Search Results (42)

Background: Unlike most cancers, breast cancer poses a persistent risk of distant recurrence—often years after initial treatment—making long-term risk stratification uniquely challenging. Current tools fall short in predicting late metastatic events, particularly for early-stage patients. Methods: We present an interpretable machine learning (ML) pipeline to predict distant recurrence-free survival at 5, 10, and 15 years, integrating Bayesian network-based causal feature selection, deep feed-forward neural network models (DNMs), and SHAP-based interpretation. Using electronic health record (EHR)-based clinical data from over 6000 patients, we first applied the Markov blanket and interactive risk factor learner (MBIL) to identify minimally sufficient predictor subsets. These were then used to train optimized DNM classifiers, with hyperparameters tuned via grid search and benchmarked against models from 10 traditional ML methods and models trained using all predictors. Results: Our best models achieved area under the curve (AUC) scores of 0.79, 0.83, and 0.89 for 5-, 10-, and 15-year predictions, respectively—substantially outperforming baselines. MBIL reduced input dimensionality by over 80% without sacrificing accuracy. Importantly, MBIL-selected features (e.g., nodal status, hormone receptor expression, tumor size) overlapped strongly with top SHAP contributors, reinforcing interpretability. Calibration plots further demonstrated close agreement between predicted probabilities and observed recurrence rates. The percentage performance improvement due to grid search ranged from 25.3% to 60%. Conclusions: This study demonstrates that combining causal selection, deep learning, and grid search improves prediction accuracy, transparency, and calibration for long-horizon breast cancer recurrence risk. The proposed framework is well-positioned for clinical use, especially to guide long-term follow-up and therapy decisions in early-stage patients. Full article

We introduce a quantum integrated-information measure $\Phi$ for multipartite states within the Relational Quantum Dynamics (RQD) framework. $\Phi \left(\rho \right)$ is defined as the minimum quantum Jensen–Shannon distance between an n-partite density operator $\rho$ and any product state over a bipartition of its subsystems. We prove that its square root induces a genuine metric on state space and that $\Phi$ is monotonic under all completely positive trace-preserving maps. Restricting the search to bipartitions yields a unique optimal split and a unique closest product state. From this geometric picture, we derive a canonical entanglement witness directly tied to $\Phi$ and construct an integration dendrogram that reveals the full hierarchical correlation structure of $\rho$. We further show that there always exists an “optimal observer”—a channel or basis—that preserves $\Phi$ better than any alternative. Finally, we propose a quantum Markov blanket theorem: the boundary of the optimal bipartition isolates subsystems most effectively. Our framework unites categorical enrichment, convex-geometric methods, and operational tools, forging a concrete bridge between integrated information theory and quantum information science. Full article

Cuffless continuous blood pressure (BP) monitoring is essential for personal health management. However, its accuracy is challenged by the diversity and heterogeneity of physiological data sources. We propose a multi-source feature selection framework based on Markov blanket theory and the concept of causal invariance. We extracted 218 BP-related photoplethysmography (PPG) features from three heterogeneous datasets (differing in subject population, acquisition devices, and methods) and constructed a causal feature set using the Multi-Dataset Stable Feature Selection via Ensemble Markov Blanket (MDSFS-EMB) algorithm. BP estimation was then performed using four machine learning models. The MDSFS-EMB algorithm integrated PPFS and HITON-MB, enabling adaptability to different data scales and distribution scenarios. It employed Gaussian Copula Mutual Information, which was robust to outliers and capable of modeling nonlinear relationships. To validate the effectiveness of the selected feature set, we conducted experiments using an independent external validation dataset and explored the impact of data segmentation strategies on model prediction outcomes. The results demonstrated that the MDSFS-EMB algorithm has advantages in feature selection efficiency, prediction accuracy, and generalization capability. This study innovatively explores the causal relationships between PPG features and BP across multiple data sources, providing a clinically applicable approach for cuffless BP estimation. Full article

