Synthetic benchmark - #62

Merged

ArcaneEmergence merged 41 commits into

mainfrom

experiment/synth_bench

Jun 19, 2026

Commits on Oct 14, 2025

cleanup unused files
ArcaneEmergence
committed
feature: Use AutoNormal guide instead of AutoMultivariateNormal guide due to computation and memory problems.
ArcaneEmergence
committed
refactor: renaming variables of posterior bfdr thresholding
ArcaneEmergence
committed
figures: small improvements on figures: 1. shorter titles, 2. make save and show figure optional, 3. legend frameon off and add titles, 4. changed indentation to spaces
ArcaneEmergence
committed
refactor: cleanup unused files
ArcaneEmergence
committed
update cluster params
ArcaneEmergence
committed
feature: return mean_over_cell posterior parameters
ArcaneEmergence
committed
add estimate_sim_params.ipynb
ArcaneEmergence
committed
feature: new version of synthetic benchmark snakemake pipeline. 1. Optimized for HPC to avoid spawning many small jobs, instead uses multiprocessing to run in parallel. 2. Additional logging of fig…
ArcaneEmergence
committed

Commits on Oct 22, 2025

Commits on Dec 1, 2025

feature: resample so that sampled N_binder / N_total ~ p_binding_ratio
ArcaneEmergence
committed

Commits on Dec 2, 2025

Commits on Mar 16, 2026

Commits on Mar 18, 2026

feature: save BEAMT results to csv
ArcaneEmergence
committed

Commits on Mar 24, 2026

Update Figure design
ArcaneEmergence
committed

Commits on Apr 8, 2026

feature: clonotype median aggregation model
ArcaneEmergence
committed

Commits on Jun 19, 2026

Figure: Add notebooks for figure plotting and add environment.yaml files for a minimal and full setup.
ArcaneEmergence
committed