Microorganisms naturally form community ecosystems to improve fitness in diverse environments and... more Microorganisms naturally form community ecosystems to improve fitness in diverse environments and conduct otherwise intractable processes. Microbial communities are therefore central to biogeochemical cycling, human health, agricultural productivity, and technologies as nuanced as nanotechnology-enabled devices; however, the combinatorial scaling of exchanges with the environment that predicate community functions are experimentally untenable. Several computational tools have been presented to capture these exchanges, yet, no attempt has been made to understand the total information flow to a community from its environment. We therefore adapted a recently developed model for singular organisms, which blends molecular communication and the Shannon Information theory to quantify information flow, to communities and exemplify this expanded model on idealized communities: one ofEscherichia coli(E. coli) andPseudomonas fluorescensto emulate an ecological community and the other ofBactero...
Traumatic brain injury and neuro-degenerative diseases leave people dependent and with a low qual... more Traumatic brain injury and neuro-degenerative diseases leave people dependent and with a low quality of life. Several technologies have been proposed to connect the central nervous system to silicon circuitry and thereby circumvent the damaged nervous tissue that is impairing normal function. These technologies rely upon a language of subtle movements within a patient’s capability to direct computer operations, however, selecting the proper abstraction for even a task as simple as moving a computer cursor can be challenging. Involuntary movements can create noise and false positives for the brain-computer-interface (BCI) receptors, and non-intuitive abstractions can be a barrier for adoption by neurologically damaged patients. We therefore introduce Visualization of Arrow Movements (VAM) as a set of mental tasks for controlling cursor movements in a BCI system. The performance of VAM was evaluated by six untrained subjects via 10-fold cross validation using band power and k-Nearest ...
Understanding cellular engagement with its environment is essential to control and monitor metabo... more Understanding cellular engagement with its environment is essential to control and monitor metabolism. Molecular Communication theory (MC) offers a computational means to identify environmental perturbations that direct or signify cellular behaviors by quantifying the information about a molecular environment that is transmitted through a metabolic system. We developed an model that integrates conventional flux balance analysis metabolic modeling (FBA) and MC to mechanistically expand the scope of MC, and thereby uniquely blends mechanistic biology and information theory to understand how substrate consumption is captured reaction activity, metabolite excretion, and biomass growth. This is enabled by defining several channels through which environmental information transmits in a metabolic network. The information flow in bits that is calculated through this workflow further determines the maximal metabolic effect of environmental perturbations on cellular metabolism and behaviors, ...
The human gut functions through a complex system of interactions between the host human tissue an... more The human gut functions through a complex system of interactions between the host human tissue and the microbes which inhabit it. These diverse interactions are difficult to model or examine under controlled laboratory conditions.
Part of the Biochemical and Biomolecular Engineering Commons, Bioinformatics Commons, Biological ... more Part of the Biochemical and Biomolecular Engineering Commons, Bioinformatics Commons, Biological Engineering Commons, Biology Commons, Biomaterials Commons, Biomechanics and Biotransport Commons, Catalysis and Reaction Engineering Commons, Computational Engineering Commons, Computer Engineering Commons, Molecular, Cellular, and Tissue Engineering Commons, Nanoscience and Nanotechnology Commons, and the Other Biomedical Engineering and Bioengineering Commons
Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication, 2018
Signal transduction pathways are chemical communication channels embedded in biological cells, an... more Signal transduction pathways are chemical communication channels embedded in biological cells, and they propagate information from the environment to regulate cell growth and proliferation, among other cell's behaviors. Disruptions in the normal functionalities of these channels, mostly resulting from mutations in the underlying genetic code, can be leading causes of diseases, such as cancer. Motivated by the increasing availability of public data on genetic code expression in cell tissue samples, i.e., transcriptomics, and the emerging field of molecular communication, a novel data-driven approach based on experimental data mining and communication theory is proposed in this paper. This approach is an alternative to existing computational models of these pathways in the context of cancer, which often appear to oversimplify the complexity of the underlying mechanisms. In contrast, a computational methodology is here derived to estimate the difference in information propagation p...