The Thoughtseeds Framework introduces a novel computational approach to modeling thought dynamics in meditative states, conceptualizing thoughtseeds as dynamic attentional agents that integrate information. This hierarchical model, structured as nested Markov blankets, comprises three interconnected levels: (i) knowledge domains as information repositories, (ii) the Thoughtseed Network where thoughtseeds compete, and (iii) meta-cognition regulating awareness. It simulates focused-attention Vipassana meditation via rule-based training informed by empirical neuroscience research on attentional stability and neural dynamics. Four states—breath_control, mind_wandering, meta_awareness, and redirect_breath—emerge organically from thoughtseed interactions, demonstrating self-organizing dynamics. Results indicate that experts sustain control dominance to reinforce focused attention, while novices exhibit frequent, prolonged mind_wandering episodes, reflecting beginner instability. Integrating Global Workspace Theory and the Intrinsic Ignition Framework, the model elucidates how thoughtseeds shape a unitary meditative experience through meta-awareness, balancing epistemic and pragmatic affordances via active inference. Synthesizing computational modeling with phenomenological insights, it provides an embodied perspective on cognitive state emergence and transitions, offering testable predictions about meditation skill development. The framework yields insights into attention regulation, meta-cognitive awareness, and meditation state emergence, establishing a versatile foundation for future research into diverse meditation practices (e.g., Open Monitoring, Non-Dual Awareness), cognitive development across the lifespan, and clinical applications in mindfulness-based interventions for attention disorders, advancing our understanding of the nature of mind and thought. Full article

Understanding and evaluating directed acyclic graphs (DAGs) is crucial for causal discovery, particularly in high-dimensional and small-sample datasets such as microbial abundance data. This study introduces DAGMetrics, an R package designed to comprehensively evaluate and compare DAGs. The package provides descriptive and comparative metrics, streamlining the assessment of outputs from various structure learning algorithms. It was applied to datasets generated for potato tubers and soils from different terroirs (continental and island) and stages (at harvest and post-harvest). Using a comprehensive set of descriptive and comparative metrics, DAGMetrics facilitated model selection by identifying balanced and robust DAGs. The PC algorithm with Spearman correlation produced DAGs with moderate complexity and high stability across scaling and transformation setups. Additionally, the package enabled detailed exploration of the Markov blanket space, revealing small Markov blankets (up to seven nodes) and numerous isolated nodes. Identified matching edges between Markov blankets across different terroirs and stages aligned with known microbial interactions, highlighting the package’s utility in facilitating the discovery of biologically meaningful relationships. This study illustrates the utility of DAGMetrics in providing objective and reproducible tools for DAG evaluation along with its potential application in agronomic and other domains involving complex structured data. Full article

Active inference under the Free Energy Principle has been proposed as an across-scales compatible framework for understanding and modelling behaviour and self-maintenance. Crucially, a collective of active inference agents can, if they maintain a group-level Markov blanket, constitute a larger group-level active inference agent with a generative model of its own. This potential for computational scale-free structures speaks to the application of active inference to self-organizing systems across spatiotemporal scales, from cells to human collectives. Due to the difficulty of reconstructing the generative model that explains the behaviour of emergent group-level agents, there has been little research on this kind of multi-scale active inference. Here, we propose a data-driven methodology for characterising the relation between the generative model of a group-level agent and the dynamics of its constituent individual agents. We apply methods from computational cognitive modelling and computational psychiatry, applicable for active inference as well as other types of modelling approaches. Using a simple Multi-Armed Bandit task as an example, we employ the new ActiveInference.jl library for Julia to simulate a collective of agents who are equipped with a Markov blanket. We use sampling-based parameter estimation to make inferences about the generative model of the group-level agent, and we show that there is a non-trivial relationship between the generative models of individual agents and the group-level agent they constitute, even in this simple setting. Finally, we point to a number of ways in which this methodology might be applied to better understand the relations between nested active inference agents across scales. Full article

Engine fault diagnosis is a critical task in automotive aftermarket management. Developing appropriate fault-labeled datasets can be challenging due to nonlinearity variations and divergence in feature distribution among different engine kinds or operating scenarios. To solve this task, this study experimentally measures audio emission signals from compression ignition engines in different vehicles, simulating injector failures, intake hose failures, and absence of failures. Based on these faults, a hybrid approach is applied to classify different conditions that help the planning and decision-making of the automobile industry. The proposed hybrid approach combines the wavelet packet transform (WPT), Markov blanket feature selection, random convolutional kernel transform (ROCKET), tree-structured Parzen estimator (TPE) for hyperparameters tuning, and ten machine learning (ML) classifiers, such as ridge regression, quadratic discriminant analysis (QDA), naive Bayes, k-nearest neighbors (k-NN), support vector machine (SVM), multilayer perceptron (MLP), random forest (RF), extra trees (ET), gradient boosting machine (GBM), and LightGBM. The audio data are broken down into sub-time series with various frequencies and resolutions using the WPT. These data are subsequently utilized as input for obtaining an informative feature subset using a Markov blanket-based selection method. This feature subset is then fed into the ROCKET method, which is paired with ML classifiers, and tuned using Optuna using the TPE approach. The generalization performance applying the proposed hybrid approach outperforms other standard ML classifiers. Full article

