Merge f09cb23 into d5c1e9b

CHANGELOG.rst

@@ -3,6 +3,7 @@
 
 Added
 ^^^^^
+* `@senwu`_: Add sparse logistic regression support.
 * `@j-rausch`_: Added unit tests for changed lingual parsing pipeline.
 * `@senwu`_: Support Python 3.7.
 * `@lukehsiao`_: Allow user to change featurization settings by providing
@@ -16,6 +17,8 @@ Added
 
 Changed
 ^^^^^^^
+* `@senwu`_: Reorganize the disc model structure.
+  (`#126 <https://github.com/HazyResearch/fonduer/pull/126>`_)
 * `@j-rausch`_: Speed-up of ``spacy_parser``. We split the lingual parsing 
   pipeline into two stages. First, we parse structure and gather all 
   sentences for a document. Then, we merge and feed all sentences per

src/fonduer/learning/__init__.py

@@ -1,5 +1,14 @@
 from fonduer.learning.disc_models.logistic_regression import LogisticRegression
-from fonduer.learning.disc_models.rnn.lstm import LSTM
+from fonduer.learning.disc_models.lstm import LSTM
+from fonduer.learning.disc_models.sparse_logistic_regression import (
+    SparseLogisticRegression
+)
 from fonduer.learning.gen_learning import GenerativeModel, GenerativeModelAnalyzer
 
-__all__ = ["GenerativeModel", "GenerativeModelAnalyzer", "LogisticRegression", "LSTM"]
+__all__ = [
+    "GenerativeModel",
+    "GenerativeModelAnalyzer",
+    "LogisticRegression",
+    "LSTM",
+    "SparseLogisticRegression",
+]

src/fonduer/learning/disc_learning.py

@@ -151,14 +151,14 @@ def train(
             diffs = Y_train.max(axis=1) - Y_train.min(axis=1)
             train_idxs = np.where(diffs > 1e-6)[0]
 
+        self.model_kwargs = self._update_kwargs(X_train, **kwargs)
+
         _X_train, _Y_train = self._preprocess_data(
             X_train, Y_train, idxs=train_idxs, train=True
         )
         if X_dev is not None:
             _X_dev, _Y_dev = self._preprocess_data(X_dev, Y_dev)
 
-        self.model_kwargs = self._update_kwargs(_X_train, **kwargs)
-
         if "host_device" not in self.model_kwargs:
             self.model_kwargs["host_device"] = "CPU"
             self.logger.info("Using CPU...")

src/fonduer/learning/disc_models/rnn/layers.py → src/fonduer/learning/disc_models/layers/rnn.py

@@ -1,5 +1,5 @@
 """
-A recurrent neural network model.
+A recurrent neural network module.
 """
 
 import torch
@@ -66,8 +66,6 @@ def forward(self, x, x_mask, state_word):
         x      : batch_size * length
         x_mask : batch_size * length
         """
-        # print("lstm forward...")
-        # print(x.size(), x_mask.size(), state_word.size())
         x_emb = self.drop(self.lookup(x))
         output_word, state_word = self.word_lstm(x_emb, state_word)
         output_word = self.drop(output_word)

src/fonduer/learning/disc_models/layers/sparse_linear.py

@@ -0,0 +1,46 @@
+"""
+A sparse linear module.
+"""
+
+import math
+
+import torch
+import torch.nn as nn
+
+
+class SparseLinear(nn.Module):
+    def __init__(self, num_features, num_classes, bias=False, padding_idx=0):
+
+        super(SparseLinear, self).__init__()
+
+        self.num_features = num_features
+        self.num_classes = num_classes
+        self.padding_idx = padding_idx
+
+        self.weight = nn.Embedding(
+            self.num_features, self.num_classes, padding_idx=self.padding_idx
+        )
+        if bias:
+            self.bias = nn.Parameter(torch.Tensor(self.num_classes))
+        else:
+            self.bias = None
+
+        self.reset_parameters()
+
+    def reset_parameters(self):
+        stdv = 1. / math.sqrt(self.num_features)
+        self.weight.weight.data.uniform_(-stdv, stdv)
+        if self.bias is not None:
+            self.bias.data.uniform_(-stdv, stdv)
+        if self.padding_idx is not None:
+            self.weight.weight.data[self.padding_idx].fill_(0)
+
+    def forward(self, x, w):
+        """
+        x : batch_size * length, the feature indices
+        w : batch_size * length, the weight for each feature
+        """
+        if self.bias is None:
+            return (w.unsqueeze(2) * self.weight(x)).sum(dim=1)
+        else:
+            return (w.unsqueeze(2) * self.weight(x)).sum(dim=1) + self.bias

src/fonduer/learning/disc_models/logistic_regression.py

@@ -62,7 +62,7 @@ def _update_kwargs(self, X, **model_kwargs):
         :param X: The input data of the model
         :param model_kwargs: The arguments of the model
         """
-        model_kwargs["input_dim"] = X[0][1].shape[1]
+        model_kwargs["input_dim"] = X[1].shape[1]
         return model_kwargs
 
     def _build_model(self, model_kwargs):

src/fonduer/learning/disc_models/rnn/lstm.py → src/fonduer/learning/disc_models/lstm.py

@@ -4,8 +4,8 @@
 from scipy.sparse import issparse
 
 from fonduer.learning.disc_learning import NoiseAwareModel
-from fonduer.learning.disc_models.rnn.layers import RNN
-from fonduer.learning.disc_models.rnn.utils import (
+from fonduer.learning.disc_models.layers.rnn import RNN
+from fonduer.learning.disc_models.utils import (
     SymbolTable,
     mark_sentence,
     mention_to_tokens,
@@ -131,7 +131,7 @@ def _update_kwargs(self, X, **model_kwargs):
                 model_kwargs[key] = settings[key]
 
         model_kwargs["relation_arity"] = len(X[0][0])
-        model_kwargs["input_dim"] = X[0][1].shape[1] + len(X[0][0]) * model_kwargs[
+        model_kwargs["input_dim"] = X[1].shape[1] + len(X[0][0]) * model_kwargs[
             "hidden_dim"
         ] * (2 if model_kwargs["bidirectional"] else 1)
 