Proceedings of the Sixth Annual ACM International Conference on Nanoscale Computing and Communication
The natural communication ability of cells is explored in this paper by providing preliminary res... more The natural communication ability of cells is explored in this paper by providing preliminary results in the estimation of the Mutual Information (MI) of signaling pathway communication channels. These results, based on an application of Molecular Communication (MC) and information theory concepts to multi-scale integrated Flux-Balance Analysis (iFBA) models are a first step to evaluate the potential of cells and their biochemical processes as a substrate for enabling engineered MC channels for the future internet of Bio-Nano Things.
2013 Ieee 8th International Conference on Industrial and Information Systems, Dec 1, 2013
ABSTRACT In this paper we present brain maps constructed for Visualization of Arrow Movement (VAM... more ABSTRACT In this paper we present brain maps constructed for Visualization of Arrow Movement (VAM) mental tasks with EEG signals recorded from 20 locations on the scalp. Method of Common Spatial Patterns (CSP) is employed to generate the spatial maps after filtering raw EEG signals into nine different frequency bands. Separate CSPs were obtained for six subjects who participated in this study. These brain maps show distinct spatial patterns that can be used for distinguishing two mental tasks in VAM. For every subject, optimal frequency range which is useful in distinguishing mental tasks in VAM was obtained.
A set of new mental tasks that can be used with Brain Computer Interface systems are introduced. ... more A set of new mental tasks that can be used with Brain Computer Interface systems are introduced. New mental tasks are natural to perform for controlling a cursor on a computer screen to select icons. With the help of three healthy subjects, performance of new mental tasks was evaluated and compared with that of popular motor imagery mental tasks. Three subjects who participated in this study showed better or equally good performance with new mental tasks as compared to motor imagery mental tasks.
A simple method is developed for selecting effective channels and feature dimensions automaticall... more A simple method is developed for selecting effective channels and feature dimensions automatically at the training stage of BCI systems. The method is applied on feature vectors constructed with all the EEG channels used for recording. Performance was evaluated with EEG data which was preprocessed by band pass filtering and feature vectors constructed by band powers. The classification method used in the evaluation is k Nearest Neighbor classifier, which is sensitive to number of dimensions in the feature vectors. It was found that new method can effectively select features and reduce channels and thereby improve accuracy and efficiency of BCI systems.
Microorganisms naturally form community ecosystems to improve fitness in diverse environments and... more Microorganisms naturally form community ecosystems to improve fitness in diverse environments and conduct otherwise intractable processes. Microbial communities are therefore central to biogeochemical cycling, human health, agricultural productivity, and technologies as nuanced as nanotechnology-enabled devices; however, the combinatorial scaling of exchanges with the environment that predicate community functions are experimentally untenable. Several computational tools have been presented to capture these exchanges, yet, no attempt has been made to understand the total information flow to a community from its environment. We therefore adapted a recently developed model for singular organisms, which blends molecular communication and the Shannon Information theory to quantify information flow, to communities and exemplify this expanded model on idealized communities: one ofEscherichia coli(E. coli) andPseudomonas fluorescensto emulate an ecological community and the other ofBactero...
Traumatic brain injury and neuro-degenerative diseases leave people dependent and with a low qual... more Traumatic brain injury and neuro-degenerative diseases leave people dependent and with a low quality of life. Several technologies have been proposed to connect the central nervous system to silicon circuitry and thereby circumvent the damaged nervous tissue that is impairing normal function. These technologies rely upon a language of subtle movements within a patient’s capability to direct computer operations, however, selecting the proper abstraction for even a task as simple as moving a computer cursor can be challenging. Involuntary movements can create noise and false positives for the brain-computer-interface (BCI) receptors, and non-intuitive abstractions can be a barrier for adoption by neurologically damaged patients. We therefore introduce Visualization of Arrow Movements (VAM) as a set of mental tasks for controlling cursor movements in a BCI system. The performance of VAM was evaluated by six untrained subjects via 10-fold cross validation using band power and k-Nearest ...
Understanding cellular engagement with its environment is essential to control and monitor metabo... more Understanding cellular engagement with its environment is essential to control and monitor metabolism. Molecular Communication theory (MC) offers a computational means to identify environmental perturbations that direct or signify cellular behaviors by quantifying the information about a molecular environment that is transmitted through a metabolic system. We developed an model that integrates conventional flux balance analysis metabolic modeling (FBA) and MC to mechanistically expand the scope of MC, and thereby uniquely blends mechanistic biology and information theory to understand how substrate consumption is captured reaction activity, metabolite excretion, and biomass growth. This is enabled by defining several channels through which environmental information transmits in a metabolic network. The information flow in bits that is calculated through this workflow further determines the maximal metabolic effect of environmental perturbations on cellular metabolism and behaviors, ...
