18 skills found
Quantco / TabmatEfficient matrix representations for working with tabular data
cognitoware / RoboticsProbabilistic state estimation for robotics applications. Bayes filters include Kalman, Markov chains; Gaussian, uniform and discrete mapping probability distributions representations; Distribution sampling, marginalization, multiplication; Distribution composition independent pairs and Bayes rule; Linear algebra, matrix, vector, inverse, square root, LU decomposition, Cholesky decomposition; piecewise linear approximation of functions; Sensor models, Markov action chains <X,U,X>.
NREL-Sienna / PowerNetworkMatrices.jlMethods to generate matrix representations of power systems matrices
majeau-bettez / Ecospold2matrixClass for recasting Ecospold2 LCA dataset into Leontief matrix representations or Supply and Use Tables
zehsilva / Sparse Poisson FactorizationPoisson Matrix and Tensor Factorization with sparse input and internal representations
hellpig / SU Toolsmany powerful tools for studying irreducible representations of SU(n), including making animations of hadron flavor-state multiplets
xhweei / Hypergraph Learning Based Discriminative Band SelectionFor hyperspectral images (HSIs), it is a challenging task to select discriminative bands due to the lack of labeled samples and complex noise. In this article, we present a novel local-view-assisted discriminative band selection method with hypergraph autolearning (LvaHAl) to solve these problems from both local and global perspectives. Specifically, the whole band space is first randomly divided into several subspaces (LVs) of different dimensions, where each LV denotes a set of lowdimensional representations of training samples consisting of bands associated with it. Then, for different LVs, a robust hinge loss function for isolated pixels regularized by the row-sparsity is adopted to measure the importance of the corresponding bands. In order to simultaneously reduce the bias of LVs and encode the complementary information between them, samples from all LVs are further projected into the label space. Subsequently, a hypergraph model that automatically learns the hyperedge weights is presented. In this way, the local manifold structure of these projections can be preserved, ensuring that samples of the same class have a small distance. Finally, a consensus matrix is used to integrate the importance of bands corresponding to different LVs, resulting in the optimal selection of expected bands from a global perspective. The classification experiments on three HSI data sets show that our method is competitive with other comparison methods
TheShadow29 / Learn Graph LaplacianImplementation of the paper Learning Laplacian Matrix in Smooth Graph Signal Representations
johannesbrust / CRCompact representations for recursive Hessian matrix estimates
mkeeter / Teapot MrepExperiments with direct ray-tracing of Béziers using matrix representations
SibaMishra / Clustering Glossary Terms Extracted From Large Sized Software Requirements Using FastTextThis repository contains the results of automatic glossary terms extraction and their clustering considering two important qualitative attributes, i.e. feature and benefit of the original CrowdRE requirement specifications dataset. In the original CrowdRE dataset, each entry has 6 attributes, i.e., role, feature, benefit, domain, tags and date-time of creation. Since, we are interested in extracting domain-specific terms from this dataset, we only focus on feature and benefit attributes of this dataset. The dataset used in our experiments containing only the feature and benefit attributes of the original CrowdRE dataset can be viewed in the file named "CrowdRE Requirements Dataset.csv". However, the original CrowdRE dataset is devloped by P. K. Murukannaiah et al. and can be accessed from "The smarthome crowd requirements dataset", https://crowdre.github.io/murukannaiah-smarthome-requirements-dataset/, April, 2017. We have computed and reported the ground truth set for a random subset of 100 requirement specifications of the used CrowdRE dataset. In total, we have manually identified a total of 120 ground truth glossary terms with 30 overlapping clusters. The ground truth glossary terms have been calculated from the best intuition of the people (s) involved in this project in an unbiased manner, as there exists no benchmark or gold standard related to the ground truth extraction and clustering for the CrowdRE dataset. The file named "Ground Truth Clusters.docx" shows the ground truth glossary terms along with the manually formulated semantically similar clusters. Note: the clusters are separated with (######) symbol in the file. Further, the manually identified 120 glossary terms in the ground truth set are shown in the third column of the file named as "Extracted Glossary Terms (With and Without WordNet Removal) and Ground Truth Glossary Terms.csv". We have extracted a total of 143 and 292 glossary terms from the CrowdRE dataset with or without removing some words specified in the WordNet lexical database (https://wordnet.princeton.edu/) using a mature text chunking approach. The results are shown in the first and second column of the file named "Extracted Glossary Terms (With and Without WordNet Removal) and Ground Truth Glossary Terms.csv". The extracted glossary terms are trained with the help of a domain specific corpora that is most related to used CrowdRE dataset, i.e. (Wikipedia Home Automation Category for a maximum depth of two, "https://en.wikipedia.org/wiki/Category:Home_automation") and with a pre-trained word vectors UMBC webbase corpus and statmt.org news dataset trained with subwords information in wikipedia 2017 (T. Mikolov, E. Grave, P. Bojanowski, C. Puhrsch, A. Joulin. Advances in Pre-Training Distributed Word Representations) using FastText word embedding vectors (https://fasttext.cc/docs/en/english-vectors.html). The main purpose of the training is to deduce the clusters by forming a the similarity matrix for the extracted glossary terms. For this, we have used two clustering algorithms, viz. K-Means and EM clustering algorithms. The similarity matrix have been developed using the computed semantic similarity scores (cosine similarity) between the word vectors using the word embedding based FastText model. The results in terms of automated formulated clusters for the random subset of 100 requirement specifications of the CrowdRE dataset for which the ground truth glossary terms are calculated are shown in the files named "Automated Ideal (Ground Truth) Clusters.docx" and "Automated Extraction and Clustering.docx" respectively. Note: there exists a maximum of n/2 clusters for n glossary terms. For evaluating the efficacy of the clustering algorithms, we used some commonly used performance evaluation metrics like (precision, recall, f-scores). The evaluation graphs utilizing the area under curve plots (AUC) and evaluating the normalized AUC scores for all the used clustering algorithms are trained on two different datasets and the evaluation results are shown in the two separate files namely, "Cluster Plots.docx" and "Extraction +Clustering Plots.docx" respectively.
Interrupt101 / GraphTheoryGraph Algorithms is a C++ project that implements fundamental graph algorithms like Breadth-First Search (BFS) and Depth-First Search (DFS). It focuses on clear implementations of graph representations such as Adjacency Matrix, with plans for Adjacency List and Edge List. This project serves as an educational tool for understanding graph theory.
kercle / SunA toolkit that aims to provide several features with regards to special unitary groups, including the generation of matrix representations, decomposition of tensor products and more.
Bioconductor / RaggedExperimentMatrix-like representations of mutation and CN data
KacperWojciechowski / GraphCakeImplementation of graph calculations and algorithms, with matrix and list representations.
ITensor / ITensorAGP.jlAdiabatically evolve matrix product states (MPS) using matrix produect operator (MPO) representations of the adiabatic gauge potential (AGP).
bkolosk1 / Multilingual Detection Of Fake News Spreaders Via Sparse Matrix FactorizationFake news is an emerging problem in online news and social media. Efficient detection of fake news spreaders and spurious accounts across multiple languages is becoming an interesting research problem, and is the key focus of this paper. Our proposed solution to PAN 2020 fake news spreaders challenge models the accounts responsible for spreading the fake news by accounting for different types of textual features, decomposed via sparse matrix factorization, to obtain easy-to-learn-from, compact representations, including the information from multiple languages. The key contribution of this work is the exploration of how powerful and scalable matrix factorization-based classification can be in a multilingual setting, where the learner is presented with the data from multiple languages simultaneously. Finally, we explore the joint latent space, where patterns from individual languages are maintained. The proposed approach scored second on the 2020 PAN shared task for identification of fake news spreaders.