src/fonduer/learning/disc_models/sparse_logistic_regression.py

@@ -0,0 +1,152 @@
+import numpy as np
+import torch
+
+from fonduer.learning.disc_learning import NoiseAwareModel
+from fonduer.learning.disc_models.layers.sparse_linear import SparseLinear
+from fonduer.learning.disc_models.utils import pad_batch
+
+
+class SparseLogisticRegression(NoiseAwareModel):
+    def forward(self, x, w):
+        """
+        Run forward pass.
+
+        :param x: The input (batch) of the model
+        """
+        return self.sparse_linear(x, w)
+
+    def _check_input(self, X):
+        """
+        Check input format.
+
+        :param X: The input data of the model
+        """
+        return isinstance(X, tuple)
+
+    def _preprocess_data(self, X, Y=None, idxs=None, train=False):
+        """
+        Preprocess the data:
+        1. Convert sparse matrix to dense matrix.
+        2. Update the order of candidates based on feature index.
+        3. Select subset of the input if idxs exists.
+
+        :param X: The input data of the model
+        :param X: The labels of input data
+        """
+        C, F = X
+        print(F.shape)
+        print(max(F.indices))
+        id2id = dict()
+        for i in range(F.shape[0]):
+            id2id[F.row_index[i]] = i
+
+        C_ = [None] * len(C)
+        for c in C:
+            C_[id2id[c.id]] = c
+
+        if idxs is None:
+            if Y is not None:
+                return (
+                    [
+                        (
+                            C_[i],
+                            F.indices[F.indptr[i] : F.indptr[i + 1]],
+                            F.data[F.indptr[i] : F.indptr[i + 1]],
+                        )
+                        for i in range(len(C_))
+                    ],
+                    Y,
+                )
+            else:
+                return [
+                    (
+                        C_[i],
+                        F.indices[F.indptr[i] : F.indptr[i + 1]],
+                        F.data[F.indptr[i] : F.indptr[i + 1]],
+                    )
+                    for i in range(len(C_))
+                ]
+        if Y is not None:
+            return (
+                [
+                    (
+                        C_[i],
+                        F.indices[F.indptr[i] : F.indptr[i + 1]],
+                        F.data[F.indptr[i] : F.indptr[i + 1]],
+                    )
+                    for i in idxs
+                ],
+                Y[idxs],
+            )
+        else:
+            return [
+                (
+                    C_[i],
+                    F.indices[F.indptr[i] : F.indptr[i + 1]],
+                    F.data[F.indptr[i] : F.indptr[i + 1]],
+                )
+                for i in idxs
+            ]
+
+    def _update_kwargs(self, X, **model_kwargs):
+        """
+        Update the model argument.
+
+        :param X: The input data of the model
+        :param model_kwargs: The arguments of the model
+        """
+        # Add one feature for padding vector (all 0s)
+        model_kwargs["input_dim"] = X[1].shape[1] + 1
+        return model_kwargs
+
+    def _build_model(self, model_kwargs):
+        """
+        Build the model.
+
+        :param model_kwargs: The arguments of the model
+        """
+        if "input_dim" not in model_kwargs:
+            raise ValueError("Kwarg input_dim cannot be None.")
+
+        cardinality = self.cardinality if self.cardinality > 2 else 1
+        bias = False if "bias" not in model_kwargs else model_kwargs["bias"]
+
+        self.sparse_linear = SparseLinear(model_kwargs["input_dim"], cardinality, bias)
+
+    def _calc_logits(self, X, batch_size=None):
+        """
+        Calculate the logits.
+
+        :param X: The input data of the model
+        :param batch_size: The batch size
+        """
+        # Generate sparse multi-modal feature input
+        F = np.array(list(zip(*X))[1]) + 1  # Correct the index since 0 is the padding
+        V = np.array(list(zip(*X))[2])
+
+        outputs = (
+            torch.Tensor([]).cuda()
+            if self.model_kwargs["host_device"] in self.gpu
+            else torch.Tensor([])
+        )
+
+        n = len(F)
+        if batch_size is None:
+            batch_size = n
+        for batch_st in range(0, n, batch_size):
+            batch_ed = batch_st + batch_size if batch_st + batch_size <= n else n
+
+            features, _ = pad_batch(F[batch_st:batch_ed], 0)
+            values, _ = pad_batch(V[batch_st:batch_ed], 0, type="float")
+
+            if self.model_kwargs["host_device"] in self.gpu:
+                features = features.cuda()
+                values = values.cuda()
+
+            output = self.forward(features, values)
+            if self.cardinality == 2:
+                outputs = torch.cat((outputs, output.view(-1)), 0)
+            else:
+                outputs = torch.cat((outputs, output), 0)
+
+        return outputs

src/fonduer/learning/disc_models/rnn/utils.py → src/fonduer/learning/disc_models/utils.py

@@ -70,11 +70,17 @@ def mark_sentence(s, args):
     return x
 
 
-def pad_batch(batch, max_len):
+def pad_batch(batch, max_len=0, type="int"):
     """Pad the batch into matrix"""
     batch_size = len(batch)
-    max_sent_len = min(int(np.max([len(x) for x in batch])), max_len)
-    idx_matrix = np.zeros((batch_size, max_sent_len), dtype=np.int)
+    max_sent_len = int(np.max([len(x) for x in batch]))
+    if max_len > 0 and max_len < max_sent_len:
+        max_sent_len = max_len
+    if type == "float":
+        idx_matrix = np.zeros((batch_size, max_sent_len), dtype=np.float32)
+    else:
+        idx_matrix = np.zeros((batch_size, max_sent_len), dtype=np.int)
+
     for idx1, i in enumerate(batch):
         for idx2, j in enumerate(i):
             if idx2 >= max_sent_len: