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Register a new userBayesian information-theoretic calibration of patient-specific radiotherapy sensitivity parameters for informing effective scanning protocols in cancer
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With new advancements in technology, it is now possible to collect data for a variety of different metrics describing tumor growth, including tumor volume, composition, and vascularity, among others. For any proposed model of tumor growth and treatment, we observe large variability among individual patients parameter values, particularly those relating to treatment response; thus, exploiting the use of these various metrics for model calibration can be helpful to infer such patient-specific parameters both accurately and early, so that treatment protocols can be adjusted mid-course for maximum efficacy. However, taking measurements can be costly and invasive, limiting clinicians to a sparse collection schedule. As such, the determination of optimal times and metrics for which to collect data in order to best inform proper treatment protocols could be of great assistance to clinicians. In this investigation, we employ a Bayesian information-theoretic calibration protocol for experimental design in order to identify the optimal times at which to collect data for informing treatment parameters. Within this procedure, data collection times are chosen sequentially to maximize the reduction in parameter uncertainty with each added measurement, ensuring that a budget of $n$ high-fidelity experimental measurements results in maximum information gain about the low-fidelity model parameter values. In addition to investigating the optimal temporal pattern for data collection, we also develop a framework for deciding which metrics should be utilized at each data collection point. We illustrate this framework with a variety of toy examples, each utilizing a radiotherapy treatment regimen. For each scenario, we analyze the dependence of the predictive power of the low-fidelity model upon the measurement budget.
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Understanding and even defining what constitutes animal interactions remains a challenging problem. Correlational tools may be inappropriate for detecting communication between a set of many agents exhibiting nonlinear behavior. A different approach is to define coordinated motions in terms of an information theoretic channel of direct causal information flow. In this work, we consider time series data obtained by an experimental protocol of optical tracking of the insect species Chironomus riparius. The data constitute reconstructed 3-D spatial trajectories of the insects flight trajectories and kinematics. We present an application of the optimal causation entropy (oCSE) principle to identify direct causal relationships or information channels among the insects. The collection of channels inferred by oCSE describes a network of information flow within the swarm. We find that information channels with a long spatial range are more common than expected under the assumption that causal information flows should be spatially localized. The tools developed herein are general and applicable to the inference and study of intercommunication networks in a wide variety of natural settings.
Pimentel et al. (2020) recently analysed probing from an information-theoretic perspective. They argue that probing should be seen as approximating a mutual information. This led to the rather unintuitive conclusion that representations encode exactly the same information about a target task as the original sentences. The mutual information, however, assumes the true probability distribution of a pair of random variables is known, leading to unintuitive results in settings where it is not. This paper proposes a new framework to measure what we term Bayesian mutual information, which analyses information from the perspective of Bayesian agents -- allowing for more intuitive findings in scenarios with finite data. For instance, under Bayesian MI we have that data can add information, processing can help, and information can hurt, which makes it more intuitive for machine learning applications. Finally, we apply our framework to probing where we believe Bayesian mutual information naturally operationalises ease of extraction by explicitly limiting the available background knowledge to solve a task.
The overall predictive uncertainty of a trained predictor can be decomposed into separate contributions due to epistemic and aleatoric uncertainty. Under a Bayesian formulation, assuming a well-specified model, the two contributions can be exactly expressed (for the log-loss) or bounded (for more general losses) in terms of information-theoretic quantities (Xu and Raginsky, 2020). This paper addresses the study of epistemic uncertainty within an information-theoretic framework in the broader setting of Bayesian meta-learning. A general hierarchical Bayesian model is assumed in which hyperparameters determine the per-task priors of the model parameters. Exact characterizations (for the log-loss) and bounds (for more general losses) are derived for the epistemic uncertainty - quantified by the minimum excess meta-risk (MEMR)- of optimal meta-learning rules. This characterization is leveraged to bring insights into the dependence of the epistemic uncertainty on the number of tasks and on the amount of per-task training data. Experiments are presented that compare the proposed information-theoretic bounds, evaluated via neural mutual information estimators, with the performance of a novel approximate fully Bayesian meta-learning strategy termed Langevin-Stein Bayesian Meta-Learning (LS-BML).
Exploiting recent developments in information theory, we propose, illustrate, and validate a principled information-theoretic algorithm for module discovery and resulting measure of network modularity. This measure is an order parameter (a dimensionless number between 0 and 1). Comparison is made to other approaches to module-discovery and to quantifying network modularity using Monte Carlo generated Erdos-like modular networks. Finally, the Network Information Bottleneck (NIB) algorithm is applied to a number of real world networks, including the social network of coauthors at the APS March Meeting 2004.
Mathematical methods of information theory constitute essential tools to describe how stimuli are encoded in activities of signaling effectors. Exploring the information-theoretic perspective, however, remains conceptually, experimentally and computationally challenging. Specifically, existing computational tools enable efficient analysis of relatively simple systems, usually with one input and output only. Moreover, their robust and readily applicable implementations are missing. Here, we propose a novel algorithm to analyze signaling data within the framework of information theory. Our approach enables robust as well as statistically and computationally efficient analysis of signaling systems with high-dimensional outputs and a large number of input values. Analysis of the NF-kB single - cell signaling responses to TNF-a uniquely reveals that the NF-kB signaling dynamics improves discrimination of high concentrations of TNF-a with a modest impact on discrimination of low concentrations. Our readily applicable R-package, SLEMI - statistical learning based estimation of mutual information, allows the approach to be used by computational biologists with only elementary knowledge of information theory.
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