feat: adds KMeans clustering algorithm

smartcore.iml

@@ -1,8 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<module type="WEB_MODULE" version="4">
+<module type="RUST_MODULE" version="4">
   <component name="NewModuleRootManager" inherit-compiler-output="true">
     <exclude-output />
-    <content url="file://$MODULE_DIR$" />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/examples" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/tests" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/benches" isTestSource="true" />
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
     <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>

src/algorithm/neighbour/bbd_tree.rs

@@ -0,0 +1,345 @@
+use std::collections::LinkedList;
+
+use crate::linalg::Matrix;
+
+#[derive(Debug)]
+pub struct BBDTree {    
+    nodes: Vec<BBDTreeNode>,
+    index: Vec<usize>,
+    root: usize
+}
+
+#[derive(Debug)]
+struct BBDTreeNode {    
+    count: usize,
+    index: usize,
+    center: Vec<f64>,
+    radius: Vec<f64>,
+    sum: Vec<f64>,
+    cost: f64,
+    lower: Option<usize>,
+    upper: Option<usize>
+}
+
+impl BBDTreeNode {
+    fn new(d: usize) -> BBDTreeNode {
+        BBDTreeNode {
+            count: 0,
+            index: 0,
+            center: vec![0f64; d],
+            radius: vec![0f64; d],
+            sum: vec![0f64; d],
+            cost: 0f64,
+            lower: Option::None,
+            upper: Option::None
+        }
+    }
+}
+
+impl BBDTree {
+    pub fn new<M: Matrix>(data: &M) -> BBDTree {
+        let nodes = Vec::new();
+
+        let (n, _) = data.shape();
+
+        let mut index = vec![0; n];
+        for i in 0..n {
+            index[i] = i;
+        }
+
+        let mut tree = BBDTree{
+            nodes: nodes,
+            index: index,
+            root: 0
+        };
+
+        let root = tree.build_node(data, 0, n);
+
+        tree.root = root;
+
+        tree
+    }    
+
+    pub(in crate) fn clustering(&self, centroids: &Vec<Vec<f64>>, sums: &mut Vec<Vec<f64>>, counts: &mut Vec<usize>, membership: &mut Vec<usize>) -> f64 {
+        let k = centroids.len();
+
+        counts.iter_mut().for_each(|x| *x = 0);
+        let mut candidates = vec![0; k];
+        for i in 0..k {
+            candidates[i] = i;
+            sums[i].iter_mut().for_each(|x| *x = 0f64);            
+        }
+                
+        self.filter(self.root, centroids, &candidates, k, sums, counts, membership)
+    }
+
+    fn filter(&self, node: usize, centroids: &Vec<Vec<f64>>, candidates: &Vec<usize>, k: usize, sums: &mut Vec<Vec<f64>>, counts: &mut Vec<usize>, membership: &mut Vec<usize>) -> f64{
+        let d = centroids[0].len();
+
+        // Determine which mean the node mean is closest to
+        let mut min_dist = BBDTree::squared_distance(&self.nodes[node].center, &centroids[candidates[0]]);
+        let mut closest = candidates[0];
+        for i in 1..k {
+            let dist = BBDTree::squared_distance(&self.nodes[node].center, &centroids[candidates[i]]);
+            if dist < min_dist {
+                min_dist = dist;
+                closest = candidates[i];
+            }
+        }
+
+        // If this is a non-leaf node, recurse if necessary
+        if !self.nodes[node].lower.is_none() {
+            // Build the new list of candidates
+            let mut new_candidates = vec![0;k];
+            let mut newk = 0;
+
+            for i in 0..k {
+                if !BBDTree::prune(&self.nodes[node].center, &self.nodes[node].radius, &centroids, closest, candidates[i]) {
+                    new_candidates[newk] = candidates[i];
+                    newk += 1;
+                }
+            }
+
+            // Recurse if there's at least two
+            if newk > 1 {
+                let result = self.filter(self.nodes[node].lower.unwrap(), centroids, &mut new_candidates, newk, sums, counts, membership) + 
+                            self.filter(self.nodes[node].upper.unwrap(), centroids, &mut new_candidates, newk, sums, counts, membership);
+                return result;
+            }
+        }
+
+        // Assigns all data within this node to a single mean
+        for i in 0..d {
+            sums[closest][i] += self.nodes[node].sum[i];
+        }
+
+        counts[closest] += self.nodes[node].count;
+        
+        let last = self.nodes[node].index + self.nodes[node].count;
+        for i in self.nodes[node].index..last {
+            membership[self.index[i]] = closest;
+        }        
+
+        BBDTree::node_cost(&self.nodes[node], &centroids[closest])
+        
+    }
+
+    fn prune(center: &Vec<f64>, radius: &Vec<f64>, centroids: &Vec<Vec<f64>>, best_index: usize, test_index: usize) -> bool {
+        if best_index == test_index {
+            return false;
+        }
+
+        let d = centroids[0].len();
+
+        let best = &centroids[best_index];
+        let test = &centroids[test_index];
+        let mut lhs = 0f64;
+        let mut rhs = 0f64;
+        for i in 0..d {
+            let diff = test[i] - best[i];
+            lhs += diff * diff;
+            if diff > 0f64 {
+                rhs += (center[i] + radius[i] - best[i]) * diff;
+            } else {
+                rhs += (center[i] - radius[i] - best[i]) * diff;
+            }
+        }
+
+        return lhs >= 2f64 * rhs;
+    }
+
+    fn squared_distance(x: &Vec<f64>,y: &Vec<f64>) -> f64 {
+        if x.len() != y.len() {
+            panic!("Input vector sizes are different.");
+        }
+
+        let mut sum = 0f64;
+        for i in 0..x.len() {
+            sum += (x[i] - y[i]).powf(2.);
+        }
+
+        return sum;
+    }
+
+    fn build_node<M: Matrix>(&mut self, data: &M, begin: usize, end: usize) -> usize {
