Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

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

Today's Web-enabled deluge of electronic data calls for automated methods of data analysis. Machine learning provides these, developing methods that can automatically detect patterns in data and then use the uncovered patterns to predict future data. This textbook offers a comprehensive and self-contained introduction to the field of machine learning, based on a unified, probabilistic approach. The coverage combines breadth and depth, offering necessary background material on such topics as probability, optimization, and linear algebra as well as discussion of recent developments in the field, including conditional random fields, L1 regularization, and deep learning. The book is written in an informal, accessible style, complete with pseudo-code for the most important algorithms. All topics are copiously illustrated with color images and worked examples drawn from such application domains as biology, text processing, computer vision, and robotics. Rather than providing a cookbook of different heuristic methods, the book stresses a principled model-based approach, often using the language of graphical models to specify models in a concise and intuitive way. Almost all the models described have been implemented in a MATLAB software package--PMTK (probabilistic modeling toolkit)--that is freely available online. The book is suitable for upper-level undergraduates with an introductory-level college math background and beginning graduate students.

Machine Learning : A Probabilistic Perspective

From the Publisher: 
The accessible presentation of this book gives both a general view of the entire computer vision enterprise and also offers sufficient detail to be able to build useful applications. Users learn techniques that have proven to be useful by first-hand experience and a wide range of mathematical methods. A CD-ROM with every copy of the text contains source code for programming practice, color images, and illustrative movies. Comprehensive and up-to-date, this book includes essential topics that either reflect practical significance or are of theoretical importance. Topics are discussed in substantial and increasing depth. Application surveys describe numerous important application areas such as image based rendering and digital libraries. Many important algorithms broken down and illustrated in pseudo code. Appropriate for use by engineers as a comprehensive reference to the computer vision enterprise.

Computer vision : a modern approach = 计算机视觉 : 一种现代的方法

We introduce a novel latent grouping model for predicting the relevance of a new document to a user. The model assumes a latent group structure for both users and documents. We compared the model against a state-of-the-art method, the User Rating Profile model, where only users have a latent group structure. We estimate both models by Gibbs sampling. The new method predicts relevance more accurately for new documents that have few known ratings. The reason is that generalization over documents then becomes necessary and hence the two-way grouping is profitable.

/pdf/two-way-latent-grouping-model-for-user-preference-prediction-3kes27dlb9.pdf

Two-way latent grouping model for user preference prediction

Comparing frequency counts over texts or corpora is an important task in many applications and scientific disciplines. Given a text corpus, we want to test a hypothesis, such as "word X is frequent", "word X has become more frequent over time", or "word X is more frequent in male than in female speech". For this purpose we need a null model of word frequencies. The commonly used bag-of-words model, which corresponds to a Bernoulli process with fixed parameter, does not account for any structure present in natural languages. Using this model for word frequencies results in large numbers of words being reported as unexpectedly frequent. We address how to take into account the inherent occurrence patterns of words in significance testing of word frequencies. Based on studies of words in two large corpora, we propose two methods for modeling word frequencies that both take into account the occurrence patterns of words and go beyond the bag-of-words assumption. The first method models word frequencies based on the spatial distribution of individual words in the language. The second method is based on bootstrapping and takes into account only word frequency at the text level. The proposed methods are compared to the current gold standard in a series of experiments on both corpora. We find that words obey different spatial patterns in the language, ranging from bursty to non-bursty/uniform, independent of their frequency, showing that the traditional approach leads to many false positives.

/pdf/analyzing-word-frequencies-in-large-text-corpora-using-inter-41y8pqfdu7.pdf

Analyzing word frequencies in large text corpora using inter-arrival times and bootstrapping

We study discriminative joint density models, that is, generative models for the joint density p(c,x) learned by maximizing a discriminative cost function, the conditional likelihood. We use the framework to derive generative models for generalized linear models, including logistic regression, linear discriminant analysis, and discriminative mixture of unigrams. The benefits of deriving the discriminative models from joint density models are that it is easy to extend the models and interpret the results, and missing data can be treated using justified standard methods.

/pdf/on-discriminative-joint-density-modeling-59l9rlm7tl.pdf

On discriminative joint density modeling

102 Stephen Fox. Ontological uncertainty and semantic uncertainty in global network organizations. 2008. 122 p. 103 Kati Tillander, Helena Jarnstrom, Tuula Hakkarainen, Juha Laitinen, Mauri Makela, & Panu Oksa. Palokohteiden savu-, nokija kemikaalijaamat ja niiden vaikutukset tyoturvallisuuteen. Polttokokeet ja altistumisen arviointi. 2008. 67 s. 104 Eija Kupi, Sanna-Kaisa Ilomaki, Virpi Sillanpaa, Heli Talja & Antti Lonnqvist. Aineettoman paaoman riskienhallinta. Riskit ja riskienhallinnan kaytannot yrityksissa. 2008. 44 s. 105 Teemu Mutanen, Joni Niemi, Sami Nousiainen, Lauri Seitsonen & Teppo Veijonen. Cultural Event Recommendations. A Case Study. 2008. 17 p. 106 Hannele Holttinen. Tuulivoiman tuotantotilastot. Vuosiraportti 2007. 2008. 44 s. + liitt. 8 s. 107 Kari Keinanen, Jarkko Leino & Jani Suomalainen. Developing Keyboard Service for NoTA. 2008. 17 p. + app. 2 p. 108 Hannele Antikainen, Asta Back & Pirjo Nakki. Sosiaalisen median hyodyntaminen paikallisissa mediapalveluissa. 2008. 64 s. 109 Raine Hautala, Pekka Leviakangas, Jukka Rasanen, Risto Oorni, Sanna Sonninen, Pasi Vahanne, Martti Hekkanen, Mikael Ohlstrom, Bengt Tammelin, Seppo Saku & Ari Venalainen. Benefits of meteorological services in South Eastern Europe. An assessment of potential benefits in Albania, Bosnia-Herzegovina, FYR Macedonia, Moldova and Montenegro. 2008. 63 p. + app. 35 p. 110 Jaana Leikas. Ikaantyvat, teknologia ja etiikka. Nakokulmia ihmisen ja teknologian vuorovaikutustutkimukseen ja -suunnitteluun. 2008. 155 s. 111 Tomi J. Lindroos. Sectoral Approaches in the Case of the Iron and Steel Industry. 2008. 58 p. + app. 11 p.

Visual Analytics: Final report

The papers in this Special Issue present the state of the art in Visual Analytics and Knowledge Discovery and Data Mining (KDD), as well as propose potential extensions and research questions to further advance and integrate these two fields.

/pdf/introduction-to-the-special-issue-on-visual-analytics-and-200m0yrylg.pdf

Kai Puolamäki

Papers

Two-way latent grouping model for user preference prediction

Analyzing word frequencies in large text corpora using inter-arrival times and bootstrapping

On discriminative joint density modeling

Visual Analytics: Final report

Introduction to the special issue on visual analytics and knowledge discovery