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pre-nmf.cl
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pre-nmf.cl
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(defpackage :pre-nmf
(:use :cl
:hc
:linear-regression
:hjs.learn.read-data
:hjs.util.matrix))
(in-package :pre-nmf)
(defun i-thvector (numeric-dataset i)
(assert (eq (type-of numeric-dataset) 'numeric-dataset))
(assert (<= 0 i (- (length (aref (dataset-numeric-points numeric-dataset) 0)) 1)))
(assert (<= 3 (length (dataset-numeric-points numeric-dataset))))
(let* ((data (dataset-numeric-points numeric-dataset))
(n (length data))
(x-i (make-array n :element-type 'double-float)))
(dotimes (k n x-i)
(setf (aref x-i k) (aref (aref data k) i)))))
(defun vector-sum (vector)
(declare (optimize (speed 3) (debug 0) (safety 0)))
(declare (type dvec vector))
(let ((sum 0))
(dotimes (i (length vector) sum)
(setf sum (+ sum (aref vector i))))))
(defun vector-square (vector)
(let ((v-square (make-array (length vector) :element-type 'double-float)))
(dotimes (i (length vector) v-square)
(setf (aref v-square i) (* (aref vector i) (aref vector i))))))
(defun square-sum (vector)
(vector-sum (vector-square vector)))
(defun vector-mean (vector)
(/ (vector-sum vector) (length vector)))
(defun m^t (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(a (make-array (list n m) :element-type 'double-float)))
(dotimes (i n a)
(dotimes (j m)
(setf (aref a i j) (aref matrix j i))))))
(defun make-test-matrix (m n)
(let ((a (make-array (list m n) :element-type 'double-float)))
(dotimes (i m a)
(dotimes (j n)
(setf (aref a i j) (coerce (random 1.0) 'double-float))))))
(defun make-test-matrix2 (m n)
(let ((a (make-array (list m n) :element-type 'double-float)))
(dotimes (i m a)
(dotimes (j n)
(setf (aref a i j) (coerce (random 100) 'double-float))))))
(defun nmf (x k)
(let* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n)))
(dotimes (p 100)
(dotimes (i k)
(dotimes (j n)
(setf (aref v i j)
(* (aref v i j)
(aref (m*m (m^t u) x) i j)
(/ (aref (m*m (m*m (m^t u) u) v) i j))))))
(dotimes (i m)
(dotimes (j k)
(setf (aref u i j)
(* (aref u i j)
(aref (m*m x (m^t v)) i j)
(/ (aref (m*m (m*m u v) (m^t v)) i j)))))))
(values u v)))
(defun norm (matrix)
(let ((n (array-dimension matrix 0))
(m (array-dimension matrix 1))
(sum 0.0))
(dotimes (i n (* 0.5 sum))
(dotimes (j m)
(setf sum (+ sum (* (aref matrix i j) (aref matrix i j))))))))
(defun nmf2 (x k)
(do* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n)))
((< (norm (m- x (m*m u v))) 0.001) (values u v))
(dotimes (i k)
(dotimes (j n)
(setf (aref v i j)
(* (aref v i j)
(aref (m*m (m^t u) x) i j)
(/ (aref (m*m (m*m (m^t u) u) v) i j))))))
(dotimes (i m)
(dotimes (j k)
(setf (aref u i j)
(* (aref u i j)
(aref (m*m x (m^t v)) i j)
(/ (aref (m*m (m*m u v) (m^t v)) i j))))))))
(defun nmf4 (x k)
(let* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n))
(sum1 0.0)
(sum2 0.0)
(sum3 0.0)
(sum4 0.0))
(dotimes (p 100 (values u v))
(let ((uu u)
(vv v))
(dotimes (i k)
(dotimes (j n)
(setf (aref v i j)
(* (aref vv i j)
(/ (dotimes (l m sum1)
(setf sum1 (+ sum1
(* (aref uu l j) (aref x l j)
(/ (aref (m-times-n uu vv) l j))))))
(dotimes (l m sum2)
(setf sum2 (+ sum2 (aref uu l i))))))))))
