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https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#1
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29194464/computer-aided-biomarker-discovery-for-precision-medicine-data-resources-models-and-applications
#2
Yuxin Lin, Fuliang Qian, Li Shen, Feifei Chen, Jiajia Chen, Bairong Shen
Biomarkers are a class of measurable and evaluable indicators with the potential to predict disease initiation and progression. In contrast to disease-associated factors, biomarkers hold the promise to capture the changeable signatures of biological states. With methodological advances, computer-aided biomarker discovery has now become a burgeoning paradigm in the field of biomedical science. In recent years, the 'big data' term has accumulated for the systematical investigation of complex biological phenomena and promoted the flourishing of computational methods for systems-level biomarker screening...
November 29, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29192299/machine-learning-to-detect-signatures-of-disease-in-liquid-biopsies-a-user-s-guide
#3
Jina Ko, Steven N Baldassano, Po-Ling Loh, Konrad Kording, Brian Litt, David Issadore
New technologies that measure sparse molecular biomarkers from easily accessible bodily fluids (e.g. blood, urine, and saliva) are revolutionizing disease diagnostics and precision medicine. Microchip devices can measure more disease biomarkers with better sensitivity and specificity each year, but clinical interpretation of these biomarkers remains a challenge. Single biomarkers in 'liquid biopsy' often cannot accurately predict the state of a disease due to heterogeneity in phenotype and disease expression across individuals...
December 1, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/29188157/predicting-quality-of-life-changes-in-hemodialysis-patients-using-machine-learning-generation-of-an-early-warning-system
#4
Shoab Saadat, Ayesha Aziz, Hira Ahmad, Hira Imtiaz, Zara S Sohail, Alvina Kazmi, Sanaa Aslam, Naveen Naqvi, Sidra Saadat
Objective To predict changes in the quality of life scores of hemodialysis patients for the coming month and the development of an early warning system using machine learning Methods It was a prospective cohort study (one-month duration) at the dialysis center of a tertiary care hospital in Pakistan. The study started on 1st October 2016. About 78 patients have been enrolled till now. Bachelor of Medicine and Bachelor of Surgery (MBBS) qualified doctors administered a proforma with demographics and the validated Urdu version of World Health Organization Quality Of Life-BREF (WHOQOL-BREF)...
September 25, 2017: Curēus
https://www.readbyqxmd.com/read/29183230/how-good-are-publicly-available-web-services-that-predict-bioactivity-profiles-for-drug-repurposing
#5
K A Murtazalieva, D S Druzhilovskiy, R K Goel, G N Sastry, V V Poroikov
Drug repurposing provides a non-laborious and less expensive way for finding new human medicines. Computational assessment of bioactivity profiles shed light on the hidden pharmacological potential of the launched drugs. Currently, several freely available computational tools are available via the Internet, which predict multitarget profiles of drug-like compounds. They are based on chemical similarity assessment (ChemProt, SuperPred, SEA, SwissTargetPrediction and TargetHunter) or machine learning methods (ChemProt and PASS)...
October 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/29180800/electronic-health-record-driven-prediction-for-gestational-diabetes-mellitus-in-early-pregnancy
#6
Hang Qiu, Hai-Yan Yu, Li-Ya Wang, Qiang Yao, Si-Nan Wu, Can Yin, Bo Fu, Xiao-Juan Zhu, Yan-Long Zhang, Yong Xing, Jun Deng, Hao Yang, Shun-Dong Lei
Gestational diabetes mellitus (GDM) is conventionally confirmed with oral glucose tolerance test (OGTT) in 24 to 28 weeks of gestation, but it is still uncertain whether it can be predicted with secondary use of electronic health records (EHRs) in early pregnancy. To this purpose, the cost-sensitive hybrid model (CSHM) and five conventional machine learning methods are used to construct the predictive models, capturing the future risks of GDM in the temporally aggregated EHRs. The experimental data sources from a nested case-control study cohort, containing 33,935 gestational women in West China Second Hospital...
November 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29180004/estimating-a-person-s-age-from-walking-over-a-sensor-floor
#7
Raoul Hoffmann, Christl Lauterbach, Jörg Conradt, Axel Steinhage
Ageing has an effect on many parameters of the physical condition, and one of them is the way a person walks. This property, the gait pattern, can unintrusively be observed by letting people walk over a sensor floor. The electric capacitance sensors built into the floor deliver information about when and where feet get into close proximity and contact with the floor during the phases of human locomotion. We processed gait patterns recorded this way by extracting a feature vector containing the discretised distribution of occurring geometrical extents of significant sensor readings...
November 7, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29173045/multiplicity-issues-in-exploratory-subgroup-analysis
#8
Ilya Lipkovich, Alex Dmitrienko, Christoph Muysers, Bohdana Ratitch
The general topic of subgroup identification has attracted much attention in the clinical trial literature due to its important role in the development of tailored therapies and personalized medicine. Subgroup search methods are commonly used in late-phase clinical trials to identify subsets of the trial population with certain desirable characteristics. Post-hoc or exploratory subgroup exploration has been criticized for being extremely unreliable. Principled approaches to exploratory subgroup analysis based on recent advances in machine learning and data mining have been developed to address this criticism...
November 27, 2017: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/29171014/the-influence-of-big-clinical-data-and-genomics-on-precision-medicine-and-drug-development
#9
Joshua C Denny, Sara L Van Driest, Wei-Qi Wei, Dan M Roden
Drug development continues to be costly and slow, with medications failing due to lack of efficacy or presence of toxicity. The promise of pharmacogenomic discovery includes tailoring therapeutics based on an individual's genetic makeup, rational drug development, and repurposing medications. Rapid growth of large research cohorts, linked to electronic health record (EHR) data, fuels discovery of new genetic variants predicting drug action, supports Mendelian randomization experiments to show drug efficacy, and suggests new indications for existing medications...
November 24, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/29151574/machine-learning-meets-complex-networks-via-coalescent-embedding-in-the-hyperbolic-space
#10
Alessandro Muscoloni, Josephine Maria Thomas, Sara Ciucci, Ginestra Bianconi, Carlo Vittorio Cannistraci
Physicists recently observed that realistic complex networks emerge as discrete samples from a continuous hyperbolic geometry enclosed in a circle: the radius represents the node centrality and the angular displacement between two nodes resembles their topological proximity. The hyperbolic circle aims to become a universal space of representation and analysis of many real networks. Yet, inferring the angular coordinates to map a real network back to its latent geometry remains a challenging inverse problem...
November 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133589/precision-oncology-beyond-targeted-therapy-combining-omics-data-with-machine-learning-matches-the-majority-of-cancer-cells-to-effective-therapeutics
#11
Michael Q Ding, Lujia Chen, Gregory F Cooper, Jonathan D Young, Xinghua Lu
Precision oncology involves identifying drugs that will effectively treat a tumor and then prescribing an optimal clinical treatment regimen. However, most first-line chemotherapy drugs do not have biomarkers to guide their application. For molecularly targeted drugs, using the genomic status of a drug target as a therapeutic indicator has limitations. In this study, machine learning methods (e.g., deep learning) were used to identify informative features from genome scale omics data and to train classifiers for predicting the effectiveness of drugs in cancer cell lines...
November 13, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29105694/-handle-with-care-about-the-potential-unintended-consequences-of-oracular-artificial-intelligence-systems-in-medicine
#12
Federico Cabitza, Camilla Alderighi, Raffaele Rasoini, Gian Franco Gensini
Decisional support systems based on machine learning (ML) in medicine are gaining a growing interest as some recent articles have highlighted the high diagnostic accuracy exhibited by these systems in specific medical contexts. However, it is implausible that any potential advantage can be obtained without some potential drawbacks. In light of the current gaps in medical research about the side effects of the application of these new AI systems in medical practice, in this article we summarize the main unexpected consequences that may result from the widespread application of "oracular" systems, that is highly accurate systems that cannot give reasonable explanations of their advice as those endowed with predictive models developed with ML techniques usually are...
October 2017: Recenti Progressi in Medicina
https://www.readbyqxmd.com/read/29104927/retrosynthetic-reaction-prediction-using-neural-sequence-to-sequence-models
#13
Bowen Liu, Bharath Ramsundar, Prasad Kawthekar, Jade Shi, Joseph Gomes, Quang Luu Nguyen, Stephen Ho, Jack Sloane, Paul Wender, Vijay Pande
We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists...
October 25, 2017: ACS Central Science
https://www.readbyqxmd.com/read/29095704/medical-education-must-move-from-the-information-age-to-the-age-of-artificial-intelligence
#14
Steven A Wartman, C Donald Combs
Changes to the medical profession require medical education reforms that will enable physicians to more effectively enter contemporary practice. Proposals for such reforms abound. Common themes include renewed emphasis on communication, teamwork, risk-management, and patient safety. These reforms are important but insufficient. They do not adequately address the most fundamental change--the practice of medicine is rapidly transitioning from the information age to the age of artificial intelligence. Employers need physicians who: work at the top of their license, have knowledge spanning the health professions and care continuum, effectively leverage data platforms, focus on analyzing outcomes and improving performance, and communicate the meaning of the probabilities generated by massive amounts of data to patients given their unique human complexities...
