6,743 research outputs found
Automating biomedical data science through tree-based pipeline optimization
Over the past decade, data science and machine learning has grown from a
mysterious art form to a staple tool across a variety of fields in academia,
business, and government. In this paper, we introduce the concept of tree-based
pipeline optimization for automating one of the most tedious parts of machine
learning---pipeline design. We implement a Tree-based Pipeline Optimization
Tool (TPOT) and demonstrate its effectiveness on a series of simulated and
real-world genetic data sets. In particular, we show that TPOT can build
machine learning pipelines that achieve competitive classification accuracy and
discover novel pipeline operators---such as synthetic feature
constructors---that significantly improve classification accuracy on these data
sets. We also highlight the current challenges to pipeline optimization, such
as the tendency to produce pipelines that overfit the data, and suggest future
research paths to overcome these challenges. As such, this work represents an
early step toward fully automating machine learning pipeline design.Comment: 16 pages, 5 figures, to appear in EvoBIO 2016 proceeding
Learning and Interpreting Multi-Multi-Instance Learning Networks
We introduce an extension of the multi-instance learning problem where
examples are organized as nested bags of instances (e.g., a document could be
represented as a bag of sentences, which in turn are bags of words). This
framework can be useful in various scenarios, such as text and image
classification, but also supervised learning over graphs. As a further
advantage, multi-multi instance learning enables a particular way of
interpreting predictions and the decision function. Our approach is based on a
special neural network layer, called bag-layer, whose units aggregate bags of
inputs of arbitrary size. We prove theoretically that the associated class of
functions contains all Boolean functions over sets of sets of instances and we
provide empirical evidence that functions of this kind can be actually learned
on semi-synthetic datasets. We finally present experiments on text
classification, on citation graphs, and social graph data, which show that our
model obtains competitive results with respect to accuracy when compared to
other approaches such as convolutional networks on graphs, while at the same
time it supports a general approach to interpret the learnt model, as well as
explain individual predictions.Comment: JML
BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments
Advances in sequencing techniques have led to exponential growth in
biological data, demanding the development of large-scale bioinformatics
experiments. Because these experiments are computation- and data-intensive,
they require high-performance computing (HPC) techniques and can benefit from
specialized technologies such as Scientific Workflow Management Systems (SWfMS)
and databases. In this work, we present BioWorkbench, a framework for managing
and analyzing bioinformatics experiments. This framework automatically collects
provenance data, including both performance data from workflow execution and
data from the scientific domain of the workflow application. Provenance data
can be analyzed through a web application that abstracts a set of queries to
the provenance database, simplifying access to provenance information. We
evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree
assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a
RASopathy analysis workflow. We analyze each workflow from both computational
and scientific domain perspectives, by using queries to a provenance and
annotation database. Some of these queries are available as a pre-built feature
of the BioWorkbench web application. Through the provenance data, we show that
the framework is scalable and achieves high-performance, reducing up to 98% of
the case studies execution time. We also show how the application of machine
learning techniques can enrich the analysis process
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Models of incremental concept formation
Given a set of observations, humans acquire concepts that organize those observations and use them in classifying future experiences. This type of concept formation can occur in the absence of a tutor and it can take place despite irrelevant and incomplete information. A reasonable model of such human concept learning should be both incremental and capable of handling this type of complex experiences that people encounter in the real world. In this paper, we review three previous models of incremental concept formation and then present CLASSIT, a model that extends these earlier systems. All of the models integrate the process of recognition and learning, and all can be viewed as carrying out search through the space of possible concept hierarchies. In an attempt to show that CLASSIT is a robust concept formation system, we also present some empirical studies of its behavior under a variety of conditions
HYPA: Efficient Detection of Path Anomalies in Time Series Data on Networks
The unsupervised detection of anomalies in time series data has important
applications in user behavioral modeling, fraud detection, and cybersecurity.
Anomaly detection has, in fact, been extensively studied in categorical
sequences. However, we often have access to time series data that represent
paths through networks. Examples include transaction sequences in financial
networks, click streams of users in networks of cross-referenced documents, or
travel itineraries in transportation networks. To reliably detect anomalies, we
must account for the fact that such data contain a large number of independent
observations of paths constrained by a graph topology. Moreover, the
heterogeneity of real systems rules out frequency-based anomaly detection
techniques, which do not account for highly skewed edge and degree statistics.
To address this problem, we introduce HYPA, a novel framework for the
unsupervised detection of anomalies in large corpora of variable-length
temporal paths in a graph. HYPA provides an efficient analytical method to
detect paths with anomalous frequencies that result from nodes being traversed
in unexpected chronological order.Comment: 11 pages with 8 figures and supplementary material. To appear at SIAM
Data Mining (SDM 2020
High dimensional biological data retrieval optimization with NoSQL technology.
Background High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data. Results In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB. Conclusions The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART's implementation to a more scalable solution for Big Data
Mining Brain Networks using Multiple Side Views for Neurological Disorder Identification
Mining discriminative subgraph patterns from graph data has attracted great
interest in recent years. It has a wide variety of applications in disease
diagnosis, neuroimaging, etc. Most research on subgraph mining focuses on the
graph representation alone. However, in many real-world applications, the side
information is available along with the graph data. For example, for
neurological disorder identification, in addition to the brain networks derived
from neuroimaging data, hundreds of clinical, immunologic, serologic and
cognitive measures may also be documented for each subject. These measures
compose multiple side views encoding a tremendous amount of supplemental
information for diagnostic purposes, yet are often ignored. In this paper, we
study the problem of discriminative subgraph selection using multiple side
views and propose a novel solution to find an optimal set of subgraph features
for graph classification by exploring a plurality of side views. We derive a
feature evaluation criterion, named gSide, to estimate the usefulness of
subgraph patterns based upon side views. Then we develop a branch-and-bound
algorithm, called gMSV, to efficiently search for optimal subgraph features by
integrating the subgraph mining process and the procedure of discriminative
feature selection. Empirical studies on graph classification tasks for
neurological disorders using brain networks demonstrate that subgraph patterns
selected by the multi-side-view guided subgraph selection approach can
effectively boost graph classification performances and are relevant to disease
diagnosis.Comment: in Proceedings of IEEE International Conference on Data Mining (ICDM)
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