It is now well-appreciated by philosophers that contemporary large-scale ‘-omics’ studies in biology stand in non-trivial relationships to more orthodox hypothesis-driven approaches. These relationships have been clarified by Ratti (2015); however, there remains much more to be said regarding how an important field of genomics cited in that work—‘genome-wide association studies’ (GWAS)—fits into this framework. In the present article, we propose a revision to Ratti’s framework more suited to studies such as GWAS. In the process of doing so, we introduce (...) to the philosophical literature novel exploratory experiments in (phospho)proteomics, and demonstrate how these experiments interplay with the above considerations. (shrink)

Supervised machine learning has found its way into ever more areas of scientific inquiry, where the outcomes of supervised machine learning applications are almost universally classified as predictions. I argue that what researchers often present as a mere terminological particularity of the field involves the consequential transformation of tasks as diverse as classification, measurement, or image segmentation into prediction problems. Focusing on the case of machine-learning enabled poverty prediction, I explore how reframing a measurement problem as a prediction task alters (...) the primary epistemic aim of the application. Instead of measuring a property, machine learning developers conceive of their models as predicting a given measurement of this property. I argue that this _predictive reframing_ common to supervised machine learning applications is epistemically and ethically problematic, as it allows developers to externalize concerns critical to the epistemic validity and ethical implications of their model’s inferences. I further hold that the predictive reframing is not a necessary feature of supervised machine learning by offering an alternative conception of machine learning models as measurement models. An interpretation of supervised machine learning applications to measurement tasks as _automatically-calibrated model-based measurements_ internalizes questions of construct validity and ethical desirability critical to the measurement problem these applications are intended to and presented as solving. Thereby, this paper introduces an initial framework for exploring technical, historical, and philosophical research at the intersection of measurement and machine learning. (shrink)

In climate science, climate models are one of the main tools for understanding phenomena. Here, we develop a framework to assess the fitness of a climate model for providing understanding. The framework is based on three dimensions: representational accuracy, representational depth, and graspability. We show that this framework does justice to the intuition that classical process-based climate models give understanding of phenomena. While simple climate models are characterized by a larger graspability, state-of-the-art models have a higher representational accuracy and representational (...) depth. We then compare the fitness-for-providing understanding of process-based to data-driven models that are built with machine learning. We show that at first glance, data-driven models seem either unnecessary or inadequate for understanding. However, a case study from atmospheric research demonstrates that this is a false dilemma. Data-driven models can be useful tools for understanding , specifically for phenomena for which scientists can argue from the coherence of the models with background knowledge to their representational accuracy and for which the model complexity can be reduced such that they are graspable to a satisfactory extent. When citing this paper, please use the full journal title Studies in History and Philosophy of Science. (shrink)

Machine learning methods have recently created high expectations in the climate modelling context in view of addressing climate change, but they are often considered as non-physics-based ‘black boxes’ that may not provide any understanding. However, in many ways, understanding seems indispensable to appropriately evaluate climate models and to build confidence in climate projections. Relying on two case studies, we compare how machine learning and standard statistical techniques affect our ability to understand the climate system. For that purpose, we put five (...) evaluative criteria of understanding to work: intelligibility, representational accuracy, empirical accuracy, coherence with background knowledge, and assessment of the domain of validity. We argue that the two families of methods are part of the same continuum where these various criteria of understanding come in degrees, and that therefore machine learning methods do not necessarily constitute a radical departure from standard statistical tools, as far as understanding is concerned. (shrink)

There are many tangled normative and technical questions involved in evaluating the quality of software used in epidemiological simulations. In this paper we answer some of these questions and offer practical guidance to practitioners, funders, scientific journals, and consumers of epidemiological research. The heart of our paper is a case study of the Imperial College London covid-19 simulator, set in the context of recent work in epistemology of simulation and philosophy of epidemiology.

The philosophical debate around the impact of machine learning in science is often framed in terms of a choice between AI and classical methods as mutually exclusive alternatives involving difficult epistemological trade-offs. A common worry regarding machine learning methods specifically is that they lead to opaque models that make predictions but do not lead to explanation or understanding. Focusing on the field of molecular biology, I argue that in practice machine learning is often used with explanatory aims. More specifically, I (...) argue that machine learning can be tightly integrated with other, more traditional, research methods and in a clear sense can contribute to insight into the causal processes underlying phenomena of interest to biologists. One could even say that machine learning is not the end of theory in important areas of biology, as has been argued, but rather a new beginning. I support these claims with a detailed discussion of a case study involving gene regulation by microRNAs. (shrink)

The problem of epistemic opacity in Artificial Intelligence is often characterised as a problem of intransparent algorithms that give rise to intransparent models. However, the degrees of transparency of an AI model should not be taken as an absolute measure of the properties of its algorithms but of the model’s degree of intelligibility to human users. Its epistemically relevant elements are to be specified on various levels above and beyond the computational one. In order to elucidate this claim, I first (...) contrast computer models and their claims to algorithm-based universality with cybernetics-style analogue models and their claims to structural isomorphism between elements of model and target system. While analogue models aim at perceptually or conceptually accessible model-target relations, computer models give rise to a specific kind of underdetermination in these relations that needs to be addressed in specific ways. I then undertake a comparison between two contemporary AI approaches that, although related, distinctly align with the above modelling paradigms and represent distinct strategies towards model intelligibility: Deep Neural Networks and Predictive Processing. I conclude that their respective degrees of epistemic transparency primarily depend on the underlying purposes of modelling, not on their computational properties. (shrink)