Merge pull request #169 from lanl/develop

Develop

CITATION.cff

@@ -20,7 +20,7 @@ authors:
   - family-names: Alexandrov
     given-names: Boian
 title: "Tensor Extraction of Latent Features (T-ELF)"
-version: 0.0.18
+version: 0.0.19
 url: https://github.com/lanl/T-ELF
 doi: 10.5281/zenodo.10257897
 date-released: 2023-12-04

README.md

@@ -153,7 +153,7 @@ If you use T-ELF please cite.
 
 **APA:**
 ```latex
-Eren, M., Solovyev, N., Barron, R., Bhattarai, M., Truong, D., Boureima, I., Skau, E., Rasmussen, K., & Alexandrov, B. (2023). Tensor Extraction of Latent Features (T-ELF) (Version 0.0.18) [Computer software]. https://doi.org/10.5281/zenodo.10257897
+Eren, M., Solovyev, N., Barron, R., Bhattarai, M., Truong, D., Boureima, I., Skau, E., Rasmussen, K., & Alexandrov, B. (2023). Tensor Extraction of Latent Features (T-ELF) (Version 0.0.19) [Computer software]. https://doi.org/10.5281/zenodo.10257897
 ```
 
 **BibTeX:**

TELF/factorization/HNMFk.py

@@ -210,16 +210,11 @@ def fit(self, X, Ks, from_checkpoint=False, save_checkpoint=False):
         if self.n_nodes > 1:
             comm = MPI.COMM_WORLD
             rank = comm.Get_rank()
-            self.node_status = {}
-            for ii in range(1, self.n_nodes, 1):
-                self.node_status[ii] = {"free":True, "job":None}
 
         # single node processing
         else:
             comm = None
             rank = 0
-            self.node_status[0] = {"free": True, "job":None}
-
 
         #
         # Checkpointing and job setup
@@ -256,6 +251,16 @@ def fit(self, X, Ks, from_checkpoint=False, save_checkpoint=False):
                     "depth":0,
                     "parent_topic":None
                 }
+
+        # organize node status
+        if self.n_nodes > 1:
+            self.node_status = {}
+            for ii in range(1, self.n_nodes, 1):
+                self.node_status[ii] = {"free":True, "job":None}
+
+        else:
+             self.node_status = {}
+             self.node_status[0] = {"free": True, "job":None}
 
         # save data matrix
         self.X = X 
@@ -355,6 +360,9 @@ def fit(self, X, Ks, from_checkpoint=False, save_checkpoint=False):
         self.iterator = self.root
         self._prepare_iterator(self.root)
 
+        if self.verbose:
+            print("Done")
+
         return {"time":total_exec_seconds}
 
 

TELF/factorization/NMFk.py

@@ -637,8 +637,9 @@ def __init__(
         k_search_method : str, optional
             Which approach to use when searching for the rank or k. The default is "linear".\n
             * ``k_search_method='linear'`` will linearly visit each K given in ``Ks`` hyper-parameter of the ``fit()`` function.\n
-            * ``k_search_method='bst_post'`` will perform post-order binary search. When an ideal rank is found, determined by the selected ``predict_k_method``, all lower ranks are pruned from the search space.
-            * ``k_search_method='bst_pre'`` will perform pre-order binary search. When an ideal rank is found, determined by the selected ``predict_k_method``, all lower ranks are pruned from the search space.
+            * ``k_search_method='bst_post'`` will perform post-order binary search. When an ideal rank is found, determined by the selected ``predict_k_method``, all lower ranks are pruned from the search space.\n
+            * ``k_search_method='bst_pre'`` will perform pre-order binary search. When an ideal rank is found, determined by the selected ``predict_k_method``, all lower ranks are pruned from the search space.\n
+            * ``k_search_method='bst_in'`` will perform in-order binary search. When an ideal rank is found, determined by the selected ``predict_k_method``, all lower ranks are pruned from the search space.
         H_sill_thresh : float, optional
             Setting for removing higher ranks from the search space.\n
             When searching for the optimal rank with binary search using ``k_search='bst_post'`` or ``k_search='bst_pre'``, this hyper-parameter can be used to cut off higher ranks from search space.\n
@@ -694,7 +695,7 @@ def __init__(
         self.H_sill_thresh = H_sill_thresh
 
         # warnings
-        assert self.k_search_method in ["linear", "bst_pre", "bst_post"], "Invalid k_search_method method. Choose from linear, bst_pre, or bst_post."
+        assert self.k_search_method in ["linear", "bst_pre", "bst_post", "bst_in"], "Invalid k_search_method method. Choose from linear, bst_pre, bst_in, or bst_post."
         assert self.predict_k_method in ["pvalue", "WH_sill", "W_sill", "H_sill", "sill"], "Invalid predict_k_method method. Choose from pvalue, WH_sill, W_sill, H_sill, or sill. sill defaults to WH_sill."
 
         if self.predict_k_method == "sill":
@@ -863,11 +864,17 @@ def fit(self, X, Ks, name="NMFk", note=""):
             node = BST.sorted_array_to_bst(Ks)
             if self.K_search_settings["k_search_method"] == "bst_pre": 
                 Ks = list(node.preorder())
-            if self.K_search_settings["k_search_method"] == "bst_post": 
+            elif self.K_search_settings["k_search_method"] == "bst_post": 
                 Ks = list(node.postorder())
+            elif self.K_search_settings["k_search_method"] == "bst_in": 
+                Ks = list(node.inorder())
             else:
                 raise Exception("Unknown k_search_method!")
+
+            if self.verbose:
+                print(f'Performing K search with {self.K_search_settings["k_search_method"]}. Ks={Ks}')
 
