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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Gao, Jiangning, et al.
(författare)
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ACES : a machine learning toolbox for clustering analysis and visualization
- 2018
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Ingår i: BMC Genomics. - : BMC. - 1471-2164. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies that aim at explaining phenotypes or disease susceptibility by genetic or epigenetic variants often rely on clustering methods to stratify individuals or samples. While statistical associations may point at increased risk for certain parts of the population, the ultimate goal is to make precise predictions for each individual. This necessitates tools that allow for the rapid inspection of each data point, in particular to find explanations for outliers.Results: ACES is an integrative cluster- and phenotype-browser, which implements standard clustering methods, as well as multiple visualization methods in which all sample information can be displayed quickly. In addition, ACES can automatically mine a list of phenotypes for cluster enrichment, whereby the number of clusters and their boundaries are estimated by a novel method. For visual data browsing, ACES provides a 2D or 3D PCA or Heat Map view. ACES is implemented in Java, with a focus on a user-friendly, interactive, graphical interface.Conclusions: ACES has been proven an invaluable tool for analyzing large, pre-filtered DNA methylation data sets and RNA-Sequencing data, due to its ease to link molecular markers to complex phenotypes. The source code is available from https://github.com/GrabherrGroup/ACES.
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| 3. |
- Gao, Jiangning, et al.
(författare)
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Expression robust 3D face landmarking using thresholded surface normals
- 2018
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Ingår i: Pattern Recognition. - : ELSEVIER SCI LTD. - 0031-3203 .- 1873-5142. ; 78, s. 120-132
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Tidskriftsartikel (refereegranskat)abstract
- 3D face recognition is an increasing popular modality for biometric authentication, for example in the iPhoneX. Landmarking plays a significant role in region based face recognition algorithms. The accuracy and consistency of the landmarking will directly determine the effectiveness of feature extraction and hence the overall recognition performance. While surface normals have been shown to provide high performing features for face recognition, their use in landmarking has not been widely explored. To this end, a new 3D facial landmarking algorithm based on thresholded surface normal maps is proposed, which is applicable to widely used 3D face databases. The benefits of employing surface normals are demonstrated for both facial roll and yaw rotation calibration and nasal landmarks localization. Results on the Bosphorus, FRGC and BU-3DFE databases show that the detected landmarks possess high within class consistency and accuracy under different expressions. For several key landmarks the performance achieved surpasses that of state-of-the-art techniques and is also training free and computationally efficient. The use of surface normals therefore provides a useful representation of the 3D surface and the proposed landmarking algorithm provides an effective approach to localising the key nasal landmarks.
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| 4. |
- Torabi Moghadam, Behrooz, et al.
(författare)
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An unsupervised approach subgroups cancer types by distinct local DNA methylation patterns
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Cancer is one of the most common causes of death in humans. It can arise from many different cell types, and even cancers originating from the same tissue can constitute a heterogeneous group of diseases. While cytogenetics, the analysis of mutations and karyotypic alterations, has greatly improved the accuracy of diagnosis, it is likely that there are more categories in which cancers can be divided than is known today. Moreover, new biomarkers confirming existing classification schemes are desirable. Here, we interrogated the DNA methylation (DNAm) landscape as a novel indicator for discerning cancer subtypes.We developed and applied an unsupervised method, methylSaguaro, which is based on the combination of a Hidden Markov Model and a Neural Net. We first compared the concept of hypothesizing patterns and grouping to statistical methods that require a priori hypotheses to perform enrichment tests. We then analyzed samples from four cancer groups, Gliomas, Chronic Lymphocytic Leukemia (CLL), Renal Cell Carcinomas (RCC), and Acute Myeloid Leukemia (AML). On gliomas and CLL, we confirmed known cancer groupings in DNAm that perfectly correspond to known mutations. On Renal Cell Carcinomas, our method disagrees with the histological classification on 4% of the samples, and finds a novel cluster, suggesting that there might be a novel subtype that was hitherto unknown. On AML, methylSaguaro spreads the samples out on a continuous spectrum, enriching one end with patients assessed as having “poor” risk based on cytogenetics, but indicating that DNAm patterns would suggest a different risk assessment. Since methylSaguaro reports both the patterns and the specific sites behind the signals, we analyzed regions and genes indicative of subtypes across the cancers, revealing 41 genes affected by alterations in more than one cancer. In summary, we expect that DNAm, coupled with a hypothesis-free analysis method, will add to the set of clinical instruments to diagnose, assess, and treat cancer.
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