Im currenty working on a project at University, where we are using python + tensorflow and keras to train an image object detector, to detect different parts of the root system of Arabidopsis.
Our current ressults are pretty bad, as we do only have about 100 images to train the model with at this moment, but we are currently working on cultuvating more plants in order to get more images(more data) to train the tensorflow model.
We have implemented the following Mask_RCNN model:Github- Mask_RCNN tensorflow
We are looking to detect three object clases: stem, main root and secondary root.
But the model detects main roots incorrectly where the secondary roots are located.
It should be able to detect something like this:Root detection example
Training root data set that we are using right now:training images
What is the usual sample size that is used to train a neural network accurate results?
First off: I think there is no simple rule to estimate the sample size but at least it depends on:
1. Quality of your images
I downloaded the images and I think you need to preprocess them before you can use it to reduce the "problem complexity". In some projects, in which I worked with biological data, a background removal (image - low pass filter) was the key to get better results. But you should definitely remove/crop the area outside the region of your interest (like the tape and the ruler). I would try to get the cleanest data set as possible (including manually adjustments cv2/ gimp/ etc.) to focus the network to solve "the right problem".. After that you could apply some random distortion to make it also work on fuzzy/bad/realistic images as well.
2. The way you work with your data
There are a few tricks that enables you to "expand" your dataset.
Sometimes it's very helpful to let a generator method crop random small patches from your input data. This allows you to work with more batches (on small gpus) and gives your network more "variety", (just think about the conv2d task: if you don't use random cropping your filters will slide over the same areas over and over again (at the same image)). Because of the same reason: apply random distortion, flip and rotate your images.
3. Network architecture
In your case I would prefer a U-Net architecture with a last conv2d output of 3 (your classes) feature maps, a final softmax activation and an categorical_crossentropy, this enables you to play with the depth, because sometimes you need sophisticated architectures to solve a problem (close to 100%) but in your case you just want to see a first working result. So fewer layers and a simple architecture could also help you to get things work. Maybe there are some trained network weights for a U-Net which meets your requirements (search on kaggle for example). Because it is also helpful (to reduce the data you need) to use "transfer learning" -> use the first layers of an network (weights) which is already trained. Using a semantic segmentation the first filters will become something like an edge detection for the most given problems/images.
4. Your mental model of "accurate results"
This is the hardest part.. because it evolves during your project. Eg. in the same moment your networks starts to perform well on preprocessed input images you will start to think about architecture/data changes to make it work on fuzzy images as well. This is why you should start with a feasible problem but always improve your dataset (including rare kinds of roots) and tune your network architecture step by step.
Related
I am currently testing out custom object detection using the Tensorflow API. But I don't quite seem to understand the theory behind it.
So if I for example download a version of MobileNet and use it to train on, lets say, red and green apples. Does it forget all the things that is has already been trained on? And if so, why does it then benefit to use MobileNet over building a CNN from scratch.
Thanks for any answers!
Does it forget all the things that is has already been trained on?
Yes, if you re-train a CNN previously trained on a large database with a new database containing fewer classes it will "forget" the old classes. However, the old pre-training can help learning the new classes, this is a training strategy called "transfert learning" of "fine tuning" depending on the exact approach.
As a rule of thumb it is generally not a good idea to create a new network architecture from scratch as better networks probably already exist. You may want to implement your custom architecture if:
You are learning CNN's and deep learning
You have a specific need and you proved that other architectures won't fit or will perform poorly
Usually, one take an existing pre-trained network and specialize it for their specific task using transfert learning.
A lot of scientific literature is available for free online if you want to learn. you can start with the Yolo series and R-CNN, Fast-RCNN and Faster-RCNN for detection networks.
The main concept behind object detection is that it divides the input image in a grid of N patches, and then for each patch, it generates a set of sub-patches with different aspect ratios, let's say it generates M rectangular sub-patches. In total you need to classify MxN images.
In general the idea is then analyze each sub-patch within each patch . You pass the sub-patch to the classifier in your model and depending on the model training, it will classify it as containing a green apple/red apple/nothing. If it is classified as a red apple, then this sub-patch is the bounding box of the object detected.
So actually, there are two parts you are interested in:
Generating as many sub-patches as possible to cover as many portions of the image as possible (Of course, the more sub-patches, the slower your model will be) and,
The classifier. The classifier is normally an already exisiting network (MobileNeet, VGG, ResNet...). This part is commonly used as the "backbone" and it will extract the features of the input image. With the classifier you can either choose to training it "from zero", therefore your weights will be adjusted to your specific problem, OR, you can load the weigths from other known problem and use them in your problem so you won't need to spend time training them. In this case, they will also classify the objects for which the classifier was training for.
Take a look at the Mask-RCNN implementation. I find very interesting how they explain the process. In this architecture, you will not only generate a bounding box but also segment the object of interest.
[![enter image description here][1]][1]I am actually reconstructing some images using dual photography. Next, I want to train a network to reconstruct clear images by removing noise (Denoising autoencoder).
The input for training the network is reconstructed images, whereas, the output is ground truth or computer based standard test images. Now the input e.g., Lena is some how not exact version of Lena with image shifted in positions and some artifacts.
If I keep input as my reconstructed image and training output as Lena test image (computer standard test image) , will it work?
I only want to know if input/output shifted or some details missing in one of them (due to some cropping) would work.
It depends on many factors like your images for training and the architecture of the network.
However, what you want to do is to make a network that learns the noise or low level information and for this purpose Generative Adversarial Networks (GAN) are very popular. You can read about them here. Maybe, after you have tried your approach and if the results are not satisfactory then try using GANs, like, DCGAN (Deep Convolution GAN).
Also, share your outcomes with the community if you would like.
Denoising Autoencoders! Love it!
There is no reason for not training your model with those images. The autoencoder, if well trained, will eventually learn the transformation if there is enough data.
However, if you have the 'positive' images, I strongly recommend you to create your own noisy images and then train in that controlled working area. You will simplify your problem and it will be easier to solve.
What is stopping you from doing just that?
My question is about finding an efficient (mostly in term of parameters count) way to implement a sliding window in tensorflow (1.4) in order to apply a neural network through the image and produce a 2-d map with each pixel (or region) representing the network output for the corresponding receptive field (which in this case is the sliding window itself).
In practice, I'm trying to implement either a MTANN or a PatchGAN using tensorflow, but I cannot understand the implementation I found.
The two architectures can be briefly described as:
MTANN: A linear neural network with input size of [1,N,N,1] and output size [ ] is applied to an image of size [1,M,M,1] to produce a map of size [1,G,G,1], in which every pixel of the generated map corresponds to a likelihood of the corresponding NxN patch to belong to a certain class.
PatchGAN Discriminator: More general architecture, as I can understand the network that is strided through the image outputs a map itself instead of a single value, which then is combined with adjacent maps to produce the final map.
While I cannot find any tensorflow implementation of MTANN, I found the PatchGAN implementation, which is considered as a convolutional network, but I couldn't figure out how to implement this in practice.
Let's say I got a pre-trained network of which I got the output tensor. I understand that convolution is the way to go, since a convolutional layer operates over a local region of the input and what is I'm trying to do can be clearly represented as a convolutional network. However, what if I already have the network that generates the sub-maps from a given window of fixed-size?
E.g. I got a tensor
sub_map = network(input_patch)
which returns a [1,2,2,1] maps from a [1,8,8,3] image (corresponding to a 3-layer FCN with input size 8, filter size 3x3).
How can I sweep this network on [1,64,64,3] images, in order to produce a [1,64,64,1] map composed of each spatial contribution, like it happens in a convolution?
I've considered these solutions:
Using tf.image.extract_image_patches which explicitly extract all the image patches and channels in the depth dimension, but I think it would consume too many resources, as I'm switching to PatchGAN Discriminator from a full convolutional network due to memory constraints - also the composition of the final map is not so straight-forward.
Adding a convolutional layer before the network I got, but I cannot figure out what the filter (and its size) should be in this case in order to keep the pretrained model work on 8x8 images while integrating it in a model which works on bigger images.
For what I can get it should be something like whole_map = tf.nn.convolution(input=x64_images, filter=sub_map, ...) but I don't think this would work as the filter is an operator which depends on the receptive field itself.