There is a widely spread belief in the Bayesian network (BN) community that the overall accuracy of results of BN inference is not too sensitive to the precision of their parameters. We present the results of several experiments in which we put this belief to a test in the context of medical diagnostic models. We study the deterioration of accuracy under random symmetric noise but also biased noise that represents overconfidence and underconfidence of human experts.Our results demonstrate consistently, across all models studied, that while noise leads to deterioration of accuracy, small amounts of noise have minimal effect on the diagnostic accuracy of BN models. Overconfidence, common among human experts, appears to be safer than symmetric noise and much safer than underconfidence in terms of the resulting accuracy. Noise in medical laboratory results and disease nodes as well as in nodes forming the Markov blanket of the disease nodes has the largest effect on accuracy. In light of these results, knowledge engineers should moderately worry about the overall quality of the numerical parameters of BNs and direct their effort where it is most needed, as indicated by sensitivity analysis. Full article

We start from the fundamental premise that any physical interaction can be interpreted as a game. To demonstrate this, we draw upon the free energy principle and the theory of quantum reference frames. In this way, we place the game-theoretic Nash Equilibrium in a new light in so far as the incompleteness and undecidability of the concept, as well as the nature of strategies in general, can be seen as the consequences of certain no-go theorems. We show that games of the generic imitation type follow a circularity of idealization that includes the good regulator theorem, generalized synchrony, and undecidability of the Turing test. We discuss Bayesian games in the light of Bell non-locality and establish the basics of quantum games, which we relate to local operations and classical communication protocols. In this light, we also review the rationality of gaming strategies from the players’ point of view. Full article

This paper presents a novel approach to improving the detection of mild cognitive impairment (MCI) through the use of super-resolved structural magnetic resonance imaging (MRI) and optimized deep learning models. The study introduces enhancements to the perceptual quality of super-resolved 2D structural MRI images using advanced loss functions, modifications to the upscaler part of the generator, and experiments with various discriminators within a generative adversarial training setting. It empirically demonstrates the effectiveness of super-resolution in the MCI detection task, showcasing performance improvements across different state-of-the-art classification models. The paper also addresses the challenge of accurately capturing perceptual image quality, particularly when images contain checkerboard artifacts, and proposes a methodology that incorporates hyperparameter optimization through a Pareto optimal Markov blanket (POMB). This approach systematically explores the hyperparameter space, focusing on reducing overfitting and enhancing model generalizability. The research findings contribute to the field by demonstrating that super-resolution can significantly improve the quality of MRI images for MCI detection, highlighting the importance of choosing an adequate discriminator and the potential of super-resolution as a preprocessing step to boost classification model performance. Full article

A theoretical account of development in mesocortical anatomy is derived from the free energy principle, operating in a neural field with both Hebbian and anti-Hebbian neural plasticity. An elementary structural unit is proposed, in which synaptic connections at mesoscale are arranged in paired patterns with mirror symmetry. Exchanges of synaptic flux in each pattern form coupled spatial eigenmodes, and the line of mirror reflection between the paired patterns operates as a Markov blanket, so that prediction errors in exchanges between the pairs are minimized. The theoretical analysis is then compared to the outcomes from a biological model of neocortical development, in which neuron precursors are selected by apoptosis for cell body and synaptic connections maximizing synchrony and also minimizing axonal length. It is shown that this model results in patterns of connection with the anticipated mirror symmetries, at micro-, meso- and inter-arial scales, among lateral connections, and in cortical depth. This explains the spatial organization and functional significance of neuron response preferences, and is compatible with the structural form of both columnar and noncolumnar cortex. Multi-way interactions of mirrored representations can provide a preliminary anatomically realistic model of cortical information processing. Full article

