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Dissertation
Generative topic modeling in image data mining and bioinformatics studies
Doctor of Philosophy (Ph.D.), Drexel University
Dec 2012
DOI:
https://doi.org/10.17918/etd-3969
Abstract
Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model is proposed for co-existing image features and annotations, in which new latent variables are introduced to allow for more flexible sampling of word topics and visual topics. A perspective hierarchical Dirichlet process (pHDP) model is proposed to deal with user-tagged image modeling, associating image features with image tags and incorporating the user's perspectives into the image tag generation process. It's also shown that in mining large scale text corpora of natural language descriptions, the relation between semantic visual attributes and object categories can be encoded as Must-Links and Cannot-Links, which can be represented by Dirichlet-Forest prior. Novel generative topic models are also introduced to meta-genomics studies. The experimental results show that the generative topic model can be used to model the taxon abundance information obtained by the homology-based approach and study the microbial core. It also shows that latent topic modeling can be used to characterize core and distributed genes within a species and to correlate similarities between genes and their functions. A further study on the functional elements derived from the non-redundant CDs catalogue shows that the configuration of functional groups encoded in the gene-expression data of meta-genome samples can be inferred by applying probabilistic topic modeling to functional elements. Furthermore, an extended HDP model is introduced to infer functional basis from detected enterotypes. The latent topics estimated from human gut microbial samples are evidenced by the recent discoveries in fecal microbiota study, which demonstrate the effectiveness of the proposed models.
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Details
- Title
- Generative topic modeling in image data mining and bioinformatics studies
- Creators
- Xin Chen - DU
- Contributors
- Xiaohua Hu (Advisor) - Drexel University (1970-)
- Awarding Institution
- Drexel University
- Degree Awarded
- Doctor of Philosophy (Ph.D.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Resource Type
- Dissertation
- Language
- English
- Academic Unit
- College of Information Science and Technology (1995-2013); Drexel University
- Other Identifier
- 3969; 991014632063204721