yukubo / Sample Word2vec Skipgram# Copyright 2015 Google Inc. All Rights Reserved. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # ============================================================================== """Multi-threaded word2vec mini-batched skip-gram model. Trains the model described in: (Mikolov, et. al.) Efficient Estimation of Word Representations in Vector Space ICLR 2013. http://arxiv.org/abs/1301.3781 This model does traditional minibatching. The key ops used are: * placeholder for feeding in tensors for each example. * embedding_lookup for fetching rows from the embedding matrix. * sigmoid_cross_entropy_with_logits to calculate the loss. * GradientDescentOptimizer for optimizing the loss. * skipgram custom op that does input processing. """ from __future__ import absolute_import from __future__ import division from __future__ import print_function import os import sys import threading import time from six.moves import xrange # pylint: disable=redefined-builtin import numpy as np import tensorflow as tf from tensorflow.models.embedding import gen_word2vec as word2vec flags = tf.app.flags flags.DEFINE_string("save_path", None, "Directory to write the model and " "training summaries.") flags.DEFINE_string("train_data", None, "Training text file. " "E.g., unzipped file http://mattmahoney.net/dc/text8.zip.") flags.DEFINE_string( "eval_data", None, "File consisting of analogies of four tokens." "embedding 2 - embedding 1 + embedding 3 should be close " "to embedding 4." "E.g. https://word2vec.googlecode.com/svn/trunk/questions-words.txt.") flags.DEFINE_integer("embedding_size", 200, "The embedding dimension size.") flags.DEFINE_integer( "epochs_to_train", 15, "Number of epochs to train. Each epoch processes the training data once " "completely.") flags.DEFINE_float("learning_rate", 0.2, "Initial learning rate.") flags.DEFINE_integer("num_neg_samples", 100, "Negative samples per training example.") flags.DEFINE_integer("batch_size", 16, "Number of training examples processed per step " "(size of a minibatch).") flags.DEFINE_integer("concurrent_steps", 12, "The number of concurrent training steps.") flags.DEFINE_integer("window_size", 5, "The number of words to predict to the left and right " "of the target word.") flags.DEFINE_integer("min_count", 5, "The minimum number of word occurrences for it to be " "included in the vocabulary.") flags.DEFINE_float("subsample", 1e-3, "Subsample threshold for word occurrence. Words that appear " "with higher frequency will be randomly down-sampled. Set " "to 0 to disable.") flags.DEFINE_boolean( "interactive", False, "If true, enters an IPython interactive session to play with the trained " "model. E.g., try model.analogy('france', 'paris', 'russia') and " "model.nearby(['proton', 'elephant', 'maxwell']") flags.DEFINE_integer("statistics_interval", 5, "Print statistics every n seconds.") flags.DEFINE_integer("summary_interval", 5, "Save training summary to file every n seconds (rounded " "up to statistics interval.") flags.DEFINE_integer("checkpoint_interval", 600, "Checkpoint the model (i.e. save the parameters) every n " "seconds (rounded up to statistics interval.") FLAGS = flags.FLAGS class Options(object): """Options used by our word2vec model.""" def __init__(self): # Model options. # Embedding dimension. self.emb_dim = FLAGS.embedding_size # Training options. # The training text file. self.train_data = FLAGS.train_data # Number of negative samples per example. self.num_samples = FLAGS.num_neg_samples # The initial learning rate. self.learning_rate = FLAGS.learning_rate # Number of epochs to train. After these many epochs, the learning # rate decays linearly to zero and the training stops. self.epochs_to_train = FLAGS.epochs_to_train # Concurrent training steps. self.concurrent_steps = FLAGS.concurrent_steps # Number of examples for one training step. self.batch_size = FLAGS.batch_size # The number of words to predict to the left and right of the target word. self.window_size = FLAGS.window_size # The minimum number of word