(let ((uu u)
(vv v))
(dotimes (i m)
(dotimes (j k)
(setf (aref u i j)
(* (aref uu i j)
(/ (dotimes (l n sum3)
(setf sum3 (+ sum3
(* (aref vv j l) (aref x i l)
(/ (aref (m-times-n uu vv) i l))))))
(dotimes (l n sum4)
(setf sum4 (+ sum4 (aref vv j l)))))))))))))
(defun nmf-beta (x k)
(let* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n)))
(dotimes (p 100)
(let* ((u^t (m^t u))
(w (m*m u^t u)))
(dotimes (i k)
(dotimes (j n)
(setf (aref v i j)
(* (aref v i j)
(a*b-i-j u^t x i j)
(/ (a*b-i-j w v i j)))))))
(let* ((v^t (m^t v))
(ww (m*m u v)))
(dotimes (i m)
(dotimes (j k)
(setf (aref u i j)
(* (aref u i j)
(a*b-i-j x v^t i j)
(/ (a*b-i-j ww v^t i j))))))))
(values u v)))
;(declaim (inline a*b-i-j))
(defun a*b-i-j (a b i j)
(declare (type dmat a))
(declare (type dmat b))
(declare (optimize (speed 3) (debug 0) (safety 0)))
(assert (= (array-dimension a 1) (array-dimension b 0)))
(let ((k (array-dimension a 1))
(sum 0.0))
(dotimes (l k sum)
(setf sum (+ sum
(* (aref a i l) (aref b l j)))))))
(defun aux-gene (n)
(dotimes (i n)
(princ ":numeric ")))
(defun aux-gene2 (n)
(dotimes (i n)
(format t "~a " i)))
;(defun numeric-matrix (numeric-dataset)
; (let* ((data (dataset-numeric-points numeric-dataset))
; (m (length data))
; (n (length (aref data 0)))
; (a (make-array (list m n) :element-type 'double-float)))
; (dotimes (i m a)
; (dotimes (j n)
; (setf (aref a i j)
; (aref (i-thvector numeric-dataset j) i))))))
(defun pick-up-row (matrix n)
(declare (type dmat matrix))
(let* ((m (array-dimension matrix 1))
(v (make-array m :element-type 'double-float)))
(dotimes (i m v)
(setf (aref v i) (aref matrix n i)))))
(defun make-index (n)
(let ((index nil))
(dotimes (i n (reverse index))
(setf index (cons i index)))))
(defun numbering (list)
(let ((n (length list)))
(mapcar #'list
list
(make-index n))))
(defun pick-up-words (feature-matrix words-vector n)
(let ((v (numbering (coerce (pick-up-row feature-matrix n) 'list))))
(setf v (sort v #'> :key #'car))
(dotimes (j 10)
(format t "~A ~A~%" (aref words-vector (car (cdr (nth j v)))) (car (nth j v))))))
(defun pick-up-column (matrix n)
(declare (type dmat matrix))
(let* ((m (array-dimension matrix 0))
(v (make-array m :element-type 'double-float)))
(dotimes (i m v)
(setf (aref v i) (aref matrix i n)))))
(defun pick-up-articles (weight-matrix articles-vector n)
(let ((v (numbering (coerce (pick-up-column weight-matrix n) 'list))))
(setf v (sort v #'> :key #'car))
(dotimes (j 10)
(format t "~A ~A~%" (aref articles-vector (car (cdr (nth j v)))) (car (nth j v))))))
(defun make-article-id (unspecialized-dataset)
(let* ((data (dataset-points unspecialized-dataset))
(n (length data))
(x (make-array n)))
(dotimes (k n x)
(setf (aref x k) (aref (aref data k) 0)))))
(defun result-words (feature-matrix words-vector)
(let ((n (array-dimension feature-matrix 0)))
(dotimes (i n)
(format t "~%Feature ~A~%" i)
(pick-up-words feature-matrix words-vector i))))
(defun result-articles (weight-matrix articles-vector)
(let ((n (array-dimension weight-matrix 1)))
(dotimes (i n)
(format t "~%Feature ~A~%" i)
(pick-up-articles weight-matrix articles-vector i))))
(defun search-area (article-id article-area)