The accurate prediction of Li-ion battery capacity is important because it ensures mission and personnel safety during operations. However, the phenomenon of capacity recovery (CR) may impede the progress of improving battery capacity prediction performance. Therefore, in this study, we focus on the phenomenon of capacity recovery during battery degradation and propose a hybrid lithium-ion battery capacity prediction framework based on two states. First, to improve the density of capacity-related information, the simultaneous Markov blanket discovery algorithm (STMB) is used to screen the causal features of capacity from the initial feature set. Then, the life-long cycle sequence of batteries is partitioned into global degradation regions and recovery regions, as part of the proposed prediction framework. The prediction branch for the global degradation region is implemented through a long short-term memory network (LSTM) and the other prediction branch for the recovery region is implemented through Gaussian process regression (GPR). A support vector machine (SVM) model is applied to identify recovery points to switch the branch of the prediction framework. The prediction results are integrated to obtain the final prediction results. Experimental studies based on NASA’s lithium battery aging data highlight the trustworthy capacity prediction ability of the proposed method considering the capacity recovery phenomenon. In contrast to the comparative methods, the mean absolute error and the root mean square error are reduced by up to 0.0013 Ah and 0.0043 Ah, which confirms the validity of the proposed method. Full article

A rolling bearing is a complex system consisting of the inner race, outer race, rolling element, etc. The interaction of components may lead to composite faults. Selecting the features that can accurately identify the fault type from the composite fault features with causality among components is key to composite fault diagnosis. To tackle this issue, we propose a feature selection approach for composite fault diagnosis based on the causal feature network. Based on the incremental association Markov blanket discovery, we first use the algorithm to mine the causal relationships between composite fault features and construct the causal feature network. Then, we draw upon the nodes’ centrality indicators in the complex network to quantify the importance of composite fault features. We also propose the criteria for threshold selection to determine the number of features in the optimal feature subset. Experimental results on the standard dataset for composite fault diagnosis show that our approach of using the causal relationship between features and the nodes’ centrality indicators of complex network can effectively identify the key features in composite fault signals and improve the accuracy of composite fault diagnosis. Experimental results thus verify our approach’s effectiveness. Full article

This paper introduces a variational formulation of natural selection, paying special attention to the nature of ‘things’ and the way that different ‘kinds’ of ‘things’ are individuated from—and influence—each other. We use the Bayesian mechanics of particular partitions to understand how slow phylogenetic processes constrain—and are constrained by—fast, phenotypic processes. The main result is a formulation of adaptive fitness as a path integral of phenotypic fitness. Paths of least action, at the phenotypic and phylogenetic scales, can then be read as inference and learning processes, respectively. In this view, a phenotype actively infers the state of its econiche under a generative model, whose parameters are learned via natural (Bayesian model) selection. The ensuing variational synthesis features some unexpected aspects. Perhaps the most notable is that it is not possible to describe or model a population of conspecifics per se. Rather, it is necessary to consider populations of distinct natural kinds that influence each other. This paper is limited to a description of the mathematical apparatus and accompanying ideas. Subsequent work will use these methods for simulations and numerical analyses—and identify points of contact with related mathematical formulations of evolution. Full article

An ever-growing amount of accumulated data has materialized in several scientific fields, due to recent technological progress. New challenges emerge in exploiting these data and utilizing the valuable available information. Causal models are a powerful tool that can be employed towards this aim, by unveiling the structure of causal relationships between different variables. The causal structure may avail experts to better understand relationships, or even uncover new knowledge. Based on 963 patients with coronary artery disease, the robustness of the causal structure of single nucleotide polymorphisms was assessed, taking into account the value of the Syntax Score, an index that evaluates the complexity of the disease. The causal structure was investigated, both locally and globally, under different levels of intervention, reflected in the number of patients that were randomly excluded from the original datasets corresponding to two categories of the Syntax Score, zero and positive. It is shown that the causal structure of single nucleotide polymorphisms was more robust under milder interventions, whereas in the case of stronger interventions, the impact increased. The local causal structure around the Syntax Score was studied in the case of a positive Syntax Score, and it was found to be resilient, even when the intervention was strong. Consequently, employing causal models in this context may increase the understanding of the biological aspects of coronary artery disease. Full article