Why my CNN does not learn?

bencr: <p>This is a repost from the computer vision category as I didn’t see that there was an audio category <img src="https://discuss.pytorch.org/images/emoji/apple/slight_smile.png?v=12" title=":slight_smile:" class="emoji" alt=":slight_smile:" loading="lazy" width="20" height="20"></p>
<p>Here is my problem:</p>
<p>I am currently working on building a CNN for sound classification. The problem is relatively simple: I need my model to detect whether there is human speech on .wav recording sounds of a tropical ecosystem. I made a train / test set containing records of 3 seconds on which there is human speech (speech) or not (no_speech). From these 3 seconds fragments I get a mel-spectrogram of dimension 128 x 128 that is used to feed the model.</p>
<p>I checked if the script <code>Audiodataset</code> (given below) gives an expected output and I can’t find any problems. For the category “speech” the mel-spectrograms look similar to:</p>
<p><img src="https://discuss.pytorch.org/uploads/default/original/3X/6/a/6af336f8eddab6a9be60cd5dbf1a3c907e06b64d.png" alt="image" data-base62-sha1="fg7HdpbszrNs7Qles3F0BmRwT2B" width="397" height="256"></p>
<p>While the mel-spectrograms for “no-speech” look like:</p>
<p><img src="https://discuss.pytorch.org/uploads/default/original/3X/a/1/a13d282de97188454aa77de84fed39ac4387b524.png" alt="image" data-base62-sha1="n0nTR4MJ3P222vSj2xohPTTzxc0" width="396" height="257"></p>
<p>Since it is a simple binary problem I thought the a CNN would easily detect human speech but I may have been too cocky. However, it seems that after 1 or 2 epoch the model doesn’t learn anymore, i.e. the loss doesn’t decrease and the number of correct prediction stays roughly the same. I tried to play with the hyperparameters but the problem is still the same. I tried a learning rate of 0.1, 0.01 … until 1e-7. Here are the runs displayed in Tensorboard:</p>
<p><div class="lightbox-wrapper"><a class="lightbox" href="https://discuss.pytorch.org/uploads/default/original/3X/6/3/6393717dcb406bed34c7dc505e7a90cb15c53791.png" data-download-href="https://discuss.pytorch.org/uploads/default/6393717dcb406bed34c7dc505e7a90cb15c53791" title="image"><img src="https://discuss.pytorch.org/uploads/default/optimized/3X/6/3/6393717dcb406bed34c7dc505e7a90cb15c53791_2_690x404.png" alt="image" data-base62-sha1="ecTafXFTs8XhRlQccuGsxYAHaYV" width="690" height="404" srcset="https://discuss.pytorch.org/uploads/default/optimized/3X/6/3/6393717dcb406bed34c7dc505e7a90cb15c53791_2_690x404.png, https://discuss.pytorch.org/uploads/default/optimized/3X/6/3/6393717dcb406bed34c7dc505e7a90cb15c53791_2_1035x606.png 1.5x, https://discuss.pytorch.org/uploads/default/original/3X/6/3/6393717dcb406bed34c7dc505e7a90cb15c53791.png 2x" data-dominant-color="FBFBFB"><div class="meta"><svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use href="#far-image"></use></svg><span class="filename">image</span><span class="informations">1117×655 33 KB</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use href="#discourse-expand"></use></svg></div></a></div></p>
<p>Then I thought it could be due to the script itself but I cannot find anything wrong. I would be glad you could have a quick look at the script and let me know what could go wrong! If you have other ideas of why this problem may occur I would also be glad to receive some advice on how to best train my CNN <img src="https://discuss.pytorch.org/images/emoji/apple/slight_smile.png?v=12" title=":slight_smile:" class="emoji" alt=":slight_smile:" loading="lazy" width="20" height="20"></p>
<p>I based the script on the LunaTrainingApp from “Deep learning in PyTorch” by Stevens as I found the script to be elegant. Of course I modified it to match my problem.</p>
<p>Here is the script creating the input for the model (from .wav file to mel-spectrogram):</p>
<pre data-code-wrap="python"><code class="lang-python">
"""
Define a class AudioDataset which take the folder of the training / test data as input 
and make normalized mel-spectrograms out of it
Labels are also one hot encoded
"""


