Sudip Mandal

Bio: Sudip Mandal is an academic researcher from Jalpaiguri Government Engineering College. The author has contributed to research in topic(s): Gene regulatory network & Search algorithm. The author has an hindex of 7, co-authored 25 publication(s) receiving 172 citation(s). Previous affiliations of Sudip Mandal include University of Calcutta.

Construction of Gene Regulatory Networks Using Recurrent Neural Networks and Swarm Intelligence.

Abstract: We have proposed a methodology for the reverse engineering of biologically plausible gene regulatory networks from temporal genetic expression data. We have used established information and the fundamental mathematical theory for this purpose. We have employed the Recurrent Neural Network formalism to extract the underlying dynamics present in the time series expression data accurately. We have introduced a new hybrid swarm intelligence framework for the accurate training of the model parameters. The proposed methodology has been first applied to a small artificial network, and the results obtained suggest that it can produce the best results available in the contemporary literature, to the best of our knowledge. Subsequently, we have implemented our proposed framework on experimental (in vivo) datasets. Finally, we have investigated two medium sized genetic networks (in silico) extracted from GeneNetWeaver, to understand how the proposed algorithm scales up with network size. Additionally, we have implemented our proposed algorithm with half the number of time points. The results indicate that a reduction of 50% in the number of time points does not have an effect on the accuracy of the proposed methodology significantly, with a maximum of just over 15% deterioration in the worst case.

Cancer Classification Using Neural Network

Abstract: Naturally, cells in human body grow and divide in a controlled way to produce more cells to maintain health. Cancer affects human body when abnormal cells divide without control and becomes able to invade other tissues. The genetic material (DNA) of these cells becomes damaged or changed that affects normal cell growth and division. Early diagnosis is of considerable significance of the physician's skills conducted based on their knowledge and experience yet an error might occur. A range of therapies have been provided by researchers already. Use of various Artificial Intelligence methods for medical diagnosis of diseases has recently become widespread. These intelligent systems help physicians as a diagnosis assistant. Now, various Artificial Neural Network, Rough Set, Decision Tree, Bayesian Network are very popular for this purpose. In this paper, Multi layer Feed Forward Neural Network was used to detect cancer from Microarray Data and UCI Machine Learning Data. Back Propagation Rule was used for training the model. Throughout this paper, two types of validations were performed: cross validation and new case testing for above two datasets with different combination of hidden layers and corresponding nodes. It was found that, NN model can classify the data with very good accuracy and this will lead to automated medical diagnosis system for the particular disease.

FPA based optimization of drilling burr using regression analysis and ANN model

Abstract: The minimization of the burr formation in drilling process by selection of optimal process parameters is the aim of this research. The experimental study has been performed according to L27 orthogonal array for burr formation in aluminium alloy using HSS drill. The second order regression model of burr height was developed in Minitab16 from experimental data consist of process parameters i.e. spindle speed, feed rate, point angle and burr height. This model was optimized using Flower Pollination Algorithm, which helped to determine the optimal process parameters responsible for minimum burr height formation. The result shows that minimum burr height was formed for optimized values of speed 219 rpm, feed 0.04 mm/rev and point angle 113°. Next, ANN model has been developed to compare between experimental, regression and ANN model predicted burr height. For validation, new set of experiments were performed and validated with ANN and regression model with satisfactory accuracy.

Elephant swarm water search algorithm for global optimization

Abstract: The rising complexity of real-life optimization problems has constantly inspired computer researchers to develop new efficient optimization methods. Evolutionary computation and metaheuristics based on swarm intelligence are very popular nature-inspired optimization techniques. In this paper, the author has proposed a novel elephant swarm water search algorithm (ESWSA) inspired by the behaviour of social elephants, to solve different optimization problems. This algorithm is mainly based on the water search strategy of intelligent and social elephants during drought. Initially, we perform preliminary parametric sensitivity analysis for our proposed algorithm, developing guidelines for choosing the parameter values in real-life problems. In addition, the algorithm is evaluated against a number of widely used benchmark functions for global optimizations, and it is observed that the proposed algorithm has better performance for most of the cases compared with other state-of-the-art metaheuristics. Moreover, ESWSA performs better during fitness test, convergence test, computational complexity test, success rate test and scalability test for most of the benchmarks. Next, ESWSA is tested against two well-known constrained optimization problems, where ESWSA is found to be very efficient in term of execution speed and best fitness. As an application of ESWSA to real-life problem, it has been tested against a benchmark problem of computational biology, i.e., inference of Gene Regulatory Network based on Recurrent Neural Network. It has been observed that the proposed ESWSA is able to reach nearest to global minima and enabled inference of all true regulations of GRN correctly with less computational time compared with the other existing metaheuristics.

Large-Scale Recurrent Neural Network Based Modelling of Gene Regulatory Network Using Cuckoo Search-Flower Pollination Algorithm

Abstract: The accurate prediction of genetic networks using computational tools is one of the greatest challenges in the postgenomic era. Recurrent Neural Network is one of the most popular but simple approaches to model the network dynamics from time-series microarray data. To date, it has been successfully applied to computationally derive small-scale artificial and real-world genetic networks with high accuracy. However, they underperformed for large-scale genetic networks. Here, a new methodology has been proposed where a hybrid Cuckoo Search-Flower Pollination Algorithm has been implemented with Recurrent Neural Network. Cuckoo Search is used to search the best combination of regulators. Moreover, Flower Pollination Algorithm is applied to optimize the model parameters of the Recurrent Neural Network formalism. Initially, the proposed method is tested on a benchmark large-scale artificial network for both noiseless and noisy data. The results obtained show that the proposed methodology is capable of increasing the inference of correct regulations and decreasing false regulations to a high degree. Secondly, the proposed methodology has been validated against the real-world dataset of the DNA SOS repair network of Escherichia coli. However, the proposed method sacrifices computational time complexity in both cases due to the hybrid optimization process.

Machine learning

Abstract: Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Particle Swarm Optimization Feature Selection for Breast Cancer Recurrence Prediction

Abstract: Women who have recovered from breast cancer (BC) always fear its recurrence. The fact that they have endured the painstaking treatment makes recurrence their greatest fear. However, with current advancements in technology, early recurrence prediction can help patients receive treatment earlier. The availability of extensive data and advanced methods make accurate and fast prediction possible. This research aims to compare the accuracy of a few existing data mining algorithms in predicting BC recurrence. It embeds a particle swarm optimization as feature selection into three renowned classifiers, namely, naive Bayes, K-nearest neighbor, and fast decision tree learner, with the objective of increasing the accuracy level of the prediction model.