V2 sweep: move MM notebooks, update templates, add experiments.tsv

- Move all MM notebooks (templates + outputs) to model_comparisons/
- Update MM template defaults to match best experiment config
- Add new params: dispersion_prior_mean/alpha, residual_library_encoder,
  library_obs_w_prior_rate, decoder_cov_weight_l2, decoder_bias_multiplier
- Add 2-mode attribution (with/without covariates) + 5-mode analysis + LISI
- Update RNA template: same new params, max_epochs=5000
- Create experiments.tsv: 69 experiments across 4 eras

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: vitkl

docs/notebooks/model_comparisons/bone_marrow_gamma_poisson_early_stopping.ipynb

@@ -0,0 +1,70 @@
+name	type	era	results_folder	label	notebook	status	dispersion_prior_mean	dispersion_prior_alpha	decoder_weight_l2	decoder_cov_weight_l2	init_decoder_bias	bg_init_gene_fraction	library_log_vars_weight	library_log_means_centering_sensitivity_rna	library_log_means_centering_sensitivity_atac	regularise_background	residual_library_encoder	library_obs_w_prior_rate	early_stopping_min_delta_per_feature	stratify_validation_key	max_epochs	notes
+exp1_rna_bg_noctr	rna	1	results/exp1_rna_bg_noctr/model	RNA: bg=T, ctr=OFF	bone_marrow_gp_es_exp1_out.ipynb	completed								1
+exp2_rna_nobg_noctr	rna	1	results/exp2_rna_nobg_noctr/model	RNA: bg=F, ctr=OFF	bone_marrow_gp_es_exp2_out.ipynb	completed								0
+exp3_rna_bg_ctr	rna	1	results/exp3_rna_bg_ctr/model	RNA: bg=T, ctr=ON	bone_marrow_gp_es_exp3_out.ipynb	completed							1.0		1
+exp4_rna_nobg_ctr	rna	1	results/exp4_rna_nobg_ctr/model	RNA: bg=F, ctr=ON	bone_marrow_gp_es_exp4_out.ipynb	completed							1.0		0
+exp5_mm_noctr	multimodal	1	results/exp5_mm_noctr/model	MM: ctr=OFF	bone_marrow_mm_es_exp5_out.ipynb	completed								0
+exp6_mm_ctr_rna	multimodal	1	results/exp6_mm_ctr_rna/model	MM: ctr=RNA	bone_marrow_mm_es_exp6_out.ipynb	completed							1.0
+exp7_mm_ctr_both	multimodal	1	results/exp7_mm_ctr_both/model	MM: ctr=RNA+ATAC	bone_marrow_mm_es_exp7_out.ipynb	completed							1.0	0.2
+exp8_mm_ctr_both_lowes	multimodal	1	results/exp8_mm_ctr_both_lowes/model	MM: ctr=both, lowES	bone_marrow_mm_es_exp8_out.ipynb	completed							1.0	0.2			3e-05
+exp9_rna_nobg_ctr_lowes	rna	1	results/exp9_rna_nobg_ctr_lowes/model	RNA: ctr=ON, lowES	bone_marrow_gp_es_exp9_out.ipynb	completed							1.0				3e-05
+exp10a_mm_libvar_0.1	multimodal	1	results/exp10a_mm_libvar_0.1/model	MM: ctr=both, libvar=0.1	bone_marrow_mm_es_exp10a_out.ipynb	completed						0.1
+exp10b_mm_libvar_0.2	multimodal	1	results/exp10b_mm_libvar_0.2/model	MM: ctr=both, libvar=0.2	bone_marrow_mm_es_exp10b_out.ipynb	completed						0.2
+exp11_mm_learnable_scale	multimodal	1	results/exp11_mm_learnable_scale/model	MM: ctr=both, learnable scale	bone_marrow_mm_es_exp11_out.ipynb	completed										learnable modality scaling
+exp12_rna_libvar_0.2	rna	1	results/exp12_rna_libvar_0.2/model	RNA: ctr=ON, libvar=0.2	bone_marrow_gp_es_exp12_out.ipynb	completed						0.2
+exp8stratified	multimodal	2	results/exp8stratified/model	MM: ctr=both, stratified	bone_marrow_mm_es_exp8stratified_out.ipynb	completed							1.0	0.2			3e-05	l1_cell_type+batch
+exp9stratified	rna	2	results/exp9stratified/model	RNA: ctr=ON, stratified	bone_marrow_gp_es_exp9stratified_out.ipynb	completed							1.0				3e-05	l1_cell_type+batch