(if (= article-id (aref (car article-area) 0))
(aref (car article-area) 1)
(search-area article-id (cdr article-area))))
(defun pick-up-articles2 (weight-matrix articles-vector article-area n)
(let ((v (numbering (coerce (pick-up-column weight-matrix n) 'list))))
(setf v (sort v #'> :key #'car))
(dotimes (j 10)
(format t "~A,~A~%" (aref articles-vector (car (cdr (nth j v))))
(search-area (parse-integer (aref articles-vector (car (cdr (nth j v)))))
article-area)))))
(defun result-articles2 (weight-matrix articles-vector article-area)
(let ((n (array-dimension weight-matrix 1)))
(dotimes (i n)
(format t "Feature ~A~%" i)
(pick-up-articles2 weight-matrix articles-vector article-area i))))
(defun set-data (file-name)
(progn
(defparameter dataset (read-data-from-file file-name :external-format :utf-8))
(defparameter article-id (make-article-id dataset))
(defparameter numeric-dataset (pick-and-specialize-data dataset
:range
(rest (make-range
(length (dataset-dimensions dataset))))
:data-types
(make-data-types (length (rest
(make-range (length (dataset-dimensions dataset))))))))
(defparameter words (dataset-dimensions numeric-dataset))
(defparameter matrix (numeric-matrix numeric-dataset))))
(defun nmf-analysis (matrix k)
(progn
(time (multiple-value-setq (weight feature) (nmf-gamma matrix k)))
(result-words feature words)
(result-articles weight article-id)
(norm (m- matrix (m-times-n weight feature)))))
(defun make-range (n)
(let ((range nil))
(dotimes (i n (reverse range))
(setf range (cons i range)))))
(defun make-data-types (n)
(let ((data-types nil))
(dotimes (i n data-types)
(setf data-types (cons :numeric data-types)))))
(defun pick-up-no-feature-words (feature-matrix words-vector n)
(let ((v (numbering (coerce (pick-up-row feature-matrix n) 'list))))
(setf v (sort v #'< :key #'car))
(dotimes (j 10)
(format t "~A~%" (aref words-vector (car (cdr (nth j v))))))))
(defun result-no-feature-words (feature-matrix words-vector)
(let ((n (array-dimension feature-matrix 0)))
(dotimes (i n)
(format t "~%Feature ~A~%" i)
(pick-up-no-feature-words feature-matrix words-vector i))))
(defun word-distance (feature-matrix word-index1 word-index2 &optional (distance-fn #'euclidean))
(let ((v1 (pick-up-column feature-matrix word-index1))
(v2 (pick-up-column feature-matrix word-index2)))
; (d 0.0))
; (dotimes (i (array-dimension feature-matrix 0) (sqrt d))
; (setf d (+ d (* (- (aref v1 i) (aref v2 i)) (- (aref v1 i) (aref v2 i))))))))
(funcall distance-fn v1 v2)))
(defun make-word-distance-matrix (feature-matrix)
(let* ((n (array-dimension feature-matrix 1))
(word-distance-matrix (make-array (list n n) :element-type 'double-float)))
(dotimes (i n word-distance-matrix)
(dotimes (j n)
(setf (aref word-distance-matrix i j)
(word-distance feature-matrix i j))))))
(defun pick-up-similar-words (word-distance-matrix words-vector word-index)
(let ((v (numbering (coerce (pick-up-row word-distance-matrix word-index) 'list))))
(setf v (sort v #'< :key #'car))
(dotimes (j 20)
(format t "~A ~A~%" (aref words-vector (car (cdr (nth j v)))) (car (nth j v))))))
(defun article-distance (weight-matrix article-index1 article-index2 &optional (distance-fn #'cosine))
(let ((v1 (pick-up-row weight-matrix article-index1))
