physics.bio-ph

arXiv:2305.03340v2 Announce Type: replace-cross Abstract: As Evolutionary Dynamics moves from the realm of theory into application, algorithms are needed to move beyond simple models. Yet few such methods exist in the literature. Ecological and physiological factors are known to be central to evolution in realistic contexts, but accounting for them generally renders problems intractable to existing methods. We introduce a formulation of evolutionary games which accounts for ecology and physiology by modeling both as computations and use this to analyze the problem of directed evolution via methods from Reinforcement Learning. This combination enables us to develop first-of-their-kind results on the algorithmic problem of learning to control an evolving population of cells. We prove a complexity bound on eco-evolutionary control in situations with limited prior knowledge of cellular physiology or ecology, give the first results on the most general version of the mathematical problem of directed evolution, and establish a new link between AI and biology.

arXiv:2412.18406v1 Announce Type: cross Abstract: Mechanobiology is gaining more and more traction as the fundamental role of physical forces in biological function becomes clearer. Forces at the microscale are often measured indirectly using inverse problems such as Traction Force Microscopy because biological experiments are hard to access with physical probes. In contrast with the experimental nature of biology and physics, these measurements do not come with error bars, confidence regions, or p-values. The aim of this manuscript is to publicize this issue and to propose a first step towards a remedy in the form of a general reconstruction framework that enables hypothesis testing.

arXiv:2408.17139v2 Announce Type: replace Abstract: We present flow matching for reaction coordinates (FMRC), a novel deep learning algorithm designed to identify optimal reaction coordinates (RC) in biomolecular reversible dynamics. FMRC is based on the mathematical principles of lumpability and decomposability, which we reformulate into a conditional probability framework for efficient data-driven optimization using deep generative models. While FMRC does not explicitly learn the well-established transfer operator or its eigenfunctions, it can effectively encode the dynamics of leading eigenfunctions of the system transfer operator into its low-dimensional RC space. We further quantitatively compare its performance with several state-of-the-art algorithms by evaluating the quality of Markov state models (MSM) constructed in their respective RC spaces, demonstrating the superiority of FMRC in three increasingly complex biomolecular systems. In addition, we successfully demonstrated the efficacy of FMRC for bias deposition in the enhanced sampling of a simple model system. Finally, we discuss its potential applications in downstream applications such as enhanced sampling methods and MSM construction.

arXiv:2412.07514v2 Announce Type: replace-cross Abstract: Physics-based dynamic models (PBDMs) are simplified representations of complex dynamical systems. PBDMs take specific processes within a complex system and assign a fragment of variables and an accompanying set of parameters to depict the processes. As this often leads to suboptimal parameterisation of the system, a key challenge requires refining the empirical parameters and variables to reduce uncertainties while maintaining the model s explainability and enhancing its predictive accuracy. We demonstrate that a hybrid mosquito population dynamics model, which integrates a PBDM with Physics-Informed Neural Networks (PINN), retains the explainability of the PBDM by incorporating the PINN-learned model parameters in place of its empirical counterparts. Specifically, we address the limitations of traditional PBDMs by modelling the parameters of larva and pupa development rates using a PINN that encodes complex, learned interactions of air temperature, precipitation and humidity. Our results demonstrate improved mosquito population simulations including the difficult-to-predict mosquito population peaks. This opens the possibility of hybridisation concept application on other complex systems based on PBDMs such as cancer growth to address the challenges posed by scarce and noisy data, and to numerical weather prediction and climate modelling to overcome the gap between physics-based and data-driven weather prediction models.

arXiv:2412.17542v1 Announce Type: new Abstract: Whole-body hemodynamics simulators, which model blood flow and pressure waveforms as functions of physiological parameters, are now essential tools for studying cardiovascular systems. However, solving the corresponding inverse problem of mapping observations (e.g., arterial pressure waveforms at specific locations in the arterial network) back to plausible physiological parameters remains challenging. Leveraging recent advances in simulation-based inference, we cast this problem as statistical inference by training an amortized neural posterior estimator on a newly built large dataset of cardiac simulations that we publicly release. To better align simulated data with real-world measurements, we incorporate stochastic elements modeling exogenous effects. The proposed framework can further integrate in-vivo data sources to refine its predictive capabilities on real-world data. In silico, we demonstrate that the proposed framework enables finely quantifying uncertainty associated with individual measurements, allowing trustworthy prediction of four biomarkers of clinical interest--namely Heart Rate, Cardiac Output, Systemic Vascular Resistance, and Left Ventricular Ejection Time--from arterial pressure waveforms and photoplethysmograms. Furthermore, we validate the framework in vivo, where our method accurately captures temporal trends in CO and SVR monitoring on the VitalDB dataset. Finally, the predictive error made by the model monotonically increases with the predicted uncertainty, thereby directly supporting the automatic rejection of unusable measurements.

arXiv:2412.17793v1 Announce Type: cross Abstract: Singular Spectrum Analysis (SSA) occupies a prominent place in the real signal analysis toolkit alongside Fourier and Wavelet analysis. In addition to the two aforementioned analyses, SSA allows the separation of patterns directly from the data space into the data space, with data that need not be strictly stationary, continuous, or even normally sampled. In most cases, SSA relies on a combination of Hankel or Toeplitz matrices and Singular Value Decomposition (SVD). Like Fourier and Wavelet analysis, SSA has its limitations. The main bottleneck of the method can be summarized in three points. The first is the diagonalization of the Hankel/Toeplitz matrix, which can become a major problem from a memory and/or computational point of view if the time series to be analyzed is very long or heavily sampled. The second point concerns the size of the analysis window, typically denoted as 'L', which will affect the detection of patterns in the time series as well as the dimensions of the Hankel/Toeplitz matrix. Finally, the third point concerns pattern reconstruction: how to easily identify in the eigenvector/eigenvalue space which patterns should be grouped. We propose to address each of these issues by describing a hopefully effective approach that we have been developing for over 10 years and that has yielded good results in our research work.