Atoms and Patterns Stabilization

[Jennifer-Foltz]

Good afternoon! I recently have run into large changes in the atoms (A) and (P) matrix values when running CoGAPS across multiple nSets. In a previous issue, these numbers were mentioned as a metric to determine if CoGAPS had stabilized, so I found this a bit concerning. Can you help me understand what is happening here, and point me to a solution? Thank you in advance! (Include the full parameters to help)

-- Standard Parameters --
nPatterns            25 
nIterations          1e+05 
seed                 891 
sparseOptimization   TRUE 
distributed          single-cell 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

-- Distributed CoGAPS Parameters -- 
nSets          6 
cut            25 
minNS          3 
maxNS          9 
[1] 33650 21914
[1] 14160 21914

This is CoGAPS version 3.14.0 
Running single-cell CoGAPS on /tmp/90251.tmpdir/Rtmp31EVRF/file62dc263e1.mtx (14160 genes and 21914 samples) with parameters:

-- Standard Parameters --
nPatterns            25 
nIterations          1e+05 
seed                 891 
sparseOptimization   TRUE 
distributed          single-cell 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

-- Distributed CoGAPS Parameters -- 
nSets          6 
cut            25 
minNS          3 
maxNS          9 

14160 gene names provided
first gene name: FAM87B 

21914 sample names provided
first sample name: 56546_tube1_AAACCTGCACGGCGTT-1 

Creating subsets...
set sizes (min, mean, max): (3652, 3652.333, 3654)
Running Across Subsets...

    worker 2 is starting!
    worker 4 is starting!
Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:01:26)
    worker 1 is starting!
    worker 6 is starting!
    worker 3 is starting!
    worker 5 is starting!
-- Equilibration Phase --
5000 of 100000, Atoms: 100971(A), 52232(P), ChiSq: 468311360, Time: 03:28:08 / 206:51:55
10000 of 100000, Atoms: 132274(A), 61924(P), ChiSq: 466190848, Time: 09:57:29 / 271:50:33
15000 of 100000, Atoms: 147622(A), 64281(P), ChiSq: 465477408, Time: 17:28:09 / 302:57:29
20000 of 100000, Atoms: 157316(A), 65815(P), ChiSq: 465079392, Time: 25:23:51 / 319:39:54
25000 of 100000, Atoms: 165574(A), 67174(P), ChiSq: 464867552, Time: 33:37:39 / 330:19:17
30000 of 100000, Atoms: 172295(A), 68477(P), ChiSq: 464668896, Time: 42:07:54 / 338:07:31
35000 of 100000, Atoms: 179143(A), 69047(P), ChiSq: 464584608, Time: 50:52:01 / 344:12:38
40000 of 100000, Atoms: 184012(A), 69617(P), ChiSq: 464515392, Time: 59:49:42 / 349:18:55
45000 of 100000, Atoms: 189512(A), 69805(P), ChiSq: 464441792, Time: 68:54:57 / 353:19:43
50000 of 100000, Atoms: 196919(A), 68410(P), ChiSq: 464404192, Time: 78:14:55 / 357:11:07
55000 of 100000, Atoms: 206964(A), 64601(P), ChiSq: 464468192, Time: 87:40:43 / 360:20:54
60000 of 100000, Atoms: 808401(A), 12023(P), ChiSq: 500546240, Time: 96:09:45 / 359:07:47
65000 of 100000, Atoms: 1055385(A), 8298(P), ChiSq: 527779296, Time: 103:43:00 / 354:42:26
70000 of 100000, Atoms: 950700(A), 7337(P), ChiSq: 533742400, Time: 112:06:23 / 353:24:58
75000 of 100000, Atoms: 924196(A), 7082(P), ChiSq: 539779776, Time: 120:40:25 / 352:40:01
80000 of 100000, Atoms: 948739(A), 6947(P), ChiSq: 541298112, Time: 129:33:54 / 352:45:34
85000 of 100000, Atoms: 1000041(A), 6826(P), ChiSq: 543738112, Time: 138:59:54 / 354:05:43
90000 of 100000, Atoms: 1064006(A), 6708(P), ChiSq: 546889728, Time: 148:56:49 / 356:23:28
95000 of 100000, Atoms: 1251780(A), 8249(P), ChiSq: 534668288, Time: 159:05:50 / 358:46:42