(v2 (pick-up-row weight-matrix article-index2)))
;(d 0.0))
; (dotimes (i (array-dimension weight-matrix 1) (sqrt d))
;(setf d (+ d (* (- (aref v1 i) (aref v2 i)) (- (aref v1 i) (aref v2 i))))))))
(funcall distance-fn v1 v2)))
(defun make-article-distance-matrix (weight-matrix)
(let* ((m (array-dimension weight-matrix 0))
(article-distance-matrix (make-array (list m m) :element-type 'double-float)))
(dotimes (i m article-distance-matrix)
(dotimes (j m)
(setf (aref article-distance-matrix i j)
(article-distance weight-matrix i j))))))
(defun pick-up-similar-articles (article-distance-matrix articles-vector article-index)
(let ((v (numbering (coerce (pick-up-column article-distance-matrix article-index) 'list))))
(setf v (sort v #'< :key #'car))
(dotimes (j 10)
(format t "~A ~A~%" (aref articles-vector (car (cdr (nth j v)))) (car (nth j v))))))
(defun make-word-data-file (feature-matrix)
(let ((n (array-dimension feature-matrix 1)))
(dotimes (i n)
(format t "~%~A ~A ~A~%" (aref feature-matrix 0 i) (aref feature-matrix 1 i)
(aref feature-matrix 2 i)))))
(defun make-article-data-file (weight-matrix)
(let ((m (array-dimension weight-matrix 0)))
(dotimes (i m)
(format t "~%~A ~A ~A~%" (aref weight-matrix i 0) (aref weight-matrix i 1)
(aref weight-matrix i 2)))))
(defun pre-normalize (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(u (make-array (list m n) :element-type 'double-float)))
(dotimes (i m)
(dotimes (j n)
(setf (aref u i j) (aref matrix i j))))
(dotimes (i m u)
(dotimes (j n)
(let ((sum 0.0))
(setf (aref u i j)
(/ (aref matrix i j)
(dotimes (l n (sqrt sum))
(setf sum (+ sum (expt (aref matrix l j) 2)))))))))))
(defun normalize (weight feature)
(let* ((k (array-dimension weight 1))
(n (array-dimension feature 1))
(v (make-array (list k n) :element-type 'double-float)))
(dotimes (i k)
(dotimes (j n)
(let ((sum 0.0))
(setf (aref v i j)
(* (aref feature i j)
(dotimes (l k (sqrt sum))
(setf sum (+ sum (expt (aref weight l i) 2)))))))))
(values (pre-normalize weight) v)))
(defun nmf-gamma0 (x k)
(declare (optimize (speed 3) (debug 0) (safety 0))
(type dmat x))
(let* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n)))
(dotimes (p 100)
(let* ((u^t (m^t u))
(w (m*m u^t u)))
(dotimes (i k)
(dotimes (j n)
(setf (aref v i j)
(* (aref v i j)
(a*b-i-j u^t x i j)
(/ (a*b-i-j w v i j)))))))
(let* ((v^t (m^t v))
(ww (m*m u v)))
(dotimes (i m)
(dotimes (j k)
(setf (aref u i j)
(* (aref u i j)
(a*b-i-j x v^t i j)
(/ (a*b-i-j ww v^t i j))))))))
(normalize u v)))
(defun nmf-gamma (x k)
(declare (type dmat x))
(let* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n)))
(declare (type dmat u))
(declare (type dmat v))
(dotimes (p 100)
(let* ((u^t (m^t u))
(w (m-times-n u^t u)))
(declare (type dmat u^t))
(declare (type dmat w))
(dotimes (i k)
(dotimes (j n)
(setf (aref v i j)
(* (aref v i j)
(a*b-i-j u^t x i j)
(/ (a*b-i-j w v i j)))))))
(let* ((v^t (m^t v))
(ww (m-times-n u v)))
(declare (type dmat v^t))
(declare (type dmat ww))
(dotimes (i m)
(dotimes (j k)
(setf (aref u i j)
(* (aref u i j)
(a*b-i-j x v^t i j)
(/ (a*b-i-j ww v^t i j)))))))
(print (norm (m- x (m-times-n u v)))))
;;(normalize u v)))
(values u v)))
(defun nmf-gamma-norm (x k)
