Recently, biologists have argued that data - driven biology fosters a new scientific methodology; namely, one that is irreducible to traditional methodologies of molecular biology defined as the discovery strategies elucidated by mechanistic philosophy. Here I show how data - driven studies can be included into the traditional mechanistic approach in two respects. On the one hand, some studies provide eliminative inferential procedures to prioritize and develop mechanistic hypotheses. On the other, different studies play an exploratory role in providing useful (...) generalizations to complement the procedure of prioritization. Overall this paper aims to shed light on the structure of contemporary research in molecular biology. (shrink)

Causality offers the first comprehensive coverage of causal analysis in many sciences, including recent advances using graphical methods. Pearl presents a unified account of the probabilistic, manipulative, counterfactual and structural approaches to causation, and devises simple mathematical tools for analyzing the relationships between causal connections, statistical associations, actions and observations. The book will open the way for including causal analysis in the standard curriculum of statistics, artificial intelligence, business, epidemiology, social science and economics.

Reasons are given to justify the claim that computer simulations and computational science constitute a distinctively new set of scientific methods and that these methods introduce new issues in the philosophy of science. These issues are both epistemological and methodological in kind.

Starting with some illustrative examples, I develop a systematic account of a specific type of experimentation--an experimentation which is not, as in the "standard view", driven by specific theories. It is typically practiced in periods in which no theory or--even more fundamentally--no conceptual framework is readily available. I call it exploratory experimentation and I explicate its systematic guidelines. From the historical examples I argue furthermore that exploratory experimentation may have an immense, but hitherto widely neglected, epistemic significance.

Computer simulations are often claimed to be opaque and thus to lack transparency. But what exactly is the opacity of simulations? This paper aims to answer that question by proposing an explication of opacity. Such an explication is needed, I argue, because the pioneering definition of opacity by P. Humphreys and a recent elaboration by Durán and Formanek are too narrow. While it is true that simulations are opaque in that they include too many computations and thus cannot be checked (...) by hand, this doesn’t exhaust what we might want to call the opacity of simulations. I thus make a fresh start with the natural idea that the opacity of a method is its disposition to resist knowledge and understanding. I draw on recent work on understanding and elaborate the idea by a systematic investigation into what type of knowledge and what type of understanding are required if opacity is to be avoided and why the required sort of understanding, in particular, is difficult to achieve. My proposal is that a method is opaque to the degree that it’s difficult for humans to know and to understand why its outcomes arise. This proposal allows for a comparison between different methods regarding opacity. It further refers to a kind of epistemic access that is important in scientific work with simulations. (shrink)

This article considers the issue of opacity as a problem for socially consequential mechanisms of classification and ranking, such as spam filters, credit card fraud detection, search engines, news trends, market segmentation and advertising, insurance or loan qualification, and credit scoring. These mechanisms of classification all frequently rely on computational algorithms, and in many cases on machine learning algorithms to do this work. In this article, I draw a distinction between three forms of opacity: opacity as intentional corporate or state (...) secrecy, opacity as technical illiteracy, and an opacity that arises from the characteristics of machine learning algorithms and the scale required to apply them usefully. The analysis in this article gets inside the algorithms themselves. I cite existing literatures in computer science, known industry practices, and do some testing and manipulation of code as a form of lightweight code audit. I argue that recognizing the distinct forms of opacity that may be coming into play in a given application is a key to determining which of a variety of technical and non-technical solutions could help to prevent harm. (shrink)

We argue that artificial networks are explainable and offer a novel theory of interpretability. Two sets of conceptual questions are prominent in theoretical engagements with artificial neural networks, especially in the context of medical artificial intelligence: Are networks explainable, and if so, what does it mean to explain the output of a network? And what does it mean for a network to be interpretable? We argue that accounts of “explanation” tailored specifically to neural networks have ineffectively reinvented the wheel. In (...) response to, we show how four familiar accounts of explanation apply to neural networks as they would to any scientific phenomenon. We diagnose the confusion about explaining neural networks within the machine learning literature as an equivocation on “explainability,” “understandability” and “interpretability.” To remedy this, we distinguish between these notions, and answer by offering a theory and typology of interpretation in machine learning. Interpretation is something one does to an explanation with the aim of producing another, more understandable, explanation. As with explanation, there are various concepts and methods involved in interpretation: Total or Partial, Global or Local, and Approximative or Isomorphic. Our account of “interpretability” is consistent with uses in the machine learning literature, in keeping with the philosophy of explanation and understanding, and pays special attention to medical artificial intelligence systems. (shrink)

