The embodiments herein disclose a method and system for designing molecules by using a machine learning algorithm. The method includes representing molecular structures included in a dataset by using a Simplified Molecular Input Line Entry System (SMILES), where the SMILES uses a series of characters, converting a SMILES representation of the molecular structures into a binary representation, pre-training a stack of Restricted Boltzmann Machines (RBMs) by using the binary representation of the molecular structures, constructing a Deep Boltzmann Machine (DBM) by using the stack of the RBMs, determining limited molecular property data for a subset of the molecule structures in the dataset, training the DBM with the limited molecular property data, combining the pre-trained stack of the RBMs and the trained DBM in a Bayesian inference framework, and generating a sample of molecules with target properties by using the Bayesian inference framework.