(declare (type dmat x))
(do* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n)))
((< (norm (m- x (m-times-n u v))) 0.1) (normalize u v))
(print (norm (m- x (m-times-n u v))))
(let* ((u^t (m^t u))
(w (m-times-n u^t u)))
(dotimes (i k)
(dotimes (j n)
(setf (aref v i j)
(* (aref v i j)
(a*b-i-j u^t x i j)
(/ (a*b-i-j w v i j)))))))
(let* ((v^t (m^t v))
(ww (m-times-n u v)))
(dotimes (i m)
(dotimes (j k)
(setf (aref u i j)
(* (aref u i j)
(a*b-i-j x v^t i j)
(/ (a*b-i-j ww v^t i j)))))))))
(defun word-clustering-vector (feature-matrix)
(let* ((n (array-dimension feature-matrix 1))
(v (make-array n)))
(dotimes (i n v)
(setf (aref v i)
(max-index (pick-up-column feature-matrix i))))))
(defun feature-vector (feature-matrix)
(let* ((n (array-dimension feature-matrix 1))
(v (make-array n)))
(dotimes (i n v)
(setf (aref v i)
(aref feature-matrix (aref (word-clustering-vector feature-matrix) i) i)))))
(defun max-index (vector)
(let* ((v (coerce vector 'list))
(w (numbering v)))
(setf w (sort w #'> :key #'car))
(second (car w))))
(defun word-clustering (feature-matrix words-vector)
(mapcar #'list
(coerce (word-clustering-vector feature-matrix) 'list)
(coerce words-vector 'list)
(coerce (feature-vector feature-matrix) 'list)))
(defun result-word-clustering (feature-matrix words-vector)
(let ((v (sort (sort (word-clustering feature-matrix words-vector) #'> :key #'third) #'< :key #'first)))
(dotimes (i (length words-vector))
(format t "~%~A ~A ~A~%"
(first (nth i v)) (second (nth i v)) (third (nth i v))))))
(defun article-clustering-vector (weight-matrix)
(let* ((m (array-dimension weight-matrix 0))
(v (make-array m)))
(dotimes (i m v)
(setf (aref v i)
(max-index (pick-up-row weight-matrix i))))))
(defun weight-vector (weight-matrix)
(let* ((m (array-dimension weight-matrix 0))
(v (make-array m)))
(dotimes (i m v)
(setf (aref v i)
(aref weight-matrix i (aref (article-clustering-vector weight-matrix) i))))))
(defun article-clustering (weight-matrix articles-vector)
(mapcar #'list
(coerce (article-clustering-vector weight-matrix) 'list)
(coerce articles-vector 'list)
(coerce (weight-vector weight-matrix) 'list)))
(defun result-article-clustering (weight-matrix articles-vector)
(let ((v (sort (sort (article-clustering weight-matrix articles-vector) #'> :key #'third) #'< :key #'first)))
(dotimes (i (length articles-vector))
(format t "~%~A ~A ~A~%"
(first (nth i v)) (second (nth i v)) (third (nth i v))))))
(defun consensus-matrix0 (feature-matrix)
(let* ((n (array-dimension feature-matrix 1))
(v (word-clustering-vector feature-matrix))
(c (make-array (list n n))))
(dotimes (i n c)
(dotimes (j n)
(setf (aref c i j)
(if (= (aref v i) (aref v j))
1
0))))))
(defun consensus-matrix (weight-matrix)
(let* ((n (array-dimension weight-matrix 0))
(v (article-clustering-vector weight-matrix))
(c (make-array (list n n))))
(dotimes (i n c)
(dotimes (j n)
(setf (aref c i j)
(if (= (aref v i) (aref v j))
1
0))))))
(defun average-consensus-matrix (matrix k &optional (count 50))
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(average-c (make-array (list m m) :initial-element 0.0d0 :element-type 'double-float))
(c (make-array (list m m)))
(u (make-array (list m k)))
(v (make-array (list k n))))
