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At least 487 records · Page 27Linked to original sources
PubMed1995

Graph-theoretic approach to RNA modeling using comparative data.

We have examined the utility of a graph-theoretic algorithm for building comparative RNA models. The method uses a maximum weighted matching algorithm to find the optimal set of basepairs given the mutual information for all pairs of alignment positions. In all cases examined, the technique generated models similar to those based on conventional comparative analysis. Any set of pairwise interactions can be suggested including pseudoknots. Here we describe the details of the method and demonstrate its implementation on tRNA where many secondary and tertiary base-pairs are accurately predicted. We also examine the usefulness of the method for the identification of shared structural features in families of RNAs isolated by artificial selection methods such as SELEX.

Algorithms↗
PubMed1993

Structuration and acquisition of medical knowledge. Using UMLS in the conceptual graph formalism.

The use of a taxonomy, such as the concept type lattice (CTL) of Conceptual Graphs, is a central structuring piece in a knowledge-based system. The knowledge it contains is constantly used by the system, and its structure provides a guide for the acquisition of other pieces of knowledge. We show how UMLS can be used as a knowledge resource to build a CTL and how the CTL can help the process of acquisition for other kinds of knowledge. We illustrate this method in the context of the MENELAS natural language understanding project.

Artificial Intelligence↗
PubMed1977

A straight-line graph for leg-length discrepancies.

A graphic method is presented that facilitates the recording and interpretation of data in cases of leg-length discrepancy. It provides a mechanism for predicting future growth that automatically takes into account the child's growth percentile and the degree of growth inhibition in the short leg. It can be used to predict the effects of corrective surgical procedures and to choose a surgical timetable. A series of cases of epiphyseodesis is presented, showing the straight-line graph method to be significantly more accurate than the so-called growth-remaining method, particularly in cases of growth inhibition.

Adolescent↗
PubMed1995

A conceptual graphs modeling of UMLS components.

The Unified Medical Language System (UMLS) of the U.S. National Library of Medicine is a complex collection of terms, concepts, and relationships derived from standard classifications. Potential applications would benefit from a high level representation of its components. This paper proposes a conceptual representation of both the Metathesaurus and the Semantic Network of the UMLS based on conceptual graphs. It shows that the addition of a dictionary of concepts to the UMLS knowledge base allows the capability to exploit it pertinently. This dictionary defines more precisely the core concepts and adds constraints on their use. Constraints are dedicated to guide an "intelligent" browsing of the UMLS knowledge sources.

Dictionaries as Topic↗
PubMed1995

Representing clinical narratives using conceptual graphs.

The analysis of medical narratives and the generation of natural language expressions are strongly dependent on the existence of an adequate representation language. Such a language has to be expressive enough in order to handle the complexity of human reasoning in the domain. Sowa's Conceptual Graphs (CG) are an answer, and this paper presents a multilingual implementation, using French, English and German. Current developments demonstrate the feasibility of an approach to natural Language Understanding where semantic aspects are dominant, in contrast to syntax driven methods. The basic idea is to aggregate blocks of words according to semantic compatibility rules, following a method called Proximity Processing. The CG representation is gradually built, starting from single words in a semantic lexicon, to finally give a complete representation of the sentence under the form of a single CG. The process is dependent on specific rules of the medical domain, and for this reason is largely controlled by the declarative knowledge of the medical Linguistic Knowledge Base.

Artificial Intelligence↗
PubMed1997

Diagnosis of breast cancer by measuring nuclear disorder using planar graphs.

OBJECTIVE: To achieve a classifier of breast lesions to distinguish benign from malignant mammary lesions by quantifying nuclear disorder in epithelial cell groups from smears obtained by fine needle aspiration. STUDY DESIGN: The study included 95 cases of breast cancer (289 groups) and 47 of benign breast lesions (150 groups), diagnosed by cytology. Information from planar graphs (mean of nuclear distances, standard deviation, maximum and minimum distance between nuclei) was used, and an algorithm constructed for this purpose was applied. The data were classified by double methodology--discriminant analysis, and classification and regression trees (CART)--to determine which achieved the best results. RESULTS: CART selected the standard deviation of nuclear distances with accurate classification in 95.7% of benign lesions and 97.9% of malignant. Discriminant analysis constructed the discriminant function using the mean of nuclear distances and its standard deviation, with results similar to those of CART. CONCLUSION: The classifier based on nuclear disorder that we constructed proved to be rapid, simple and effective for malignant-benign discrimination in breast lesions and should be of diagnostic assistance.

Breast Neoplasms↗
PubMed1999

Segmentation of tissue architecture by distance graph matching.

BACKGROUND: Characterization of tissues can be based on the topographical relationship between the cells. Such characterization should be insensitive to distortions intrinsic to the acquisition of biological preparation. In this paper, a method for the robust segmentation of tissues based on the spatial distribution of cells is proposed. MATERIALS AND METHODS: The neighborhood of each cell in the tissue is modeled by the distances to the surrounding cells. Comparison with an example or prototype neighborhood reveals topographical similarity between tissue and prototype. Processing of all cells in the tissue extracts the regions with tissue architecture similar to the given example. RESULTS: Comparison with other topographical-segmentation methods shows that the proposed method is better suited for partitioning tissue architecture. As an example, the quantification of the structural integrity in rat hippocampi after ischemia is demonstrated. In contrast to other methods, the algorithm correlates well with expert evaluation. CONCLUSIONS: The present method reduces the nonbiological variation in the analysis of tissue sections and thus improves confidence in the result. The method can be applied to any field where regular patterns have to be detected, as long as the directional distribution of neighbors may be neglected.

Algorithms↗
PubMed1986

Number of receptor sites from Scatchard and Klotz graphs: complementary approaches.

Estimates of number of receptor sites and evaluation of the complexity of the binding process require collection of a spectrum of binding measurements and selection of a theoretical model to fit the experimental data. The appropriateness of the measurements and of the model can be visually judged on graphic displays of the model-data fitting curves in Scatchard and semilogarithmic coordinates. This approach is helpful for detecting the two types of errors most frequently found in reports of binding studies: (1) underestimating the number of binding sites, and (2) failure to recognize the complexity of the binding process. While the former is readily recognizable on semilogarithmic but not on Scatchard plots of the model fitting the data, the latter might not be apparent on either plot. Collection of extensive measurements over a wide range of ligand concentrations with graphic display of the model-data fitting curves in Scatchard and semilogarithmic coordinates should be used to recognize and prevent both errors.

Humans↗
PubMed2002

Graphing survival curve estimates for time-dependent covariates.

Graphical representation of statistical results is often used to assist readers in the interpretation of the findings. This is especially true for survival analysis where there is an interest in explaining the patterns of survival over time for specific covariates. For fixed categorical covariates, such as a group membership indicator, Kaplan-Meier estimates (1958) can be used to display the curves. For time-dependent covariates this method may not be adequate. Simon and Makuch (1984) proposed a technique that evaluates the covariate status of the individuals remaining at risk at each event time. The method takes into account the change in an individual's covariate status over time. The survival computations are the same as the Kaplan-Meier method, in that the conditional survival estimates are the function of the ratio of the number of events to the number at risk at each event time. The difference between the two methods is that the individuals at risk within each level defined by the covariate is not fixed at time 0 in the Simon and Makuch method as it is with the Kaplan-Meier method. Examples of how the two methods can differ for time dependent covariates in Cox proportional hazards regression analysis are presented.

Adolescent↗
PubMed1982

Linkage graphs.

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Biopolymers↗