from torch.utils.data import Dataset
from pydub import AudioSegment
from sklearn.preprocessing import LabelEncoder
from fs import open_fs
from fs.osfs import OSFS

import numpy as np
import librosa
import torch
import os

class AudioDataset(Dataset):
    def __init__(self, data_root, n_fft, hop_length, n_mels):
        self.data_root_fs = open_fs(data_root)
        self.samples = []
        self.n_fft = n_fft
        self.hop_length = hop_length
        self.n_mels = n_mels
        self.class_encode = LabelEncoder()
        self._init_dataset()

    def __len__(self):
        return len(self.samples)

    def __getitem__(self, idx):
        
        audio_filepath, label = self.samples[idx]
        
        with self.data_root_fs.open(audio_filepath, 'rb') as audio_fd:
            audio_file = AudioSegment.from_file(audio_fd)
        
        #audio_file = AudioSegment.from_file(audio_filepath)
        array_audio = np.array(audio_file.get_array_of_samples(), dtype=float)
        
        mel = self.to_mel_spectrogram(array_audio)
        #mel_norm = self.normalize_row_matrix(mel)
        mel_norm_tensor = torch.tensor(mel)
        mel_norm_tensor = mel_norm_tensor.unsqueeze(0)
        
        label_encoded = self.one_hot_sample(label)
        label_class = torch.argmax(label_encoded)
        
        return (mel_norm_tensor, label_class)
    
    
    def _init_dataset(self):
        
        folder_names = set()
        for match in self.data_root_fs.glob("*/*.wav"):
            folder = match.path.split('/')[-2]
            folder_names.add(folder)
            self.samples.append((match.path, folder))
        self.class_encode.fit(list(folder_names))
                
    def to_mel_spectrogram(self, x):

        sgram = librosa.stft(x, n_fft=self.n_fft, hop_length=self.hop_length)
        sgram_mag, _ = librosa.magphase(sgram)
        mel_scale_sgram = librosa.feature.melspectrogram(S=sgram_mag, sr=16000, n_mels=self.n_mels)
        mel_sgram = librosa.amplitude_to_db(mel_scale_sgram)
        return mel_sgram
    
    def normalize_row_matrix(self, mat):

        mean_rows = mat.mean(axis=1)
        std_rows = mat.std(axis=1)
        normalized_array = (mat - mean_rows[:, np.newaxis]) / std_rows[:, np.newaxis]
        return normalized_array
    
    def to_one_hot(self, codec, values):
        value_idxs = codec.transform(values)
        return torch.eye(len(codec.classes_))[value_idxs]

    def one_hot_sample(self, label):
        t_label = self.to_one_hot(self.class_encode, [label])
        return t_label

</code></pre>
<p>The model itself, which basically performs 2D convolutions on the mel-spectrogram:</p>
<pre data-code-wrap="python"><code class="lang-python">import torch
import torch.nn as nn
import torch.nn.functional as F
import math

class VADNet(nn.Module):
    def __init__(self, in_channels=1, conv_channels=8):
        super().__init__()

        self.tail_batchnorm = nn.BatchNorm2d(1)

        self.block1 = ConvBlock(in_channels, conv_channels)
        self.block2 = ConvBlock(conv_channels, conv_channels * 2)
        self.block3 = ConvBlock(conv_channels * 2, conv_channels * 4)
        self.block4 = ConvBlock(conv_channels * 4, conv_channels * 8)

        self.head_linear = nn.Linear(8 * 8 * conv_channels * 8, 2)

        self._init_weights()

    def _init_weights(self):
        for m in self.modules():
            if type(m) in {
                nn.Linear,
                nn.Conv3d,
                nn.Conv2d,
                nn.ConvTranspose2d,
                nn.ConvTranspose3d,
            }:
                nn.init.kaiming_normal_(
                    m.weight.data, a=0, mode='fan_out', nonlinearity='relu',
                )
                if m.bias is not None:
                    fan_in, fan_out = \
                        nn.init._calculate_fan_in_and_fan_out(m.weight.data)
                    bound = 1 / math.sqrt(fan_out)
                    nn.init.normal_(m.bias, -bound, bound)