(dotimes (l count average-c)
(multiple-value-setq (u v) (nmf-gamma matrix k))
(setf c (consensus-matrix u))
(dotimes (i m)
(dotimes (j m)
(setf (aref average-c i j)
(/ (+ (* l (aref average-c i j)) (aref c i j))
(+ l 1))))))))
(defun make-distance-matrix (similarity-matrix)
(let* ((n (array-dimension similarity-matrix 0))
(distance-matrix (make-array (list n n) :element-type 'double-float)))
(dotimes (i n distance-matrix)
(dotimes (j n)
(setf (aref distance-matrix i j) (- 1.0 (aref similarity-matrix i j)))))))
(defun nmf-delta (x k)
(declare (type dmat x))
(let* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n)))
(declare (type dmat u))
(declare (type dmat v))
(dotimes (p 100 (values u v))
(let* ((u^t (m^t u))
(w (m-times-n u^t u)))
(dotimes (i k)
(dotimes (j n)
(setf (aref v i j)
(* (aref v i j)
(a*b-i-j u^t x i j)
(/ (a*b-i-j w v i j)))))))
(let* ((v^t (m^t v))
(ww (m-times-n u v)))
(dotimes (i m)
(dotimes (j k)
(setf (aref u i j)
(* (aref u i j)
(a*b-i-j x v^t i j)
(/ (a*b-i-j ww v^t i j)))))))
(multiple-value-setq (u v) (normalize u v)))))
(defun m-times-n (a b)
(declare (optimize (speed 3) (debug 0) (safety 0)))
(declare (type dmat a))
(declare (type dmat b))
(assert (= (array-dimension a 1) (array-dimension b 0)))
(let* ((m (array-dimension a 0))
(n (array-dimension b 1))
(c (make-array (list m n) :element-type 'double-float)))
(declare (type dmat c))
(dotimes (i m c)
(dotimes (j n)
(setf (aref c i j) (a*b-i-j a b i j))))))
(defun rho-k (matrix k)
(let* ((avc (average-consensus-matrix matrix k))
(d (make-distance-matrix avc))
(u (cophenetic-matrix d)))
(cophenetic-cc d u)))
(defun norm-nmf (matrix k)
(multiple-value-setq (u v) (nmf-gamma matrix k))
(norm (m- matrix (m-times-n u v))))
(defun KL-nmf (x k)
(declare (type dmat x))
(let* ((m (array-dimension x 0))
(n (array-dimension x 1))
(u (make-test-matrix m k))
(v (make-test-matrix k n)))
(dotimes (p 30 (normalize u v))
(let ((uv (m-times-n u v)))
(dotimes (i m)
(dotimes (l k)
(setf (aref u i l)
(* (aref u i l)
(aux-kl-1 x uv v i l))))))
(let ((old-u (copy-matrix u)))
(dotimes (i m)
(dotimes (l k)
(setf (aref u i l)
(* (aref u i l)
(/ (vector-sum (pick-up-column old-u l))))))))
(let ((uv (m-times-n u v)))
(dotimes (l k)
(dotimes (j n)
(setf (aref v l j)
(* (aref v l j)
(aux-kl-2 x uv u l j)))))))))
(defun aux-kl-1 (x uv v i l)
(declare (optimize (speed 3) (debug 0) (safety 0)))
(declare (type dmat x))
(declare (type dmat uv))
(declare (type dmat v))
(let* ((n (array-dimension x 1))
(a (make-array n :element-type 'double-float)))
(declare (type dvec a))
(dotimes (j n (vector-sum a))
(setf (aref a j)
(* (aref x i j)
(/ (aref uv i j))
(aref v l j))))))
(defun aux-kl-2 (x uv u l j)
(declare (optimize (speed 3) (debug 0) (safety 0)))
(declare (type dmat x))
(declare (type dmat uv))
(declare (type dmat u))
(let* ((m (array-dimension x 0))
(b (make-array m :element-type 'double-float)))
(declare (type dvec b))
(dotimes (i m (vector-sum b))
(setf (aref b i)
(* (aref x i j)
(/ (aref uv i j))
(aref u i l))))))
(defun copy-matrix (matrix)
(declare (type dmat matrix))
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(w (make-array (list m n) :element-type 'double-float)))
(dotimes (i m w)