Many of the computing systems programmed using Machine Learning are opaque: it is difficult to know why they do what they do or how they work. Explainable Artificial Intelligence aims to develop analytic techniques that render opaque computing systems transparent, but lacks a normative framework with which to evaluate these techniques’ explanatory successes. The aim of the present discussion is to develop such a framework, paying particular attention to different stakeholders’ distinct explanatory requirements. Building on an analysis of “opacity” from (...) philosophy of science, this framework is modeled after accounts of explanation in cognitive science. The framework distinguishes between the explanation-seeking questions that are likely to be asked by different stakeholders, and specifies the general ways in which these questions should be answered so as to allow these stakeholders to perform their roles in the Machine Learning ecosystem. By applying the normative framework to recently developed techniques such as input heatmapping, feature-detector visualization, and diagnostic classification, it is possible to determine whether and to what extent techniques from Explainable Artificial Intelligence can be used to render opaque computing systems transparent and, thus, whether they can be used to solve the Black Box Problem. (shrink)

Simple idealized models seem to provide more understanding than opaque, complex, and hyper-realistic models. However, an increasing number of scientists are going in the opposite direction by utilizing opaque machine learning models to make predictions and draw inferences, suggesting that scientists are opting for models that have less potential for understanding. Are scientists trading understanding for some other epistemic or pragmatic good when they choose a machine learning model? Or are the assumptions behind why minimal models provide understanding misguided? In (...) this paper, using the case of deep neural networks, I argue that it is not the complexity or black box nature of a model that limits how much understanding the model provides. Instead, it is a lack of scientific and empirical evidence supporting the link that connects a model to the target phenomenon that primarily prohibits understanding. (shrink)

I analyze the exploratory function of two main modeling practices: targetless fictional models and hypothetical perspectival models. In both cases, I argue, modelers invite us to imagine or conceive something about the target system, which is known to be either nonexistent or just hypothetical. I clarify the kind of imagining or conceiving involved in each modeling practice, and I show how each—in its own right—delivers important modal knowledge. I illustrate these two kinds of exploratory models with Maxwell’s ether model and (...) supersymmetric particle models at the Large Hadron Collider. (shrink)

Several philosophical issues in connection with computer simulations rely on the assumption that results of simulations are trustworthy. Examples of these include the debate on the experimental role of computer simulations :483–496, 2009; Morrison in Philos Stud 143:33–57, 2009), the nature of computer data Computer simulations and the changing face of scientific experimentation, Cambridge Scholars Publishing, Barcelona, 2013; Humphreys, in: Durán, Arnold Computer simulations and the changing face of scientific experimentation, Cambridge Scholars Publishing, Barcelona, 2013), and the explanatory power of (...) computer simulations :277–292, 2008; Durán in Int Stud Philos Sci 31:27–45, 2017). The aim of this article is to show that these authors are right in assuming that results of computer simulations are to be trusted when computer simulations are reliable processes. After a short reconstruction of the problem of epistemic opacity, the article elaborates extensively on computational reliabilism, a specified form of process reliabilism with computer simulations located at the center. The article ends with a discussion of four sources for computational reliabilism, namely, verification and validation, robustness analysis for computer simulations, a history of successful implementations, and the role of expert knowledge in simulations. (shrink)

Since its introduction, multivariate pattern analysis, or ‘neural decoding’, has transformed the field of cognitive neuroscience. Underlying its influence is a crucial inference, which we call the decoder’s dictum: if information can be decoded from patterns of neural activity, then this provides strong evidence about what information those patterns represent. Although the dictum is a widely held and well-motivated principle in decoding research, it has received scant philosophical attention. We critically evaluate the dictum, arguing that it is false: decodability is (...) a poor guide for revealing the content of neural representations. However, we also suggest how the dictum can be improved on, in order to better justify inferences about neural representation using MVPA. (shrink)

Taking scientific practice as its starting point, this book charts the complex territory of models used in science. It examines what scientific models are and what their function is. Reliance on models is pervasive in science, and scientists often need to construct models in order to explain or predict anything of interest at all. The diversity of kinds of models one finds in science – ranging from toy models and scale models to theoretical and mathematical models – has attracted attention (...) not only from scientists, but also from philosophers, sociologists, and historians of science. This has given rise to a wide variety of case studies that look at the different uses to which models have been put in specific scientific contexts. By exploring current debates on the use and building of models via cutting-edge examples drawn from physics and biology, the book provides broad insight into the methodology of modelling in the natural sciences. It pairs specific arguments with introductory material relating to the ontology and the function of models, and provides some historical context to the debates as well as a sketch of general positions in the philosophy of scientific models in the process. (shrink)

