sequences, the PRECIS component allows users to generate structured protein family reports from sets of related Swiss-Prot entries. These reports may then be augmented with pertinent sentences extracted from online biomedical literature via support vector machine and rule-based sentence classification systems.


AVAILABILITY
http://umber.sbs.man.ac.uk/dbbrowser/metis/
20514902
A CHIM-based interactive Tchebycheff procedure for multiple objective decision making
This study presents a new solution procedure for multiple objective programming (MOP). It applies the concept of the normal boundary intersection (NBI) within the framework of the interactive weighted Tchebycheff procedure (IWTP). The proposed procedure is a collaborative approach to overcome the weak points inherent in both the NBI method and IWTP. In order to control the solution procedure of pinpointing a final solution properly, we parameterized the Pareto-frontier via a set of reference point vectors based on the convex hull of individual maxima (CHIM) instead of using the varying weights of each objective. Using well-distributed reference point vectors, we could identify well-distributed Pareto-optimal solutions, thereby eliminating the IWTP filtering stages and reducing the chance of missing the best compromise solution from the decision maker (DM)'s utility point of view. Moreover, by working with a sequence of progressively smaller subsets of reference point vectors, the DM can identify a final solution at earlier stages than with the IWTP.
14157019
Projections of Binary Linear Codes onto Larger Fields
We study certain projections of binary linear codes onto larger fields. These projections include the well-known projection of the extended Golay [24,12,8] code onto the hexacode over $\mbox{GF}(4)$ and the projection of the Reed--Muller code R(2,5) onto the unique self-dual [8,4,4] code over $\mbox{GF}(4)$. We give a characterization of these projections, and we construct several binary linear codes which have best known optimal parameters, for instance, [20,11,5], [40,22,8], [48,21,12], and [72,31,16]. We also relate the automorphism group of a quaternary code to that of the corresponding binary code.
488943
A Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model
In modern biology, one of the most important research problems is to understand how protein sequences fold into their native 3D structures. To investigate this problem at a high level, one wishes to analyze the protein landscapes, i.e., the structures of the space of all protein sequences and their native 3D structures. Perhaps the most basic computational problem at this level is to take a target 3D structure as input and design a fittest protein sequence with respect to one or more fitness functions of the target 3D structure. We develop a toolbox of combinatorial techniques for protein landscape analysis in the Grand Canonical model of Sun, Brem, Chan, and Dill. The toolbox is based on linear programming, network flow, and a linear-size representation of all minimum cuts of a network. It not only substantially expands the network flow technique for protein sequence design in Kleinberg's seminal work but also is applicable to a considerably broader collection of computational problems than those considered by Kleinberg. We have used this toolbox to obtain a number of efficient algorithms and hardness results. We have further used the algorithms to analyze 3D structures drawn from the Protein Data Bank and have discovered some novel relationships between such native 3D structures and the Grand Canonical model.
6080724
BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature
MOTIVATION
Contrasts are useful conceptual vehicles for learning processes and exploratory research of the unknown. For example, contrastive information between proteins can reveal what similarities, divergences and relations there are of the two proteins, leading to invaluable insights for better understanding about the proteins. Such contrastive information are found to be reported in the biomedical literature. However, there have been no reported attempts in current biomedical text mining work that systematically extract and present such useful contrastive information from the literature for exploitation.


RESULTS
Our BioContrasts system extracts protein-protein contrastive information from MEDLINE abstracts and presents the information to biologists in a web-application for exploitation. Contrastive information are identified in the text abstracts with contrastive negation patterns such as 'A but not B'. A total of 799 169 pairs of contrastive expressions were successfully extracted from 2.5 million MEDLINE abstracts. Using grounding of contrastive protein names to Swiss-Prot entries, we were able to produce 41 471 pieces of contrasts between Swiss-Prot protein entries. These contrastive pieces of information are then presented via a user-friendly interactive web portal that can be exploited for applications such as the refinement of biological pathways.


AVAILABILITY
BioContrasts can be accessed at http://biocontrasts.i2r.a-star.edu.sg. It is also mirrored at http://biocontrasts.biopathway.org.


SUPPLEMENTARY INFORMATION
Supplementary materials are available at Bioinformatics online.
18935022
Dynamically mapping tasks with priorities and multiple deadlines in a heterogeneous environment
In a distributed heterogeneous computing system, the resources have different capabilities and tasks have different requirements. To maximize the performance of the system, it is essential to assign the resources to tasks (match) and order the execution of tasks on each resource (schedule) to exploit the heterogeneity of the resources and tasks. Dynamic mapping (defined as matching and scheduling) is performed when the arrival of tasks is not known a priori. In the heterogeneous environment considered in this study, tasks arrive randomly, tasks are independent (i.e., no inter-task communication), and tasks have priorities and multiple soft deadlines. The value of a task is calculated based on the priority of the task and the completion time of the task with respect to its deadlines. The goal of a dynamic mapping heuristic in this research is to maximize the value accrued of completed tasks in a given interval of time. This research proposes, evaluates, and compares eight dynamic mapping heuristics. Two static mapping schemes (all arrival information of tasks are known) are designed also for comparison. The performance of the best heuristics is 84% of a calculated upper bound for the scenarios considered.