occurrences for it to be included in the # vocabulary. self.min_count = FLAGS.min_count # Subsampling threshold for word occurrence. self.subsample = FLAGS.subsample # How often to print statistics. self.statistics_interval = FLAGS.statistics_interval # How often to write to the summary file (rounds up to the nearest # statistics_interval). self.summary_interval = FLAGS.summary_interval # How often to write checkpoints (rounds up to the nearest statistics # interval). self.checkpoint_interval = FLAGS.checkpoint_interval # Where to write out summaries. self.save_path = FLAGS.save_path # Eval options. # The text file for eval. self.eval_data = FLAGS.eval_data class Word2Vec(object): """Word2Vec model (Skipgram).""" def __init__(self, options, session): self._options = options self._session = session self._word2id = {} self._id2word = [] self.build_graph() self.build_eval_graph() self.save_vocab() self._read_analogies() def _read_analogies(self): """Reads through the analogy question file. Returns: questions: a [n, 4] numpy array containing the analogy question's word ids. questions_skipped: questions skipped due to unknown words. """ questions = [] questions_skipped = 0 with open(self._options.eval_data, "rb") as analogy_f: for line in analogy_f: if line.startswith(b":"): # Skip comments. continue words = line.strip().lower().split(b" ") ids = [self._word2id.get(w.strip()) for w in words] if None in ids or len(ids) != 4: questions_skipped += 1 else: questions.append(np.array(ids)) print("Eval analogy file: ", self._options.eval_data) print("Questions: ", len(questions)) print("Skipped: ", questions_skipped) self._analogy_questions = np.array(questions, dtype=np.int32) def forward(self, examples, labels): """Build the graph for the forward pass.""" opts = self._options # Declare all variables we need. # Embedding: [vocab_size, emb_dim] init_width = 0.5 / opts.emb_dim emb = tf.Variable( tf.random_uniform( [opts.vocab_size, opts.emb_dim], -init_width, init_width), name="emb") self._emb = emb # Softmax weight: [vocab_size, emb_dim]. Transposed. sm_w_t = tf.Variable( tf.zeros([opts.vocab_size, opts.emb_dim]), name="sm_w_t") # Softmax bias: [emb_dim]. sm_b = tf.Variable(tf.zeros([opts.vocab_size]), name="sm_b") # Global step: scalar, i.e., shape []. self.global_step = tf.Variable(0, name="global_step") # Nodes to compute the nce loss w/ candidate sampling. labels_matrix = tf.reshape( tf.cast(labels, dtype=tf.int64), [opts.batch_size, 1]) # Negative sampling. sampled_ids, _, _ = (tf.nn.fixed_unigram_candidate_sampler( true_classes=labels_matrix, num_true=1, num_sampled=opts.num_samples, unique=True, range_max=opts.vocab_size, distortion=0.75, unigrams=opts.vocab_counts.tolist())) # Embeddings for examples: [batch_size, emb_dim] example_emb = tf.nn.embedding_lookup(emb, examples) # Weights for labels: [batch_size, emb_dim] true_w = tf.nn.embedding_lookup(sm_w_t, labels) # Biases for labels: [batch_size, 1] true_b = tf.nn.embedding_lookup(sm_b, labels) # Weights for sampled ids: [num_sampled, emb_dim] sampled_w = tf.nn.embedding_lookup(sm_w_t, sampled_ids) # Biases for sampled ids: [num_sampled, 1] sampled_b = tf.nn.embedding_lookup(sm_b, sampled_ids) # True logits: [batch_size, 1] true_logits = tf.reduce_sum(tf.mul(example_emb, true_w), 1) + true_b # Sampled logits: [batch_size, num_sampled] # We replicate sampled noise lables for all examples in the batch # using the matmul. sampled_b_vec = tf.reshape(sampled_b, [opts.num_samples]) sampled_logits = tf.matmul(example_emb, sampled_w, transpose_b=True) + sampled_b_vec return true_logits, sampled_logits def nce_loss(self, true_logits, sampled_logits): """Build the graph for the NCE loss.""" # cross-entropy(logits, labels) opts = self._options true_xent = tf.nn.sigmoid_cross_entropy_with_logits( true_logits, tf.ones_like(true_logits)) sampled_xent = tf.nn.sigmoid_cross_entropy_with_logits( sampled_logits, tf.zeros_like(sampled_logits)) # NCE-loss is the sum of the true and noise (sampled words) # contributions, averaged over the batch. nce_loss_tensor = (tf.reduce_sum(true_xent) + tf.reduce_sum(sampled_xent)) / opts.batch_size return nce_loss_tensor def optimize(self, loss): """Build the graph to optimize the loss function.""" # Optimizer nodes. # Linear learning rate decay. opts = self._options words_to_train = float(opts.words_per_epoch * opts.epochs_to_train) lr = opts.learning_rate * tf.maximum( 0.0001, 1.0 - tf.cast(self._words, tf.float32) / words_to_train) self._lr = lr optimizer = tf.train.GradientDescentOptimizer(lr) train = optimizer.minimize(loss, global_step=self.global_step, gate_gradients=optimizer.GATE_NONE) self._train = train def build_eval_graph(self): """Build the eval graph.""" # Eval graph # Each analogy task is to predict the 4th word (d) given three # words: a, b, c. E.g., a=italy, b=rome, c=france, we should # predict d=paris. # The eval feeds three vectors of word ids for a, b, c, each of # which is of size N, where N is the number of analogies we want to # evaluate in one batch. analogy_a = tf.placeholder(dtype=tf.int32) # [N] analogy_b = tf.placeholder(dtype=tf.int32) # [N] analogy_c = tf.placeholder(dtype=tf.int32) # [N] # Normalized word embeddings of shape [vocab_size, emb_dim]. nemb = tf.nn.l2_normalize(self._emb, 1) # Each row of a_emb, b_emb, c_emb is a word's embedding vector. # They all have the shape [N, emb_dim] a_emb = tf.gather(nemb, analogy_a) # a's embs b_emb = tf.gather(nemb, analogy_b) # b's embs c_emb = tf.gather(nemb, analogy_c) # c's embs # We expect that d's embedding vectors on the unit hyper-sphere is # near: c_emb + (b_emb - a_emb), which has the shape [N, emb_dim]. target = c_emb + (b_emb - a_emb) # Compute cosine distance between each pair of target and vocab. # dist has shape [N, vocab_size]. dist = tf.matmul(target, nemb, transpose_b=True) # For each question (row in dist), find the top 4 words. _, pred_idx = tf.nn.top_k(dist, 4) # Nodes for computing neighbors for a given word according to # their cosine distance. nearby_word = tf.placeholder(dtype=tf.int32) # word id nearby_emb = tf.gather(nemb, nearby_word) nearby_dist = tf.matmul(nearby_emb, nemb, transpose_b=True) nearby_val, nearby_idx = tf.nn.top_k(nearby_dist, min(1000, self._options.vocab_size)) # Nodes in the construct graph which are used by training and # evaluation to run/feed/fetch. self._analogy_a = analogy_a self._analogy_b = analogy_b self._analogy_c = analogy_c self._analogy_pred_idx = pred_idx self._nearby_word = nearby_word self._nearby_val = nearby_val self._nearby_idx = nearby_idx def build_graph(self): """Build the graph for the full model.""" opts = self._options # The training data. A text file. (words, counts, words_per_epoch, self._epoch, self._words, examples, labels) = word2vec.skipgram(filename=opts.train_data, batch_size=opts.batch_size, window_size=opts.window_size, min_count=opts.min_count, subsample=opts.subsample) (opts.vocab_words, opts.vocab_counts, opts.words_per_epoch) = self._session.run([words, counts, words_per_epoch]) opts.vocab_size = len(opts.vocab_words) print("Data file: ", opts.train_data) print("Vocab size: ", opts.vocab_size - 1, " + UNK") print("Words per epoch: ", opts.words_per_epoch) self._examples = examples self._labels = labels self._id2word = opts.vocab_words for i, w in enumerate(self._id2word): self._word2id[w] = i true_logits, sampled_logits = self.forward(examples, labels) loss = self.nce_loss(true_logits, sampled_logits) tf.scalar_summary("NCE loss", loss) self._loss = loss self.optimize(loss) # Properly initialize all variables. tf.initialize_all_variables().run() self.saver = tf.train.Saver() def save_vocab(self): """Save the vocabulary to a file so the model can be reloaded.""" opts = self._options with open(os.path.join(opts.save_path, "vocab.txt"), "w") as f: for i in xrange(opts.vocab_size): f.write("%s %d\n" % (tf.compat.as_text(opts.vocab_words[i]), opts.vocab_counts[i])) def _train_thread_body(self): initial_epoch, = self._session.run([self._epoch]) while True: _, epoch = self._session.run([self._train, self._epoch]) if epoch != initial_epoch: break def train(self): """Train the model.""" opts = self._options initial_epoch, initial_words = self._session.run([self._epoch, self._words]) summary_op = tf.merge_all_summaries() summary_writer = tf.train.SummaryWriter(opts.save_path, graph_def=self._session.graph_def) workers = [] for _ in xrange(opts.concurrent_steps): t = threading.Thread(target=self._train_thread_body) t.start() workers.append(t) last_words, last_time, last_summary_time = initial_words, time.time(), 0 last_checkpoint_time = 0 while True: time.sleep(opts.statistics_interval) # Reports our progress once a while. (epoch, step, loss, words, lr) = self._session.run( [self._epoch, self.global_step, self._loss, self._words, self._lr]) now = time.time() last_words, last_time, rate = words, now, (words - last_words) / ( now - last_time) print("Epoch %4d Step %8d: lr = %5.3f loss = %6.2f words/sec = %8.0f\r" % (epoch, step, lr, loss, rate), end="") sys.stdout.flush() if now - last_summary_time > opts.summary_interval: summary_str = self._session.run(summary_op) summary_writer.add_summary(summary_str, step) last_summary_time = now if now - last_checkpoint_time > opts.checkpoint_interval: self.saver.save(self._session, opts.save_path + "model", global_step=step.astype(int)) last_checkpoint_time = now if epoch != initial_epoch: break for t in workers: t.join() return epoch def _predict(self, analogy): """Predict the top 4 answers for analogy questions.""" idx, = self._session.run([self._analogy_pred_idx], { self._analogy_a: analogy[:, 0], self._analogy_b: analogy[:, 1], self._analogy_c: analogy[:, 2] }) return idx def eval(self): """Evaluate analogy questions and reports accuracy.""" # How many questions we get right at precision@1. correct = 0 total = self._analogy_questions.shape[0] start = 0 while start < total: limit = start + 2500 sub = self._analogy_questions[start:limit, :] idx = self._predict(sub) start = limit for question in xrange(sub.shape[0]): for j in xrange(4): if idx[question, j] == sub[question, 3]: # Bingo! We predicted correctly. E.g., [italy, rome, france, paris]. correct += 1 break elif idx[question, j] in sub[question, :3]: # We need to skip words already in the question. continue else: # The correct label is not the precision@1 break print() print("Eval %4d/%d accuracy = %4.1f%%" % (correct, total, correct * 100.0 / total)) def analogy(self, w0, w1, w2): """Predict word w3 as in w0:w1 vs w2:w3.""" wid = np.array([[self._word2id.get(w, 0) for w in [w0, w1, w2]]]) idx = self._predict(wid) for c in [self._id2word[i] for i in idx[0, :]]: if c not in [w0, w1, w2]: return c return "unknown" def nearby(self, words, num=20): """Prints out nearby words given a list of words.""" ids = np.array([self._word2id.get(x, 0) for x in words]) vals, idx = self._session.run( [self._nearby_val, self._nearby_idx], {self._nearby_word: ids}) for i in xrange(len(words)): print("\n%s\n=====================================" % (words[i])) for (neighbor, distance) in zip(idx[i, :num], vals[i, :num]): print("%-20s %6.4f" % (self._id2word[neighbor], distance)) def _start_shell(local_ns=None): # An interactive shell is useful for debugging/development. import IPython user_ns = {} if local_ns: user_ns.update(local_ns) user_ns.update(globals()) IPython.start_ipython(argv=[], user_ns=user_ns) def main(_): """Train a word2vec model.""" if not FLAGS.train_data or not FLAGS.eval_data or not FLAGS.save_path: print("--train_data --eval_data and --save_path must be specified.") sys.exit(1) opts = Options() with tf.Graph().as_default(), tf.Session() as session: with tf.device("/cpu:0"): model = Word2Vec(opts, session) for _ in xrange(opts.epochs_to_train): model.train() # Process one epoch model.eval() # Eval analogies. # Perform a final save. model.saver.save(session, os.path.join(opts.save_path, "model.ckpt"), global_step=model.global_step) if FLAGS.interactive: # E.g., # [0]: model.analogy('france', 'paris', 'russia') # [1]: model.nearby(['proton', 'elephant', 'maxwell']) _start_shell(locals()) if __name__ == "__main__": tf.app.run()
