{"id":9588,"date":"2020-09-07T09:04:41","date_gmt":"2020-09-07T09:04:41","guid":{"rendered":"https:\/\/www.experfy.com\/blog\/?p=9588"},"modified":"2023-11-09T06:12:33","modified_gmt":"2023-11-09T06:12:33","slug":"how-to-build-a-regression-model-in-python","status":"publish","type":"post","link":"https:\/\/www.experfy.com\/blog\/bigdata-cloud\/how-to-build-a-regression-model-in-python\/","title":{"rendered":"How to Build a Regression Model in Python"},"content":{"rendered":"\t\t
\n\t\t\t\t\t\t
\n\t\t\t\t\t\t
\n\t\t\t\t\t
\n\t\t\t
\n\t\t\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

A Detailed and Visual Step-by-Step Walkthrough<\/em><\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

If you are an aspiring data scientist or a veteran data scientist, this article is for you! In this article, we will be building a simple regression model in Python. To spice things up a bit, we will not be using the widely popular and ubiquitous\u00a0Boston Housing<\/em>\u00a0dataset but instead, we will be using a simple Bioinformatics dataset. Particularly, we will be using the\u00a0Delaney Solubility<\/em><\/strong>\u00a0dataset that represents an important physicochemical property in computational drug discovery.<\/p>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\n

The aspiring data scientist will find the step-by-step tutorial particularly accessible while the veteran data scientist may want to find a new challenging dataset for which to try out their state-of-the-art machine learning algorithm or workflow.<\/p>\n\n\n

\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

1. What we are Building Today?<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

A regression model! And we are going to use Python to do that. While we\u2019re at it, we are going to use a bioinformatics dataset (technically, it\u2019s cheminformatics dataset) for the model building.<\/p>\n\n\n\n

Particularly, we are going to predict the LogS value which is the aqueous solubility of small molecules. The aqueous solubility value is a relative measure of the ability of a molecule to be soluble in water. It is an important physicochemical property of effective drugs.<\/p>\n\n\n\n

What better way to get acquainted with the concept of what we are building today than a cartoon illustration!<\/p>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t
\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

2. Delaney Solubility Dataset<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

2.1. Data Understanding<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
\n\t\t\t\t\t\t
\n\t\t\t\t\t
\n\t\t\t
\n\t\t\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

As the name implies, the\u00a0Delaney solubility<\/em><\/strong>\u00a0dataset is comprised of the\u00a0aqueous solubility<\/em><\/strong>\u00a0values along with their corresponding chemical structure for a set of 1,144 molecules. For those, outside the field of biology there are some terms that we will spend some time on clarifying.<\/p>\n\n\n\n

Molecules<\/em><\/strong>\u00a0or sometimes referred to as small molecules or compounds are chemical entities that are made up of atoms. Let\u2019s use some analogy here and let\u2019s think of atoms as being equivalent to Lego blocks where 1 atom being 1 Lego block. When we use several Lego blocks to build something whether it be a house, a car or some abstract entity; such constructed entities are comparable to molecules. Thus, we can refer to the specific arrangement and connectivity of atoms to form a molecule as the\u00a0chemical structure<\/em><\/strong>.<\/p>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

So how does each of the entities that you are building differ? Well, they differ by the spatial connectivity of the blocks (i.e. how the individual blocks are connected). In chemical terms, each molecules differ by their chemical structures. Thus, if you alter the connectivity of the blocks, consequently you would have effectively altered the entity that you are building. For molecules, if atom types (e.g. carbon, oxygen, nitrogen, sulfur, phosphorus, fluorine, chlorine, etc.) or groups of atoms (e.g. hydroxy, methoxy, carboxy, ether, etc.) are altered then the molecules would also be altered consequently becoming a new chemical entity (i.e. that is a new molecule is produced).<\/p>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\n

To become an effective drug, molecules will need to be uptake and distributed in the human body and such property is directly governed by the\u00a0aqueous solubility<\/em><\/strong>. Solubility is an important property that researchers take into consideration in the design and development of therapeutic drugs. Thus, a potent drug that is unable to reach the desired destination target owing to its poor solubility would be a poor drug candidate.<\/p>\n\n\n

\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

2.2. Retrieving the Dataset<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

The aqueous solubility dataset as performed by Delaney in the research paper entitled\u00a0ESOL: Estimating Aqueous Solubility Directly from Molecular Structure<\/a>\u00a0is available as a\u00a0Supplementary file<\/a>. For your convenience, we have also downloaded the entire\u00a0Delaney solubility dataset<\/strong><\/a>\u00a0and made it available on the\u00a0Data Professor GitHub<\/a>.<\/p>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\n
\n

\n
Preview of the raw version of the Delaney solubility dataset.<\/strong>\u00a0The\u00a0full version<\/a>\u00a0is available on the\u00a0Data Professor GitHub<\/a>.<\/figcaption>\n<\/figure>\n<\/div>\n\n\n\n

CODE PRACTICE<\/strong><\/p>\n\n\n\n

Let\u2019s get started, shall we?<\/p>\n\n\n\n

Fire up Google Colab or your Jupyter Notebook and run the following code cells.<\/p>\n\n\n\n

\u00a0<\/div>\n\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

CODE EXPLANATION<\/strong><\/p>\n\n\n\n

Let\u2019s now go over what each code cells mean.<\/p>\n\n\n\n

The\u00a0first code cell<\/strong>,<\/p>\n\n\n\n