We are sceptical of concerns over the opacity of algorithmic decision tools. While transparency and explainability are certainly important desiderata in algorithmic governance, we worry that automated decision-making is being held to an unrealistically high standard, possibly owing to an unrealistically high estimate of the degree of transparency attainable from human decision-makers. In this paper, we review evidence demonstrating that much human decision-making is fraught with transparency problems, show in what respects AI fares little worse or better and argue that (...) at least some regulatory proposals for explainable AI could end up setting the bar higher than is necessary or indeed helpful. The demands of practical reason require the justification of action to be pitched at the level of practical reason. Decision tools that support or supplant practical reasoning should not be expected to aim higher than this. We cast this desideratum in terms of Daniel Dennett’s theory of the “intentional stance” and argue that since the justification of action for human purposes takes the form of intentional stance explanation, the justification of algorithmic decisions should take the same form. In practice, this means that the sorts of explanations for algorithmic decisions that are analogous to intentional stance explanations should be preferred over ones that aim at the architectural innards of a decision tool. (shrink)

As Aristotle stated, scientific explanation is based on deductive argument--yet, Wesley C. Salmon points out, not all deductive arguments are qualified explanations. The validity of the explanation must itself be examined. _Four Decades of Scientific Explanation_ provides a comprehensive account of the developments in scientific explanation that transpired in the last four decades of the twentieth century. It continues to stand as the most comprehensive treatment of the writings on the subject during these years. Building on the historic 1948 essay (...) by Carl G. Hempel and Paul Oppenheim, "Studies in the Logic of Explanation,” which introduced the deductive-nomological model on which most work on scientific explanation was based for the following four decades, Salmon goes beyond this model's inherent basis of describing empirical knowledge to tells us “not only _what,_ but also _why_.” Salmon examines the predominant models in chronological order and describes their development, refinement, and criticism or rejection. _Four Decades of Scientific Explanation_ underscores the need for a consensus of approach and ongoing evaluations of methodology in scientific explanation, with the goal of providing a better understanding of natural phenomena. (shrink)

Recent claims, mainly from computer scientists, concerning a largely automated and model-free data-intensive science have been countered by critical reactions from a number of philosophers of science. The debate suffers from a lack of detail in two respects, regarding the actual methods used in data-intensive science and the specific ways in which these methods presuppose theoretical assumptions. I examine two widely-used algorithms, classificatory trees and non-parametric regression, and argue that these are theory-laden in an external sense, regarding the framing of (...) research questions, but not in an internal sense concerning the causal structure of the examined phenomenon. With respect to the novelty of data-intensive science, I draw an analogy to exploratory as opposed to theory-directed experimentation. (shrink)

The view that the brain is a sort of computer has functioned as a theoretical guideline both in cognitive science and, more recently, in neuroscience. But since we can view every physical system as a computer, it has been less than clear what this view amounts to. By considering in some detail a seminal study in computational neuroscience, I first suggest that neuroscientists invoke the computational outlook to explain regularities that are formulated in terms of the information content of electrical (...) signals. I then indicate why computational theories have explanatory force with respect to these regularities:in a nutshell, they underscore correspondence relations between formal/mathematical properties of the electrical signals and formal/mathematical properties of the represented objects. I finally link my proposal to the philosophical thesis that content plays an essential role in computational taxonomy. (shrink)

With In Search of Mechanisms, Carl F. Craver and Lindley Darden offer both a descriptive and an instructional account of how biologists discover mechanisms. Drawing on examples from across the life sciences and through the centuries, Craver and Darden compile an impressive toolbox of strategies that biologists have used and will use again to reveal the mechanisms that produce, underlie, or maintain the phenomena characteristic of living things. They discuss the questions that figure in the search for mechanisms, characterizing the (...) experimental, observational, and conceptual considerations used to answer them, all the while providing examples from the history of biology to highlight the kinds of evidence and reasoning strategies employed to assess mechanisms. At a deeper level, Craver and Darden pose a systematic view of what biology is, of how biology makes progress, of how biological discoveries are and might be made, and of why knowledge of biological mechanisms is important for the future of the human species. (shrink)

Since its introduction, multivariate pattern analysis, or ‘neural decoding’, has transformed the field of cognitive neuroscience. Underlying its influence is a crucial inference, which we call the decoder’s dictum: if information can be decoded from patterns of neural activity, then this provides strong evidence about what information those patterns represent. Although the dictum is a widely held and well-motivated principle in decoding research, it has received scant philosophical attention. We critically evaluate the dictum, arguing that it is false: decodability is (...) a poor guide for revealing the content of neural representations. However, we also suggest how the dictum can be improved on, in order to better justify inferences about neural representation using MVPA. 1Introduction 2A Brief Primer on Neural Decoding: Methods, Application, and Interpretation 2.1What is multivariate pattern analysis? 2.2The informational benefits of multivariate pattern analysis 3Why the Decoder’s Dictum Is False 3.1We don’t know what information is decoded 3.2The theoretical basis for the dictum 3.3Undermining the theoretical basis 4Objections and Replies 4.1Does anyone really believe the dictum? 4.2Good decoding is not enough 4.3Predicting behaviour is not enough 5Moving beyond the Dictum 6Conclusion. (shrink)