Novel Geometric Approach for Global Alignment of PPI Networks
Authors: Yangwei Liu, Hu Ding, Danyang Chen, Jinhui Xu
AAAI 2017 | Conference PDF | Archive PDF | Plain Text | LLM Run Details
| Reproducibility Variable | Result | LLM Response |
|---|---|---|
| Research Type | Experimental | Experiments We compare our algorithm with 4 popular alignment algorithms, including Iso Rank, MI-GRAAL, GHOST and NETAL. We choose the value of λ and μ in Geo Align using a 10-fold cross-validation on the NAPAbench CG data optimizing the specificity. Datasets For synthetic data, we use the NAPAbench (Sahraeian and Yoon 2012), which is a widely accepted synthetic benchmark dataset with functional annotation of proteins. [...] Results on Synthetic Dataset Results on the NAPAbench dataset are summarized in Tables 1 to 3. Note that for MNE, smaller value is better, while for other metrics, larger value is better. The best performer in each row is shown in black. |
| Researcher Affiliation | Academia | Yangwei Liu,1 Hu Ding,2 Danyang Chen,1 Jinhui Xu1 1Department of Computer Science and Engineering, State University of New York at Buffalo 2Department of Computer Science and Engineering, Michigan State University |
| Pseudocode | Yes | Algorithm 1 Structure Preserving Embedding; Algorithm 2 Preprocessing; Algorithm 3 Iterative Closest Point; Algorithm 4 Geo Align |
| Open Source Code | No | The paper does not include any explicit statement about providing open-source code for the described methodology, nor does it provide a link to a code repository. |
| Open Datasets | Yes | For synthetic data, we use the NAPAbench (Sahraeian and Yoon 2012), which is a widely accepted synthetic benchmark dataset with functional annotation of proteins. [...] For real world data, we use the PPI networks of C.elegans, D.melanogaster, S.cerevisiae, and H.sapiens from the Iso Base data set (Park et al. 2011). |
| Dataset Splits | Yes | We choose the value of λ and μ in Geo Align using a 10-fold cross-validation on the NAPAbench CG data optimizing the specificity. |
| Hardware Specification | No | The paper does not provide specific hardware details (e.g., GPU/CPU models, processor types, memory amounts) used for running its experiments. |
| Software Dependencies | No | The paper does not provide specific ancillary software details, such as library or solver names with version numbers, needed to replicate the experiments. |
| Experiment Setup | No | The paper states that the values of λ and μ were chosen using cross-validation ('We choose the value of λ and μ in Geo Align using a 10-fold cross-validation...'), but it does not explicitly list their specific values or other concrete hyperparameter settings. |