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Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change. Theoretical work and empirical…
Vision Transformers (ViT)s have shown great performance in self-supervised learning of global and local representations that can be transferred to downstream applications. Inspired by these results, we introduce a novel self-supervised…
Some low-$n$ kink-ballooning modes not far from marginal stability are shown to exhibit a bifurcation between two very distinct nonlinear paths that depends sensitively on the background transport levels and linear perturbation amplitudes.…
Generative AI has received significant attention among a spectrum of diverse industrial and academic domains, thanks to the magnificent results achieved from deep generative models such as generative pre-trained transformers (GPT) and…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
Sensor drift is a major problem in chemical sensors that requires addressing for reliable and accurate detection of chemical analytes. In this paper, we develop a causal convolutional neural network (CNN) with a Discrete Cosine Transform…
Spiking Neural Networks (SNNs) offer a promising alternative to traditional deep learning frameworks, since they provide higher computational efficiency due to event-driven information processing. SNNs distribute the analog values of pixel…
Positron emission tomography (PET) is a critical tool for diagnosing tumors and neurological disorders but poses radiation risks to patients, particularly to sensitive populations. While reducing injected radiation dose mitigates this risk,…
The regulatory mechanisms driving progression of the yeast cell cycle appears to be comprised of an interacting network of transcription factors (TFs), cyclin-dependent kinases (CDK) and ubiquitin ligases. From a systems perspective the…
Random Matrix Theory (RMT) is applied to analyze weight matrices of Deep Neural Networks (DNNs), including both production quality, pre-trained models such as AlexNet and Inception, and smaller models trained from scratch, such as LeNet5…
Genes/Proteins do not work alone within our body, rather as a group they perform certain activities indicated as pathways. Signalling transduction pathways (STPs) are some of the important pathways that transmit biological signals from…
SCN2A encodes the alpha subunit of the voltage-gated sodium channel Nav1.2, which is involved in action potential initiation and backpropagation in glutamatergic neurons. Mutations in the gene lead to SCN2A-related disorders, which are…
By use of complex network dynamics and graph-based machine learning, we identified critical determinants of lineage-specific plasticity across the single-cell transcriptomics of pediatric high-grade glioma (pHGGs) subtypes: IDHWT…
Designing Doppler-resilient unimodular discrete phase-coded waveforms (DPWs) with low delay-Doppler sidelobes is critical for multiple-input multiple-output (MIMO) radar. Existing block coordinate descent (BCD) methods suffer from high…
Wireless image transmission underpins diverse networked intelligent services and becomes an increasingly critical issue. Existing works have shown that deep learning-based joint source-channel coding (JSCC) is an effective framework to…
The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of…
Disordered Quantum many-body Systems (DQS) and Quantum Neural Networks (QNN) have many structural features in common. However, a DQS is essentially an initialized QNN with random weights, often leading to non-random outcomes. In this work,…
Stepwise signals are ubiquitous in single-molecule detections, where abrupt changes in signal levels typically correspond to molecular conformational changes or state transitions. However, these features are inevitably obscured by noise,…
Cells sense their surrounding by employing intracellular signaling pathways that transmit hormonal signals from the cell membrane to the nucleus. TGF-$\beta$/SMAD signaling encodes various cell fates, controls tissue homeostasis and is…