Bridging heterogeneous mutation data to enhance disease gene discovery.

Bridging heterogeneous mutation data fills in the gap between various data categories and propels discovery of disease-related genes. It is known that genome-wide association study (GWAS) infers significant mutation associations that link genotype and phenotype. However, due to the differences of size and quality between GWAS studies, not all de facto vital variations are able to pass the multiple testing. In the meantime, mutation events widely reported in literature unveil typical functional biological process, including mutation types like gain of function and loss of function. To bring together the heterogeneous mutation data, we propose a 'Gene-Disease Association prediction by Mutation Data Bridging (GDAMDB)' pipeline with a statistic generative model. The model learns the distribution parameters of mutation associations and mutation types and recovers false-negative GWAS mutations that fail to pass significant test but represent supportive evidences of functional biological process in literature. Eventually, we applied GDAMDB in Alzheimer's disease (AD) and predicted 79 AD-associated genes. Besides, 12 of them from the original GWAS, 60 of them are supported to be AD-related by other GWAS or literature report, and rest of them are newly predicted genes. Our model is capable of enhancing the GWAS-based gene association discovery by well combining text mining results. The positive result indicates that bridging the heterogeneous mutation data is contributory for the novel disease-related gene discovery.

A Machine Learning Approach to Identifying the Thought Markers of Suicidal Subjects: A Prospective Multicenter Trial.

Death by suicide demonstrates profound personal suffering and societal failure. While basic sciences provide the opportunity to understand biological markers related to suicide, computer science provides opportunities to understand suicide thought markers. In this novel prospective, multimodal, multicenter, mixed demographic study, we used machine learning to measure and fuse two classes of suicidal thought markers: verbal and nonverbal. Machine learning algorithms were used with the subjects' words and vocal characteristics to classify 379 subjects recruited from two academic medical centers and a rural community hospital into one of three groups: suicidal, mentally ill but not suicidal, or controls. By combining linguistic and acoustic characteristics, subjects could be classified into one of the three groups with up to 85% accuracy. The results provide insight into how advanced technology can be used for suicide assessment and prevention.

A Controlled Trial Using Natural Language Processing to Examine the Language of Suicidal Adolescents in the Emergency Department.

What adolescents say when they think about or attempt suicide influences the medical care they receive. Mental health professionals use teenagers' words, actions, and gestures to gain insight into their emotional state and to prescribe what they believe to be optimal care. This prescription is often inconsistent among caregivers, however, and leads to varying outcomes. This variation could be reduced by applying machine learning as an aid in clinical decision support. We designed a prospective clinical trial to test the hypothesis that machine learning methods can discriminate between the conversation of suicidal and nonsuicidal individuals. Using semisupervised machine learning methods, the conversations of 30 suicidal adolescents and 30 matched controls were recorded and analyzed. The results show that the machines accurately distinguished between suicidal and nonsuicidal teenagers.