+        let (_, d) = data.shape();
+
+        // Allocate the node
+        let mut node = BBDTreeNode::new(d);
+
+        // Fill in basic info
+        node.count = end - begin;
+        node.index = begin;
+
+        // Calculate the bounding box
+        let mut lower_bound = vec![0f64; d];
+        let mut upper_bound = vec![0f64; d];
+
+        for i in 0..d {
+            lower_bound[i] = data.get(self.index[begin],i);
+            upper_bound[i] = data.get(self.index[begin],i);
+        }
+
+        for i in begin..end {
+            for j in 0..d {
+                let c = data.get(self.index[i], j);
+                if lower_bound[j] > c {
+                    lower_bound[j] = c;
+                }
+                if upper_bound[j] < c {
+                    upper_bound[j] = c;
+                }
+            }
+        }
+
+        // Calculate bounding box stats
+        let mut max_radius = -1.;
+        let mut split_index = 0;
+        for i in 0..d {
+            node.center[i] = (lower_bound[i] + upper_bound[i]) / 2.;
+            node.radius[i] = (upper_bound[i] - lower_bound[i]) / 2.;
+            if node.radius[i] > max_radius {
+                max_radius = node.radius[i];
+                split_index = i;
+            }
+        }
+
+        // If the max spread is 0, make this a leaf node
+        if max_radius < 1E-10 {
+            node.lower = Option::None;
+            node.upper = Option::None;
+            for i in 0..d {
+                node.sum[i] = data.get(self.index[begin], i);
+            }
+            
+            if end > begin + 1 {
+                let len = end - begin;
+                for i in 0..d {
+                    node.sum[i] *= len as f64;
+                }
+            }
+
+            node.cost = 0f64;
+            return self.add_node(node);
+        }
+
+        // Partition the data around the midpoint in this dimension. The
+        // partitioning is done in-place by iterating from left-to-right and
+        // right-to-left in the same way that partioning is done in quicksort.
+        let split_cutoff = node.center[split_index];
+        let mut i1 = begin;
+        let mut i2 = end - 1;
+        let mut size = 0;
+        while i1 <= i2 {
+            let mut i1_good = data.get(self.index[i1], split_index) < split_cutoff;
+            let mut i2_good = data.get(self.index[i2], split_index) >= split_cutoff;
+
+            if !i1_good && !i2_good {
+                let temp = self.index[i1];
+                self.index[i1] = self.index[i2];
+                self.index[i2] = temp;
+                i1_good = true;
+                i2_good = true;
+            }
+
+            if i1_good {
+                i1 += 1;
+                size += 1;
+            }
+
+            if i2_good {
+                i2 -= 1;
+            }
+        }
+
+        // Create the child nodes
+        node.lower = Option::Some(self.build_node(data, begin, begin + size));
+        node.upper = Option::Some(self.build_node(data, begin + size, end));
+
+        // Calculate the new sum and opt cost
+        for i in 0..d {
+            node.sum[i] = self.nodes[node.lower.unwrap()].sum[i] + self.nodes[node.upper.unwrap()].sum[i];
+        }
+
+        let mut mean = vec![0f64; d];
+        for i in 0..d {
+            mean[i] = node.sum[i] / node.count as f64;
+        }
+
+        node.cost = BBDTree::node_cost(&self.nodes[node.lower.unwrap()], &mean) + BBDTree::node_cost(&self.nodes[node.upper.unwrap()], &mean);
+
+        self.add_node(node)
+    }
+
+    fn node_cost(node: &BBDTreeNode, center: &Vec<f64>) -> f64 {
+        let d = center.len();
+        let mut scatter = 0f64;
+        for i in 0..d {
+            let x = (node.sum[i] / node.count as f64) - center[i];
+            scatter += x * x;
+        }
+        node.cost + node.count as f64 * scatter
+    }
+
+    fn add_node(&mut self, new_node: BBDTreeNode) -> usize{
+        let idx = self.nodes.len();
+        self.nodes.push(new_node);
+        idx
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*; 
+    use crate::linalg::naive::dense_matrix::DenseMatrix;    
+
+    #[test]
+    fn fit_predict_iris() {             
+
+        let data = DenseMatrix::from_array(&[
+            &[5.1, 3.5, 1.4, 0.2],
+            &[4.9, 3.0, 1.4, 0.2],
+            &[4.7, 3.2, 1.3, 0.2],
+            &[4.6, 3.1, 1.5, 0.2],
+            &[5.0, 3.6, 1.4, 0.2],
+            &[5.4, 3.9, 1.7, 0.4],
+            &[4.6, 3.4, 1.4, 0.3],
+            &[5.0, 3.4, 1.5, 0.2],
+            &[4.4, 2.9, 1.4, 0.2],
+            &[4.9, 3.1, 1.5, 0.1],
+            &[7.0, 3.2, 4.7, 1.4],
+            &[6.4, 3.2, 4.5, 1.5],
+            &[6.9, 3.1, 4.9, 1.5],
+            &[5.5, 2.3, 4.0, 1.3],
+            &[6.5, 2.8, 4.6, 1.5],
+            &[5.7, 2.8, 4.5, 1.3],
+            &[6.3, 3.3, 4.7, 1.6],
+            &[4.9, 2.4, 3.3, 1.0],
+            &[6.6, 2.9, 4.6, 1.3],
+            &[5.2, 2.7, 3.9, 1.4]]);        
+
+        let tree = BBDTree::new(&data);        
+
+        let centroids = vec![
+            vec![4.86, 3.22, 1.61, 0.29],
+            vec![6.23, 2.92, 4.48, 1.42]
+        ];
+
+        let mut sums = vec![
+            vec![0f64; 4],
+            vec![0f64; 4]
+        ];
+
+        let mut counts = vec![11, 9];
+
+        let mut membership = vec![0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1];
+
+        let dist = tree.clustering(&centroids, &mut sums, &mut counts, &mut membership);        
+        assert!((dist - 10.68).abs() < 1e-2);
+        assert!((sums[0][0] - 48.6).abs() < 1e-2);
+        assert!((sums[1][3] - 13.8).abs() < 1e-2);
+        assert_eq!(membership[17], 1);        
+            
+    }
+
+}

src/algorithm/neighbour/mod.rs

@@ -1,5 +1,6 @@
 pub mod cover_tree;
 pub mod linear_search;
+pub mod bbd_tree;
 
 pub enum KNNAlgorithmName {
     CoverTree,

src/classification/decision_tree.rs

@@ -412,7 +412,7 @@ mod tests {
     #[test]
     fn fit_predict_iris() {             
 
-        let x = DenseMatrix::from_2d_array(&[
+        let x = DenseMatrix::from_array(&[
             &[5.1, 3.5, 1.4, 0.2],
             &[4.9, 3.0, 1.4, 0.2],
             &[4.7, 3.2, 1.3, 0.2],
@@ -444,7 +444,7 @@ mod tests {
     #[test]
     fn fit_predict_baloons() {             
 
-        let x = DenseMatrix::from_2d_array(&[
+        let x = DenseMatrix::from_array(&[
             &[1.,1.,1.,0.],
             &[1.,1.,1.,0.],
             &[1.,1.,1.,1.],

src/classification/logistic_regression.rs

@@ -192,19 +192,26 @@ impl<M: Matrix> LogisticRegression<M> {
     }
 
     pub fn predict(&self, x: &M) -> M::RowVector {
+        let n = x.shape().0;
+        let mut result = M::zeros(1, n);
         if self.num_classes == 2 {            
             let (nrows, _) = x.shape();
             let x_and_bias = x.v_stack(&M::ones(nrows, 1));
             let y_hat: Vec<f64> = x_and_bias.dot(&self.weights.transpose()).to_raw_vector();
-            M::from_vec(1, nrows, y_hat.iter().map(|y_hat| self.classes[if y_hat.sigmoid() > 0.5 { 1 } else { 0 }]).collect()).to_row_vector()         
+            for i in 0..n {
+                result.set(0, i, self.classes[if y_hat[i].sigmoid() > 0.5 { 1 } else { 0 }]);
+            }            
 
         } else {
             let (nrows, _) = x.shape();
             let x_and_bias = x.v_stack(&M::ones(nrows, 1));        
             let y_hat = x_and_bias.dot(&self.weights.transpose());            
             let class_idxs = y_hat.argmax();
-            M::from_vec(1, nrows, class_idxs.iter().map(|class_idx| self.classes[*class_idx]).collect()).to_row_vector()
+            for i in 0..n {
+                result.set(0, i, self.classes[class_idxs[i]]);
+            }            
         }
+        result.to_row_vector()
     }
 
     pub fn coefficients(&self) -> M {
@@ -242,7 +249,7 @@ mod tests {
     #[test]
     fn multiclass_objective_f() { 
 
-        let x = DenseMatrix::from_2d_array(&[
+        let x = DenseMatrix::from_array(&[
             &[1., -5.],
             &[ 2.,  5.],
             &[ 3., -2.],
@@ -282,7 +289,7 @@ mod tests {
     #[test]
     fn binary_objective_f() { 
 
-        let x = DenseMatrix::from_2d_array(&[
+        let x = DenseMatrix::from_array(&[
             &[1., -5.],
             &[ 2.,  5.],
             &[ 3., -2.],
@@ -323,7 +330,7 @@ mod tests {
     #[test]
     fn lr_fit_predict() {             
 
-        let x = DenseMatrix::from_2d_array(&[
+        let x = DenseMatrix::from_array(&[
             &[1., -5.],
             &[ 2.,  5.],
             &[ 3., -2.],

src/classification/random_forest.rs

@@ -128,7 +128,7 @@ mod tests {
     #[test]
     fn fit_predict_iris() {             
 
-        let x = DenseMatrix::from_2d_array(&[
+        let x = DenseMatrix::from_array(&[
             &[5.1, 3.5, 1.4, 0.2],
             &[4.9, 3.0, 1.4, 0.2],
             &[4.7, 3.2, 1.3, 0.2],

src/cluster/kmeans.rs

@@ -0,0 +1,220 @@
+extern crate rand;
+
+use rand::Rng;
+
+use crate::linalg::Matrix;
+use crate::algorithm::neighbour::bbd_tree::BBDTree;
+
+#[derive(Debug)]
+pub struct KMeans {    
+    k: usize,
+    y: Vec<usize>,
+    size: Vec<usize>,
+    distortion: f64,
+    centroids: Vec<Vec<f64>>
+}
+
+#[derive(Debug, Clone)]
+pub struct KMeansParameters {  
+    pub max_iter: usize
+}
+
+impl Default for KMeansParameters {
+    fn default() -> Self { 
+        KMeansParameters {
+            max_iter: 100
+        }
+     }
+}
+
+impl KMeans{
+    pub fn new<M: Matrix>(data: &M, k: usize, parameters: KMeansParameters) -> KMeans {
+
+        let bbd = BBDTree::new(data);
+
+        if k < 2 {
+            panic!("Invalid number of clusters: {}", k);
+        }
+
+        if parameters.max_iter <= 0 {
+            panic!("Invalid maximum number of iterations: {}", parameters.max_iter);
+        }
+
+        let (n, d) = data.shape();
+                
+        let mut distortion = std::f64::MAX;
+        let mut y = KMeans::kmeans_plus_plus(data, k);
+        let mut size = vec![0; k];
+        let mut centroids = vec![vec![0f64; d]; k];
+
+        for i in 0..n {
+            size[y[i]] += 1;
+        }
+
+        for i in 0..n {
+            for j in 0..d {
+                centroids[y[i]][j] += data.get(i, j);
+            }
+        }
+
+        for i in 0..k {
+            for j in 0..d {
+                centroids[i][j] /= size[i] as f64;
+            }
+        }        
+
+        let mut sums = vec![vec![0f64; d]; k];
+        for _ in 1..= parameters.max_iter {
+            let dist = bbd.clustering(&centroids, &mut sums, &mut size, &mut y);
+            for i in 0..k {
+                if size[i] > 0 {
+                    for j in 0..d {
+                        centroids[i][j] = sums[i][j] as f64 / size[i] as f64;
+                    }
+                }
+            }
+
+            if distortion <= dist {
+                break;
+            } else {
+                distortion = dist;
+            }
+            
+        }        
+
+        KMeans{
+            k: k,
+            y: y,
+            size: size,
+            distortion: distortion,
+            centroids: centroids
+        }
+    }
+
+    pub fn predict<M: Matrix>(&self, x: &M) -> M::RowVector {
+        let (n, _) = x.shape();        
+        let mut result = M::zeros(1, n); 
+
+        for i in 0..n {
+
+            let mut min_dist = std::f64::MAX;
+            let mut best_cluster = 0;
+
+            for j in 0..self.k {
+                let dist = KMeans::squared_distance(&x.get_row_as_vec(i), &self.centroids[j]);                
+                if dist < min_dist {
+                    min_dist = dist;
+                    best_cluster = j;
+                }
+            }            
+            result.set(0, i, best_cluster as f64);
+        }
+
+        result.to_row_vector()
+    }
+
+    fn kmeans_plus_plus<M: Matrix>(data: &M, k: usize) -> Vec<usize>{
+        let mut rng = rand::thread_rng();        
+        let (n, _) = data.shape();
+        let mut y = vec![0; n];
+        let mut centroid = data.get_row_as_vec(rng.gen_range(0, n));
+
+        let mut d = vec![std::f64::MAX; n];
+        
+        // pick the next center
+        for j in 1..k {
+            // Loop over the samples and compare them to the most recent center.  Store
+            // the distance from each sample to its closest center in scores.
+            for i in 0..n {
+                // compute the distance between this sample and the current center
+                let dist = KMeans::squared_distance(&data.get_row_as_vec(i), &centroid);
+                
+                if dist < d[i] {
+                    d[i] = dist;
+                    y[i] = j - 1;
+                }
+            }
+
+            let sum: f64 = d.iter().sum();
+            let cutoff = rng.gen::<f64>() * sum;
+            let mut cost = 0f64;
+            let index = 0;
+            for index in 0..n {
+                cost += d[index];
+                if cost >= cutoff {
+                    break;
+                }
+            }
+
+            centroid = data.get_row_as_vec(index);
+        }
+
+        for i in 0..n {
+            // compute the distance between this sample and the current center
+            let dist = KMeans::squared_distance(&data.get_row_as_vec(i), &centroid);            
+            
+            if dist < d[i] {
+                d[i] = dist;
+                y[i] = k - 1;
+            }
+        }
+
+        y
+    }
+
+    fn squared_distance(x: &Vec<f64>,y: &Vec<f64>) -> f64 {
+        if x.len() != y.len() {
+            panic!("Input vector sizes are different.");
+        }
+
+        let mut sum = 0f64;
+        for i in 0..x.len() {
+            sum += (x[i] - y[i]).powf(2.);
+        }
+
+        return sum;
+    }
+    
+}
+
+
+#[cfg(test)]
+mod tests {
+    use super::*; 
+    use crate::linalg::naive::dense_matrix::DenseMatrix;
+
+    #[test]
+    fn fit_predict_iris() {  
+        let x = DenseMatrix::from_array(&[
+            &[5.1, 3.5, 1.4, 0.2],
+            &[4.9, 3.0, 1.4, 0.2],
+            &[4.7, 3.2, 1.3, 0.2],
+            &[4.6, 3.1, 1.5, 0.2],
+            &[5.0, 3.6, 1.4, 0.2],
+            &[5.4, 3.9, 1.7, 0.4],
+            &[4.6, 3.4, 1.4, 0.3],
+            &[5.0, 3.4, 1.5, 0.2],
+            &[4.4, 2.9, 1.4, 0.2],
+            &[4.9, 3.1, 1.5, 0.1],
+            &[7.0, 3.2, 4.7, 1.4],
+            &[6.4, 3.2, 4.5, 1.5],
+            &[6.9, 3.1, 4.9, 1.5],
+            &[5.5, 2.3, 4.0, 1.3],
+            &[6.5, 2.8, 4.6, 1.5],
+            &[5.7, 2.8, 4.5, 1.3],
+            &[6.3, 3.3, 4.7, 1.6],
+            &[4.9, 2.4, 3.3, 1.0],
+            &[6.6, 2.9, 4.6, 1.3],
+            &[5.2, 2.7, 3.9, 1.4]]);                
+
+        let kmeans = KMeans::new(&x, 2, Default::default());
+
+        let y = kmeans.predict(&x);
+
+        for i in 0..y.len() {
+            assert_eq!(y[i] as usize, kmeans.y[i]);
+        }        
+        
+    }
+    
+}

src/cluster/mod.rs

@@ -0,0 +1 @@
+pub mod kmeans;

src/lib.rs

@@ -1,5 +1,6 @@
 pub mod classification;
 pub mod regression;
+pub mod cluster;
 pub mod linalg;
 pub mod math;
 pub mod error;

src/linalg/mod.rs

@@ -12,10 +12,6 @@ pub trait Matrix: Clone + Debug {
 
     fn to_row_vector(self) -> Self::RowVector;
 
-    fn from_array(nrows: usize, ncols: usize, values: &[f64]) -> Self;
-    
-    fn from_vec(nrows: usize, ncols: usize, values: Vec<f64>) -> Self;
-
     fn get(&self, row: usize, col: usize) -> f64; 
 
     fn get_row_as_vec(&self, row: usize) -> Vec<f64>;

src/linalg/naive/dense_matrix.rs

@@ -14,11 +14,19 @@ pub struct DenseMatrix {
 
 impl DenseMatrix {  
     
-    pub fn from_2d_array(values: &[&[f64]]) -> DenseMatrix {
+    fn new(nrows: usize, ncols: usize, values: Vec<f64>) -> DenseMatrix {
-        DenseMatrix::from_2d_vec(&values.into_iter().map(|row| Vec::from(*row)).collect())
+        DenseMatrix {
+            ncols: ncols,
+            nrows: nrows,
+            values: values
+        }
     } 
 
-    pub fn from_2d_vec(values: &Vec<Vec<f64>>) -> DenseMatrix {
+    pub fn from_array(values: &[&[f64]]) -> DenseMatrix {
+        DenseMatrix::from_vec(&values.into_iter().map(|row| Vec::from(*row)).collect())
+    }
+
+    pub fn from_vec(values: &Vec<Vec<f64>>) -> DenseMatrix {
         let nrows = values.len();
         let ncols = values.first().unwrap_or_else(|| panic!("Cannot create 2d matrix from an empty vector")).len();
         let mut m = DenseMatrix {
@@ -112,25 +120,13 @@ impl Matrix for DenseMatrix {
     type RowVector = Vec<f64>;
 
     fn from_row_vector(vec: Self::RowVector) -> Self{
-        DenseMatrix::from_vec(1, vec.len(), vec)
+        DenseMatrix::new(1, vec.len(), vec)
     }
 
     fn to_row_vector(self) -> Self::RowVector{
         self.to_raw_vector()
     }     
 
-    fn from_array(nrows: usize, ncols: usize, values: &[f64]) -> DenseMatrix {
-        DenseMatrix::from_vec(nrows, ncols, Vec::from(values)) 
-    }
- 
-    fn from_vec(nrows: usize, ncols: usize, values: Vec<f64>) -> DenseMatrix {
-        DenseMatrix {
-            ncols: ncols,
-            nrows: nrows,
-            values: values
-        }
-    }  
-
     fn get(&self, row: usize, col: usize) -> f64 {
         self.values[col*self.nrows + row]
     }
@@ -255,7 +251,7 @@ impl Matrix for DenseMatrix {
         let ncols = cols.len();
         let nrows = rows.len();
 
-        let mut m = DenseMatrix::from_vec(nrows, ncols, vec![0f64; nrows * ncols]);
+        let mut m = DenseMatrix::new(nrows, ncols, vec![0f64; nrows * ncols]);
 
         for r in rows.start..rows.end {
             for c in cols.start..cols.end {
@@ -731,7 +727,7 @@ impl Matrix for DenseMatrix {
     }
 
     fn fill(nrows: usize, ncols: usize, value: f64) -> Self {
-        DenseMatrix::from_vec(nrows, ncols, vec![value; ncols * nrows])
+        DenseMatrix::new(nrows, ncols, vec![value; ncols * nrows])
     }
 
     fn add_mut(&mut self, other: &Self) -> &Self {
@@ -998,7 +994,7 @@ mod tests {
     fn from_to_row_vec() { 
 
         let vec = vec![ 1.,  2.,  3.];
-        assert_eq!(DenseMatrix::from_row_vector(vec.clone()), DenseMatrix::from_vec(1, 3, vec![1., 2., 3.]));
+        assert_eq!(DenseMatrix::from_row_vector(vec.clone()), DenseMatrix::new(1, 3, vec![1., 2., 3.]));
         assert_eq!(DenseMatrix::from_row_vector(vec.clone()).to_row_vector(), vec![1., 2., 3.]);
 
     }
@@ -1006,9 +1002,9 @@ mod tests {
     #[test]
     fn qr_solve_mut() { 
 
-            let mut a = DenseMatrix::from_2d_array(&[&[0.9, 0.4, 0.7], &[0.4, 0.5, 0.3], &[0.7, 0.3, 0.8]]);
+            let mut a = DenseMatrix::from_array(&[&[0.9, 0.4, 0.7], &[0.4, 0.5, 0.3], &[0.7, 0.3, 0.8]]);
-            let b = DenseMatrix::from_2d_array(&[&[0.5, 0.2],&[0.5, 0.8], &[0.5, 0.3]]);
+            let b = DenseMatrix::from_array(&[&[0.5, 0.2],&[0.5, 0.8], &[0.5, 0.3]]);
-            let expected_w = DenseMatrix::from_array(3, 2, &[-0.20, 0.87, 0.47, -1.28, 2.22, 0.66]);
+            let expected_w = DenseMatrix::new(3, 2, vec![-0.20, 0.87, 0.47, -1.28, 2.22, 0.66]);
             let w = a.qr_solve_mut(b);   
             assert!(w.approximate_eq(&expected_w, 1e-2));
     }
@@ -1016,9 +1012,9 @@ mod tests {
     #[test]
     fn svd_solve_mut() { 
 