    def forward(self, input_batch):
        bn_output = self.tail_batchnorm(input_batch)

        block_out = self.block1(bn_output)
        block_out = self.block2(block_out)
        block_out = self.block3(block_out)
        block_out = self.block4(block_out)

        conv_flat = block_out.view(block_out.size(0),-1)
        linear_output = self.head_linear(conv_flat)

        return linear_output


class ConvBlock(nn.Module):
    def __init__(self, in_channels, conv_channels):
        super().__init__()

        self.conv1 = nn.Conv2d(
            in_channels, conv_channels, kernel_size=3, padding=1, bias=True,
        )
        self.relu1 = nn.ReLU(inplace=True)
        self.conv2 = nn.Conv2d(
            conv_channels, conv_channels, kernel_size=3, padding=1, bias=True,
        )
        self.relu2 = nn.ReLU(inplace=True)

        self.maxpool = nn.MaxPool2d(2, 2)

    def forward(self, input_batch):
        block_out = self.conv1(input_batch)
        block_out = self.relu1(block_out)
        block_out = self.conv2(block_out)
        block_out = self.relu2(block_out)

        return self.maxpool(block_out)
</code></pre>
<p>And the script that I use for training the model:</p>
<pre data-code-wrap="python"><code class="lang-python">import torch
import torch.nn as nn
import argparse
import numpy as np

import logging
logging.basicConfig(level = logging.INFO)
log = logging.getLogger(__name__)

from torch.optim import SGD
from torch.utils.tensorboard import SummaryWriter
from torch.utils.data import DataLoader
from sklearn.metrics import confusion_matrix

from dataset_loader.audiodataset import AudioDataset
from models.vadnet import VADNet
from utils.earlystopping import EarlyStopping


class VADTrainingApp:
    
    def __init__(self, sys_argv=None):
        
        parser = argparse.ArgumentParser()
        
        parser.add_argument("--train_path",
                           help='Path to the training set',
                           required=True,
                           type=str,
        )
        
        parser.add_argument("--test_path",
                           help='Path to the testing set',
                           required=True,
                           type=str,
        )
        
        parser.add_argument("--save_path",
                           help='Path to saving the model',
                           required=True,
                           type=str,
        )
        
        parser.add_argument("--save_es",
            help='Save the checkpoints of early stopping call',
            default="checkpoint.pt",
            type=str,
        )
        
        parser.add_argument('--num-workers',
            help='Number of worker processes for background data loading',
            default=8,
            type=int,
        )
        
        parser.add_argument("--batch_size",
                            help='Batch size to use for training',
                            default=32,
                            type=int,)
        
        parser.add_argument('--epochs',
            help='Number of epochs to train for',
            default=50,
            type=int,
        )
        
        parser.add_argument('--lr',
            help='Learning rate for th stochastic gradient descent',
            default=0.001,
            type=float,
        )
        
        self.cli_args = parser.parse_args(sys_argv)
        
        # related to the hardware
        self.use_cuda = torch.cuda.is_available()
        self.device = torch.device("cuda" if self.use_cuda else "cpu")
        
        # directly related to the neural network
        self.model = self.initModel()
        self.optimizer = self.initOptimizer()
        
        # For early stopping
        self.patience = 7
        
        # For metrics
        self.METRICS_LABELS_NDX = 0
        self.METRICS_PREDS_NDX = 1
        self.METRICS_LOSS_NDX = 2
        self.METRICS_SIZE = 3
        
    def initModel(self):
        """Initialize the model, if GPU available computation done there"""       
        model = VADNet()
        model = model.double()
        
        if self.use_cuda:
            log.info("Using CUDA; {} devices".format(torch.cuda.device_count()))
            if torch.cuda.device_count() &gt; 1:
                model = nn.DataParallel(model)
            model = model.to(self.device)
        return model
               
    def initOptimizer(self):
        
        return SGD(self.model.parameters(), lr=self.cli_args.lr)#, momentum=0.8, weight_decay=0.01)
    
    def adjust_learning_rate(self):
        """Sets the learning rate to the initial LR decayed by a factor of 10 every 20 epochs"""
        self.cli_args.lr = self.cli_args.lr * (0.1 ** (self.cli_args.epochs // 20))
        for param_group in self.optimizer.param_groups:
            param_group['lr'] = self.cli_args.lr
    
    def initTrainDL(self):
        
        trainingset = AudioDataset(self.cli_args.train_path, 
                                   n_fft=1024, 
                                   hop_length=376, 
                                   n_mels=128)
        
        batch_size = self.cli_args.batch_size
        if self.use_cuda:
            batch_size *= torch.cuda.device_count()
               
        trainLoader = DataLoader(trainingset,
                                batch_size = batch_size, 
                                shuffle=True, 
                                num_workers=self.cli_args.num_workers,
                                pin_memory=self.use_cuda)
        return trainLoader
    
    def initTestDL(self):
        
        testset = AudioDataset(self.cli_args.test_path, 
                                   n_fft=1024, 
                                   hop_length=376, 
                                   n_mels=128)
        
        batch_size = self.cli_args.batch_size
        if self.use_cuda:
            batch_size *= torch.cuda.device_count()
               
        testLoader = DataLoader(testset,
                                batch_size = batch_size, 
                                shuffle=True, 
                                num_workers=self.cli_args.num_workers,
                                pin_memory=self.use_cuda)
        return testLoader
    
    def main(self):
        
        log.info("Start training, {}".format(self.cli_args))
        
        train_dl = self.initTrainDL()
        test_dl = self.initTestDL()
        
        trn_writer = SummaryWriter(log_dir='runs' + '-trn')
        val_writer = SummaryWriter(log_dir='runs' + '-val')
        
        early_stopping = EarlyStopping(patience=self.patience, path=self.cli_args.save_es, verbose=True)

        for epoch_ndx in range(1, self.cli_args.epochs + 1):
            log.info("Epoch {} / {}".format(epoch_ndx, self.cli_args.epochs))
            
            # Adjust the new learning rate
            self.adjust_learning_rate()
            
            # Train the model's parameters
            metrics_t = self.do_training(train_dl)
            self.logMetrics(metrics_t, trn_writer, epoch_ndx)

            # Test the model
            metrics_v = self.do_val(test_dl, val_writer)
            self.logMetrics(metrics_v, val_writer, epoch_ndx, train=False)
            
            # Add the mean loss of the val for the epoch
            early_stopping(metrics_v[self.METRICS_LOSS_NDX].mean(), self.model)

            if early_stopping.early_stop:
                print("Early stopping")
                break
        
        # Save the model once all epochs have been completed
        torch.save(self.model.state_dict(), self.cli_args.save_path)
        
    def do_training(self, train_dl):
        """Training loop"""
        self.model.train()
        
        # Initiate a 3 dimension tensor to store loss, labels and prediction
        trn_metrics = torch.zeros(self.METRICS_SIZE, len(train_dl.dataset), device=self.device)
        
        for batch_ndx, batch_tup in enumerate(train_dl):

            if batch_ndx%100==0:
                log.info("TRAINING --&gt; Batch {} / {}".format(batch_ndx, len(train_dl)))
            
            self.optimizer.zero_grad()
            
            loss = self.ComputeBatchLoss(batch_ndx, 
                                        batch_tup, 
                                        self.cli_args.batch_size,
                                        trn_metrics)

            loss.backward()
            self.optimizer.step()
            
        return trn_metrics.to('cpu')
    
    def do_val(self, test_dl, early_stop):
        """Validation loop"""
        with torch.no_grad(): 
            self.model.eval()
            
            val_metrics = torch.zeros(self.METRICS_SIZE, len(test_dl.dataset), device=self.device)
                
            for batch_ndx, batch_tup in enumerate(test_dl):
                
                if batch_ndx%100==0:
                    log.info("VAL --&gt; Batch {} / {}".format(batch_ndx, len(test_dl)))
                    
                loss = self.ComputeBatchLoss(batch_ndx, 
                                            batch_tup, 
                                            self.cli_args.batch_size,
                                            val_metrics)
                
        return val_metrics.to('cpu')  
       
    def ComputeBatchLoss(self, batch_ndx, batch_tup, batch_size, metrics_mat):
        """
        Return a tensor the loss of the batch
        """

        imgs, labels = batch_tup
        imgs = imgs.to(device=self.device, non_blocking=True)
        labels = labels.to(device=self.device, non_blocking=True)  
        
        outputs = self.model(imgs)
        _, predicted = torch.max(outputs, dim=1)

        loss_func = nn.CrossEntropyLoss(reduction="none")
        loss = loss_func(outputs, labels)

        start_ndx = batch_ndx * self.cli_args.batch_size
        end_ndx = start_ndx + labels.size(0)

        metrics_mat[self.METRICS_LABELS_NDX, start_ndx:end_ndx] = labels.detach()
        metrics_mat[self.METRICS_PREDS_NDX, start_ndx:end_ndx] = predicted.detach()
        metrics_mat[self.METRICS_LOSS_NDX, start_ndx:end_ndx] = loss.detach()
            
        return loss.mean()
        
    def logMetrics(self, metrics_mat, writer, epoch_ndx, train=True):
        """
        Function to compute custom metrics: accurracy and recall for both classes
        and % of correct predictions. Log the metrics in a tensorboard writer
        """ 
        
        # Confusion matrix to compute precision / recall for each class
        tn, fp, fn, tp = torch.tensor(confusion_matrix(metrics_mat[self.METRICS_LABELS_NDX], 
                                                       metrics_mat[self.METRICS_PREDS_NDX], 
                                                       labels=[0,1]).ravel())
        
        precision_no_speech = tp / (tp + fp)
        recall_no_speech = tp / (tp + fn)
        
        # class speech is labelled 0, so true positive = true negative for speech
        precision_speech = tn / (tn + fn)
        recall_speech = tn / (fp + tn)
        
        # % of correct predictions - optional metrics that are nice
        no_speech_count = (metrics_mat[self.METRICS_LABELS_NDX] == 0).sum()
        speech_count = (metrics_mat[self.METRICS_LABELS_NDX] == 1).sum()
            
        no_speech_correct = ((metrics_mat[self.METRICS_PREDS_NDX] == 0) &amp; (metrics_mat[self.METRICS_LABELS_NDX] == 0)).sum()
        speech_correct = ((metrics_mat[self.METRICS_PREDS_NDX] == 1) &amp; (metrics_mat[self.METRICS_LABELS_NDX] == 1)).sum()
            
        correct_all = (speech_correct + no_speech_correct) / float(speech_count + no_speech_count) * 100
        correct_speech = speech_correct / float(speech_count) * 100
        correct_no_speech = no_speech_correct / float(no_speech_count) * 100
        
        loss = metrics_mat[self.METRICS_LOSS_NDX].mean()
        
        writer.add_scalar("loss", loss, epoch_ndx)
        
        writer.add_scalar("precision/no_speech", precision_no_speech, epoch_ndx)
        writer.add_scalar("recall/no_speech", recall_no_speech, epoch_ndx)
        writer.add_scalar("precision/speech", precision_speech, epoch_ndx)
        writer.add_scalar("recall/speech", recall_speech, epoch_ndx)
        
        writer.add_scalar("correct/all", correct_all, epoch_ndx)
        writer.add_scalar("correct/speech", correct_speech, epoch_ndx)
        writer.add_scalar("correct/no_speech", correct_no_speech, epoch_ndx)
        
        if train:
            log.info("[TRAINING] loss: {}, correct/all: {}% , correct/speech: {}%, correct/no_speech: {}%".format(loss, 
                                                   correct_all,
                                                   correct_speech,
                                                   correct_no_speech))                    
        else:
            log.info("[VAL] loss: {}, correct/all: {}% , correct/speech: {}%, correct/no_speech: {}%".format(loss, 
                                                   correct_all,
                                                   correct_speech,
                                                   correct_no_speech))  
                     
        
if __name__ == "__main__":
    VADTrainingApp().main()
</code></pre>
<p>I tried to fit the model on a small subset of the data but the problem remains. I would be very grateful for any help as this problem is getting frustrating <img src="https://discuss.pytorch.org/images/emoji/apple/slight_smile.png?v=12" title=":slight_smile:" class="emoji" alt=":slight_smile:" loading="lazy" width="20" height="20"></p>
<p>Thank you!</p>