+exp10bstratified	multimodal	2	results/exp10bstratified/model	MM: libvar=0.2, stratified	bone_marrow_mm_es_exp10bstratified_out.ipynb	completed						0.2					l1_cell_type+batch
+exp11stratified	multimodal	2	results/exp11stratified/model	MM: learnable scale, stratified	bone_marrow_mm_es_exp11stratified_out.ipynb	completed									l1_cell_type+batch		learnable scale, stratified
+exp12stratified	rna	2	results/exp12stratified/model	RNA: libvar=0.2, stratified	bone_marrow_gp_es_exp12stratified_out.ipynb	completed						0.2					l1_cell_type+batch
+exp10bstratified_filtered	multimodal	2	results/exp10bstratified_filtered/model	MM: libvar=0.2, strat, ATAC>2k	bone_marrow_mm_es_exp10bstratified_filtered_out.ipynb	completed						0.2					l1_cell_type+batch		ATAC>2k
+exp10bstratified_lowes	multimodal	2	results/exp10bstratified_lowes/model	MM: libvar=0.2, strat, lowES=1e-4	bone_marrow_mm_es_exp10bstratified_lowes_out.ipynb	completed						0.2				0.0001	l1_cell_type+batch
+exp11stratified_lowes	multimodal	2	results/exp11stratified_lowes/model	MM: learnable scale, strat, lowES	bone_marrow_mm_es_exp11stratified_lowes_out.ipynb	completed									0.0001	l1_cell_type+batch		learnable scale
+exp10bstratified_filtered_lowes	multimodal	2	results/exp10bstratified_filtered_lowes/model	MM: libvar=0.2, ATAC>2k, lowES	bone_marrow_mm_es_exp10bstratified_filtered_lowes_out.ipynb	completed						0.2				0.0001	l1_cell_type+batch		ATAC>2k
+exp10bstratified_filtered_lowes_libvar05	multimodal	2	results/exp10bstratified_filtered_lowes_libvar05/model	MM: libvar=0.5, ATAC>2k, lowES	bone_marrow_mm_es_exp10bstratified_filtered_lowes_libvar05_out.ipynb	completed						0.5				0.0001	l1_cell_type+batch		ATAC>2k
+exp10bstratified_filtered_lowes2_libvar05	multimodal	2	results/exp10bstratified_filtered_lowes2_libvar05/model	MM: libvar=0.5, ATAC>2k, ES=2e-4	bone_marrow_mm_es_exp10bstratified_filtered_lowes2_libvar05_out.ipynb	completed						0.5				0.0002	l1_cell_type+batch		ATAC>2k
+exp10bstratified_filtered_lowes_ataclr2	multimodal	2	results/exp10bstratified_filtered_lowes_ataclr2/model	MM: ATAC LR 2x	bone_marrow_mm_es_exp10bstratified_filtered_lowes_ataclr2_out.ipynb	completed									0.0001	l1_cell_type+batch		ATAC LR 2x
+exp10bstratified_filtered_lowes2_libvar10	multimodal	2	results/exp10bstratified_filtered_lowes2_libvar10/model	MM: libvar=1.0, ES=2e-4	bone_marrow_mm_es_exp10bstratified_filtered_lowes2_libvar10_out.ipynb	completed						1.0				0.0002	l1_cell_type+batch
+exp12stratified_filtered_lowes2_libvar10	rna	2	results/exp12stratified_filtered_lowes2_libvar10/model	RNA: libvar=1.0, ES=2e-4	bone_marrow_gp_es_exp12stratified_filtered_lowes2_libvar10_out.ipynb	completed						1.0				0.0002	l1_cell_type+batch
+exp10bstratified_filtered_lowes2_libvar05_repeat2	multimodal	2	results/exp10bstratified_filtered_lowes2_libvar05_repeat2/model	MM: libvar=0.5, ES=2e-4, repeat	bone_marrow_mm_es_exp10bstratified_filtered_lowes2_libvar05_repeat2_out.ipynb	completed						0.5				0.0002	l1_cell_type+batch		repeat2
+exp10bstratified_filtered_lowes2_libvar02_ataclibvar15	multimodal	2	results/exp10bstratified_filtered_lowes2_libvar02_ataclibvar15/model	MM: RNA-lv=0.2, ATAC-lv=1.5	bone_marrow_mm_es_exp10bstratified_filtered_lowes2_libvar02_ataclibvar15_out.ipynb	completed						0.2				0.0002	l1_cell_type+batch		per-modality libvar, ATAC-lv=1.5
