Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

CA : A Cancer Journal for Clinicians

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

Driven by high-throughput sequencing techniques, modern genomic and clinical studies are in a strong need of integrative machine learning models for better use of vast volumes of heterogeneous information in the deep understanding of biological systems and the development of predictive models. How data from multiple sources (called multi-view data) are incorporated in a learning system is a key step for successful analysis. In this article, we provide a comprehensive review on omics and clinical data integration techniques, from a machine learning perspective, for various analyses such as prediction, clustering, dimension reduction and association. We shall show that Bayesian models are able to use prior information and model measurements with various distributions; tree-based methods can either build a tree with all features or collectively make a final decision based on trees learned from each view; kernel methods fuse the similarity matrices learned from individual views together for a final similarity matrix or learning model; network-based fusion methods are capable of inferring direct and indirect associations in a heterogeneous network; matrix factorization models have potential to learn interactions among features from different views; and a range of deep neural networks can be integrated in multi-modal learning for capturing the complex mechanism of biological systems.

A review on machine learning principles for multi-view biological data integration.

Background
Non-negative matrix factorization (NMF) has been introduced as an important method for mining biological data. Though there currently exists packages implemented in R and other programming languages, they either provide only a few optimization algorithms or focus on a specific application field. There does not exist a complete NMF package for the bioinformatics community, and in order to perform various data mining tasks on biological data.

/pdf/the-non-negative-matrix-factorization-toolbox-for-biological-2rchvp6m7e.pdf

The non-negative matrix factorization toolbox for biological data mining

In the context of highly scalable distributed resource management architectures for grid computing, we present a genetic algorithm based scheduler. A scheduler must use the available resources efficiently, while satisfying competing and mutually conflicting goals. The grid workload may consist of multiple jobs, with quality-of-service constraints. A directed acyclic graph (DAG) represents each job, taking into account arbitrary precedence constraints and arbitrary processing time. The scheduler has been designed to be compatible with other tools being developed by our grid research group. We present the design, implementation and test results for such a scheduler in which we minimize make-span, idle time of the available computational resources, turn-around time and the specified deadlines provided by users. The architecture is hierarchical and the scheduler is usable at either the lowest or the higher tiers. It can also be used in both the intra-grid of a large organization and in a research grid consisting of large clusters, connected through a high bandwidth dedicated network.

/pdf/genetic-algorithm-based-scheduler-for-computational-grids-33okp3phre.pdf

Genetic algorithm based scheduler for computational grids

Genomic profiles among different breast cancer survivors who received similar treatment may provide clues about the key biological processes involved in the cells and finding the right treatment. More specifically, such profiling may help personalize the treatment based on the patients' gene expression. In this paper, we present a hierarchical machine learning system that predicts the 5-year survivability of the patients who underwent though specific therapy; The classes are built on the combination of two parts that are the survivability information and the given therapy. For the survivability information part, it defines whether the patient survives the 5-years interval or deceased. While the therapy part denotes the therapy has been taken during that interval, which includes hormone therapy, radiotherapy, or surgery, which totally forms six classes. The Model classifies one class vs. the rest at each node, which makes the tree-based model creates five nodes. The model is trained using a set of standard classifiers based on a comprehensive study dataset that includes genomic profiles and clinical information of 347 patients. A combination of feature selection methods and a prediction method are applied on each node to identify the genes that can predict the class at that node, the identified genes for each class may serve as potential biomarkers to the class's treatment for better survivability. The results show that the model identifies the classes with high-performance measurements. An exhaustive analysis based on relevant literature shows that some of the potential biomarkers are strongly related to breast cancer survivability and cancer in general.

/pdf/a-machine-learning-approach-for-identifying-gene-biomarkers-1773bkskh6.pdf

A Machine Learning Approach for Identifying Gene Biomarkers Guiding the Treatment of Breast Cancer.

In wireless mobile communication systems, radio spectrum is a limited resource. However, efficient use of available channels has been shown to improve the system capacity. The role of a channel assignment scheme is to allocate channels to cells or mobiles in such a way as to minimize call blocking or call dropping probabilities, and also to maximize the quality of service. Channel assignment is known to be an NP-hard optimization problem. In this paper, we have developed an evolutionary strategy (ES) which optimizes the channel assignment. The proposed ES approach uses an efficient problem representation as well as an appropriate fitness function. Our paper deals with a novel hybrid channel assignment based scheme called D-ring. Our D-ring method yields a faster running time and simpler objective function. We also propose a novel way of generating the initial population which reduces the number of channels reassignments and therefore yields a faster running time and may generate a possibly better initial parent. We have obtained better results (as well as faster running time) than a similar approach in literature.

/pdf/a-hybrid-channel-assignment-approach-using-an-efficient-53s8ymt2c2.pdf

Alioune Ngom

Papers

A review on machine learning principles for multi-view biological data integration.

The non-negative matrix factorization toolbox for biological data mining

Genetic algorithm based scheduler for computational grids

A Machine Learning Approach for Identifying Gene Biomarkers Guiding the Treatment of Breast Cancer.

A hybrid channel assignment approach using an efficient evolutionary strategy in wireless mobile networks