Sudip Mandal

Bio: Sudip Mandal is an academic researcher from Jalpaiguri Government Engineering College. The author has contributed to research in topics: Gene regulatory network & Search algorithm. The author has an hindex of 7, co-authored 25 publications receiving 172 citations. 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.

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.

Reverse engineering of gene regulatory networks based on S-systems and Bat algorithm.

Abstract: The correct inference of gene regulatory networks for the understanding of the intricacies of the complex biological regulations remains an intriguing task for researchers. With the availability of large dimensional microarray data, relationships among thousands of genes can be simultaneously extracted. Among the prevalent models of reverse engineering genetic networks, S-system is considered to be an efficient mathematical tool. In this paper, Bat algorithm, based on the echolocation of bats, has been used to optimize the S-system model parameters. A decoupled S-system has been implemented to reduce the complexity of the algorithm. Initially, the proposed method has been successfully tested on an artificial network with and without the presence of noise. Based on the fact that a real-life genetic network is sparsely connected, a novel Accumulative Cardinality based decoupled S-system has been proposed. The cardinality has been varied from zero up to a maximum value, and this model has been implemented for the reconstruction of the DNA SOS repair network of Escherichia coli. The obtained results have shown significant improvements in the detection of a greater number of true regulations, and in the minimization of false detections compared to other existing methods.

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.