Defining subtypes of complex diseases such as cancer and stratifying patient groups with the same disease but different subtypes for targeted treatments is important for personalized and precision medicine. Approaches that incorporate multi-omic data are more advantageous to those using only one data type for patient clustering and disease subtype discovery. However, it is challenging to integrate multi-omic data as they are heterogeneous and noisy. In this paper, we present Affinity Network Fusion (ANF) to integrate multi-omic data for patient clustering. ANF first constructs patient affinity networks for each omic data type, and then calculates a fused network for spectral clustering. We applied ANF to a processed harmonized cancer dataset downloaded from GDC data portal consisting of 2193 patients, and generated promising results on clustering patients into correct disease types. Moreover, we developed a semi-supervised model combining ANF and neural network for few-shot learning. In several cases, the model can achieve greater than 90 acccuracy on test set with training less than 1 of the data. This demonstrates the power of ANF in learning a good representation of patients, and shows the great potential of semi-supervised learning in cancer patient clustering.
Mining multi-omic data has been a hot topic in recent years @cite_7 @cite_9 . Many approaches are based on probabilistic modeling usually involving a set of latent variables with a prior distribution. For instance, iCluster @cite_10 , a widely used cancer patient clustering method, assumes different types of omic data share a common latent feature space that can be jointly learned from multi-omic data. KMeans clustering is then performed on the learned latent features. Other approaches incorporate domain knowledge such as biological networks into probabilistic modeling. For instance, PARADIGM @cite_6 converted NCI pathway databases into a factor graph in which each gene is a factor incorporating several kinds of information, a natural'' way for integrating multi-omic data.
@cite_9 @cite_10 @cite_6 @cite_7
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We introduce a generative probabilistic model for segmentation of tumors in multi-dimensional images. The model allows for different tumor boundaries in each channel, reflecting difference in tumor appearance across modalities.We augment a probabilistic atlas of healthy tissue priors with a latent atlas of the lesion and derive the estimation algorithm to extract tumor boundaries and the latent atlas from the image data. We present experiments on 25 glioma patient data sets, demonstrating significant improvement over the traditional multivariate tumor segmentation. With the advances and increasing sophistication in data collection techniques, we are facing with large amounts of data collected from multiple heterogeneous sources in many applications. For example, in the study of Alzheimer's Disease (AD), different types of measurements such as neuroimages, gene protein expression data, genetic data etc. are often collected and analyzed together for improved predictive power. It is believed that a joint learning of multiple data sources is beneficial as different data sources may contain complementary information, and feature-pruning and data source selection are critical for learning interpretable models from high-dimensional data. Very often the collected data comes with block-wise missing entries; for example, a patient without the MRI scan will have no information in the MRI data block, making his her overall record incomplete. There has been a growing interest in the data mining community on expanding traditional techniques for single-source complete data analysis to the study of multi-source incomplete data. The key challenge is how to effectively integrate information from multiple heterogeneous sources in the presence of block-wise missing data. In this paper we first investigate the situation of complete data and present a unified bi-level" learning model for multi-source data. Then we give a natural extension of this model to the more challenging case with incomplete data. Our major contributions are threefold: (1) the proposed models handle both feature-level and source-level analysis in a unified formulation and include several existing feature learning approaches as special cases; (2) the model for incomplete data avoids direct imputation of the missing elements and thus provides superior performances. Moreover, it can be easily generalized to other applications with block-wise missing data sources; (3) efficient optimization algorithms are presented for both the complete and incomplete models. We have performed comprehensive evaluations of the proposed models on the application of AD diagnosis. Our proposed models compare favorably against existing approaches. Mining patterns in graphs has become an important issue in real applications, such as bioinformatics and web mining. We address a graph clustering problem where a cluster is a set of densely connected nodes, under a practical setting that 1) the input is multiple graphs which share a set of nodes but have different edges and 2) a true cluster cannot be found in all given graphs. For this problem, we propose a probabilistic generative model and a robust learning scheme based on variational Bayesian estimation. A key feature of our probabilistic framework is that not only nodes but also given graphs can be clustered at the same time, allowing our model to capture clusters found in only part of all given graphs. We empirically evaluated the effectiveness of the proposed framework on not only a variety of synthetic graphs but also real gene networks, demonstrating that our proposed approach can improve the clustering performance of competing methods in both synthetic and real data. We present a new method for clustering based on compression. The method does not use subject-specific features or background knowledge, and works as follows: First, we determine a parameter-free, universal, similarity distance, the normalized compression distance or NCD, computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normalized information distance, co-developed by one of the authors, is provably optimal. However, the optimality comes at the price of using the noncomputable notion of Kolmogorov complexity. We propose axioms to capture the real-world setting, and show that the NCD approximates optimality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (ternary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics, we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis.