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 104668 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 177 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 158 times

OrderTest1.png (123.89 KiB) Viewed 104667 times

OrderTest2.png (125.93 KiB) Viewed 104667 times

OrderTest3.png (124.98 KiB) Viewed 104667 times

OrderTest4.png (118.33 KiB) Viewed 104667 times

OrderTest5.png (120.74 KiB) Viewed 104667 times

OrderTest6.png (119.39 KiB) Viewed 104667 times

OrderTest7.png (122.01 KiB) Viewed 104667 times

OrderTest8.png (120.05 KiB) Viewed 104667 times

[lsand039]

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

run.sh4genes.png (123.89 KiB) Viewed 104664 times

./run.sh BDe: Score: -nan

BDe4genes.png (123.89 KiB) Viewed 104664 times

./run.sh BIC: Score : 30.882

BIC4genes.png (17.92 KiB) Viewed 104664 times

./run.sh AIC: Score : 8.000

AIC4genes.png (17.92 KiB) Viewed 104664 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 104664 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 172 times

(1)mh.txt

Forced arcs

(17 Bytes) Downloaded 169 times

ROC: 0.731618

(1)ROC-AD.png (11.07 KiB) Viewed 104662 times

(1)ROC-nonAD.png (11.06 KiB) Viewed 104662 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 104663 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 175 times

(2)mnh.txt

Forced Arcs

(401 Bytes) Downloaded 169 times

ROC: 0.717182

(2)ROC-nonAD.png (11.09 KiB) Viewed 104662 times

(2)ROC-AD.png (11.04 KiB) Viewed 104662 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 104663 times

Background knowledge files:

(3)mnh.txt

Forbidden Arcs

(540 Bytes) Downloaded 159 times

(3)mh.txt

Forced arcs

(16 Bytes) Downloaded 178 times

ROC: 0.73061

(3)ROC-nonAD.png (11.11 KiB) Viewed 104662 times

(3)ROC-AD.png (11.08 KiB) Viewed 104662 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 104661 times

Background knowledge files:

(5)mh.txt

forced arcs

(16 Bytes) Downloaded 152 times

(5)mnh.txt

forbidden arcs

(434 Bytes) Downloaded 161 times

ROC: 0.717238

(5)ROC-AD.png (11.07 KiB) Viewed 104661 times

(5)ROC-nonAD.png (11.18 KiB) Viewed 104661 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 167 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 104660 times

ROC: 0.7192

(6)aROC-AD.png (11.2 KiB) Viewed 104659 times

(6)aROC-nonAD.png (11.23 KiB) Viewed 104659 times

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

(6)b.png (106.25 KiB) Viewed 104660 times

ROC: 0.736538

(6)bROC-AD.png (11.08 KiB) Viewed 104659 times

(6)bROC-nonAD.png (11.08 KiB) Viewed 104659 times

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

(6)c.png (103.69 KiB) Viewed 104660 times

ROC: 0.736538

(6)cROC-AD.png (11.3 KiB) Viewed 104659 times

(6)cROC-nonAD.png (10.97 KiB) Viewed 104659 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 104657 times

The scores for the other structure:

(6)scores.xlsx

(5.9 KiB) Downloaded 160 times

Background knowledge files:

(4)mh.txt

forced arcs

(16 Bytes) Downloaded 166 times

(4)mnh.txt

forbidden arcs

(1008 Bytes) Downloaded 165 times

ROC: 0.741332

(4)ROC-AD.png (11.13 KiB) Viewed 104657 times

(4)ROC-nonAD.png (11.16 KiB) Viewed 104657 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)