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

Abstract. In this note, we argue that the outputs of causal discovery algorithms should not usually be considered end results but rather starting points and hypotheses for further study. The incentive to explore this topic came from a recent study by Krich et al. (2020), which gives a good introduction to estimating causal networks in biosphere–atmosphere interaction but confines the scope by investigating the outcome of a single algorithm. We aim to give a broader perspective to this study and to illustrate how not only different algorithms but also different initial states and prior information of possible causal model structures affect the outcome. We provide a proof-of-concept demonstration of how to incorporate expert domain knowledge with causal structure discovery and remark on how to detect and take into account over-fitting and concept drift.


https://bg.copernicus.org/articles/19/2095/2022/bg-19-2095-2022.pdf

Technical note: Incorporating expert domain knowledge into causal structure discovery workflows

We study a class of generalized models of gauge mediated supersymmetry breaking (GMSB). We find the parameters and the full particle spectrum of the minimal supersymmetric standard model (MSSM) for all GMSB models with messenger multiplicities that satisfy the perturbativity of the gauge couplings up to the GUT scale. We give a detailed description of the algorithm that has been used to predict all the unmeasured parameters of the MSSM by taking (one-loop) radiative effects into account. We also calculate the branching ratio $BR(b \to s \gamma)$ and find that it always turns out to be larger than the standard model prediction. However, we find that the branching ratio typically remains within the current experimental bounds, except for some special cases with a light charged Higgs boson, or a small supersymmetry breaking scale and a negative $\mu$-parameter.

Radiative symmetry breaking and the ${b \to s \gamma}$ decay in generalized GMSB models

The outcome of the explorative data analysis (EDA) phase is vital for successful data analysis. EDA is more effective when the user interacts with the system used to carry out the exploration. In the recently proposed paradigm of iterative data mining the user controls the exploration by inputting knowledge in the form of patterns observed during the process. The system then shows the user views of the data that are maximally informative given the user's current knowledge. Although this scheme is good at showing surprising views of the data to the user, there is a clear shortcoming: the user cannot steer the process. In many real cases we want to focus on investigating specific questions concerning the data. This paper presents the Human Guided Data Exploration framework, generalising previous research. This framework allows the user to incorporate existing knowledge into the exploration process, focus on exploring a subset of the data, and compare different complex hypotheses concerning relations in the data. The framework utilises a computationally efficient constrained randomisation scheme. To showcase the framework, we developed a free open-source tool, using which the empirical evaluation on real-world datasets was carried out. Our evaluation shows that the ability to focus on particular subsets and being able to compare hypotheses are important additions to the interactive iterative data mining process.

Human-Guided Data Exploration.

Today's ever-increasing amount of data places new demands on cognitive ergonomics and requires new design ideas to ensure successful human–data interaction. Our aim is to identify the cognitive factors that require attention when designing systems to improve decision-making based on large amounts of data. We designed an experiment that simulates the typical cognitive demands people encounter in data analysis situations. We demonstrate some essential cognitive limitations using a behavioural experiment with 20 participants. The studied task presented the participants with critical and noncritical attributes that contained information on two groups of people. They had to select the response option (group) with a higher frequency of critical attributes. The results showed that accuracy of judgement decreased as the amount of information increased, and that judgement was affected by irrelevant information. Our results thus demonstrate critical cognitive limitations when people utilise data and suggest a cognitive bias in data-based decision-making. Therefore, when designing for cognition, we should consider the human cognitive limitations that are manifested in a data analysis context and develop general cognitive ergonomics guidelines for design to support the utilisation of data and improve data-based decision-making.

https://dl.acm.org/doi/pdf/10.1145/3335082.3335112

Cognitive ergonomics for data analysis

Neogene cooling and aridifi cation in the Northern Hemisphere have long been recognized, but there are no studies comparing patterns of aridity gradients or differences between North America and Eurasia. Large herbivorous mammals are an excellent source for understanding large-scale environmental and climatic patterns because their molar crown height (hypsodonty) refl ects both habitat and precipitation. The temporal development of hypsodonty in the North American Great Plains is well studied, but both spatial detail and comparisons with patterns in Eurasia are lacking. Here we use a methodology based on community levels of hypsodonty to estimate precipitation during the Neogene (the past 23 Ma). We show that aridifi cation was more profound and occurred ~5 Ma earlier in North America than in Eurasia. By combining our results with existing climate model output and new sensitivity experiments, we show how these changes were infl uenced by ocean heat transport and atmospheric circulation patterns. We further suggest that asymmetric dispersal of large mammals between Eurasia and North America was related to the contrasting humidity regimes between the continents.

Kai Puolamäki

Papers

Technical note: Incorporating expert domain knowledge into causal structure discovery workflows

Radiative symmetry breaking and the ${b \to s \gamma}$ decay in generalized GMSB models

Human-Guided Data Exploration.

Cognitive ergonomics for data analysis

Neogene aridifi cation of the Northern Hemisphere