(dotimes (j n)
(setf (aref w i j) (aref matrix i j))))))
(defun partition-matrix (matrix word-clustering-vector)
(declare (type dmat matrix))
(declare (type (SIMPLE-ARRAY T (*)) word-clustering-vector))
(let* ((m (array-dimension matrix 0))
;(n (array-dimension matrix 1))
(p (number-of-n word-clustering-vector 0))
(q (number-of-n word-clustering-vector 1))
(a (make-array (list m p) :element-type 'double-float))
(b (make-array (list m q) :element-type 'double-float)))
(dotimes (i m)
(dotimes (j p)
(setf (aref a i j)
(aref (jth-n-column matrix word-clustering-vector j 0) i))))
(dotimes (i m (values a b))
(dotimes (j q)
(setf (aref b i j)
(aref (jth-n-column matrix word-clustering-vector j 1) i))))))
(defun number-of-n (clustering-vector n)
(declare (type (SIMPLE-ARRAY T (*)) clustering-vector))
(let ((sum 0))
(dotimes (i (length clustering-vector) sum)
(when (= (svref clustering-vector i) n)
(setf sum (+ 1 sum))))))
(defun correspond-column-number (word-clustering-vector j p)
(declare (type (SIMPLE-ARRAY T (*)) word-clustering-vector))
(let ((sum 0))
(do ((i 0 (+ i 1)))
((= (- sum 1) j) (- i 1))
(when (= (svref word-clustering-vector i) p)
(setf sum (+ 1 sum))))))
(defun jth-n-column (matrix word-clustering-vector j n)
(pick-up-column matrix (correspond-column-number word-clustering-vector j n)))
(defun with-index (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(matrix-with-index (make-array
(list (+ m 1) (+ n 1))
:element-type 'double-float)))
(setf (aref matrix-with-index 0 0) -1.0d0)
(dotimes (j n)
(setf (aref matrix-with-index 0 (+ j 1)) (coerce j 'double-float)))
(dotimes (i m)
(setf (aref matrix-with-index (+ i 1) 0) (coerce i 'double-float)))
(dotimes (i m matrix-with-index)
(dotimes (j n)
(setf (aref matrix-with-index (+ i 1) (+ j 1))
(aref matrix i j))))))
(defun without-index (matrix-with-index)
(let* ((m (- (array-dimension matrix-with-index 0) 1))
(n (- (array-dimension matrix-with-index 1) 1))
(matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m matrix)
(dotimes (j n)
(setf (aref matrix i j) (aref matrix-with-index (+ i 1) (+ j 1)))))))
(defun make-new-words-vector (words-vector word-clustering-vector p)
(let* ((n (number-of-n word-clustering-vector p))
(new-words-vector (make-array n)))
(dotimes (i n new-words-vector)
(setf (aref new-words-vector i)
(aref words-vector (correspond-column-number word-clustering-vector i p))))))
(defun hierarchical-nmf-analysis (matrix words-vector)
(progn
(time (multiple-value-setq (weight feature) (nmf-gamma matrix 2)))
(setf new-words-vector (make-new-words-vector words-vector (word-clustering-vector feature) 0))
(multiple-value-setq (m0 m1) (partition-matrix matrix (word-clustering-vector feature)))
(result-words feature words-vector)
(values (array-dimension m0 1) (array-dimension m1 1))))
(defun enhanced-matrix0 (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(new-matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m new-matrix)
(dotimes (j n)
(setf (aref new-matrix i j)
(expt (aref matrix i j) 2))))))
(defun enhanced-matrix1 (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(new-matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m new-matrix)
(dotimes (j n)
(if (= (aref matrix i j) 0.0d0)
