In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...) particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...) particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

Deep learning is a kind of machine learning which happens in a certain type of artificial neural networks called deep networks. Artificial deep networks, which exhibit many similarities with biological ones, have consistently shown human-like performance in many intelligent tasks. This poses the question whether this performance is caused by such similarities. After reviewing the structure and learning processes of artificial and biological neural networks, we outline two important reasons for the success of deep learning, namely the extraction of successively (...) higher level features and the multiple layer structure, which are closely related to each other. Then some indications about the framing of this heated debate are given. After that, an assessment of the value of artificial deep networks as models of the human brain is given from the similarity perspective of model representation. Finally, a new version of computational functionalism is proposed which addresses the specificity of deep neural computation better than classic, program based computational functionalism. (shrink)

We argue that mechanistic models elaborated by machine learning cannot be explanatory by discussing the relation between mechanistic models, explanation and the notion of intelligibility of models. We show that the ability of biologists to understand the model that they work with severely constrains their capacity of turning the model into an explanatory model. The more a mechanistic model is complex, the less explanatory it will be. Since machine learning increases its performances when more components are added, then it generates (...) models which are not intelligible, and hence not explanatory. (shrink)

Classic conceptions of model simplicity for machine learning are mainly based on the analysis of the structure of the model. Bayesian, Frequentist, information theoretic and expressive power concepts are the best known of them, which are reviewed in this work, along with their underlying assumptions and weaknesses. These approaches were developed before the advent of the Big Data deluge, which has overturned the importance of structural simplicity. The computational simplicity concept is presented, and it is argued that it is more (...) encompassing and closer to actual machine learning practices than the classic ones. In order to process the huge datasets which are commonplace nowadays, the computational complexity of the learning algorithm is the decisive factor to assess the viability of a machine learning strategy, while the classic accounts of simplicity play a surrogate role. Some of the desirable features of computational simplicity derive from its reliance on the learning system concept, which integrates key aspects of machine learning that are ignored by the classic concepts. Moreover, computational simplicity is directly associated with energy efficiency. In particular, the question of whether the maximum possibly achievable predictive accuracy should be attained, no matter the economic cost of the associated energy consumption pattern, is considered. (shrink)

One of the best known arguments against the connectionist approach to artificial intelligence and cognitive science is that neural networks are black boxes, i.e., there is no understandable account of their operation. This difficulty has impeded efforts to explain how categories arise from raw sensory data. Moreover, it has complicated investigation about the role of symbols and language in cognition. This state of things has been radically changed by recent experimental findings in artificial deep learning research. Two kinds of artificial (...) deep learning networks, namely the convolutional neural network and the generative adversarial network have been found to possess the capability to build internal states that are interpreted by humans as complex visual categories, without any specific hints or any grammatical processing. This emergent ability suggests that those categories do not depend on human knowledge or the syntactic structure of language, while they do rely on their visual context. This supports a mild form of empiricism, while it does not assume that computational functionalism is true. Some consequences are extracted regarding the debate about amodal and grounded representations in the human brain. Furthermore, new avenues for research on cognitive science are open. (shrink)