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Models developed using machine learning are increasingly prevalent in scientific research. At the same time, these models are notoriously opaque. Explainable AI aims to mitigate the impact of opacity by rendering opaque models transparent. More than being just the solution to a problem, however, Explainable AI can also play an invaluable role in scientific exploration. This paper describes how post-hoc analytic techniques from Explainable AI can be used to refine target phenomena in medical science, to identify starting points for future investigations of (potentially) causal relationships, and to generate possible explanations of target phenomena in cognitive science. In this way, this paper describes how Explainable AI—over and above machine learning itself—contributes to the efficiency and scope of data-driven scientific research.

Models developed using machine learning (ML) are increasingly prevalent in scientific research. Because many of these models are opaque, techniques from Explainable AI (XAI) have been developed to render them transparent. But XAI is more than just the solution to the problems that opacity poses—it also plays an invaluable exploratory role. In this paper, we demonstrate that current XAI techniques can be used to (1) better understand what an ML model is a model of, (2) engage in causal inference over high-dimensional nonlinear systems, and (3) generate algorithmic-level hypotheses in cognitive science.

This chapter provides an overview of the basic research strategies and analytic techniques deployed in computational cognitive neuroscience. On the one hand, “top-down” (or reverse-engineering) strategies are used to infer, from formal characterizations of behavior and cognition, the computational properties of underlying neural mechanisms. On the other hand, “bottom-up” research strategies are used to identify neural mechanisms and to reconstruct their computational capacities. Both of these strategies rely on experimental techniques familiar from other branches of neuroscience, including functional magnetic resonance imaging, single-cell recording, and electroencephalography. What sets computational cognitive neuroscience apart, however, is the explanatory role of analytic techniques from disciplines as varied as computer science, statistics, machine learning, and mathematical physics. These techniques serve to describe neural mechanisms computationally, but also to drive the process of scientific discovery by influencing which kinds of mechanisms are most likely to be identified. For this reason, understanding the nature and unique appeal of computational cognitive neuroscience requires not just an understanding of the basic research strategies that are involved, but also of the formal methods and tools that are being deployed, including those of probability theory, dynamical systems theory, and graph theory.

This paper considers the way mathematical and computational models are used in network neuroscience to deliver mechanistic explanations. Two case studies are considered: Recent work on klinotaxis by Caenorhabditis elegans, and a longstanding research effort on the network basis of schizophrenia in humans. These case studies illustrate the various ways in which network, simulation and dynamical models contribute to the aim of representing and understanding network mechanisms in the brain, and thus, of delivering mechanistic explanations. After outlining this mechanistic construal of network neuroscience, two concerns are addressed. In response to the concern that functional network models are non-explanatory, it is argued that functional network models are in fact explanatory mechanism sketches. In response to the concern that models which emphasize a network’s organization over its composition do not explain mechanistically, it is argued that this emphasis is both appropriate and consistent with the principles of mechanistic explanation. What emerges is an improved understanding of the ways in which mathematical and computational models are deployed in network neuroscience, as well as an improved conception of mechanistic explanation in general.

This chapter subsumes David Marr’s levels of analysis account of explanation in cognitive science under the framework of mechanistic explanation: Answering the questions that define each one of Marr’s three levels is tantamount to describing the component parts and operations of mechanisms, as well as their organization, behavior, and environmental context. By explicating these questions and showing how they are answered in several different cognitive science research programs, this chapter resolves some of the ambiguities that remain in Marr’s account, and shows that many different areas and traditions of cognitive scientific research can be unified under the mechanistic framework.

Bayesian reverse-engineering is a research strategy for developing three-level explanations of behavior and cognition. Starting from a computational-level analysis of behavior and cognition as optimal probabilistic inference, Bayesian reverse-engineers apply numerous tweaks and heuristics to formulate testable hypotheses at the algorithmic and implementational levels. In so doing, they exploit recent technological advances in Bayesian artificial intelligence, machine learning, and statistics, but also consider established principles from cognitive psychology and neuroscience. Although these tweaks and heuristics are highly pragmatic in character and are often deployed unsystematically, Bayesian reverse-engineering avoids several important worries that have been raised about the explanatory credentials of Bayesian cognitive science: the worry that the lower levels of analysis are being ignored altogether; the challenge that the mathematical models being developed are unfalsifiable; and the charge that the terms ‘optimal’ and ‘rational’ have lost their customary normative force. But while Bayesian reverse-engineering is therefore a viable and productive research strategy, it is also no fool-proof recipe for explanatory success.

The philosophical conception of mechanistic explanation is grounded on a limited number of canonical examples. These examples provide an overly narrow view of contemporary scientific practice, because they do not reflect the extent to which the heuristic strategies and descriptive practices that contribute to mechanistic explanation have evolved beyond the well-known methods of decomposition, localization, and pictorial representation. Recent examples from evolutionary robotics and network approaches to biology and neuroscience demonstrate the increasingly important role played by computer simulations and mathematical representations in the epistemic practices of mechanism discovery and mechanism description. These examples also indicate that the scope of mechanistic explanation must be re-examined: With new and increasingly powerful methods of discovery and description comes the possibility of describing mechanisms far more complex than traditionally assumed.

Whereas most branches of neuroscience are thought to provide mechanistic explanations, systems neuroscience is not. Two reasons are traditionally cited in support of this conclusion. First, systems neuroscientists rarely, if ever, rely on the dual strategies of decomposition and localization. Second, they typically emphasize organizational properties over the properties of individual components. In this paper, I argue that neither reason is conclusive: researchers might rely on alternative strategies for mechanism discovery, and focusing on organization is often appropriate and consistent with the norms of mechanistic explanation. Thus, many explanations in systems neuroscience can also be viewed as mechanistic explanations.