We propose an effective machine learning approach to identify group of interacting single nucleotide polymorphisms (SNPs), which contribute most to the breast cancer (BC) risk by assuming dependencies among BCAC iCOGS SNPs. We adopt a gradient tree boosting method followed by an adaptive iterative SNP search to capture complex non-linear SNP-SNP interactions and consequently, obtain group of interacting SNPs with high BC risk-predictive potential. We also propose a support vector machine formed by the identified SNPs to classify BC cases and controls. Our approach achieves mean average precision (mAP) of 72.66, 67.24 and 69.25 in discriminating BC cases and controls in KBCP, OBCS and merged KBCP-OBCS sample sets, respectively. These results are better than the mAP of 70.08, 63.61 and 66.41 obtained by using a polygenic risk score model derived from 51 known BC-associated SNPs, respectively, in KBCP, OBCS and merged KBCP-OBCS sample sets. BC subtype analysis further reveals that the 200 identified KBCP SNPs from the proposed method performs favorably in classifying estrogen receptor positive (ER+) and negative (ER−) BC cases both in KBCP and OBCS data. Further, a biological analysis of the identified SNPs reveals genes related to important BC-related mechanisms, estrogen metabolism and apoptosis.
We propose a unified approach to automatic foreign accent recognition. It takes advantage of recent technology advances in both linguistics and acoustics based modeling techniques in automatic speech recognition (ASR) while overcoming the issue of a lack of a large set of transcribed data often required in designing state-of-the-art ASR systems. The key idea lies in defining a common set of fundamental units "universally" across all spoken accents such that any given spoken utterance can be transcribed with this set of "accentuniversal" units. In this study, we adopt a set of units describing manner and place of articulation as speech attributes. These units exist in most spoken languages and they can be reliably modeled and extracted to represent foreign accent cues. We also propose an i-vector representation strategy to model the feature streams formed by concatenating these units. Testing on both the Finnish national foreign language certificate (FSD) corpus and the English NIST 2008 SRE corpus, the experimental results with the proposed approach demonstrate a significant system performance improvement with p-value < 0.05 over those with the conventional spectrum-based techniques. We observed up to a 15% relative error reduction over the already very strong i-vector accented recognition system when only manner information is used. Additional improvement is obtained by adding place of articulation clues along with context information. Furthermore, diagnostic information provided by the proposed approach can be useful to the designers to further enhance the system performance.
Breast cancer (BC) is a multifactorial disease and the most common cancer in women worldwide. We describe a machine learning approach to identify a combination of interacting genetic variants (SNPs) and demographic risk factors for BC, especially factors related to both familial history (Group 1) and oestrogen metabolism (Group 2), for predicting BC risk. This approach identifies the best combinations of interacting genetic and demographic risk factors that yield the highest BC risk prediction accuracy. In tests on the Kuopio Breast Cancer Project (KBCP) dataset, our approach achieves a mean average precision (mAP) of 77.78 in predicting BC risk by using interacting genetic and Group 1 features, which is better than the mAPs of 74.19 and 73.65 achieved using only Group 1 features and interacting SNPs, respectively. Similarly, using interacting genetic and Group 2 features yields a mAP of 78.00, which outperforms the system based on only Group 2 features, which has a mAP of 72.57. Furthermore, the gene interaction maps built from genes associated with SNPs that interact with demographic risk factors indicate important BC-related biological entities, such as angiogenesis, apoptosis and oestrogen-related networks. The results also show that demographic risk factors are individually more important than genetic variants in predicting BC risk.
i-Vector based recognition is a well-established technique in state-of-the-art speaker and language recognition but its use in dialect and accent classification has received less attention. In this work, we extensively experiment with the spectral feature based i-vector system on Finnish foreign accent recognition task. Parameters of the system are initially tuned with the CallFriend corpus. Then the optimized system is applied to the Finnish national foreign language certificate (FSD) corpus. The availability of suitable Finnish language corpora to estimate the hyper-parameters is necessarily limited in comparison to major languages such as English. In addition, it is not immediately clear which factors affect the foreign accent detection performance most. To this end, we assess the effect of three different components of the foreign accent recognition: (1) recognition system parameters, (2) data used for estimating hyper-parameters and (3) language aspects. We find out that training the hyper-parameters from non-matched dataset yields poor detection error rates in comparison to training from application-specific dataset. We also observed that, the mother tongue of speakers with higher proficiency in Finnish are more difficult to detect than of those speakers with lower proficiency. Analysis on age factor suggests that mother tongue detection in older speaker groups is easier than in younger speaker groups. This suggests that mother tongue traits might be more preserved in older speakers when speaking the second language in comparison to younger speakers.
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