-            let mut a = DenseMatrix::from_2d_array(&[&[0.9, 0.4, 0.7], &[0.4, 0.5, 0.3], &[0.7, 0.3, 0.8]]);
+            let mut a = DenseMatrix::from_array(&[&[0.9, 0.4, 0.7], &[0.4, 0.5, 0.3], &[0.7, 0.3, 0.8]]);
-            let b = DenseMatrix::from_2d_array(&[&[0.5, 0.2],&[0.5, 0.8], &[0.5, 0.3]]);
+            let b = DenseMatrix::from_array(&[&[0.5, 0.2],&[0.5, 0.8], &[0.5, 0.3]]);
-            let expected_w = DenseMatrix::from_array(3, 2, &[-0.20, 0.87, 0.47, -1.28, 2.22, 0.66]);
+            let expected_w = DenseMatrix::new(3, 2, vec![-0.20, 0.87, 0.47, -1.28, 2.22, 0.66]);
             let w = a.svd_solve_mut(b);  
             assert!(w.approximate_eq(&expected_w, 1e-2));            
     }
@@ -1026,16 +1022,16 @@ mod tests {
     #[test]
     fn h_stack() { 
 
-            let a = DenseMatrix::from_2d_array(
+            let a = DenseMatrix::from_array(
                 &[
                     &[1., 2., 3.],
                     &[4., 5., 6.],
                     &[7., 8., 9.]]);
-            let b = DenseMatrix::from_2d_array(
+            let b = DenseMatrix::from_array(
                 &[
                     &[1., 2., 3.],
                     &[4., 5., 6.]]);
-            let expected = DenseMatrix::from_2d_array(
+            let expected = DenseMatrix::from_array(
                 &[
                     &[1., 2., 3.], 
                     &[4., 5., 6.], 
@@ -1049,17 +1045,17 @@ mod tests {
     #[test]
     fn v_stack() { 
 
-            let a = DenseMatrix::from_2d_array(
+            let a = DenseMatrix::from_array(
                 &[
                     &[1., 2., 3.],
                     &[4., 5., 6.],
                     &[7., 8., 9.]]);
-            let b = DenseMatrix::from_2d_array(
+            let b = DenseMatrix::from_array(
                 &[
                     &[1., 2.],
                     &[3., 4.],
                     &[5., 6.]]);
-            let expected = DenseMatrix::from_2d_array(
+            let expected = DenseMatrix::from_array(
                 &[
                     &[1., 2., 3., 1., 2.], 
                     &[4., 5., 6., 3., 4.], 
@@ -1071,16 +1067,16 @@ mod tests {
     #[test]
     fn dot() { 
 
-            let a = DenseMatrix::from_2d_array(
+            let a = DenseMatrix::from_array(
                 &[
                     &[1., 2., 3.],
                     &[4., 5., 6.]]);
-            let b = DenseMatrix::from_2d_array(
+            let b = DenseMatrix::from_array(
                 &[
                     &[1., 2.],
                     &[3., 4.],
                     &[5., 6.]]);
-            let expected = DenseMatrix::from_2d_array(
+            let expected = DenseMatrix::from_array(
                 &[
                     &[22., 28.], 
                     &[49., 64.]]);
@@ -1091,12 +1087,12 @@ mod tests {
     #[test]
     fn slice() { 
 
-            let m = DenseMatrix::from_2d_array(
+            let m = DenseMatrix::from_array(
                 &[
                     &[1., 2., 3., 1., 2.], 
                     &[4., 5., 6., 3., 4.], 
                     &[7., 8., 9., 5., 6.]]);
-            let expected = DenseMatrix::from_2d_array(
+            let expected = DenseMatrix::from_array(
                 &[
                     &[2., 3.], 
                     &[5., 6.]]);
@@ -1107,15 +1103,15 @@ mod tests {
 
     #[test]
     fn approximate_eq() {             
-            let m = DenseMatrix::from_2d_array(
+            let m = DenseMatrix::from_array(
                 &[
                     &[2., 3.], 
                     &[5., 6.]]);
-            let m_eq = DenseMatrix::from_2d_array(
+            let m_eq = DenseMatrix::from_array(
                 &[
                     &[2.5, 3.0], 
                     &[5., 5.5]]);
-            let m_neq = DenseMatrix::from_2d_array(
+            let m_neq = DenseMatrix::from_array(
                 &[
                     &[3.0, 3.0], 
                     &[5., 6.5]]);            
@@ -1135,8 +1131,8 @@ mod tests {
 