JuanFMontesinos: <p>Well ijt’s difficult to say.<br>
I would use Binary Cross entropy rather than cross entropy as you have a binary case.</p>
<p>I also would do a pooling in after the CNN. Think that those features are spatial and you don’t really care about where the speech is located in the original mel. It also forces each neuron in the linear layer to distinguish between speech/non-speech.</p>
<p>Rather than taking a subset, take a single batch, load it in the gpu and backprop with a simple clean script. This can help you to debug whether there is a bad network desing or a bug in the code.</p>
<p>If everything is okay then I would start from checking the dataset and making sure it works as supposed. If it does you can go for a simpler problem. For example, two clean different categories. Using enhanced speech where the human voice is clearly predominant. In short you have to be sure the task is suitable.</p>

bencr: <blockquote>
<p>I also would do a pooling in after the CNN</p>
</blockquote>
<p>Do you mean, after the the 4th block to do a MaxPooling across the time axis to get a 1D array of frequencies?</p>

puranjay_mishra: <p>I’m just a begginer, but i have gone through the Google’s speech recognition API. What they do is record 3-5 seconds of background noise, and then use the intensity of recorded background noise as base level. Any substantial change in this intensity triggers its recording and the pre-trained speech recognition determines wether the sound is a spoken word(say the wake word) or just a random sound.<br>
Coming to the your CNN implementation , it really depends on one question . Can you differentiate between human speech and no human speech pictures? if yes then the CNN ideally would work. Also does the spectrogram show difference between noise and human speech?<br>
The implementation , as Juan said above has only 1 minor issue. Use BinaryCrossEntropy for binary classification. I doubt that not using maxpool matters much , however it is something you should play around with. Take inspiration from other successful NN for the task. You can also do  transfer learning , however this might be an overkill.</p>

JuanFMontesinos: <p>Well everything depends on if you are interested on frequency info or temporal info.<br>
In short, if you look at CNN design through time, at the beggining people used to flatten features and send then to a linear layer.</p>
<p>Nowadays the common way is to use a pooling to get a 1D array and send that to a linear layer.<br>
Note that you are not interested in keeping the spatial features. So imagine your output is 256x8x8.</p>
<p>If you have the speech at the beginning of the track, the elements with useful info would be the [:,:,:]4 ones in the left.<br>
With max pooling the linear layer faces a simpler task.</p>

bencr: <p>Okay, thanks for the tip!</p>
<p>So I have been running a simplified version of my script and now the model is able to learn. I also tried to build a model based on 1D convolutions: the “time” axis becomes channels. I was reading that it makes more sense theoretically. It seems to work OK and way faster than the conv2D (due to less parameters)</p>
<p>However, I have another question regarding the training of the model. My dataset is very imbalanced: 95% of no speech for 5% of speech and it seems that the model struggle to “learn” what speech look like - I get up to 60% accuracy for speech. Is there any method or architecture I should look for to improve the performance on such dataset?</p>
<p>Note that the dataset is artifically created: I overlapped VoxCeleb / Librispeech voices on only 5% of the ecosystem record. This percentage was decided based on the real-life occurrence of human sound in an ecosystem.</p>
<p>Would it be better to build a balanced dataset for the model to better “learn” what speech look like, even though this is not a realistic situation. Or is it better to focus on improving the model with the 5% occurrence of speech?</p>
<p>Thanks for the help!</p>

puranjay_mishra: <p>Building a balanced data set is always better. Try image augmentation. But such a disparity (95-5)  would be hard to overcome even with image augmentation.</p>