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 study the phenomenological aspects of supersymmetric SU(5) grand unified theories with nonuniversal gaugino masses. For large $\mathrm{tan}\ensuremath{\beta},$ we investigate constraints from the requirement of successful electroweak symmetry breaking, the positivity of stau mass squared, and the $\stackrel{\ensuremath{\rightarrow}}{b}s\ensuremath{\gamma}$ decay rate. In the allowed region, the nature of the lightest supersymmetric particle is determined. Examples of mass spectra are given. We also calculate loop corrections to the bottom mass due to superpartners.

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Phenomenological constraints on SUSY SU(5) GUTs with nonuniversal gaugino masses

We explore the use of eye movements as a source of implicit relevance feedback information. We construct a controlled information retrieval experiment where the relevance of each text is known, and test usefulness of implicit relevance feedback with it. If perceived relevance of a text can be predicted from eye movements, eye movement signal must contain information on the relevance. The result is that relevance can be predicted to a considerable extent with discriminative hidden Markov models, and clearly better than randomly already with simple linear models of time-averaged data.

/pdf/implicit-relevance-feedback-from-eye-movements-4gn1fraqsz.pdf

Implicit relevance feedback from eye movements

We introduce an expectation maximization-type (EM) algorithm for maximum likelihood optimization of conditional densities. It is applicable to hidden variable models where the distributions are from the exponential family. The algorithm can alternatively be viewed as automatic step size selection for gradient ascent, where the amount of computation is traded off to guarantees that each step increases the likelihood. The tradeoff makes the algorithm computationally more feasible than the earlier conditional EM. The method gives a theoretical basis for extended Baum Welch algorithms used in discriminative hidden Markov models in speech recognition, and compares favourably with the current best method in the experiments.

/pdf/expectation-maximization-algorithms-for-conditional-1igm8bm236.pdf

Expectation maximization algorithms for conditional likelihoods

Hypothesis testing using constrained null models can be used to compute the significance of data mining results given what is already known about the data. We study the novel problem of finding the smallest set of patterns that explains most about the data in terms of a global p value. The resulting set of patterns, such as frequent patterns or clusterings, is the smallest set that statistically explains the data. We show that the newly formulated problem is, in its general form, NP-hard and there exists no efficient algorithm with finite approximation ratio. However, we show that in a special case a solution can be computed efficiently with a provable approximation ratio. We find that a greedy algorithm gives good results on real data and that, using our approach, we can formulate and solve many known data-mining tasks. We demonstrate our method on several data mining tasks. We conclude that our framework is able to identify in various settings a small set of patterns that statistically explains the data and to formulate data mining problems in the terms of statistical significance.

A statistical significance testing approach to mining the most informative set of patterns

It is known that periods of intense social interaction result in shared patterns in collaborators' physiological signals. However, applied quantitative research on collaboration is hindered due to scarcity of objective metrics of teamwork effectiveness. Indeed, especially in the domain of productive, ecologically-valid activity such as programming, there is a lack of evidence for the most effective, affordable and reliable measures of collaboration quality. In this study we investigate synchrony in physiological signals between collaborating computer science students performing pair-programming exercises in a class room environment. We recorded electrocardiography over the course of a 60 minute programming session, using lightweight physiological sensors. We employ correlation of heart-rate variability features to study social psychophysiological compliance of the collaborating students. We found evident physiological compliance in collaborating dyads' heart-rate variability signals. Furthermore, dyads' self-reported workload was associated with the physiological compliance. Our results show viability of a novel approach to field measurement using lightweight devices in an uncontrolled environment, and suggest that self-reported collaboration quality can be assessed via physiological signals.

/pdf/cognitive-collaboration-found-in-cardiac-physiology-study-in-h2vofqqd7x.pdf

Kai Puolamäki

Papers

Phenomenological constraints on SUSY SU(5) GUTs with nonuniversal gaugino masses

Implicit relevance feedback from eye movements

Expectation maximization algorithms for conditional likelihoods

A statistical significance testing approach to mining the most informative set of patterns

Cognitive Collaboration Found in Cardiac Physiology: Study in Classroom Environment.