GEO datasets

[lsand039]

I'm trying to use Jinang's code to score my structures, but I keep running into this error:

Screenshot from 2017-10-05 09-30-37.png (64.03 KiB) Viewed 146497 times

I've specified my structure as "Benestructure.graph.txt" and my data as "2254Sx4G.csv". I'm currently at a loss on how to fix it. I've tried googling for solutions, but I'm unfortunately not familiar enough with python codes.

Below are all the files downloaded from his code and my files.

bayesian_causal_model.git.tar.gz

(652.42 KiB) Downloaded 186 times

[lsand039]

Bene seems to always output a fully connected graph that follows the same order as the variables are listed in the datafile.

Datafiles.xlsx

Sheet number of data corresponds to test number data was used for.

(445.27 KiB) Downloaded 167 times

OrderTest1.png (123.89 KiB) Viewed 146496 times

OrderTest2.png (125.93 KiB) Viewed 146496 times

OrderTest3.png (124.98 KiB) Viewed 146496 times

OrderTest4.png (118.33 KiB) Viewed 146496 times

OrderTest5.png (120.74 KiB) Viewed 146496 times

OrderTest6.png (119.39 KiB) Viewed 146496 times

OrderTest7.png (122.01 KiB) Viewed 146496 times

OrderTest8.png (120.05 KiB) Viewed 146496 times

[lsand039]

Different structures based off Bene-command:
./run.sh: Score: -nan

run.sh4genes.png (123.89 KiB) Viewed 146493 times

./run.sh BDe: Score: -nan

BDe4genes.png (123.89 KiB) Viewed 146493 times

./run.sh BIC: Score : 30.882

BIC4genes.png (17.92 KiB) Viewed 146493 times

./run.sh AIC: Score : 8.000

AIC4genes.png (17.92 KiB) Viewed 146493 times

[lsand039]

I don't have a score for the fully connected Bene structure, but here's the structure for (1): best scoring structure without background knowledge 1st and 2nd degree genes of Alzheimer. This structure was consistent in paths 2, 3, and 5.

(1).png (76.78 KiB) Viewed 146493 times

I ordered the 1st & 2nd degree genes of Alzheimer's according to correlations. The clinical variables were forced to have arcs with Alzheimer's.
Background knowledge files:

(1)mnh.txt

forbidden arcs

(684 Bytes) Downloaded 181 times

(1)mh.txt

Forced arcs

(17 Bytes) Downloaded 178 times

ROC: 0.731618

(1)ROC-AD.png (11.07 KiB) Viewed 146491 times

(1)ROC-nonAD.png (11.06 KiB) Viewed 146491 times

[lsand039]

I don't have a score for the fully connected Bene structure, but here's the structure for (2): best scoring structure with background knowledge 1st and 2nd degree genes of Alzheimer. This structure was consistent in paths 2, 3, and 5.

(2).png (77.53 KiB) Viewed 146492 times

I ordered the 1st & 2nd degree genes of Alzheimer's according to correlations. The clinical variables were forced to have arcs with Alzheimer's.
Background knowledge files:

(2)mh.txt

Forced Arcs

(16 Bytes) Downloaded 184 times

(2)mnh.txt

Forced Arcs

(401 Bytes) Downloaded 177 times

ROC: 0.717182

(2)ROC-nonAD.png (11.09 KiB) Viewed 146491 times

(2)ROC-AD.png (11.04 KiB) Viewed 146491 times

[lsand039]

I don't have a score for the fully connected Bene structure, but here's the structure for (3): best scoring structure without background knowledge 1st and 2nd degree genes of Alzheimer and KEGG genes 4th degree MB with no background knowledge. This structure was consistent in paths 2, 3, and 5.

(3).png (59 KiB) Viewed 146492 times

Background knowledge files:

(3)mnh.txt

Forbidden Arcs

(540 Bytes) Downloaded 168 times

(3)mh.txt

Forced arcs

(16 Bytes) Downloaded 188 times

ROC: 0.73061

(3)ROC-nonAD.png (11.11 KiB) Viewed 146491 times

(3)ROC-AD.png (11.08 KiB) Viewed 146491 times

[lsand039]

I don't have a score for the fully connected Bene structure, but here's the structure for (5): best scoring structure with background knowledge 1st and 2nd degree genes of Alzheimer and KEGG genes 3rd & 4th degree MB with background knowledge. This structure was consistent in paths 2, 3, and 5.

(5).png (88.39 KiB) Viewed 146490 times

Background knowledge files:

(5)mh.txt

forced arcs

(16 Bytes) Downloaded 161 times

(5)mnh.txt

forbidden arcs

(434 Bytes) Downloaded 169 times

ROC: 0.717238

(5)ROC-AD.png (11.07 KiB) Viewed 146490 times

(5)ROC-nonAD.png (11.18 KiB) Viewed 146490 times

[lsand039]

I don't have a score for the fully connected Bene structure, but here's the structure for (6): best scoring structure with background knowledge 1st and 2nd degree genes of Alzheimer KEGG genes 3rd, 4th , &5th degree MB with background knowledge. The BaNJo runs did not agree on a single structure. Here are the scores & log likelihood %:

(6) scores.xlsx

(5.39 KiB) Downloaded 175 times

Here are the top 3 structures. They only accounted for 92% of the log likelihood. There were 2 other structures that would've summed >95%. Please let me know if I should have them posted.
Top scoring structure: 45.89% of total log likelihood score

(6)a.png (104.73 KiB) Viewed 146489 times

ROC: 0.7192

(6)aROC-AD.png (11.2 KiB) Viewed 146488 times

(6)aROC-nonAD.png (11.23 KiB) Viewed 146488 times

2nd top scoring structure: 36.08% of total log likelihood score

(6)b.png (106.25 KiB) Viewed 146489 times

ROC: 0.736538

(6)bROC-AD.png (11.08 KiB) Viewed 146488 times

(6)bROC-nonAD.png (11.08 KiB) Viewed 146488 times

3rd top structure: 9.99% of total log likelihood score

(6)c.png (103.69 KiB) Viewed 146489 times

ROC: 0.736538

(6)cROC-AD.png (11.3 KiB) Viewed 146488 times

(6)cROC-nonAD.png (10.97 KiB) Viewed 146488 times

[lsand039]

Here's the structure for (4): best scoring structure without background knowledge 1st and 2nd degree genes of Alzheimer and KEGG genes 4th&5th degree MB with no background knowledge.
This is the highest scoring structure is below:

(4).png (137.95 KiB) Viewed 146486 times

The scores for the other structure:

(6)scores.xlsx

(5.9 KiB) Downloaded 167 times

Background knowledge files:

(4)mh.txt

forced arcs

(16 Bytes) Downloaded 173 times

(4)mnh.txt

forbidden arcs

(1008 Bytes) Downloaded 174 times

ROC: 0.741332

(4)ROC-AD.png (11.13 KiB) Viewed 146486 times

(4)ROC-nonAD.png (11.16 KiB) Viewed 146486 times

[lsand039]

Here are the arcs that were different in a couple (6)'s top scoring graphs:
CAPN2->MCL1 (not in A)
UQCRC1->MCL1 (not in B,C)

PPP3CB->NFKB2 (not in B)
UQCRC2->NFKB2 (not in A,C)

MCL1->CAPN2 (not in B,C)
Alzheimer->CAPN2 (not in A)

YWHAZ->APBB1 (not in B,C)
SNCA->APBB1 (not in A)

PPP3CB->MYO1F (not in A,B)
ATP2A2->MYO1F (not in C)

PPP3CB->NFKB2; (not in B)
UQCRC2->NFKB2; (not in B)