Related papers: Ribosome Flow Model with Extended Objects
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
Forecasting high-dimensional, PDE-governed dynamics remains a core challenge for generative modeling. Existing autoregressive and diffusion-based approaches often suffer cumulative errors and discretisation artifacts that limit long,…
We introduce a model for stochastic transport on a one-dimensional substrate with particles assuming different conformations during their stepping cycles. These conformations correspond to different footprints on the substrate: in order to…
The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied Totally Asymmetric Exclusion…
Fundamental biological processes such as transcription and translation, where a genetic sequence is sequentially read by a macromolecule, have been well described by a classical model of non-equilibrium statistical physics, the totally…
We study the mean velocity and diffusion constant in three related models of molecular Brownian ratchets. Brownian ratchets can be used to describe translocation of biopolymers like DNA through nanopores in cells in the presence of…
We introduce Robust Bayesian Sequential Borrowing (RBSB), a framework for extrapolating evidence across adjacent subgroups in multi-population clinical programmes where studies are conducted in sequence and populations are ordered by…
The challenges in feature selection, particularly in balancing model accuracy, interpretability, and computational efficiency, remain a critical issue in advancing machine learning methodologies. To address these complexities, this study…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…
Residual moveout (RMO) provides critical information for travel time tomography. The current industry-standard method for fitting RMO involves scanning high-order polynomial equations. However, this analytical approach does not accurately…
Model extrapolation to unseen flow is one of the biggest challenges facing data-driven turbulence modeling, especially for models with high dimensional inputs that involve many flow features. In this study we review previous efforts on…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
Amoeboid cell motility is essential for a wide range of biological processes including wound healing, embryonic morphogenesis, and cancer metastasis. It relies on complex dynamical patterns of cell shape changes that pose long-standing…
Diffusion models deliver high-fidelity generation but remain slow at inference time due to many sequential network evaluations. We find that standard timestep conditioning becomes a key bottleneck for few-step sampling. Motivated by…
Cell migration is crucial to many physiological and pathological processes. During migration, a cell adapts its morphology, including the overall morphology and nucleus morphology, in response to various cues in complex microenvironments,…
Recurrent Neural Networks (RNNs) have achieved remarkable performance on a range of tasks. A key step to further empowering RNN-based approaches is improving their explainability and interpretability. In this work we present MEME: a model…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
Ribosome-targeting antibiotics, such as chloramphenicol, stall elongating ribosomes during protein synthesis, disrupting mRNA translation. These antibiotic-induced pauses occur stochastically, alter collective ribosome dynamics and…
Self-supervised learning through masked autoencoders has attracted great attention for remote sensing (RS) foundation model (FM) development, enabling improved representation learning across diverse sensors and downstream tasks. However,…
Recent studies show that using diffusion models for time series signal reconstruction holds great promise. However, such approaches remain largely unexplored in the domain of medical time series. The unique characteristics of the…