Sasitharan Balasubramaniam

Sasitharan Balasubramaniam, Samitha Somathilaka, Sehee Sun et al.

Artificial Intelligence (AI) and Machine Learning (ML) are weaving their way into the fabric of society, where they are playing a crucial role in numerous facets of our lives. As we witness the increased deployment of AI and ML in various types of devices, we benefit from their use into energy-efficient algorithms for low powered devices. In this paper, we investigate a scale and medium that is far smaller than conventional devices as we move towards molecular systems that can be utilized to perform machine learning functions, i.e., Molecular Machine Learning (MML). Fundamental to the operation of MML is the transport, processing, and interpretation of information propagated by molecules through chemical reactions. We begin by reviewing the current approaches that have been developed for MML, before we move towards potential new directions that rely on gene regulatory networks inside biological organisms as well as their population interactions to create neural networks. We then investigate mechanisms for training machine learning structures in biological cells based on calcium signaling and demonstrate their application to build an Analog to Digital Converter (ADC). Lastly, we look at potential future directions as well as challenges that this area could solve.

Adrian Ratwatte, Samitha Somathilaka, Sasitharan Balasubramaniam et al.

The Gene Regulatory Network (GRN) of biological cells governs a number of key functionalities that enables them to adapt and survive through different environmental conditions. Close observation of the GRN shows that the structure and operational principles resembles an Artificial Neural Network (ANN), which can pave the way for the development of Biological Artificial Intelligence. In particular, a gene's transcription and translation process resembles a sigmoidal-like property based on transcription factor inputs. In this paper, we develop a mathematical model of gene-perceptron using a dual-layered transcription-translation chemical reaction model, enabling us to transform a GRN into a Gene Regulatory Neural Network (GRNN). We perform stability analysis for each gene-perceptron within the fully-connected GRNN sub network to determine temporal as well as stable concentration outputs that will result in reliable computing performance. We focus on a non-linear classifier application for the GRNN, where we analyzed generic multi-layer GRNNs as well as E.Coli GRNN that is derived from trans-omic experimental data. Our analysis found that varying the parameters of the chemical reactions can allow us shift the boundaries of the classification region, laying the platform for programmable GRNNs that suit diverse application requirements.

Samitha Somathilaka, Daniel P. Martins, Xu Li et al.

Bacterial cells are sensitive to a range of external signals used to learn the environment. These incoming external signals are then processed using a Gene Regulatory Network (GRN), exhibiting similarities to modern computing algorithms. An in-depth analysis of gene expression dynamics suggests an inherited Gene Regulatory Neural Network (GRNN) behavior within the GRN that enables the cellular decision-making based on received signals from the environment and neighbor cells. In this study, we extract a sub-network of \textit{Pseudomonas aeruginosa} GRN that is associated with one virulence factor: pyocyanin production as a use case to investigate the GRNN behaviors. Further, using Graph Neural Network (GNN) architecture, we model a single species biofilm to reveal the role of GRNN dynamics on ecosystem-wide decision-making. Varying environmental conditions, we prove that the extracted GRNN computes input signals similar to natural decision-making process of the cell. Identifying of neural network behaviors in GRNs may lead to more accurate bacterial cell activity predictive models for many applications, including human health-related problems and agricultural applications. Further, this model can produce data on causal relationships throughout the network, enabling the possibility of designing tailor-made infection-controlling mechanisms. More interestingly, these GRNNs can perform computational tasks for bio-hybrid computing systems.

Jacob Clouse, Thomas Ramsey, Samitha Somathilaka et al.

As the demand for more efficient and adaptive computing grows, nature-inspired architectures offer promising alternatives to conventional electronic designs. Microfluidic platforms, drawing on biological forms and fluid dynamics, present a compelling foundation for low-power, high-resilience computing in environments where electronics are unsuitable. This study explores a hybrid reservoir computing system based on a dragonfly-wing inspired microfluidic chip, which encodes temporal input patterns as fluid interactions within the micro channel network. The system operates with three dye-based inlet channels and three camera-monitored detection areas, transforming discrete spatial patterns into dynamic color output signals. These reservoir output signals are then modified and passed to a simple and trainable readout layer for pattern classification. Using a combination of raw reservoir outputs and synthetically generated outputs, we evaluated system performance, system clarity, and data efficiency. The results demonstrate consistent classification accuracies up to $91\%$, even with coarse resolution and limited training data, highlighting the viability of the microfluidic reservoir computing.

