Phylodynamic inference with the bounded coalescent: a point process perspective

arXiv:2609.29035 · stat.ME, q-bio.PE · Submitted 2026-09-24 · Read on arXiv

stat.ME, q-bio.PE

Submitted: 2026-09-24

Updated: 2026-09-24

Code: https://github.com/JuliaPalacios/phylodyn

Terminology

• Bayesian Inference — 3× in this paper · explained in 5 episodes
• On-Line Encyclopedia of Integer Sequences — 3× in this paper
• Data Augmentation — 2× in this paper · explained in 7 episodes
• Adam — 1× in this paper · explained in 2 episodes
• Aggregation — 1× in this paper · explained in 1 episode
• Calibration — 1× in this paper · explained in 7 episodes
• Computational Biology — 1× in this paper · explained in 2 episodes
• Degeneracy — 1× in this paper · explained in 3 episodes
• Generative AI — 1× in this paper · explained in 2 episodes
• Regularization — 1× in this paper · explained in 3 episodes
• Systematic Bias — 1× in this paper · explained in 3 episodes
• Uncertainty Quantification — 1× in this paper · explained in 8 episodes

Sources

• Lecture Notes: Temporal Point Processes and the Conditional Intensity Function

Related papers

• Doubly robust inference via calibration
• Bayesian Empirical Bayes: Simultaneous Inference from Probabilistic Symmetries
• Optimal Watermark Localization in Mixed-Source Large Language Model Texts
• Flexible Nonparametric Inference for Causal Effects under the Front-Door Model
• A Greedy PDE Router for Blending Neural Operators and Classical Methods
• Policy Learning with Weak Signals