+exp10bstratified_filtered_lowes2_libvar05_bgprior1	multimodal	2	results/exp10bstratified_filtered_lowes2_libvar05_bgprior1/model	MM: libvar=0.5, bg G(1,1)	bone_marrow_mm_es_exp10bstratified_filtered_lowes2_libvar05_bgprior1_out.ipynb	completed						0.5				0.0002	l1_cell_type+batch		bg_prior_beta=1
+exp12stratified_filtered_lowes2_libvar05	rna	2	results/exp12stratified_filtered_lowes2_libvar05/model	RNA: libvar=0.5, ES=2e-4	bone_marrow_gp_es_exp12stratified_filtered_lowes2_libvar05_out.ipynb	completed						0.5				0.0002	l1_cell_type+batch
+exp12stratified_filtered_lowes2_libvar05_bgprior1	rna	2	results/exp12stratified_filtered_lowes2_libvar05_bgprior1/model	RNA: libvar=0.5, bg G(1,1)	bone_marrow_gp_es_exp12stratified_filtered_lowes2_libvar05_bgprior1_out.ipynb	failed						0.5				0.0002	l1_cell_type+batch		FAILED wandb
+exp12stratified_filtered_lowes2_libvar02_bgprior1	rna	2	results/exp12stratified_filtered_lowes2_libvar02_bgprior1/model	RNA: libvar=0.2, bg G(1,1)	bone_marrow_gp_es_exp12stratified_filtered_lowes2_libvar02_bgprior1_out.ipynb	completed						0.2				0.0002	l1_cell_type+batch		bg G(1,1)
+exp12stratified_filtered_lowes2_libvar02_bgprior033	rna	2	results/exp12stratified_filtered_lowes2_libvar02_bgprior033/model	RNA: libvar=0.2, bg G(1,3)	bone_marrow_gp_es_exp12stratified_filtered_lowes2_libvar02_bgprior033_out.ipynb	completed						0.2				0.0002	l1_cell_type+batch		bg G(1,3)
+exp12stratified_filtered_lowes2_libvar05_bgprior033	rna	2	results/exp12stratified_filtered_lowes2_libvar05_bgprior033/model	RNA: libvar=0.5, bg G(1,3)	bone_marrow_gp_es_exp12stratified_filtered_lowes2_libvar05_bgprior033_out.ipynb	completed						0.5				0.0002	l1_cell_type+batch		bg G(1,3)
+mm_es_libvar05_dwl2_00001	multimodal	3	results/mm_es_libvar05_dwl2_00001/model	MM: dwl2=1e-5	bone_marrow_mm_es_libvar05_dwl2_00001_out.ipynb	completed			0.0001								0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_0001	multimodal	3	results/mm_es_libvar05_dwl2_0001/model	MM: dwl2=1e-3	bone_marrow_mm_es_libvar05_dwl2_0001_out.ipynb	completed			0.001								0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_001	multimodal	3	results/mm_es_libvar05_dwl2_001/model	MM: dwl2=0.01	bone_marrow_mm_es_libvar05_dwl2_001_out.ipynb	completed			0.01								0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_01	multimodal	3	results/mm_es_libvar05_dwl2_01/model	MM: dwl2=0.1	bone_marrow_mm_es_libvar05_dwl2_01_out.ipynb	completed			0.1								0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_1	multimodal	3	results/mm_es_libvar05_dwl2_1/model	MM: dwl2=1.0	bone_marrow_mm_es_libvar05_dwl2_1_out.ipynb	completed			1.0								0	0.0002	l1_cell_type+batch
+mm_es_libvar05_bias_mean	multimodal	3	results/mm_es_libvar05_bias_mean/model	MM: bias=mean	bone_marrow_mm_es_libvar05_bias_mean_out.ipynb	completed			0.0		mean							0	0.0002	l1_cell_type+batch
+mm_es_libvar05_bias_mean_bg02	multimodal	3	results/mm_es_libvar05_bias_mean_bg02/model	MM: bias=mean, bg=0.2	bone_marrow_mm_es_libvar05_bias_mean_bg02_out.ipynb	completed			0.0		mean	0.2						0	0.0002	l1_cell_type+batch
