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Positive and negative dependence are fundamental concepts that characterize the attractive and repulsive behavior of random subsets. Although some probabilistic models are known to exhibit positive or negative dependence, it is challenging…
Photon counting spectral CT (PCCT) can produce reconstructed attenuation maps in different energy channels, reflecting energy properties of the scanned object. Due to the limited photon numbers and the non-ideal detector response of each…
Deep supervised neural networks trained to classify objects have emerged as popular models of computation in the primate ventral stream. These models represent information with a high-dimensional distributed population code, implying that…
The use of deep learning to undertake shape analysis of the complexities of the human head holds great promise. However, there have traditionally been a number of barriers to accurate modelling, especially when operating on both a global…
Denoising diffusion probabilistic models (DDPMs) and generative adversarial networks (GANs) are popular generative models for neural vocoders. The DDPMs and GANs can be characterized by the iterative denoising framework and adversarial…
The p53 protein is well-known for its tumour suppressor function. The p53-MDM2 negative feedback loop constitutes the core module of a network of regulatory interactions activated under cellular stress. In normal cells, the level of p53…
The cambium is a meristematic tissue in plant stems. Here, cell divisions occur that are required for radial growth of plant stems. Daughters of cell divisions within the cambium differentiate into woody xylem cells towards the inside of…
We introduce and analyze a mathematical model for the regeneration of planarian flatworms. This system of differential equations incorporates dynamics of head and tail cells which express positional control genes that in turn translate into…
Morphogens are proteins, often produced in a localised region, whose concentrations spatially demarcate regions of differing gene expression in developing embryos. The boundaries of expression must be set accurately and in proportion to the…
Chromatin regulators can alter transcriptional programs by modifying the accessibility of regulatory DNA elements. Understanding how regulatory sequences differ between wild-type (WT) and knockout (KO) conditions is crucial for deciphering…
In clinical examinations and diagnoses, low-dose computed tomography (LDCT) is crucial for minimizing health risks compared with normal-dose computed tomography (NDCT). However, reducing the radiation dose compromises the signal-to-noise…
Differentially-Private SGD (DP-SGD) and its adaptive variant DP-Adam are powerful techniques to protect user privacy when using sensitive data to train neural networks. During training, converting model weights and activations into…
The pedunculopontine nucleus (PPN) is a heterogeneous brainstem locomotor hub implicated in Parkinson's disease and potentially relevant for its treatment. We propose single-compartment, conductance-based models for three classes of PPN…
The evolution of the Schr\"{o}dinger-cat states in a dissipative parametric amplifier is examined. The main tool in the analysis is the normally ordered characteristic function. Squeezing, photon-number distribution and reduced factorial…
Recent studies have introduced a new class of generative models for synthesizing implicit neural representations (INRs) that capture arbitrary continuous signals in various domains. These models opened the door for domain-agnostic…
Deep Feedback Models (DFMs) are a new class of stateful neural networks that combine bottom up input with high level representations over time. This feedback mechanism introduces dynamics into otherwise static architectures, enabling DFMs…
We present a new modeling approach for G protein coupled receptors signaling systems, that take into account the compartmentalization of receptors and their effectors, both at plasma membrane and in dynamic intra-cellular vesicles called…
Interacting quantum spin models are remarkably useful for describing different types of physical, chemical, and biological systems. Significant understanding of their equilibrium properties has been achieved to date, especially for the case…
Riboswitches, structured elements in the untranslated regions of messenger RNAs, regulate gene expression by binding specific metabolites. We introduce a kinetic network model that describes the functions of riboswitches at the systems…
Many patterning events in multi-cellular organisms rely on cell-to-cell contact signaling, such as the Notch pathway in metazoans. A particularly interesting phenomenon in this form of communication is lateral inhibition where a cell that…