The ultimate goal is to apply this small network to big images (eg. 1024x1024) in an efficient way, since my current model downscales progressively the images and wouldn't fit in memory due to the huge number of parameters.
Can anyone help me to get a better understanding of what I am missing?
Thank you
I found an interesting video by Andrew Ng exactly on how to implement a sliding window using a convolutional layer.
The problem here was that I was thinking at the number of layers as a variable that is dependent on a fixed input/output shape, while it should be the opposite.
In principle, a saved model should only contain the learned filters for each level and as long as the filter shapes are compatible with the layers' input/output depth. Thus, applying a different (ie. bigger) spatial resolution to the network input produces a different output shape, which can be seen as an application of the neural network to a sliding windows sweeping across the input image.
I'm using cnn built by keras(tensorflow) to do visual recognition.
I wonder if there is a way to know what my own tensorflow model "see".
Google had a news showing the cat face in the AI brain.
https://www.smithsonianmag.com/innovation/one-step-closer-to-a-brain-79159265/
Can anybody tell me how to take out the image in my own cnn networks.
For example, what my own cnn model recognize a car?
We have to distinguish between what Tensorflow actually see:
As we go deeper into the network, the feature maps look less like the
original image and more like an abstract representation of it. As you
can see in block3_conv1 the cat is somewhat visible, but after that it
becomes unrecognizable. The reason is that deeper feature maps encode
high level concepts like “cat nose” or “dog ear” while lower level
feature maps detect simple edges and shapes. That’s why deeper feature
maps contain less information about the image and more about the class
of the image. They still encode useful features, but they are less
visually interpretable by us.
and what we can reconstruct from it as a result of some kind of reverse deconvolution (which is not a real math deconvolution in fact) process.
To answer to your real question, there is a lot of good example solution out there, one you can study it with success: Visualizing output of convolutional layer in tensorflow.
When you are building a model to perform visual recognition, you actually give it similar kinds of labelled data or pictures in this case to it to recognize so that it can modify its weights according to the training data. If you wish to build a model that can recognize a car, you have to perform training on a large train data containing labelled pictures. This type of recognition is basically a categorical recognition.
You can experiment with the MNIST dataset which provides with a dataset of pictures of digits for image recognition.
Open CV provides a simple API to detect and extract faces from given images. ( I do not think it works perfectly fine though because I experienced that it cuts frames from the input pictures that have nothing to do with face images. )
I wonder if tensorflow API can be used for face detection. I failed finding relevant information but hoping that maybe an experienced person in the field can guide me on this subject. Can tensorflow's object detection API be used for face detection as well in the same way as Open CV does? (I mean, you just call the API function and it gives you the face image from the given input image.)
You can, but some work is needed.
First, take a look at the object detection README. There are some useful articles you should follow. Specifically: (1) Configuring an object detection pipeline, (3) Preparing inputs and (3) Running locally. You should start with an existing architecture with a pre-trained model. Pretrained models can be found in Model Zoo, and their corresponding configuration files can be found here.
The most common pre-trained models in Model Zoo are on COCO dataset. Unfortunately this dataset doesn't contain face as a class (but does contain person).
Instead, you can start with a pre-trained model on Open Images, such as faster_rcnn_inception_resnet_v2_atrous_oid, which does contain face as a class.
Note that this model is larger and slower than common architectures used on COCO dataset, such as SSDLite over MobileNetV1/V2. This is because Open Images has a lot more classes than COCO, and therefore a well working model need to be much more expressive in order to be able to distinguish between the large amount of classes and localizing them correctly.
Since you only want face detection, you can try the following two options:
If you're okay with a slower model which will probably result in better performance, start with faster_rcnn_inception_resnet_v2_atrous_oid, and you can only slightly fine-tune the model on the single class of face.
If you want a faster model, you should probably start with something like SSDLite-MobileNetV2 pre-trained on COCO, but then fine-tune it on the class of face from a different dataset, such as your own or the face subset of Open Images.
Note that the fact that the pre-trained model isn't trained on faces doesn't mean you can't fine-tune it to be, but rather that it might take more fine-tuning than a pre-trained model which was pre-trained on faces as well.
just increase the shape of the input, I tried and it's work much better