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

The term “Linked Data” refers to a set of best practices for publishing and connecting structured data on the Web. These best practices have been adopted by an increasing number of data providers over the last three years, leading to the creation of a global data space containing billions of assertions— the Web of Data. In this article, the authors present the concept and technical principles of Linked Data, and situate these within the broader context of related technological developments. They describe progress to date in publishing Linked Data on the Web, review applications that have been developed to exploit the Web of Data, and map out a research agenda for the Linked Data community as it moves forward.

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Linked Data - the story so far

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

The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method.

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The PSIPRED protein structure prediction server.

The paradigmatic shift from a Web of manual interactions to a Web of programmatic interactions driven by Web services is creating unprecedented opportunities for the formation of online business-to-business (B2B) collaborations. In particular, the creation of value-added services by composition of existing ones is gaining a significant momentum. Since many available Web services provide overlapping or identical functionality, albeit with different quality of service (QoS), a choice needs to be made to determine which services are to participate in a given composite service. This paper presents a middleware platform which addresses the issue of selecting Web services for the purpose of their composition in a way that maximizes user satisfaction expressed as utility functions over QoS attributes, while satisfying the constraints set by the user and by the structure of the composite service. Two selection approaches are described and compared: one based on local (task-level) selection of services and the other based on global allocation of tasks to services using integer programming.

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QoS-aware middleware for Web services composition

Integrated access to multiple distributed and autonomous RDF data sources is a key challenge for many semantic web applications. As a reaction to this challenge, SPARQL, the W3C Recommendation for an RDF query language, supports querying of multiple RDF graphs. However, the current standard does not provide transparent query federation, which makes query formulation hard and lengthy. Furthermore, current implementations of SPARQL load all RDF graphs mentioned in a query to the local machine. This usually incurs a large overhead in network traffic, and sometimes is simply impossible for technical or legal reasons. To overcome these problems we present DARQ, an engine for federated SPARQL queries. DARQ provides transparent query access to multiple SPARQL services, i.e., it gives the user the impression to query one single RDF graph despite the real data being distributed on the web. A service description language enables the query engine to decompose a query into sub-queries, each of which can be answered by an individual service. DARQ also uses query rewriting and cost-based query optimization to speed-up query execution. Experiments show that these optimizations significantly improve query performance even when only a very limited amount of statistical information is available. DARQ is available under GPL License at http://darq.sf.net/.

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Querying distributed RDF data sources with SPARQL

We present Stratosphere, an open-source software stack for parallel data analysis. Stratosphere brings together a unique set of features that allow the expressive, easy, and efficient programming of analytical applications at very large scale. Stratosphere's features include "in situ" data processing, a declarative query language, treatment of user-defined functions as first-class citizens, automatic program parallelization and optimization, support for iterative programs, and a scalable and efficient execution engine. Stratosphere covers a variety of "Big Data" use cases, such as data warehousing, information extraction and integration, data cleansing, graph analysis, and statistical analysis applications. In this paper, we present the overall system architecture design decisions, introduce Stratosphere through example queries, and then dive into the internal workings of the system's components that relate to extensibility, programming model, optimization, and query execution. We experimentally compare Stratosphere against popular open-source alternatives, and we conclude with a research outlook for the next years.

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The Stratosphere platform for big data analytics

Motivation Text mining has become an important tool for biomedical research. The most fundamental text-mining task is the recognition of biomedical named entities (NER), such as genes, chemicals and diseases. Current NER methods rely on pre-defined features which try to capture the specific surface properties of entity types, properties of the typical local context, background knowledge, and linguistic information. State-of-the-art tools are entity-specific, as dictionaries and empirically optimal feature sets differ between entity types, which makes their development costly. Furthermore, features are often optimized for a specific gold standard corpus, which makes extrapolation of quality measures difficult. Results We show that a completely generic method based on deep learning and statistical word embeddings [called long short-term memory network-conditional random field (LSTM-CRF)] outperforms state-of-the-art entity-specific NER tools, and often by a large margin. To this end, we compared the performance of LSTM-CRF on 33 data sets covering five different entity classes with that of best-of-class NER tools and an entity-agnostic CRF implementation. On average, F1-score of LSTM-CRF is 5% above that of the baselines, mostly due to a sharp increase in recall. Availability and implementation The source code for LSTM-CRF is available at https://github.com/glample/tagger and the links to the corpora are available at https://corposaurus.github.io/corpora/ . Contact habibima@informatik.hu-berlin.de.

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Deep learning with word embeddings improves biomedical named entity recognition.

Motivation: The accurate identification of chemicals in text is important for many applications, including computer-assisted reconstruction of metabolic networks or retrieval of information about substances in drug development. But due to the diversity of naming conventions and traditions for such molecules, this task is highly complex and should be supported by computational tools. Results: We present ChemSpot, a named entity recognition (NER) tool for identifying mentions of chemicals in natural language texts, including trivial names, drugs, abbreviations, molecular formulas and International Union of Pure and Applied Chemistry entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a hybrid approach combining a Conditional Random Field with a dictionary. It achieves an F1 measure of 68.1% on the SCAI corpus, outperforming the only other freely available chemical NER tool, OSCAR4, by 10.8 percentage points. Availability: ChemSpot is freely available at: http://www.informatik.hu-berlin.de/wbi/resources Contact: leser@informatik.hu-berlin.de

ChemSpot: a hybrid system for chemical named entity recognition

Many applications work with graph-structured data. As graphs grow in size, indexing becomes essential to ensure sufficient query performance. We present the GRIPP index structure (GRaph Indexing based on Pre- and Postorder numbering) for answering reachability queries in graphs. GRIPP requires only linear time and space. Using GRIPP, we can answer reachability queries on graphs with 5 million nodes on average in less than 5 milliseconds, which is unrivaled by previous methods. We evaluate the performance and scalability of our approach on real and synthetic random and scale-free graphs and compare our approach to existing indexing schemes. GRIPP is implemented as stored procedure inside a relational database management system and can therefore very easily be integrated into existing graph-oriented applications.

Ulf Leser

Papers

Querying distributed RDF data sources with SPARQL

The Stratosphere platform for big data analytics

Deep learning with word embeddings improves biomedical named entity recognition.

ChemSpot: a hybrid system for chemical named entity recognition

Fast and practical indexing and querying of very large graphs