Frances Cleary, Witawas Srisa-an, Beatriz Gil et al.

On garment intelligence influenced by artificial neural networks and neuromorphic computing is emerging as a research direction in the e-textile sector. In particular, bio inspired Spiking Neural Networks mimicking the workings of the brain show promise in recent ICT research applications. Taking such technological advancements and new research directions driving forward the next generation of e-textiles and smart materials, we present a wearable micro Brain capable of event driven artificial spiking neural network computation in a fabric based environment. We demonstrate a wearable Brain SNN prototype with multi-layer computation, enabling scalability and flexibility in terms of modifications for hidden layers to be augmented to the network. The wearable micro Brain provides a low size, weight and power artificial on-garment intelligent wearable solution with embedded functionality enabling offline adaptive learning through the provision of interchangeable resistor synaptic weightings. The prototype has been evaluated for fault tolerance, where we have determine the robustness of the circuit when certain parts are damaged. Validations were also conducted for movements to determine if the circuit can still perform accurate computation.

Mohd Siblee Islam, Stepan Ivanov, Hamdan Awan et al.

This article uses Deep Learning technologies to safeguard DNA sequencing against Bio-Cyber attacks. We consider a hybrid attack scenario where the payload is encoded into a DNA sequence to activate a Trojan malware implanted in a software tool used in the sequencing pipeline in order to allow the perpetrators to gain control over the resources used in that pipeline during sequence analysis. The scenario considered in the paper is based on perpetrators submitting synthetically engineered DNA samples that contain digitally encoded IP address and port number of the perpetrators machine in the DNA. Genetic analysis of the samples DNA will decode the address that is used by the software trojan malware to activate and trigger a remote connection. This approach can open up to multiple perpetrators to create connections to hijack the DNA sequencing pipeline. As a way of hiding the data, the perpetrators can avoid detection by encoding the address to maximise similarity with genuine DNAs, which we showed previously. However, in this paper we show how Deep Learning can be used to successfully detect and identify the trigger encoded data, in order to protect a DNA sequencing pipeline from trojan attacks. The result shows nearly up to 100% accuracy in detection in such a novel Trojan attack scenario even after applying fragmentation encryption and steganography on the encoded trigger data. In addition, feasibility of designing and synthesizing encoded DNA for such Trojan payloads is validated by a wet lab experiment.

Frances Cleary, David Henshall, Sasitharan Balasubramaniam

E-textiles has received tremendous attention in recent years due to the capability of integrating sensors into a garment to provide high precision sensing of the human body. Besides sensing, a number of solutions for e-textile garments have also integrated wireless interfaces allowing these sensing data to be transmitted and also sensors that allow users to provide instructions through touching. While this has provided a new level of sensing that can result in unprecedented applications, there has been little attention placed on on-body computing for e-textiles. Facilitating computing on e-textiles can result in a new form of On-body Edge Computing, where sensor information are processed very close to the body before being transmitted to an external device or wireless access point. This form of computing can provide new security and data privacy capabilities and at the same time provide opportunities for new energy harvesting mechanisms to process the data through the garment. This paper proposes this concept through embroidered Programmable Logic Array (PLA) integrated into e-textiles. In the way that PLAs have programmable logic circuits by interconnecting different AND, NOT and OR gates, we propose e-textile based gates that are sewn into a garment and connected through conductive thread stitching. Two designs are proposed and this includes Single and Multi-Layered PLA. Experimental validations have been conducted at the individual gates as well as the entire PLA circuits to determine the voltage utilization as well as logic computing reliability. Our proposed approach can usher in a new form of On-Body Edge Computing for e-textile garments for future wearable technologies

Dixon Vimalajeewa, Subhasis Thakur, John Breslin et al.

