Identifying the Attractors of Gene Regulatory Networks from Expression Data under Uncertainty: An Interpretable Approach

In systems biology, attractor landscape analysis of gene regulatory networks is recognized as a powerful computational tool for studying various cellular states from proliferation and differentiation to senescence and apoptosis. Therefore, accurate identification of attractors plays a critical role in determination of the cell fates. On the other hand, in a real biological circuit, genetic/epigenetic alterations as well as varying environmental factors drastically take effect on the location, characteristics, and even the number of attractors. The central question is: Given a temporal gene expression profile of a real gene regulatory network, how can the attractors be robustly identified in the presence of huge amount of uncertainty? This paper addresses this question using a novel approach based on Zadeh Computing with Words. The proposed scheme could effectively identify the attractors from temporal gene expression data in terms of both fuzzy logic-based and linguistic descriptions which are simply interpretable by human experts. Therefore, this method can be considered as an effective step towards interpretable artificial intelligence. Without loss of generality, genetic toggle switch is considered as the case study. The nonlinear dynamics of this benchmark gene regulatory network is computationally modeled by the notion of uncertain stochastic differential equations. The results of in-silico study demonstrate the efficiency and robustness of the proposed method.

Universal Swarm Computing by Nanorobots

Realization of universal computing units for nanorobots is highly promising in creating new and wide arrays of applications, particularly in the realm of distributed computation. However, such realization is also a challenging problem due to the physical limitations of nanometer-sized designs such as in computation, sensory and perception as well as actuation. This paper proposes a theoretical foundation for solving this problem based on a novel notion of distributed swarm computing by basis agents (BAs). The proposed BA is an abstract model for nanorobots that can compute a very simple basis function called B-function. It is mathematically shown here that a swarm of BAs has the universal function approximation property and can accurately approximate functions. It is then analytically demonstrated that a swarm of BAs can be easily reprogrammed to compute desired functions simply by adjusting the concentrations of BAs in the environment. We further propose a specific structure for BAs which enable them to perform distributed computing such as in the aqueous environment of living tissues and nanomedicine. The hardware complexity of this structure aims to remain low to be more reasonably realizable by today technology. Finally, the performance of the proposed approach is illustrated by a simulation example.

Robust Control of Nanoscale Drug Delivery System in Atherosclerosis: A Mathematical Approach

This paper proposes a mathematical approach for robust control of a nanoscale drug delivery system in treatment of atherosclerosis. First, a new nonlinear lumped model is introduced for mass transport in the arterial wall, and its accuracy is evaluated in comparison with the original distributed-parameter model. Then, based on the notion of sliding-mode control, an abstract model is designed for a smart drug delivery nanoparticle. In contrast to the competing strategies on nanorobotics, the proposed nanoparticles carry simpler hardware to penetrate the interior arterial wall and become more technologically feasible. Finally, from this lumped model and the nonlinear control theory, the overall system's stability is mathematically proven in the presence of uncertainty. Simulation results on a well-known model, and comparisons with earlier benchmark approaches, reveals that even when the LDL concentration in the lumen is high, the proposed nanoscale drug delivery system successfully reduces the drug consumption levels by as much as 16% and the LDL level in the Endothelium, Intima, Internal Elastic Layer (IEL) and Media layers of an unhealthy arterial wall by as much as 14.6%, 50.5%, 51.8%, and 64.4%, respectively.

Descriptive evaluation of students using fuzzy approximate reasoning

In recent years, descriptive evaluation has been introduced as a new model for educational evaluation of Iranian students. The current descriptive evaluation method is based on four-valued logic. Assessing all students with only four values is led to a lack of relative justice and the creation of unrealistic equality. Also, the complexity of the evaluation process in the current method increases teacher errors likelihood. As a suitable solution, in this paper, a fuzzy descriptive evaluation system has been proposed. The proposed method is based on fuzzy logic, which is an infinite-valued logic and it can perform approximate reasoning on natural language propositions. By the proposed fuzzy system, student assessment is performed over the school year with infinite values instead of four values. But to eliminate the diversity of assigned values to students, at the end of the school year, the calculated values for each student will be rounded to the nearest value of the four standard values of the current descriptive evaluation system. It can be implemented easily in an appropriate smartphone app, which makes it much easier for the teachers to evaluate the evaluation process. In this paper, the evaluation process of the elementary third-grade mathematics course in Iran during the period from the beginning of the MEHR (The Seventh month of Iran) to the end of BAHMAN (The Eleventh Month of Iran) is examined by the proposed system. To evaluate the validity of this system, the proposed method has been simulated in MATLAB software.

A knowledge-based intelligent system for control of dirt recognition process in the smart washing machines

In this paper, we propose an intelligence approach based on fuzzy logic to modeling human intelligence in washing clothes. At first, an intelligent feedback loop is designed for perception-based sensing of dirt inspired by human color understanding. Then, when color stains leak out of some colored clothes the human probabilistic decision making is computationally modeled to detect this stain leakage and thus the problem of recognizing dirt from stain can be considered in the washing process. Finally, we discuss the fuzzy control of washing clothes and design and simulate a smart controller based on the fuzzy intelligence feedback loop.