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

‡We describe the use of singular value decomposition in transforming genome-wide expression data from genes 3 arrays space to reduced diagonalized ‘‘eigengenes’’ 3 ‘‘eigenarrays’’ space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent noise or experimental artifacts enables meaningful comparison of the expression of different genes across different arrays in different experiments. Sorting the data according to the eigengenes and eigenarrays gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype, respectively. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.

Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2017.0387

Opportunities and obstacles for deep learning in biology and medicine.

The major change in the second edition of this book is the addition of a new chapter on probabilistic retrieval. This chapter has been included because I think this is one of the most interesting and active areas of research in information retrieval. There are still many problems to be solved so I hope that this particular chapter will be of some help to those who want to advance the state of knowledge in this area. All the other chapters have been updated by including some of the more recent work on the topics covered. In preparing this new edition I have benefited from discussions with Bruce Croft, The material of this book is aimed at advanced undergraduate information (or computer) science students, postgraduate library science students, and research workers in the field of IR. Some of the chapters, particularly Chapter 6 * , make simple use of a little advanced mathematics. However, the necessary mathematical tools can be easily mastered from numerous mathematical texts that now exist and, in any case, references have been given where the mathematics occur. I had to face the problem of balancing clarity of exposition with density of references. I was tempted to give large numbers of references but was afraid they would have destroyed the continuity of the text. I have tried to steer a middle course and not compete with the Annual Review of Information Science and Technology. Normally one is encouraged to cite only works that have been published in some readily accessible form, such as a book or periodical. Unfortunately, much of the interesting work in IR is contained in technical reports and Ph.D. theses. For example, most the work done on the SMART system at Cornell is available only in reports. Luckily many of these are now available through the National Technical Information Service (U.S.) and University Microfilms (U.K.). I have not avoided using these sources although if the same material is accessible more readily in some other form I have given it preference. I should like to acknowledge my considerable debt to many people and institutions that have helped me. Let me say first that they are responsible for many of the ideas in this book but that only I wish to be held responsible. My greatest debt is to Karen Sparck Jones who taught me to research information retrieval as an experimental science. Nick Jardine and Robin …

Information retrieval

Preprocessing is one of the key components in a typical text classification framework. This paper aims to extensively examine the impact of preprocessing on text classification in terms of various aspects such as classification accuracy, text domain, text language, and dimension reduction. For this purpose, all possible combinations of widely used preprocessing tasks are comparatively evaluated on two different domains, namely e-mail and news, and in two different languages, namely Turkish and English. In this way, contribution of the preprocessing tasks to classification success at various feature dimensions, possible interactions among these tasks, and also dependency of these tasks to the respective languages and domains are comprehensively assessed. Experimental analysis on benchmark datasets reveals that choosing appropriate combinations of preprocessing tasks, rather than enabling or disabling them all, may provide significant improvement on classification accuracy depending on the domain and language studied on.

The impact of preprocessing on text classification

A great amount of machine learning techniques have been applied to problems where data is collected over an extended period of time. However, the disadvantage with many real-world applications is that the distribution underlying the data is likely to change over time. In these situations, a problem that many global eager learners face is their inability to adapt to local concept drift. Concept drift in spam is particularly difficult as the spammers actively change the nature of their messages to elude spam filters. Algorithms that track concept drift must be able to identify a change in the target concept (spam or legitimate e-mails) without direct knowledge of the underlying shift in distribution. In this paper we show how a previously successful instance-based reasoning e-mail filtering model can be improved in order to better track concept drift in spam domain. Our proposal is based on the definition of two complementary techniques able to select both terms and e-mails representative of the current situation. The enhanced system is evaluated against other well-known successful lazy learning approaches in two scenarios, all within a cost-sensitive framework. The results obtained from the experiments carried out are very promising and back up the idea that instance-based reasoning systems can offer a number of advantages tackling concept drift in dynamic problems, as in the case of the anti-spam filtering domain.

Applying lazy learning algorithms to tackle concept drift in spam filtering

In this paper we show an instance-based reasoning e-mail filtering model that outperforms classical machine learning techniques and other successful lazy learners approaches in the domain of anti-spam filtering. The architecture of the learning-based anti-spam filter is based on a tuneable enhanced instance retrieval network able to accurately generalize e-mail representations. The reuse of similar messages is carried out by a simple unanimous voting mechanism to determine whether the target case is spam or not. Previous to the final response of the system, the revision stage is only performed when the assigned class is spam whereby the system employs general knowledge in the form of meta-rules.

SpamHunting: An instance-based reasoning system for spam labelling and filtering

Gene expression profiles are composed of thousands of genes at the same time, representing the complex relationships between them. One of the well-known constraints specifically related to microarray data is the large number of genes in comparison with the small number of available experiments or cases. In this context, the ability of design methods capable of overcoming current limitations of state-of-the-art algorithms is crucial to the development of successful applications. This paper presents gene-CBR, a hybrid model that can perform cancer classification based on microarray data. The system employs a case-based reasoning model that incorporates a set of fuzzy prototypes, a growing cell structure network and a set of rules to provide an accurate diagnosis. The hybrid model has been implemented and tested with microarray data belonging to bone marrow cases from forty-three adult patients with cancer plus a group of six cases corresponding to healthy persons.

gene‐CBR: A CASE‐BASED REASONIG TOOL FOR CANCER DIAGNOSIS USING MICROARRAY DATA SETS

In this paper we analyse the strengths and weaknesses of the mainly used feature selection methods in text categorization when they are applied to the spam problem domain. Several experiments with different feature selection methods and content-based filtering techniques are carried out and discussed. Information Gain, χ2-text, Mutual Information and Document Frequency feature selection methods have been analysed in conjunction with Naive Bayes, boosting trees, Support Vector Machines and ECUE models in different scenarios. From the experiments carried out the underlying ideas behind feature selection methods are identified and applied for improving the feature selection process of SpamHunting, a novel anti-spam filtering software able to accurate classify suspicious e-mails.

/pdf/a-comparative-performance-study-of-feature-selection-methods-1362fykbix.pdf

A comparative performance study of feature selection methods for the anti-spam filtering domain

Early work on case-based reasoning (CBR) reported in the literature shows the importance of soft computing techniques applied to different stages of the classical four-step CBR life cycle. This correspondence proposes a reduction technique based on rough sets theory capable of minimizing the case memory by analyzing the contribution of each case feature. Inspired by the application of the minimum description length principle, the method uses the granularity of the original data to compute the relevance of each attribute. The rough feature weighting and selection method is applied as a preprocessing step prior to the generation of a fuzzy rule system, which is employed in the revision phase of the proposed CBR system. Experiments using real oceanographic data show that the rough sets reduction method maintains the accuracy of the employed fuzzy rules, while reducing the computational effort needed in its generation and increasing the explanatory strength of the fuzzy rules

/pdf/reducing-the-memory-size-of-a-fuzzy-case-based-reasoning-3483ys22q9.pdf

Fernando Díaz

Papers

Applying lazy learning algorithms to tackle concept drift in spam filtering

SpamHunting: An instance-based reasoning system for spam labelling and filtering

gene‐CBR: A CASE‐BASED REASONIG TOOL FOR CANCER DIAGNOSIS USING MICROARRAY DATA SETS

A comparative performance study of feature selection methods for the anti-spam filtering domain

Reducing the Memory Size of a Fuzzy Case-Based Reasoning System Applying Rough Set Techniques