(setf (aref new-matrix i j) 0.01d0)
(setf (aref new-matrix i j)
(expt (aref matrix i j) 2)))))))
(defun enhanced-matrix (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(new-matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m new-matrix)
(dotimes (j n)
(if (= (aref matrix i j) 0.0d0)
(setf (aref new-matrix i j) 0.01d0)
(setf (aref new-matrix i j) (aref matrix i j)))))))
(defun dfreq (matrix word-id)
(assert (<= 0 word-id (- (array-dimension matrix 1) 1)))
(let ((v (pick-up-column matrix word-id)))
(number-of-non-zero-elements v)))
(defun number-of-non-zero-elements (vector)
(let ((n (length vector))
(sum 0))
(dotimes (i n sum)
(setf sum (if (zerop (aref vector i))
(+ sum 0)
(+ sum 1))))))
(defun tf*idf (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(new-matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m new-matrix)
(dotimes (j n)
(setf (aref new-matrix i j)
(* (aref matrix i j)
(log (/ m (dfreq matrix j)))))))))
(defun normalized-tf*idf (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(new-matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m new-matrix)
(dotimes (j n)
(setf (aref new-matrix i j)
(* (tf2 matrix i j)
(log (/ m (dfreq matrix j)))))))))
(defun tf (matrix i j)
(let ((v (pick-up-row matrix i)))
(/ (log (+ 1.0 (aref matrix i j)))
(log (vector-sum v)))))
(defun tf2 (matrix i j)
(let ((v (pick-up-row matrix i)))
(/ (log (+ 1.0 (aref matrix i j)))
(log (number-of-non-zero-elements v)))))
(defun word-weighting (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(new-matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m new-matrix)
(dotimes (j n)
(setf (aref new-matrix i j)
(* (local-weight matrix i j)
(global-weight matrix j)))))))
(defun local-weight (matrix i j)
(if (zerop (aref matrix i j))
0
(+ 1.0 (sqrt (- (aref matrix i j) 0.5)))))
(defun global-weight (matrix j)
(sqrt (- (/ (vector-sum (pick-up-column matrix j))
(number-of-non-zero-elements (pick-up-column matrix j)))
0.90)))
(defun normalization (matrix)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(new-matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m new-matrix)
(dotimes (j n)
(setf (aref new-matrix i j)
(* (aref matrix i j)
(normalization-factor matrix i)))))))
(defun normalization-factor (matrix i)
(let ((n (array-dimension matrix 1))
(sum 0.0))
(dotimes (j n (/ (sqrt sum)))
(setf sum (+ sum (expt (aref matrix i j) 2))))))
(defun scale-transformation (matrix scale)
(let* ((m (array-dimension matrix 0))
(n (array-dimension matrix 1))
(new-matrix (make-array (list m n) :element-type 'double-float)))
(dotimes (i m new-matrix)
(dotimes (j n)
(setf (aref new-matrix i j)
(* (aref matrix i j)
(expt 10 scale)))))))
(defun +phi (matrix i j)
(/ (non-zero (aref matrix i j))
(number-of-non-zero-elements (pick-up-row matrix i))))
(defun -phi (matrix i j)
(/ (non-zero (aref matrix i j))
(number-of-non-zero-elements (pick-up-column matrix j))))
(defun delta (matrix i h)
(let ((n (array-dimension matrix 1))
(sum 0.0))
(dotimes (j n sum)
(setf sum (+ sum
(* (+phi matrix i j)
(-phi matrix h j)))))))
(defun cluster-number (matrix)
(let ((m (array-dimension matrix 0))
(sum 0.0))
(dotimes (i m sum)
(setf sum (+ sum (delta matrix i i))))))