The human gut functions through a complex system of interactions between the host human tissue an... more The human gut functions through a complex system of interactions between the host human tissue and the microbes which inhabit it. These diverse interactions are difficult to model or examine under controlled laboratory conditions.
Part of the Biochemical and Biomolecular Engineering Commons, Bioinformatics Commons, Biological ... more Part of the Biochemical and Biomolecular Engineering Commons, Bioinformatics Commons, Biological Engineering Commons, Biology Commons, Biomaterials Commons, Biomechanics and Biotransport Commons, Catalysis and Reaction Engineering Commons, Computational Engineering Commons, Computer Engineering Commons, Molecular, Cellular, and Tissue Engineering Commons, Nanoscience and Nanotechnology Commons, and the Other Biomedical Engineering and Bioengineering Commons
Proceedings of the 5th ACM International Conference on Nanoscale Computing and Communication, 2018
Signal transduction pathways are chemical communication channels embedded in biological cells, an... more Signal transduction pathways are chemical communication channels embedded in biological cells, and they propagate information from the environment to regulate cell growth and proliferation, among other cell's behaviors. Disruptions in the normal functionalities of these channels, mostly resulting from mutations in the underlying genetic code, can be leading causes of diseases, such as cancer. Motivated by the increasing availability of public data on genetic code expression in cell tissue samples, i.e., transcriptomics, and the emerging field of molecular communication, a novel data-driven approach based on experimental data mining and communication theory is proposed in this paper. This approach is an alternative to existing computational models of these pathways in the context of cancer, which often appear to oversimplify the complexity of the underlying mechanisms. In contrast, a computational methodology is here derived to estimate the difference in information propagation p...
Proceedings of the Sixth Annual ACM International Conference on Nanoscale Computing and Communication
The natural communication ability of cells is explored in this paper by providing preliminary res... more The natural communication ability of cells is explored in this paper by providing preliminary results in the estimation of the Mutual Information (MI) of signaling pathway communication channels. These results, based on an application of Molecular Communication (MC) and information theory concepts to multi-scale integrated Flux-Balance Analysis (iFBA) models are a first step to evaluate the potential of cells and their biochemical processes as a substrate for enabling engineered MC channels for the future internet of Bio-Nano Things.
2013 Ieee 8th International Conference on Industrial and Information Systems, Dec 1, 2013
ABSTRACT In this paper we present brain maps constructed for Visualization of Arrow Movement (VAM... more ABSTRACT In this paper we present brain maps constructed for Visualization of Arrow Movement (VAM) mental tasks with EEG signals recorded from 20 locations on the scalp. Method of Common Spatial Patterns (CSP) is employed to generate the spatial maps after filtering raw EEG signals into nine different frequency bands. Separate CSPs were obtained for six subjects who participated in this study. These brain maps show distinct spatial patterns that can be used for distinguishing two mental tasks in VAM. For every subject, optimal frequency range which is useful in distinguishing mental tasks in VAM was obtained.
A set of new mental tasks that can be used with Brain Computer Interface systems are introduced. ... more A set of new mental tasks that can be used with Brain Computer Interface systems are introduced. New mental tasks are natural to perform for controlling a cursor on a computer screen to select icons. With the help of three healthy subjects, performance of new mental tasks was evaluated and compared with that of popular motor imagery mental tasks. Three subjects who participated in this study showed better or equally good performance with new mental tasks as compared to motor imagery mental tasks.
A simple method is developed for selecting effective channels and feature dimensions automaticall... more A simple method is developed for selecting effective channels and feature dimensions automatically at the training stage of BCI systems. The method is applied on feature vectors constructed with all the EEG channels used for recording. Performance was evaluated with EEG data which was preprocessed by band pass filtering and feature vectors constructed by band powers. The classification method used in the evaluation is k Nearest Neighbor classifier, which is sensitive to number of dimensions in the feature vectors. It was found that new method can effectively select features and reduce channels and thereby improve accuracy and efficiency of BCI systems.
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