10,434 research outputs found
Semi-supervised model-based clustering with controlled clusters leakage
In this paper, we focus on finding clusters in partially categorized data
sets. We propose a semi-supervised version of Gaussian mixture model, called
C3L, which retrieves natural subgroups of given categories. In contrast to
other semi-supervised models, C3L is parametrized by user-defined leakage
level, which controls maximal inconsistency between initial categorization and
resulting clustering. Our method can be implemented as a module in practical
expert systems to detect clusters, which combine expert knowledge with true
distribution of data. Moreover, it can be used for improving the results of
less flexible clustering techniques, such as projection pursuit clustering. The
paper presents extensive theoretical analysis of the model and fast algorithm
for its efficient optimization. Experimental results show that C3L finds high
quality clustering model, which can be applied in discovering meaningful groups
in partially classified data
How to Explain Individual Classification Decisions
After building a classifier with modern tools of machine learning we
typically have a black box at hand that is able to predict well for unseen
data. Thus, we get an answer to the question what is the most likely label of a
given unseen data point. However, most methods will provide no answer why the
model predicted the particular label for a single instance and what features
were most influential for that particular instance. The only method that is
currently able to provide such explanations are decision trees. This paper
proposes a procedure which (based on a set of assumptions) allows to explain
the decisions of any classification method.Comment: 31 pages, 14 figure
A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature
We participated, in the Article Classification and the Interaction Method
subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of
the BioCreative III Challenge. For the ACT, we pursued an extensive testing of
available Named Entity Recognition and dictionary tools, and used the most
promising ones to extend our Variable Trigonometric Threshold linear
classifier. For the IMT, we experimented with a primarily statistical approach,
as opposed to employing a deeper natural language processing strategy. Finally,
we also studied the benefits of integrating the method extraction approach that
we have used for the IMT into the ACT pipeline. For the ACT, our linear article
classifier leads to a ranking and classification performance significantly
higher than all the reported submissions. For the IMT, our results are
comparable to those of other systems, which took very different approaches. For
the ACT, we show that the use of named entity recognition tools leads to a
substantial improvement in the ranking and classification of articles relevant
to protein-protein interaction. Thus, we show that our substantially expanded
linear classifier is a very competitive classifier in this domain. Moreover,
this classifier produces interpretable surfaces that can be understood as
"rules" for human understanding of the classification. In terms of the IMT
task, in contrast to other participants, our approach focused on identifying
sentences that are likely to bear evidence for the application of a PPI
detection method, rather than on classifying a document as relevant to a
method. As BioCreative III did not perform an evaluation of the evidence
provided by the system, we have conducted a separate assessment; the evaluators
agree that our tool is indeed effective in detecting relevant evidence for PPI
detection methods.Comment: BMC Bioinformatics. In Pres
Representing and analysing molecular and cellular function in the computer
Determining the biological function of a myriad of genes, and understanding how they interact to yield a living cell, is the major challenge of the post genome-sequencing era. The complexity of biological systems is such that this cannot be envisaged without the help of powerful computer systems capable of representing and analysing the intricate networks of physical and functional interactions between the different cellular components. In this review we try to provide the reader with an appreciation of where we stand in this regard. We discuss some of the inherent problems in describing the different facets of biological function, give an overview of how information on function is currently represented in the major biological databases, and describe different systems for organising and categorising the functions of gene products. In a second part, we present a new general data model, currently under development, which describes information on molecular function and cellular processes in a rigorous manner. The model is capable of representing a large variety of biochemical processes, including metabolic pathways, regulation of gene expression and signal transduction. It also incorporates taxonomies for categorising molecular entities, interactions and processes, and it offers means of viewing the information at different levels of resolution, and dealing with incomplete knowledge. The data model has been implemented in the database on protein function and cellular processes 'aMAZE' (http://www.ebi.ac.uk/research/pfbp/), which presently covers metabolic pathways and their regulation. Several tools for querying, displaying, and performing analyses on such pathways are briefly described in order to illustrate the practical applications enabled by the model
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