+mm_es_libvar05_bg_gene02	multimodal	3	results/mm_es_libvar05_bg_gene02/model	MM: bg=0.2	bone_marrow_mm_es_libvar05_bg_gene02_out.ipynb	completed			0.0			0.2						0	0.0002	l1_cell_type+batch
+mm_es_libvar05_bias_topN_bg02	multimodal	3	results/mm_es_libvar05_bias_topN_bg02/model	MM: bias=topN, bg=0.2	bone_marrow_mm_es_libvar05_bias_topN_bg02_out.ipynb	completed			0.0		topN	0.2						0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_001_bias_mean_bg02	multimodal	3	results/mm_es_libvar05_dwl2_001_bias_mean_bg02/model	MM: dwl2=0.01+bias+bg	bone_marrow_mm_es_libvar05_dwl2_001_bias_mean_bg02_out.ipynb	completed			0.01		mean	0.2						0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_01_bias_mean_bg02	multimodal	3	results/mm_es_libvar05_dwl2_01_bias_mean_bg02/model	MM: dwl2=0.1+bias+bg	bone_marrow_mm_es_libvar05_dwl2_01_bias_mean_bg02_out.ipynb	completed			0.1		mean	0.2						0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_001_bias_mean_bg02_repeat2	multimodal	3	results/mm_es_libvar05_dwl2_001_bias_mean_bg02_repeat2/model	MM: dwl2=0.01+bias+bg repeat	bone_marrow_mm_es_libvar05_dwl2_001_bias_mean_bg02_repeat2_out.ipynb	completed			0.01		mean	0.2						0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_01_bias_mean_bg02_repeat2	multimodal	3	results/mm_es_libvar05_dwl2_01_bias_mean_bg02_repeat2/model	MM: dwl2=0.1+bias+bg repeat	bone_marrow_mm_es_libvar05_dwl2_01_bias_mean_bg02_repeat2_out.ipynb	completed			0.1		mean	0.2						0	0.0002	l1_cell_type+batch
+mm_es_libvar05_dwl2_01_bias_mean_batchbg02	multimodal	3	results/mm_es_libvar05_dwl2_01_bias_mean_batchbg02/model	MM: BEST — dwl2=0.1+bias+batchbg	bone_marrow_mm_es_libvar05_dwl2_01_bias_mean_batchbg02_out.ipynb	completed			0.1		mean	0.2						0	0.0002	l1_cell_type+batch
+mm_v2_disp3_dwl2_01_atacsens02	multimodal	4	results/mm_v2_disp3_dwl2_01_atacsens02/model	MM v2: baseline	bone_marrow_mm_v2_disp3_dwl2_01_atacsens02_out.ipynb	pending	3.0	9.0	0.1		mean	0.2	0.5	1.0	0.2	0	True		0.0002	l1_cell_type+batch		baseline
+mm_v2_disp3_dwl2_01_atacsens10	multimodal	4	results/mm_v2_disp3_dwl2_01_atacsens10/model	MM v2: atacsens=1.0	bone_marrow_mm_v2_disp3_dwl2_01_atacsens10_out.ipynb	pending	3.0	9.0	0.1		mean	0.2	0.5	1.0	1.0	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp3_dwl2_1_atacsens02	multimodal	4	results/mm_v2_disp3_dwl2_1_atacsens02/model	MM v2: dwl2=1.0	bone_marrow_mm_v2_disp3_dwl2_1_atacsens02_out.ipynb	pending	3.0	9.0	1.0		mean	0.2	0.5	1.0	0.2	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp3_dwl2_1_atacsens10	multimodal	4	results/mm_v2_disp3_dwl2_1_atacsens10/model	MM v2: dwl2=1.0, atacsens=1.0	bone_marrow_mm_v2_disp3_dwl2_1_atacsens10_out.ipynb	pending	3.0	9.0	1.0		mean	0.2	0.5	1.0	1.0	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp2_dwl2_01_atacsens02	multimodal	4	results/mm_v2_disp2_dwl2_01_atacsens02/model	MM v2: disp=2.0	bone_marrow_mm_v2_disp2_dwl2_01_atacsens02_out.ipynb	pending	2.0	9.0	0.1		mean	0.2	0.5	1.0	0.2	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp2_dwl2_01_atacsens10	multimodal	4	results/mm_v2_disp2_dwl2_01_atacsens10/model	MM v2: disp=2.0, atacsens=1.0	bone_marrow_mm_v2_disp2_dwl2_01_atacsens10_out.ipynb	pending	2.0	9.0	0.1		mean	0.2	0.5	1.0	1.0	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp2_dwl2_1_atacsens02	