Example #1
0
    def _testPerplexityOnRealData(self):
        dtype = np.float64 # DTYPE

        rd.seed(0xBADB055)
        data = DataSet.from_files(words_file=AclWordPath, links_file=AclCitePath)
        with open(AclDictPath, "rb") as f:
            dic = pkl.load(f)

        data.convert_to_dtype(dtype)
        data.convert_to_undirected_graph()
        data.convert_to_binary_link_matrix()
        data.prune_and_shuffle(min_doc_len=MinDocLen, min_link_count=MinLinkCount)

        # IDF frequency for when we print out the vocab later
        freq = np.squeeze(np.asarray(data.words.sum(axis=0)))
        scale = np.reciprocal(1 + freq)

        # Initialise the model
        K = TopicCount
        model      = rtm.newModelAtRandom(data, K, dtype=dtype)
        queryState = rtm.newQueryState(data, model)
        trainPlan  = rtm.newTrainPlan(iterations=50, logFrequency=LogFreq, fastButInaccurate=False, debug=True)

        # Train the model, and the immediately save the result to a file for subsequent inspection
        model, query, (bndItrs, bndVals, bndLikes) = rtm.train (data, model, queryState, trainPlan)
#        with open(newModelFileFromModel(model), "wb") as f:
#            pkl.dump ((model, query, (bndItrs, bndVals, bndLikes)), f)

        # Plot the evolution of the bound during training.
        fig, ax1 = plt.subplots()
        ax1.plot(bndItrs, bndVals, 'b-')
        ax1.set_xlabel('Iterations')
        ax1.set_ylabel('Bound', color='b')

        ax2 = ax1.twinx()
        ax2.plot(bndItrs, bndLikes, 'r-')
        ax2.set_ylabel('Likelihood', color='r')

        fig.show()
        plt.show()

        # Print out the most likely topic words
        # scale = np.reciprocal(1 + np.squeeze(np.array(data.words.sum(axis=0))))
        vocab = rtm.wordDists(model)
        topWordCount = 10
        kTopWordInds = [self.topWordInds(vocab[k,:], topWordCount) for k in range(K)]

        like = rtm.log_likelihood(data, model, query)
        perp = perplexity_from_like(like, data.word_count)

        print ("Prior %s" % (str(model.topicPrior)))
        print ("Perplexity: %f\n\n" % perp)

        for k in range(model.K):
            print("\nTopic %d\n=============================" % k)
            print("\n".join("%-20s\t%0.4f" % (dic[kTopWordInds[k][c]], vocab[k][kTopWordInds[k][c]]) for c in range(topWordCount)))
Example #2
0
    def testMapOnRealData(self):
        dtype = np.float64 # DTYPE

        rd.seed(0xBADB055)
        data = DataSet.from_files(words_file=AclWordPath, links_file=AclCitePath)
        with open(AclDictPath, "rb") as f:
            dic = pkl.load(f)

        data.convert_to_dtype(dtype)
        data.convert_to_undirected_graph()
        data.convert_to_binary_link_matrix()
        data.prune_and_shuffle(min_doc_len=MinDocLen, min_link_count=MinLinkCount)

        trainData, testData = data.doc_completion_split()

        for pseudoNegCount in (5, 10, 25, 50, 100):
            rd.seed(0xC0FFEE)

            # Initialise the model
            K = TopicCount
            model      = rtm.newModelAtRandom(trainData, K, dtype=dtype, pseudoNegCount=data.doc_count * pseudoNegCount)
            queryState = rtm.newQueryState(trainData, model)
            trainPlan  = rtm.newTrainPlan(iterations=50, logFrequency=LogFreq, fastButInaccurate=False, debug=True)

            # Train the model, and the immediately save the result to a file for subsequent inspection
            model, topics, (bndItrs, bndVals, bndLikes) = rtm.train(trainData, model, queryState, trainPlan)
    #        with open(newModelFileFromModel(model), "wb") as f:
    #            pkl.dump ((model, query, (bndItrs, bndVals, bndLikes)), f)

            # Plot the evolution of the bound during training.
            fig, ax1 = plt.subplots()
            ax1.plot(bndItrs, bndVals, 'b-')
            ax1.set_xlabel('Iterations')
            ax1.set_ylabel('Bound', color='b')

            ax2 = ax1.twinx()
            ax2.plot(bndItrs, bndLikes, 'r-')
            ax2.set_ylabel('Likelihood', color='r')

            fig.show()
            plt.show()

            # Print out the most likely topic words
            # scale = np.reciprocal(1 + np.squeeze(np.array(data.words.sum(axis=0))))
            vocab = rtm.wordDists(model)
            topWordCount = 10
            kTopWordInds = [self.topWordInds(vocab[k, :], topWordCount) for k in range(K)]

            like = rtm.log_likelihood(trainData, model, topics)
            perp = perplexity_from_like(like, trainData.word_count)

            # print ("Prior %s" % (str(model.topicPrior)))
            print ("Pseudo Neg-Count: %d " % pseudoNegCount)
            print ("\tTrain Perplexity: %f\n\n" % perp)

            # for k in range(model.K):
            #     print ("\nTopic %d\n=============================" % k)
            #     print ("\n".join("%-20s\t%0.4f" % (dic[kTopWordInds[k][c]], vocab[k][kTopWordInds[k][c]]) for c in range(topWordCount)))

            min_probs  = rtm.min_link_probs(model, topics, testData.links)
            link_probs = rtm.link_probs(model, topics, min_probs)
            try:
                map = mean_average_prec(testData.links, link_probs)
            except:
                print ("Unexpected error")

            print("\tThe Mean-Average-Precision is %.3f" % map)