87,242 research outputs found
Machine Learning Models for High-dimensional Biomedical Data
abstract: The recent technological advances enable the collection of various complex, heterogeneous and high-dimensional data in biomedical domains. The increasing availability of the high-dimensional biomedical data creates the needs of new machine learning models for effective data analysis and knowledge discovery. This dissertation introduces several unsupervised and supervised methods to help understand the data, discover the patterns and improve the decision making. All the proposed methods can generalize to other industrial fields.
The first topic of this dissertation focuses on the data clustering. Data clustering is often the first step for analyzing a dataset without the label information. Clustering high-dimensional data with mixed categorical and numeric attributes remains a challenging, yet important task. A clustering algorithm based on tree ensembles, CRAFTER, is proposed to tackle this task in a scalable manner.
The second part of this dissertation aims to develop data representation methods for genome sequencing data, a special type of high-dimensional data in the biomedical domain. The proposed data representation method, Bag-of-Segments, can summarize the key characteristics of the genome sequence into a small number of features with good interpretability.
The third part of this dissertation introduces an end-to-end deep neural network model, GCRNN, for time series classification with emphasis on both the accuracy and the interpretation. GCRNN contains a convolutional network component to extract high-level features, and a recurrent network component to enhance the modeling of the temporal characteristics. A feed-forward fully connected network with the sparse group lasso regularization is used to generate the final classification and provide good interpretability.
The last topic centers around the dimensionality reduction methods for time series data. A good dimensionality reduction method is important for the storage, decision making and pattern visualization for time series data. The CRNN autoencoder is proposed to not only achieve low reconstruction error, but also generate discriminative features. A variational version of this autoencoder has great potential for applications such as anomaly detection and process control.Dissertation/ThesisDoctoral Dissertation Industrial Engineering 201
Image mining: issues, frameworks and techniques
[Abstract]: Advances in image acquisition and storage technology have led to tremendous growth in significantly large and detailed image databases. These images, if analyzed, can reveal useful information to the human users. Image mining deals with the extraction of implicit knowledge, image data relationship, or other patterns not explicitly stored in the images. Image mining is more than just an extension of data mining to image domain. It is an
interdisciplinary endeavor that draws upon expertise in
computer vision, image processing, image retrieval, data
mining, machine learning, database, and artificial
intelligence. Despite the development of many
applications and algorithms in the individual research
fields cited above, research in image mining is still in its infancy. In this paper, we will examine the research issues in image mining, current developments in image mining, particularly, image mining frameworks, state-of-the-art techniques and systems. We will also identify some future research directions for image mining at the end of this paper
On the Effect of Semantically Enriched Context Models on Software Modularization
Many of the existing approaches for program comprehension rely on the
linguistic information found in source code, such as identifier names and
comments. Semantic clustering is one such technique for modularization of the
system that relies on the informal semantics of the program, encoded in the
vocabulary used in the source code. Treating the source code as a collection of
tokens loses the semantic information embedded within the identifiers. We try
to overcome this problem by introducing context models for source code
identifiers to obtain a semantic kernel, which can be used for both deriving
the topics that run through the system as well as their clustering. In the
first model, we abstract an identifier to its type representation and build on
this notion of context to construct contextual vector representation of the
source code. The second notion of context is defined based on the flow of data
between identifiers to represent a module as a dependency graph where the nodes
correspond to identifiers and the edges represent the data dependencies between
pairs of identifiers. We have applied our approach to 10 medium-sized open
source Java projects, and show that by introducing contexts for identifiers,
the quality of the modularization of the software systems is improved. Both of
the context models give results that are superior to the plain vector
representation of documents. In some cases, the authoritativeness of
decompositions is improved by 67%. Furthermore, a more detailed evaluation of
our approach on JEdit, an open source editor, demonstrates that inferred topics
through performing topic analysis on the contextual representations are more
meaningful compared to the plain representation of the documents. The proposed
approach in introducing a context model for source code identifiers paves the
way for building tools that support developers in program comprehension tasks
such as application and domain concept location, software modularization and
topic analysis
JUNIPR: a Framework for Unsupervised Machine Learning in Particle Physics
In applications of machine learning to particle physics, a persistent
challenge is how to go beyond discrimination to learn about the underlying
physics. To this end, a powerful tool would be a framework for unsupervised
learning, where the machine learns the intricate high-dimensional contours of
the data upon which it is trained, without reference to pre-established labels.
In order to approach such a complex task, an unsupervised network must be
structured intelligently, based on a qualitative understanding of the data. In
this paper, we scaffold the neural network's architecture around a
leading-order model of the physics underlying the data. In addition to making
unsupervised learning tractable, this design actually alleviates existing
tensions between performance and interpretability. We call the framework
JUNIPR: "Jets from UNsupervised Interpretable PRobabilistic models". In this
approach, the set of particle momenta composing a jet are clustered into a
binary tree that the neural network examines sequentially. Training is
unsupervised and unrestricted: the network could decide that the data bears
little correspondence to the chosen tree structure. However, when there is a
correspondence, the network's output along the tree has a direct physical
interpretation. JUNIPR models can perform discrimination tasks, through the
statistically optimal likelihood-ratio test, and they permit visualizations of
discrimination power at each branching in a jet's tree. Additionally, JUNIPR
models provide a probability distribution from which events can be drawn,
providing a data-driven Monte Carlo generator. As a third application, JUNIPR
models can reweight events from one (e.g. simulated) data set to agree with
distributions from another (e.g. experimental) data set.Comment: 37 pages, 24 figure
Hierarchically Clustered Representation Learning
The joint optimization of representation learning and clustering in the
embedding space has experienced a breakthrough in recent years. In spite of the
advance, clustering with representation learning has been limited to flat-level
categories, which often involves cohesive clustering with a focus on instance
relations. To overcome the limitations of flat clustering, we introduce
hierarchically-clustered representation learning (HCRL), which simultaneously
optimizes representation learning and hierarchical clustering in the embedding
space. Compared with a few prior works, HCRL firstly attempts to consider a
generation of deep embeddings from every component of the hierarchy, not just
leaf components. In addition to obtaining hierarchically clustered embeddings,
we can reconstruct data by the various abstraction levels, infer the intrinsic
hierarchical structure, and learn the level-proportion features. We conducted
evaluations with image and text domains, and our quantitative analyses showed
competent likelihoods and the best accuracies compared with the baselines.Comment: 10 pages, 7 figures, Under review as a conference pape
- …