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

Morphometric tools for landmark data: geometry and biology

A Survey on semi-supervised feature selection methods

Problem Given the number of times in which an unknown event has happened and failed: Required the chance that the probability of its happening in a single trial lies somewhere between any two degrees of probability that can be named. SECTION 1 Definition 1. Several events are inconsistent, when if one of them happens, none of the rest can. 2. Two events are contrary when one, or other of them must; and both together cannot happen. 3. An event is said to fail, when it cannot happen; or, which comes to the same thing, when its contrary has happened. 4. An event is said to be determined when it has either happened or failed. 5. The probability of any event is the ratio between the value at which an expectation depending on the happening of the event ought to be computed, and the value of the thing expected upon it’s 2 happening.

An essay towards solving a problem in the doctrine of chances. [Facsimil]

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways One of its main priorities is to provide easy and efficient access to its high quality curated data At present, biological pathway databases typically store their contents in relational databases This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data The same data in a graph database can be queried more efficiently Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery The adoption of this technology greatly improved query efficiency, reducing the average query time by 93% The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage By adopting graph database technology we are providing a high performance pathway data resource to the community The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types

/pdf/reactome-graph-database-efficient-access-to-complex-pathway-4v8xihttbo.pdf

Reactome graph database: Efficient access to complex pathway data.

Relational databases have been around for many decades and are the database technology of choice for most traditional data-intensive storage and retrieval applications. Retrievals are usually accomplished using SQL, a declarative query language. Relational database systems are generally efficient unless the data contains many relationships requiring joins of large tables. Recently there has been much interest in data stores that do not use SQL exclusively, the socalled NoSQL movement. Examples are Google’s BigTable and Facebook’s Cassandra. This paper reports on a comparison of one such NoSQL graph database called Neo4j with a common relational database system, MySQL, for use as the underlying technology in the development of a software system to record and query data provenance information.

A Comparison of a Graph Database and a Relational Database

Relational databases have been around for many decades and are the database technology of choice for most traditional data-intensive storage and retrieval applications. Retrievals are usually accomplished using SQL, a declarative query language. Relational database systems are generally efficient unless the data contains many relationships requiring joins of large tables. Recently there has been much interest in data stores that do not use SQL exclusively, the so-called NoSQL movement. Examples are Google's BigTable and Facebook's Cassandra. This paper reports on a comparison of one such NoSQL graph database called Neo4j with a common relational database system, MySQL, for use as the underlying technology in the development of a software system to record and query data provenance information.

A comparison of a graph database and a relational database: a data provenance perspective

Steady state visual evoked potential (SSVEP) is the brain's natural electrical potential response for visual stimuli at specific frequencies. Using a visual stimulus flashing at some given frequency will entrain the SSVEP at the same frequency, thereby allowing determination of the subject's visual focus. The faster an SSVEP is identified, the higher information transmission rate the system achieves. Thus, an effective stimulus, defined as one with high success rate of eliciting SSVEP and high signal-noise ratio, is desired. Also, researchers observed that harmonic frequencies often appear in the SSVEP at a reduced magnitude. Are the harmonics in the SSVEP elicited by the fundamental stimulating frequency or by the artifacts of the stimuli? In this paper, we compare the SSVEP responses of three periodic stimuli: square wave (with different duty cycles), triangle wave, and sine wave to find an effective stimulus. We also demonstrate the connection between the strength of the harmonics in SSVEP and the type of stimulus.

/pdf/square-or-sine-finding-a-waveform-with-high-success-rate-of-57s5zpri72.pdf

Square or sine: finding a waveform with high success rate of eliciting SSVEP

In the context of drug discovery and development, much effort has been exerted to determine which conformers of a given molecule are responsible for the observed biological activity. In this work we aimed to predict bioactive conformers using a variant of supervised learning, named multiple-instance learning. A single molecule, treated as a bag of conformers, is biologically active if and only if at least one of its conformers, treated as an instance, is responsible for the observed bioactivity; and a molecule is inactive if none of its conformers is responsible for the observed bioactivity. The implementation requires instance-based embedding, and joint feature selection and classification. The goal of the present project is to implement multiple-instance learning in drug activity prediction, and subsequently to identify the bioactive conformers for each molecule. We encoded the 3-dimensional structures using pharmacophore fingerprints which are binary strings, and accomplished instance-based embedding using calculated dissimilarity distances. Four dissimilarity measures were employed and their performances were compared. 1-norm SVM was used for joint feature selection and classification. The approach was applied to four data sets, and the best proposed model for each data set was determined by using the dissimilarity measure yielding the smallest number of selected features. The predictive abilities of the proposed approach were compared with three classical predictive models without instance-based embedding. The proposed approach produced the best predictive models for one data set and second best predictive models for the rest of the data sets, based on the external validations. To validate the ability of the proposed approach to find bioactive conformers, 12 small molecules with co-crystallized structures were seeded in one data set. 10 out of 12 co-crystallized structures were indeed identified as significant conformers using the proposed approach. The proposed approach was proven not to suffer from overfitting and to be highly competitive with classical predictive models, so it is very powerful for drug activity prediction. The approach was also validated as a useful method for pursuit of bioactive conformers.

/pdf/implementation-of-multiple-instance-learning-in-drug-54dwar7tc4.pdf

Implementation of multiple-instance learning in drug activity prediction

There are a vast number of biology related research problems involving a combination of multiple sources of data to achieve a better understanding of the underlying problems. It is important to select and interpret the most important information from these sources. Thus it will be beneficial to have a good algorithm to simultaneously extract rules and select features for better interpretation of the predictive model. We propose an efficient algorithm, Combined Rule Extraction and Feature Elimination (CRF), based on 1-norm regularized random forests. CRF simultaneously extracts a small number of rules generated by random forests and selects important features. We applied CRF to several drug activity prediction and microarray data sets. CRF is capable of producing performance comparable with state-of-the-art prediction algorithms using a small number of decision rules. Some of the decision rules are biologically significant.

/pdf/combined-rule-extraction-and-feature-elimination-in-9cf7vxrpc9.pdf

Yixin Chen

Papers

A Comparison of a Graph Database and a Relational Database

A comparison of a graph database and a relational database: a data provenance perspective

Square or sine: finding a waveform with high success rate of eliciting SSVEP

Implementation of multiple-instance learning in drug activity prediction

Combined Rule Extraction and Feature Elimination in Supervised Classification