+
         #
         # check X format
         #

TELF/factorization/utilities/bst_helper.py

@@ -21,11 +21,19 @@ def preorder(self):
             yield from self.left.preorder()
         if self.right:
             yield from self.right.preorder()
-
+        
     def postorder(self):
-        yield self.value
+        if self.left:
+            yield from self.left.postorder()
         if self.right:
-            yield from self.right.preorder()
+            yield from self.right.postorder()
+        yield self.value
+
+    def inorder(self):
         if self.left:
-            yield from self.left.preorder()
+            yield from self.left.postorder()
+        yield self.value
+        if self.right:
+            yield from self.right.postorder()
+
 

TELF/version.py

@@ -1 +1 @@
-__version__ = '0.0.18'
+__version__ = '0.0.19'

docs/Beaver.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.pre_processing.Beaver: Fast matrix and tensor building tool &#8212; TELF 0.0.18 documentation</title>
+    <title>TELF.pre_processing.Beaver: Fast matrix and tensor building tool &#8212; TELF 0.0.19 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=4bf62f09"></script>
+    <script src="_static/documentation_options.js?v=f00aad14"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.18 documentation</p>
+    <p class="title logo__title">TELF 0.0.19 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

docs/Cheetah.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.applications.Cheetah: Advanced search by keywords and phrases &#8212; TELF 0.0.18 documentation</title>
+    <title>TELF.applications.Cheetah: Advanced search by keywords and phrases &#8212; TELF 0.0.19 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=4bf62f09"></script>
+    <script src="_static/documentation_options.js?v=f00aad14"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.18 documentation</p>
+    <p class="title logo__title">TELF 0.0.19 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

docs/HNMFk.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.HNMFk: Hierarchical Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.18 documentation</title>
+    <title>TELF.factorization.HNMFk: Hierarchical Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.19 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=4bf62f09"></script>
+    <script src="_static/documentation_options.js?v=f00aad14"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.18 documentation</p>
+    <p class="title logo__title">TELF 0.0.19 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

docs/NMFk.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.NMFk: Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.18 documentation</title>
+    <title>TELF.factorization.NMFk: Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.19 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=4bf62f09"></script>
+    <script src="_static/documentation_options.js?v=f00aad14"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.18 documentation</p>
+    <p class="title logo__title">TELF 0.0.19 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
@@ -528,6 +528,7 @@ <h1>Available Functions<a class="headerlink" href="#available-functions" title="
 <li><p><code class="docutils literal notranslate"><span class="pre">k_search_method='linear'</span></code> will linearly visit each K given in <code class="docutils literal notranslate"><span class="pre">Ks</span></code> hyper-parameter of the <code class="docutils literal notranslate"><span class="pre">fit()</span></code> function.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">k_search_method='bst_post'</span></code> will perform post-order binary search. When an ideal rank is found, determined by the selected <code class="docutils literal notranslate"><span class="pre">predict_k_method</span></code>, all lower ranks are pruned from the search space.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">k_search_method='bst_pre'</span></code> will perform pre-order binary search. When an ideal rank is found, determined by the selected <code class="docutils literal notranslate"><span class="pre">predict_k_method</span></code>, all lower ranks are pruned from the search space.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">k_search_method='bst_in'</span></code> will perform in-order binary search. When an ideal rank is found, determined by the selected <code class="docutils literal notranslate"><span class="pre">predict_k_method</span></code>, all lower ranks are pruned from the search space.</p></li>
 </ul>
 </dd>
 <dt>H_sill_thresh<span class="classifier">float, optional</span></dt><dd><p>Setting for removing higher ranks from the search space.</p>

docs/RESCALk.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.RESCALk: RESCAL with Automatic Model Determination &#8212; TELF 0.0.18 documentation</title>
+    <title>TELF.factorization.RESCALk: RESCAL with Automatic Model Determination &#8212; TELF 0.0.19 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=4bf62f09"></script>
+    <script src="_static/documentation_options.js?v=f00aad14"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.18 documentation</p>
+    <p class="title logo__title">TELF 0.0.19 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

docs/SymNMFk.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.SymNMFk: Symmetric Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.18 documentation</title>
+    <title>TELF.factorization.SymNMFk: Symmetric Non-negative Matrix Factorization with Automatic Model Determination &#8212; TELF 0.0.19 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=4bf62f09"></script>
+    <script src="_static/documentation_options.js?v=f00aad14"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.18 documentation</p>
+    <p class="title logo__title">TELF 0.0.19 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

docs/TELF.factorization.decompositions.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.decompositions package &#8212; TELF 0.0.18 documentation</title>
+    <title>TELF.factorization.decompositions package &#8212; TELF 0.0.19 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=4bf62f09"></script>
+    <script src="_static/documentation_options.js?v=f00aad14"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -128,7 +128,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.18 documentation</p>
+    <p class="title logo__title">TELF 0.0.19 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">

docs/TELF.factorization.decompositions.utilities.html

@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>TELF.factorization.decompositions.utilities package &#8212; TELF 0.0.18 documentation</title>
+    <title>TELF.factorization.decompositions.utilities package &#8212; TELF 0.0.19 documentation</title>
 
 
 
@@ -37,7 +37,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
   <script src="_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
 
-    <script src="_static/documentation_options.js?v=4bf62f09"></script>
+    <script src="_static/documentation_options.js?v=f00aad14"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
@@ -127,7 +127,7 @@
 
 
 
-    <p class="title logo__title">TELF 0.0.18 documentation</p>
+    <p class="title logo__title">TELF 0.0.19 documentation</p>
 
 </a></div>
         <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">