multimodal	4	results/mm_v2_disp2_dwl2_1_atacsens02/model	MM v2: disp=2.0, dwl2=1.0	bone_marrow_mm_v2_disp2_dwl2_1_atacsens02_out.ipynb	pending	2.0	9.0	1.0		mean	0.2	0.5	1.0	0.2	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp2_dwl2_1_atacsens10	multimodal	4	results/mm_v2_disp2_dwl2_1_atacsens10/model	MM v2: disp=2.0, dwl2=1.0, atacsens=1.0	bone_marrow_mm_v2_disp2_dwl2_1_atacsens10_out.ipynb	pending	2.0	9.0	1.0		mean	0.2	0.5	1.0	1.0	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp1_dwl2_01_atacsens02	multimodal	4	results/mm_v2_disp1_dwl2_01_atacsens02/model	MM v2: disp=1.0	bone_marrow_mm_v2_disp1_dwl2_01_atacsens02_out.ipynb	pending	1.0	9.0	0.1		mean	0.2	0.5	1.0	0.2	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp1_dwl2_01_atacsens10	multimodal	4	results/mm_v2_disp1_dwl2_01_atacsens10/model	MM v2: disp=1.0, atacsens=1.0	bone_marrow_mm_v2_disp1_dwl2_01_atacsens10_out.ipynb	pending	1.0	9.0	0.1		mean	0.2	0.5	1.0	1.0	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp1_dwl2_1_atacsens02	multimodal	4	results/mm_v2_disp1_dwl2_1_atacsens02/model	MM v2: disp=1.0, dwl2=1.0	bone_marrow_mm_v2_disp1_dwl2_1_atacsens02_out.ipynb	pending	1.0	9.0	1.0		mean	0.2	0.5	1.0	0.2	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp1_dwl2_1_atacsens10	multimodal	4	results/mm_v2_disp1_dwl2_1_atacsens10/model	MM v2: disp=1.0, dwl2=1.0, atacsens=1.0	bone_marrow_mm_v2_disp1_dwl2_1_atacsens10_out.ipynb	pending	1.0	9.0	1.0		mean	0.2	0.5	1.0	1.0	0	True		0.0002	l1_cell_type+batch
+mm_v2_disp3_dwl2_01_atacsens02_noreslib	multimodal	4	results/mm_v2_disp3_dwl2_01_atacsens02_noreslib/model	MM v2: no residual lib	bone_marrow_mm_v2_disp3_dwl2_01_atacsens02_noreslib_out.ipynb	pending	3.0	9.0	0.1		mean	0.2	0.5	1.0	0.2	0	False		0.0002	l1_cell_type+batch		residual_lib OFF
+rna_v2_disp3_dwl2_01	rna	4	results/rna_v2_disp3_dwl2_01/model	RNA v2: baseline	bone_marrow_rna_v2_disp3_dwl2_01_out.ipynb	pending	3.0	9.0	0.1		mean	0.2	0.5	1.0		0	True		0.0002	l1_cell_type+batch		baseline
+rna_v2_disp3_dwl2_1	rna	4	results/rna_v2_disp3_dwl2_1/model	RNA v2: dwl2=1.0	bone_marrow_rna_v2_disp3_dwl2_1_out.ipynb	pending	3.0	9.0	1.0		mean	0.2	0.5	1.0		0	True		0.0002	l1_cell_type+batch
+rna_v2_disp2_dwl2_01	rna	4	results/rna_v2_disp2_dwl2_01/model	RNA v2: disp=2.0	bone_marrow_rna_v2_disp2_dwl2_01_out.ipynb	pending	2.0	9.0	0.1		mean	0.2	0.5	1.0		0	True		0.0002	l1_cell_type+batch
+rna_v2_disp2_dwl2_1	rna	4	results/rna_v2_disp2_dwl2_1/model	RNA v2: disp=2.0, dwl2=1.0	bone_marrow_rna_v2_disp2_dwl2_1_out.ipynb	pending	2.0	9.0	1.0		mean	0.2	0.5	1.0		0	True		0.0002	l1_cell_type+batch
+rna_v2_disp1_dwl2_01	rna	4	results/rna_v2_disp1_dwl2_01/model	RNA v2: disp=1.0	bone_marrow_rna_v2_disp1_dwl2_01_out.ipynb	pending	1.0	9.0	0.1		mean	0.2	0.5	1.0		0	True		0.0002	l1_cell_type+batch
+rna_v2_disp1_dwl2_1	rna	4	results/rna_v2_disp1_dwl2_1/model	RNA v2: disp=1.0, dwl2=1.0	bone_marrow_rna_v2_disp1_dwl2_1_out.ipynb	pending	1.0	9.0	1.0		mean	0.2	0.5	1.0		0	True		0.0002	l1_cell_type+batch
+rna_v2_disp3_dwl2_01_noreslib	rna	4	results/rna_v2_disp3_dwl2_01_noreslib/model	RNA v2: no residual lib	bone_marrow_rna_v2_disp3_dwl2_01_noreslib_out.ipynb	pending	3.0	9.0	0.1		mean	0.2	0.5	1.0		0	False		0.0002	l1_cell_type+batch		residual_lib OFF