Paper List
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Autonomous Agents Coordinating Distributed Discovery Through Emergent Artifact Exchange
This paper addresses the fundamental limitation of current AI-assisted scientific research by enabling truly autonomous, decentralized investigation w...
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D-MEM: Dopamine-Gated Agentic Memory via Reward Prediction Error Routing
This paper addresses the fundamental scalability bottleneck in LLM agentic memory systems: the O(N²) computational complexity and unbounded API token ...
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Countershading coloration in blue shark skin emerges from hierarchically organized and spatially tuned photonic architectures inside skin denticles
This paper solves the core problem of how blue sharks achieve their striking dorsoventral countershading camouflage, revealing that coloration origina...
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Human-like Object Grouping in Self-supervised Vision Transformers
This paper addresses the core challenge of quantifying how well self-supervised vision models capture human-like object grouping in natural scenes, br...
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Hierarchical pp-Adic Framework for Gene Regulatory Networks: Theory and Stability Analysis
This paper addresses the core challenge of mathematically capturing the inherent hierarchical organization and multi-scale stability of gene regulator...
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Towards unified brain-to-text decoding across speech production and perception
This paper addresses the core challenge of developing a unified brain-to-text decoding framework that works across both speech production and percepti...
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Dual-Laws Model for a theory of artificial consciousness
This paper addresses the core challenge of developing a comprehensive, testable theory of consciousness that bridges biological and artificial systems...
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Pulse desynchronization of neural populations by targeting the centroid of the limit cycle in phase space
This work addresses the core challenge of determining optimal pulse timing and intensity for desynchronizing pathological neural oscillations when the...
Fast and Accurate Node-Age Estimation Under Fossil Calibration Uncertainty Using the Adjusted Pairwise Likelihood
Department of Statistics, University of Georgia, Athens, 30601, USA
30秒速读
IN SHORT: This paper addresses the dual challenge of computational inefficiency and sensitivity to fossil calibration errors in Bayesian divergence time estimation for large phylogenomic datasets.
核心创新
- Methodology Introduces two Adjusted Pairwise Likelihood (APW) formulations (APW1 and APW2) that use asymptotic moment-matching weights to correct composite likelihoods within a Bayesian MCMC framework.
- Methodology Demonstrates that APW methods reduce computational cost by more than an order of magnitude compared to full-likelihood methods while maintaining comparable accuracy in node-age estimation.
- Methodology Shows that APW methods exhibit greater robustness to fossil misplacement and prior misspecification due to the reduced sensitivity of composite likelihoods to local calibration errors.
主要结论
- APW methods produce node-age estimates statistically comparable to full-likelihood methods across diverse simulation scenarios, with reduced sensitivity to local calibration errors.
- Applied to a genome-scale avian dataset, APW recovered divergence time patterns consistent with recent studies while achieving a >10x reduction in computational cost.
- The robustness of APW to fossil misplacement stems from the composite likelihood's inherent property of being less sensitive to errors in individual calibration points, as demonstrated in simulations modeling various prior misspecifications.
摘要: Estimating divergence times from molecular sequence data is central to reconstructing the evolutionary history of lineages. Although Bayesian relaxed-clock methods provide a principled framework for incorporating fossil information, their dependence on repeated evaluations of the full phylogenetic likelihood makes them computationally demanding for large genomic datasets. Furthermore, because disagreements in divergence-time estimates often arise from uncertainty or error in fossil placement and prior specification, there is a need for methods that are both computationally efficient and robust to fossil-calibration uncertainty. In this study, we introduce fast and accurate alternatives based on the phylogenetic pairwise composite likelihood, presenting two adjusted pairwise likelihood (APW) formulations that employ asymptotic moment-matching weights to better approximate the behavior of the full likelihood within a Bayesian MCMC framework. Extensive simulations across diverse fossil-calibration scenarios show that APW methods produce node-age estimates comparable to those obtained from the full likelihood while offering greater robustness to fossil misplacement and prior misspecification, due to the reduced sensitivity of composite likelihoods to local calibration errors. Applied to a genome-scale dataset of modern birds, APW methods recover divergence time patterns consistent with recent studies, while reducing computational cost by more than an order of magnitude. Overall, our results demonstrate that adjusted pairwise likelihoods provide a calibration-robust and computationally efficient framework for Bayesian node dating, especially suited for large phylogenomic datasets and analyses in which fossil priors may be uncertain or imperfectly placed.