The use of Internet of Things (IoT) with the Internet of Nano Things (IoNT) can further expand decision making systems (DMS) to improve reliability as it provides a new spectrum of more granular level data to make decisions. However, growing concerns such as data security, transparency and processing capability challenge their use in real-world applications. DMS integrated with Block Chain (BC) technology can contribute immensely to overcome such challenges. The use of IoNT and IoT along with BC for making DMS has not yet been investigated. This study proposes a BC-powered IoNT (BC-IoNT) system for sensing chemicals level in the context of farm management. This is a critical application for smart farming, which aims to improve sustainable farm practices through controlled delivery of chemicals. BC-IoNT system includes a novel machine learning model formed by using the Langmuir molecular binding model and the Bayesian theory, and is used as a smart contract for sensing the level of the chemicals. A credit model is used to quantify the traceability and credibility of farms to determine if they are compliant with the chemical standards. The accuracy of detecting the chemicals of the distributed BC-IoNT approach was >90% and the centralized approach was <80%. Also, the efficiency of sensing the level of chemicals depends on the sampling frequency and variability in chemical level among farms.

Federico Tavella, Alberto Giaretta, Mauro Conti et al.

Data storage is one of the main computing issues of this century. Not only storage devices are converging to strict physical limits, but also the amount of data generated by users is growing at an unbelievable rate. To face these challenges, data centres grew constantly over the past decades. However, this growth comes with a price, particularly from the environmental point of view. Among various promising media, DNA is one of the most fascinating candidate. In our previous work, we have proposed an automated archival architecture which uses bioengineered bacteria to store and retrieve data, previously encoded into DNA. This storage technique is one example of how biological media can deliver power-efficient storing solutions. The similarities between these biological media and classical ones can also be a drawback, as malicious parties might replicate traditional attacks on the former archival system, using biological instruments and techniques. In this paper, first we analyse the main characteristics of our storage system and the different types of attacks that could be executed on it. Then, aiming at identifying on-going attacks, we propose and evaluate detection techniques, which rely on traditional metrics and machine learning algorithms. We identify and adapt two suitable metrics for this purpose, namely generalized entropy and information distance. Moreover, our trained models achieve an AUROC over 0.99 and AUPRC over 0.91.

Sergio López Bernal, Alberto Huertas Celdrán, Lorenzo Fernández Maimó et al.

Brain-Computer Interfaces (BCI) arose as systems that merge computing systems with the human brain to facilitate recording, stimulation, and inhibition of neural activity. Over the years, the development of BCI technologies has shifted towards miniaturization of devices that can be seamlessly embedded into the brain and can target single neuron or small population sensing and control. We present a motivating example highlighting vulnerabilities of two promising micron-scale BCI technologies, demonstrating the lack of security and privacy principles in existing solutions. This situation opens the door to a novel family of cyberattacks, called neuronal cyberattacks, affecting neuronal signaling. This paper defines the first two neural cyberattacks, Neuronal Flooding (FLO) and Neuronal Scanning (SCA), where each threat can affect the natural activity of neurons. This work implements these attacks in a neuronal simulator to determine their impact over the spontaneous neuronal behavior, defining three metrics: number of spikes, percentage of shifts, and dispersion of spikes. Several experiments demonstrate that both cyberattacks produce a reduction of spikes compared to spontaneous behavior, generating a rise in temporal shifts and a dispersion increase. Mainly, SCA presents a higher impact than FLO in the metrics focused on the number of spikes and dispersion, where FLO is slightly more damaging, considering the percentage of shifts. Nevertheless, the intrinsic behavior of each attack generates a differentiation on how they alter neuronal signaling. FLO is adequate to generate an immediate impact on the neuronal activity, whereas SCA presents higher effectiveness for damages to the neural signaling in the long-term.

Sergio López Bernal, Alberto Huertas Celdrán, Gregorio Martínez Pérez et al.

BCIs have significantly improved the patients' quality of life by restoring damaged hearing, sight, and movement capabilities. After evolving their application scenarios, the current trend of BCI is to enable new innovative brain-to-brain and brain-to-the-Internet communication paradigms. This technological advancement generates opportunities for attackers since users' personal information and physical integrity could be under tremendous risk. This work presents the existing versions of the BCI life-cycle and homogenizes them in a new approach that overcomes current limitations. After that, we offer a qualitative characterization of the security attacks affecting each phase of the BCI cycle to analyze their impacts and countermeasures documented in the literature. Finally, we reflect on lessons learned, highlighting research trends and future challenges concerning security on BCIs.