López-Rubio, Ezequiel and Ratti, Emanuele (2019) Data science and molecular biology: prediction and mechanistic explanation. [Preprint]

Preview	Text Data science and molecular biology.pdf Download (174kB) | Preview
	Spreadsheet Supplementary Table 1.xls Download (93kB)
Preview	Text SupplementaryTableReferenceList.pdf Download (28kB) | Preview

Abstract

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.

---

Export/Citation:

EndNote | BibTeX | Dublin Core | ASCII/Text Citation (Chicago) | HTML Citation | OpenURL

Social Networking:

Share |

---

Item Type:	Preprint
Creators:	Creators Email ORCID López-Rubio, Ezequiel ezeqlr@lcc.uma.es 0000-0001-8231-5687 Ratti, Emanuele mnl.ratti@gmail.com 0000-0003-1409-8240
Keywords:	biology; data science; machine learning; explanation; prediction
Subjects:	Specific Sciences > Biology > Molecular Biology/Genetics Specific Sciences > Computer Science Specific Sciences > Artificial Intelligence General Issues > Explanation Specific Sciences > Artificial Intelligence > Machine Learning
Depositing User:	Prof. Ezequiel López-Rubio
Date Deposited:	30 May 2019 04:46
Last Modified:	30 May 2019 04:46
Item ID:	16057
DOI or Unique Handle:	10.1007/s11229-019-02271-0
Subjects:	Specific Sciences > Biology > Molecular Biology/Genetics Specific Sciences > Computer Science Specific Sciences > Artificial Intelligence General Issues > Explanation Specific Sciences > Artificial Intelligence > Machine Learning
Date:	28 May 2019
URI:	https://philsci-archive.pitt.edu/id/eprint/16057

Monthly Views for the past 3 years

Monthly Downloads for the past 3 years

Plum Analytics

Altmetric.com

Actions (login required)

View Item