     #[test]
     fn transpose() {
-        let m = DenseMatrix::from_2d_array(&[&[1.0, 3.0], &[2.0, 4.0]]);
+        let m = DenseMatrix::from_array(&[&[1.0, 3.0], &[2.0, 4.0]]);
-        let expected = DenseMatrix::from_2d_array(&[&[1.0, 2.0], &[3.0, 4.0]]);
+        let expected = DenseMatrix::from_array(&[&[1.0, 2.0], &[3.0, 4.0]]);
         let m_transposed = m.transpose();
         for c in 0..2 {
             for r in 0..2 {

src/linalg/ndarray_bindings.rs

@@ -16,14 +16,6 @@ impl Matrix for ArrayBase<OwnedRepr<f64>, Ix2>
         self.into_shape(vec_size).unwrap()
     }
 
-    fn from_array(nrows: usize, ncols: usize, values: &[f64]) -> Self {
-        Array::from_shape_vec((nrows, ncols), values.to_vec()).unwrap()     
-    }
-    
-    fn from_vec(nrows: usize, ncols: usize, values: Vec<f64>) -> Self {
-        Array::from_shape_vec((nrows, ncols), values).unwrap()     
-    }
-
     fn get(&self, row: usize, col: usize) -> f64 {
         self[[row, col]]
     }
@@ -330,19 +322,6 @@ mod tests {
 
     }
 
-    #[test]
-    fn from_array_from_vec() { 
-
-        let a1 = arr2(&[[ 1.,  2.,  3.],
-                        [4., 5., 6.]]);
-        let a2 = Array2::from_array(2, 3, &[1., 2., 3., 4., 5., 6.]);
-        let a3 = Array2::from_vec(2, 3, vec![1., 2., 3., 4., 5., 6.]);
-        
-        assert_eq!(a1, a2);
-        assert_eq!(a1, a3);        
-
-    }
-
     #[test]
     fn vstack_hstack() { 
 

src/regression/linear_regression.rs

@@ -19,14 +19,14 @@ impl<M: Matrix> LinearRegression<M> {
 
     pub fn fit(x: &M, y: &M, solver: LinearRegressionSolver) -> LinearRegression<M>{
 
+        let b = y.transpose();
         let (x_nrows, num_attributes) = x.shape();
-        let (y_nrows, _) = y.shape();
+        let (y_nrows, _) = b.shape();
 
         if x_nrows != y_nrows {
             panic!("Number of rows of X doesn't match number of rows of Y");
         }
                 
-        let b = y.clone();
         let mut a = x.v_stack(&M::ones(x_nrows, 1));
 
         let w = match solver {
@@ -52,7 +52,7 @@ impl<M: Matrix> Regression<M> for LinearRegression<M> {
         let (nrows, _) = x.shape();
         let mut y_hat = x.dot(&self.coefficients);
         y_hat.add_mut(&M::fill(nrows, 1, self.intercept));
-        y_hat
+        y_hat.transpose()
     }
 
 }
@@ -65,7 +65,7 @@ mod tests {
     #[test]
     fn ols_fit_predict() { 
 
-            let x = DenseMatrix::from_2d_array(&[
+            let x = DenseMatrix::from_array(&[
                 &[234.289, 235.6, 159.0, 107.608, 1947., 60.323],
                 &[259.426, 232.5, 145.6, 108.632, 1948., 61.122],
                 &[258.054, 368.2, 161.6, 109.773, 1949., 60.171],
@@ -82,7 +82,8 @@ mod tests {
                 &[502.601, 393.1, 251.4, 125.368, 1960., 69.564],
                 &[518.173, 480.6, 257.2, 127.852, 1961., 69.331],
                 &[554.894, 400.7, 282.7, 130.081, 1962., 70.551]]);
-            let y = DenseMatrix::from_array(16, 1, &[83.0,  88.5,  88.2,  89.5,  96.2,  98.1,  99.0, 100.0, 101.2, 104.6, 108.4, 110.8, 112.6, 114.2, 115.7, 116.9]);        
+        
+            let y = DenseMatrix::from_array(&[&[83.0,  88.5,  88.2,  89.5,  96.2,  98.1,  99.0, 100.0, 101.2, 104.6, 108.4, 110.8, 112.6, 114.2, 115.7, 116.9]]);            
 
             let y_hat_qr = LinearRegression::fit(&x, &y, LinearRegressionSolver::QR).predict(&x);