Mining Seasonal Marine Microbial Pattern with Greedy Heuristic Clustering and Symmetrical Nonnegative Matrix Factorization

Pseudocode 1

 Input: Sequence Set 𝑋={𝑆₁,𝑆₂,…,𝑆_𝑛}, Minimum Length with Polymers l,  Neighborhood

   Parameter 𝜎, Clustering Threshold 𝛼, MinClusterSize

 Output: Clustering Result of Sequence Set 𝑋

 {

 Seed = {𝑆_𝑖};  // Initialize the Seed Sequence Set

 For (𝑖=1,𝑖≤𝑁,𝑖++)  //  Traverse the Distance of the Input sequence 𝑆_𝑖 and current Seed Set

       For (𝑘=1,𝑘<=length(Seed),𝑘++) //  Compute Distance of 𝑆_𝑖 and Seed_𝑘  (or Simmilary);

  If ∃𝑘 Meet Distance 𝑆_𝑖,Seed_𝑘≤𝛼,

   //  then Sequence𝑆_𝑖 ∈ Clustering Unit of Seed_𝑘, and output

     OTU_seed𝑘=OTU_seed𝑘+𝑆_𝑖, label(𝑆_𝑖)=arg𝑢_label(seed_𝑘);

  Else

   //  with Neighbor Sequence Expanding Method, yield to 𝜎  Neighbor Sequence  (𝑆_𝑖)

   Seed←Seed+Neighbor(𝑆_𝑖), //  Expanding Current Seed Sequence Set

   ClusterNum=ClusterNum+1;

   End If

  End For

 END For //  Travel all of Clustering Units, Subtract the Clustering Results the Parameter

    MinClusterSize

 IfCluster_𝑖<MinClusterSize,

  Reassigned (Cluster_𝑖)  //  Recluster Sequence in Clustering Units 𝑖 base on the Nearest

  Neighbor Clustering Algorithm,  Assigned to the nearest cluster units 𝑗, and 𝑗  Meet Cluster_𝑗>MinClusterSize

 End If

 }

Notes: Seed_𝑘 denotes the 𝑘th Seed Sequence in Sequence Set; Neighbor (𝑆_𝑖)  denotes 𝜎

Neighbor Sequence  (𝑆_𝑖); OTU_seed𝑘  denotes Clustering Unit of Seed_𝑘.