November 1, 2017: Academic Medicine: Journal of the Association of American Medical Colleges
https://www.readbyqxmd.com/read/29093610/automating-biomedical-evidence-synthesis-robotreviewer
#15
Iain J Marshall, Joël Kuiper, Edward Banner, Byron C Wallace
We present RobotReviewer, an open-source web-based system that uses machine learning and NLP to semi-automate biomedical evidence synthesis, to aid the practice of Evidence-Based Medicine. RobotReviewer processes full-text journal articles (PDFs) describing randomized controlled trials (RCTs). It appraises the reliability of RCTs and extracts text describing key trial characteristics (e.g., descriptions of the population) using novel NLP methods. RobotReviewer then automatically generates a report synthesising this information...
July 2017: Proceedings of the Conference on Computational Linguistics
https://www.readbyqxmd.com/read/29074332/improving-individual-predictions-machine-learning-approaches-for-detecting-and-attacking-heterogeneity-in-schizophrenia-and-other-psychiatric-diseases
#16
Hugo G Schnack
Psychiatric diseases are very heterogeneous both in clinical manifestation and etiology. With the recent rise of using machine learning techniques to attempt to diagnose and prognose these disorders, the issue of heterogeneity becomes increasingly important. With the growing interest in personalized medicine, it becomes even more important to not only classify someone as a patient with a certain disorder, its treatment needs a more precise definition of the underlying neurobiology, since different biological origins of the same disease may require (very) different treatments...
October 24, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/29073909/genotype-driven-identification-of-a-molecular-network-predictive-of-advanced-coronary-calcium-in-clinseq%C3%A2-and-framingham-heart-study-cohorts
#17
Cihan Oguz, Shurjo K Sen, Adam R Davis, Yi-Ping Fu, Christopher J O'Donnell, Gary H Gibbons
BACKGROUND: One goal of personalized medicine is leveraging the emerging tools of data science to guide medical decision-making. Achieving this using disparate data sources is most daunting for polygenic traits. To this end, we employed random forests (RFs) and neural networks (NNs) for predictive modeling of coronary artery calcium (CAC), which is an intermediate endo-phenotype of coronary artery disease (CAD). METHODS: Model inputs were derived from advanced cases in the ClinSeq®; discovery cohort (n=16) and the FHS replication cohort (n=36) from 89 (th) -99 (th) CAC score percentile range, and age-matched controls (ClinSeq®; n=16, FHS n=36) with no detectable CAC (all subjects were Caucasian males)...
October 26, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29073279/open-source-machine-learning-algorithms-for-the-prediction-of-optimal-cancer-drug-therapies
#18
Cai Huang, Roman Mezencev, John F McDonald, Fredrik Vannberg
Precision medicine is a rapidly growing area of modern medical science and open source machine-learning codes promise to be a critical component for the successful development of standardized and automated analysis of patient data. One important goal of precision cancer medicine is the accurate prediction of optimal drug therapies from the genomic profiles of individual patient tumors. We introduce here an open source software platform that employs a highly versatile support vector machine (SVM) algorithm combined with a standard recursive feature elimination (RFE) approach to predict personalized drug responses from gene expression profiles...
2017: PloS One
https://www.readbyqxmd.com/read/29065619/diagnosis-of-alzheimer-s-disease-based-on-structural-mri-images-using-a-regularized-extreme-learning-machine-and-pca-features
#19
Ramesh Kumar Lama, Jeonghwan Gwak, Jeong-Seon Park, Sang-Woong Lee
Alzheimer's disease (AD) is a progressive, neurodegenerative brain disorder that attacks neurotransmitters, brain cells, and nerves, affecting brain functions, memory, and behaviors and then finally causing dementia on elderly people. Despite its significance, there is currently no cure for it. However, there are medicines available on prescription that can help delay the progress of the condition. Thus, early diagnosis of AD is essential for patient care and relevant researches. Major challenges in proper diagnosis of AD using existing classification schemes are the availability of a smaller number of training samples and the larger number of possible feature representations...
2017: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29063545/grappling-with-the-future-use-of-big-data-for-translational-medicine-and-clinical-care
#20
S Murphy, V Castro, K Mandl
Objectives: Although patients may have a wealth of imaging, genomic, monitoring, and personal device data, it has yet to be fully integrated into clinical care. Methods: We identify three reasons for the lack of integration. The first is that "Big Data" is poorly managed by most Electronic Medical Record Systems (EMRS). The data is mostly available on "cloud-native" platforms that are outside the scope of most EMRs, and even checking if such data is available on a patient often must be done outside the EMRS...
August 2017: Yearbook of Medical Informatics
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