## Group Sybrandt

Group Description |
Sybrandt: machine learning graphs from document analysis ---------------------------------------------------------------------- MOLIERE Hypothesis Generation Network, J. Sybrandt, Clemson Univ. ---------------------------------------------------------------------- Justin Sybrandt, jsybran at clemson.edu Matrix Name: MOLIERE_2016 Hypothesis Generation Network Kind/Problem Domain: Term/Document Graph This network was presented in "MOLIERE: Automatic Biomedical Hypothesis Generation System (KDD''17)." Nodes in this network are either MEDLINE documents, UMLS terms, or n-grams we extracted through ToPMine. citation: Justin Sybrandt (Clemson University, Clemson, SC, USA), Michael Shtutman (University of South Carolina, Columbia, SC, USA) Ilya Safro (Clemson University, Clemson, SC, USA), "MOLIERE: Automatic Biomedical Hypothesis Generation System", 23rd ACM SIGKDD Conference on Knowledge Discovery and Data Mining August 13-17, 2017, Halifax, Nova Scotia - Canada https://doi.org/10.1145/3097983.3098057 The original data was 0-based with nodes numbered 0 to n-1. Converted to 1-based for the SuiteSparse Matrix Collection, July 2018. The graph has n=30,239,687 nodes. Node labels are held in the char array Problem.aux.labels. Nodes 1 to 22,281,874 all have labels starting with the capital letter "P", and are PubMed indentification numbers of the MEDLINE documents. Nodes 27,683,534 to n all start with the letter "C", and refer to UMLS terms. Nodes between these two sets of nodes refer to n-grams; none of them start with P or C (or any capital letter). The label of the kth node is also the kth line in the labels text file, and to the kth row and column of the matrix. The graph has 4,023,336 explicit zero edges, which are very important to the problem. They link automatically mined n-grams to UMLS terms representing the same concept. The goal is to find shortest-paths, so an edge of zero-length is important, and not the same as no edge at all. The pattern of the explicit zeros is held in Problem.Zeros in the MATLAB representation, and are part of the files for the Matrix Market and Rutherford-Boeing formats. To operate on the graph G in MATLAB, use G = Problem.A + 1e-100 * Problem.Zeros, or some other suitable tiny value. The nonzero edge weights in the graph range in value between 5e-15 and 3.0. There are no negative edge weights. The graph also has d=3,106,164 duplicate edges; it could be considered a multigraph. However, since the problem is to find shortest paths, the duplicate edges are not needed. The matrix in the SuiteSparse Matrix Collection holds the smallest edge weight for any duplicate. The duplicates not in the matrix are held in Problem.aux.duplicate_edges, as a d-by-3 dense matrix, where each row holds [i j eij] for the edge (i,j) with weight eij. ---------------------------------------------------------------------- Sybrandt/AGATHA_2015: deep-learning graph ---------------------------------------------------------------------- AGATHA: Automatic Graph-mining And Transformer based Hypothesis Generation Approach Justin Sybrandt, Ilya Tyagin, Michael Shtutman, Ilya Safro Clemson University paper: https://arxiv.org/abs/2002.05635. abstract: Medical research is risky and expensive. Drug discovery, as an example, requires that researchers efficiently winnow thousands of potential targets to a small candidate set for more thorough evaluation. However, research groups spend significant time and money to perform the experiments necessary to determine this candidate set long before seeing intermediate results. Hypothesis generation systems address this challenge by mining the wealth of publicly available scientific information to predict plausible research directions. We present AGATHA, a deep-learning hypothesis generation system that can introduce data-driven insights earlier in the discovery process. Through a learned ranking criteria, this system quickly prioritizes plausible term-pairs among entity sets, allowing us to recommend new research directions. We massively validate our system with a temporal holdout wherein we predict connections first introduced after 2015 using data published beforehand. We additionally explore biomedical sub-domains, and demonstrate AGATHA's predictive capacity across the twenty most popular relationship types. This system achieves best-in-class performance on an established benchmark, and demonstrates high recommendation scores across subdomains. Reproducibility: All code, experimental data, and pre-trained models are available online: http://sybrandt.com/2020/agatha . Appears in the 29TH ACM Intl. Conf. on Information and Knowledge Management, Oct 2020. https://www.cikm2020.org/ Details of this matrix: This matrix represents the semantic graph associated with the Agatha hypothesis generation system: https://arxiv.org/abs/2002.05635. The matrix was created by selecting all biomedical papers published prior to January 1st 2015. We extracted terms, phrases, entities, and author-supplied metadata keywords for each. In addition we identify all SemRep predicate arguments. Each sentence, term, phrase, entity, and predicate represents a node. Edges follow a particular schema, described in detail in the paper. Most edges indicate that two nodes co-occur. For instance, if a sentence contains a term, then an edge exists between the two nodes. We introduce a set of edges between sentences based on the nearest-neighbors network of sentence embeddings. The graph is really big, consisting of 183,964,077 nodes and 11,588,725,964 entries (half that many edges since the matrix is symmetric). Each node has a label, consisting of a character string, with a length ranging from 0 to 782 characters. The mean string lenth is 17.4. A single node (171,649,101 in 1-based notation) has a label of length zero, and is an artifact from how the original data was processed. All other node labels range in length from 3 to 782. The longest string comes from the following paper: https://pubmed.ncbi.nlm.nih.gov/183954/ which states: "The primary structure of the enzyme was determined: Ac-Met-Glu-...--Ala-Leu-Lys." To save space in the MATLAB representation, the node labels are held in a single character array, Problem.aux.names, where each label is terminated with a newline character. To extract the label of any given node, do the following: names = Problem.aux.names ; p = [1 find(names==10)+1] ; label = names (p(i):p(i+1)-2) ; For example, to list all nodes with labels of length 0 to 4: p = [1 find(names==10)+1] ; d = diff (p) ; for len = 0:4 fprintf ('\nnodes with labels of length %d:\n', len) ; nodes = find (d == len+1) ; for i = nodes fprintf ('%12d: [%s]\n', i, names (p(i):p(i+1)-2)) ; end end |
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Displaying

**all 2**collection matricesId | Name | Group | Rows | Cols | Nonzeros | Kind | Date | Download File |
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2893 | AGATHA_2015 | Sybrandt | 183,964,077 | 183,964,077 | 11,588,725,964 | Undirected Graph | 2020 | MATLAB Rutherford Boeing Matrix Market |

2810 | MOLIERE_2016 | Sybrandt | 30,239,687 | 30,239,687 | 6,669,254,694 | Undirected Weighted Graph | 2017 | MATLAB Rutherford Boeing Matrix Market |