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1. dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra

   https://doi.org/10.1101/2023.06.15.545182  

   Huang, Xin; Struck, Travis J; Davey, Sean W; Gutenkunst, Ryan N (June 2023, bioRxiv)

   Abstract Summarydadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing. Availability and Implementationdadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available athttps://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2https://cacao.jetstream-cloud.org/. 

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2. Towards instance-wise calibration: local amortized diagnostics and reshaping of conditional densities (LADaR)

   https://doi.org/10.1088/2632-2153/ae1f05  

   Dey, Biprateep; Zhao, David; Andrews, Brett H; Newman, Jeffrey A; Izbicki, Rafael; Lee, Ann B (December 2025, Machine Learning: Science and Technology)

   Abstract Key science questions, such as galaxy distance estimation and weather forecasting, often require knowing the full predictive distribution of a target variableYgiven complex inputsX. Despite recent advances in machine learning and physics-based models, it remains challenging to assess whether an initial model is calibrated for allx, and when needed, to reshape the densities ofytoward ‘instance-wise’ calibration. This paper introduces the local amortized diagnostics and reshaping of conditional densities (LADaR) framework and proposes a new computationally efficient algorithm (Cal-PIT) that produces interpretable local diagnostics and provides a mechanism for adjusting conditional density estimates (CDEs).Cal-PITlearns a single interpretable local probability–probability map from calibration data that identifies where and how the initial model is miscalibrated across feature space, which can be used to morph CDEs such that they are well-calibrated. We illustrate the LADaR framework on synthetic examples, including probabilistic forecasting from image sequences, akin to predicting storm wind speed from satellite imagery. Our main science application involves estimating the probability density functions of galaxy distances given photometric data, whereCal-PITachieves better instance-wise calibration than all 11 other literature methods in a benchmark data challenge, demonstrating its utility for next-generation cosmological analyzes⁹9Code available as a Python package here:https://github.com/lee-group-cmu/Cal-PIT.. 

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3. DELVE: feature selection for preserving biological trajectories in single-cell data

   https://doi.org/10.1038/s41467-024-46773-z  

   Ranek, Jolene S; Stallaert, Wayne; Milner, J Justin; Redick, Margaret; Wolff, Samuel C; Beltran, Adriana S; Stanley, Natalie; Purvis, Jeremy E (December 2024, Nature Communications)

   Abstract Single-cell technologies can measure the expression of thousands of molecular features in individual cells undergoing dynamic biological processes. While examining cells along a computationally-ordered pseudotime trajectory can reveal how changes in gene or protein expression impact cell fate, identifying such dynamic features is challenging due to the inherent noise in single-cell data. Here, we present DELVE, an unsupervised feature selection method for identifying a representative subset of molecular features which robustly recapitulate cellular trajectories. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effects of confounding sources of variation, and instead models cell states from dynamic gene or protein modules based on core regulatory complexes. Using simulations, single-cell RNA sequencing, and iterative immunofluorescence imaging data in the context of cell cycle and cellular differentiation, we demonstrate how DELVE selects features that better define cell-types and cell-type transitions. DELVE is available as an open-source python package:https://github.com/jranek/delve. 

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4. Heterogeneous pseudobulk simulation enables realistic benchmarking of cell-type deconvolution methods

   https://doi.org/10.1186/s13059-024-03292-w  

   Hu, Mengying; Chikina, Maria (December 2024, Genome Biology)

   Abstract BackgroundComputational cell type deconvolution enables the estimation of cell type abundance from bulk tissues and is important for understanding tissue microenviroment, especially in tumor tissues. With rapid development of deconvolution methods, many benchmarking studies have been published aiming for a comprehensive evaluation for these methods. Benchmarking studies rely on cell-type resolved single-cell RNA-seq data to create simulated pseudobulk datasets by adding individual cells-types in controlled proportions. ResultsIn our work, we show that the standard application of this approach, which uses randomly selected single cells, regardless of the intrinsic difference between them, generates synthetic bulk expression values that lack appropriate biological variance. We demonstrate why and how the current bulk simulation pipeline with random cells is unrealistic and propose a heterogeneous simulation strategy as a solution. The heterogeneously simulated bulk samples match up with the variance observed in real bulk datasets and therefore provide concrete benefits for benchmarking in several ways. We demonstrate that conceptual classes of deconvolution methods differ dramatically in their robustness to heterogeneity with reference-free methods performing particularly poorly. For regression-based methods, the heterogeneous simulation provides an explicit framework to disentangle the contributions of reference construction and regression methods to performance. Finally, we perform an extensive benchmark of diverse methods across eight different datasets and find BayesPrism and a hybrid MuSiC/CIBERSORTx approach to be the top performers. ConclusionsOur heterogeneous bulk simulation method and the entire benchmarking framework is implemented in a user friendly packagehttps://github.com/humengying0907/deconvBenchmarkingandhttps://doi.org/10.5281/zenodo.8206516, enabling further developments in deconvolution methods. 

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5. Adaptive ergodic search with energy-aware scheduling for persistent multi-robot missions

   https://doi.org/10.1007/s10514-025-10215-6  

   Naveed, Kaleb Ben; Agrawal, Devansh R; Kumar, Rahul; Panagou, Dimitra (December 2025, Autonomous Robots)

   Abstract Autonomous robots are increasingly deployed for long-term information-gathering tasks, which pose two key challenges: planning informative trajectories in environments that evolve across space and time, and ensuring persistent operation under energy constraints. This paper presents a unified framework, , that addresses both challenges through adaptive ergodic search and energy-aware scheduling in multi-robot systems. Our contributions are two-fold: (1) we model real-world variability using stochastic spatiotemporal environments, where the underlying information evolves continuously over space and time under process noise. To guide exploration, we construct a target information spatial distribution (TISD) based on clarity, a metric that captures the decay of information in the absence of observations and highlights regions of high uncertainty; and (2) we introduce ( ), an online scheduling method that enables persistent operation by coordinating rechargeable robots sharing a single mobile charging station. Unlike prior work, our approach avoids reliance on preplanned schedules, static or dedicated charging stations, and simplified robot dynamics. Instead, the scheduler supports general nonlinear models, accounts for uncertainty in the estimated position of the charging station, and handles central node failures. The proposed framework is validated through real-world hardware experiments, and feasibility guarantees are provided under specific assumptions.[Code: https://github.com/kalebbennaveed/mEclares-main.git][Experiment Video: https://www.youtube.com/watch?v=dmaZDvxJgF8] 

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