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Supplemental Information

Results for the split of 10 with 10 bits per feature (6880 total bits)

The highest Fmax at 60 committee members is at 75k, with an Fmax of 0.098

DOI: 10.7287/peerj.preprints.2197v1/supp-1

Results for the split of 16 with 16 bits per feature (11008 total bits)

The highest Fmax at 60 committee members is at 75k, with an Fmax of 0.097.

DOI: 10.7287/peerj.preprints.2197v1/supp-2

Results for the split of 4 with 4 bits per feature (2752 total bits)

The highest Fmax at 60 committee members is at 75k, with an Fmax of 0.097.

DOI: 10.7287/peerj.preprints.2197v1/supp-3

Results for the split of 16 with 4 bits per feature (2752 total bits)

The highest Fmax at 60 committee members is at 75k, with an Fmax of 0.102

DOI: 10.7287/peerj.preprints.2197v1/supp-4

Results for the split of 4 with 2 bits per feature (1376 total bits)

The highest Fmax at 60 committee members is at 75k, with an Fmax of 0.102.

DOI: 10.7287/peerj.preprints.2197v1/supp-5

Results at 75k updates for all five split treatments

The highest Fmax is achieved by the split of 16, 4 bits per feature encoding, with an Fmax of 0.103.

DOI: 10.7287/peerj.preprints.2197v1/supp-6

Specificity and sensitivity results at 75k updates for the split of 4 with 2 bits per feature treatment

Specificity at 60 committee members was 0.14, and sensitivity was 0.35.

DOI: 10.7287/peerj.preprints.2197v1/supp-7

A sample network diagram taken from the treatment of a split of 4 with 2 bits/feature at 75k updates

Out of a possible 1376 bits, the network has evolved to recognize only 118 of these. Inputs bits are green, gates are red, and outputs are blue. The inputs and gates are unordered. Note that a pair of outputs has evolved to represent a positive contact answer (the maximum is two), but that the negative contact answer evolved only one.

DOI: 10.7287/peerj.preprints.2197v1/supp-8

A histogram showing number of features recognized by each number of networks

The used encoding used is split of 4 with 2 bits/feature. A network only has to have input from one bit of a feature to recognize it.

DOI: 10.7287/peerj.preprints.2197v1/supp-9

Number of networks out of the 60 that evolved to recognize each kind of secondary structure along the two size-9 sliding windows

Encoding was split of 4, 2 bits/feature.

DOI: 10.7287/peerj.preprints.2197v1/supp-10

Number of networks out of the 60 that evolved to recognize the amino acid pair separation features

Encoding was split of 4, 2 bits/feature. Each tick shown is a different contact separation feature.

DOI: 10.7287/peerj.preprints.2197v1/supp-11

Fmax comparison of the runs for all features and the reduced features

Fmax of the original split-4, 2 bits per feature encoding with all features, and the same kind of run with the reduced feature set that only used features recognized by at least 6 of the networks from the first run.

DOI: 10.7287/peerj.preprints.2197v1/supp-12

Additional Information

Competing Interests

Claus O. Wilke is an Academic Editor for PeerJ.

Author Contributions

Samuel D Chapman performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Christoph Adami conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Claus O Wilke conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Dukka B KC conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

https://figshare.com/articles/Output_results_and_testing_contacts/3463256

Funding

This material is based in part upon work supported by the National Science Foundation under Cooperative Agreement No. DBI-0939454. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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