From e55a4a8bf8e7b69f94e35e50e4209ca651c7a8e1 Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Mon, 17 Nov 2025 16:13:22 -0800 Subject: [PATCH 1/3] chore([st]rwr): add doi --- spras/rwr.py | 2 +- spras/strwr.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/spras/rwr.py b/spras/rwr.py index e7691f160..ec5824e4d 100644 --- a/spras/rwr.py +++ b/spras/rwr.py @@ -16,7 +16,7 @@ class RWR(PRM): required_inputs = ['network','nodes'] - dois = [] + dois = ["10.1093/bioinformatics/btq680"] @staticmethod def generate_inputs(data, filename_map): diff --git a/spras/strwr.py b/spras/strwr.py index c99b39830..1844ff889 100644 --- a/spras/strwr.py +++ b/spras/strwr.py @@ -15,7 +15,7 @@ # Note: This class is almost identical to the rwr.py file. class ST_RWR(PRM): required_inputs = ['network','sources','targets'] - dois = [] + dois = ["10.1093/bioinformatics/btq680"] @staticmethod def generate_inputs(data, filename_map): From 843a1a16f1976933a81507e9d9d2ff4cbcdc3600 Mon Sep 17 00:00:00 2001 From: "Tristan F." Date: Thu, 20 Nov 2025 00:42:15 +0000 Subject: [PATCH 2/3] chore: add other DOIs --- spras/rwr.py | 4 +++- spras/strwr.py | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/spras/rwr.py b/spras/rwr.py index ec5824e4d..4edd16e41 100644 --- a/spras/rwr.py +++ b/spras/rwr.py @@ -16,7 +16,9 @@ class RWR(PRM): required_inputs = ['network','nodes'] - dois = ["10.1093/bioinformatics/btq680"] + # Paper relevant to biological applications of random walks, + # then the original TrustRank paper. + dois = ["10.1093/bioinformatics/btq680", "10.1016/b978-012088469-8/50052-8"] @staticmethod def generate_inputs(data, filename_map): diff --git a/spras/strwr.py b/spras/strwr.py index 1844ff889..e94102b8d 100644 --- a/spras/strwr.py +++ b/spras/strwr.py @@ -15,7 +15,9 @@ # Note: This class is almost identical to the rwr.py file. class ST_RWR(PRM): required_inputs = ['network','sources','targets'] - dois = ["10.1093/bioinformatics/btq680"] + # Paper relevant to biological applications of random walks, + # then the personalization-vector-based PageRank paper. + dois = ["10.1093/bioinformatics/btq680", "10.1145/511446.511513"] @staticmethod def generate_inputs(data, filename_map): From 795242bfa0f0d6ec9840848709a9b04f324d9da2 Mon Sep 17 00:00:00 2001 From: "Tristan F.-R." Date: Sat, 13 Dec 2025 20:36:31 -0800 Subject: [PATCH 3/3] docs: use pagerank paper over trustrank paper --- spras/rwr.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/spras/rwr.py b/spras/rwr.py index 4edd16e41..759df0e4f 100644 --- a/spras/rwr.py +++ b/spras/rwr.py @@ -17,8 +17,8 @@ class RWR(PRM): required_inputs = ['network','nodes'] # Paper relevant to biological applications of random walks, - # then the original TrustRank paper. - dois = ["10.1093/bioinformatics/btq680", "10.1016/b978-012088469-8/50052-8"] + # then the original personalized PageRank paper. + dois = ["10.1093/bioinformatics/btq680", "10.1145/511446.511513"] @staticmethod def generate_inputs(data, filename_map):