Larry  Kessler

Larry Kessler

1618413960

Medical Report Generation Using Deep Learning

Table of Contents

  1. Overview
  2. Prerequisites
  3. Business Problem
  4. Data Analysis
  5. ML Formulation
  6. Performance Metric
  7. Data preparation
  8. Modeling
  9. Comparison of models
  10. Model Deployment
  11. Future Works
  12. Profile
  13. References

#image-captioning #machine-learning #deep-learning #data-science #attention-model

What is GEEK

Buddha Community

Medical Report Generation Using Deep Learning
Marget D

Marget D

1618317562

Top Deep Learning Development Services | Hire Deep Learning Developer

View more: https://www.inexture.com/services/deep-learning-development/

We at Inexture, strategically work on every project we are associated with. We propose a robust set of AI, ML, and DL consulting services. Our virtuoso team of data scientists and developers meticulously work on every project and add a personalized touch to it. Because we keep our clientele aware of everything being done associated with their project so there’s a sense of transparency being maintained. Leverage our services for your next AI project for end-to-end optimum services.

#deep learning development #deep learning framework #deep learning expert #deep learning ai #deep learning services

Mikel  Okuneva

Mikel Okuneva

1603735200

Top 10 Deep Learning Sessions To Look Forward To At DVDC 2020

The Deep Learning DevCon 2020, DLDC 2020, has exciting talks and sessions around the latest developments in the field of deep learning, that will not only be interesting for professionals of this field but also for the enthusiasts who are willing to make a career in the field of deep learning. The two-day conference scheduled for 29th and 30th October will host paper presentations, tech talks, workshops that will uncover some interesting developments as well as the latest research and advancement of this area. Further to this, with deep learning gaining massive traction, this conference will highlight some fascinating use cases across the world.

Here are ten interesting talks and sessions of DLDC 2020 that one should definitely attend:

Also Read: Why Deep Learning DevCon Comes At The Right Time


Adversarial Robustness in Deep Learning

By Dipanjan Sarkar

**About: **Adversarial Robustness in Deep Learning is a session presented by Dipanjan Sarkar, a Data Science Lead at Applied Materials, as well as a Google Developer Expert in Machine Learning. In this session, he will focus on the adversarial robustness in the field of deep learning, where he talks about its importance, different types of adversarial attacks, and will showcase some ways to train the neural networks with adversarial realisation. Considering abstract deep learning has brought us tremendous achievements in the fields of computer vision and natural language processing, this talk will be really interesting for people working in this area. With this session, the attendees will have a comprehensive understanding of adversarial perturbations in the field of deep learning and ways to deal with them with common recipes.

Read an interview with Dipanjan Sarkar.

Imbalance Handling with Combination of Deep Variational Autoencoder and NEATER

By Divye Singh

**About: **Imbalance Handling with Combination of Deep Variational Autoencoder and NEATER is a paper presentation by Divye Singh, who has a masters in technology degree in Mathematical Modeling and Simulation and has the interest to research in the field of artificial intelligence, learning-based systems, machine learning, etc. In this paper presentation, he will talk about the common problem of class imbalance in medical diagnosis and anomaly detection, and how the problem can be solved with a deep learning framework. The talk focuses on the paper, where he has proposed a synergistic over-sampling method generating informative synthetic minority class data by filtering the noise from the over-sampled examples. Further, he will also showcase the experimental results on several real-life imbalanced datasets to prove the effectiveness of the proposed method for binary classification problems.

Default Rate Prediction Models for Self-Employment in Korea using Ridge, Random Forest & Deep Neural Network

By Dongsuk Hong

About: This is a paper presentation given by Dongsuk Hong, who is a PhD in Computer Science, and works in the big data centre of Korea Credit Information Services. This talk will introduce the attendees with machine learning and deep learning models for predicting self-employment default rates using credit information. He will talk about the study, where the DNN model is implemented for two purposes — a sub-model for the selection of credit information variables; and works for cascading to the final model that predicts default rates. Hong’s main research area is data analysis of credit information, where she is particularly interested in evaluating the performance of prediction models based on machine learning and deep learning. This talk will be interesting for the deep learning practitioners who are willing to make a career in this field.


#opinions #attend dldc 2020 #deep learning #deep learning sessions #deep learning talks #dldc 2020 #top deep learning sessions at dldc 2020 #top deep learning talks at dldc 2020

Few Shot Learning — A Case Study (2)

In the previous blog, we looked into the fact why Few Shot Learning is essential and what are the applications of it. In this article, I will be explaining the Relation Network for Few-Shot Classification (especially for image classification) in the simplest way possible. Moreover, I will be analyzing the Relation Network in terms of:

  1. Effectiveness of different architectures such as Residual and Inception Networks
  2. Effects of transfer learning via using pre-trained classifier on ImageNet dataset

Moreover, effectiveness will be evaluated on the accuracy, time required for training, and the number of required training parameters.

Please watch the GitHub repository to check out the implementations and keep updated with further experiments.

Introduction to Few-Shot Classification

In few shot classification, our objective is to design a method which can identify any object images by analyzing few sample images of the same class. Let’s the take one example to understand this. Suppose Bob has a client project to design a 5 class classifier, where 5 classes can be anything and these 5 classes can even change with time. As discussed in previous blog, collecting the huge amount of data is very tedious task. Hence, in such cases, Bob will rely upon few shot classification methods where his client can give few set of example images for each classes and after that his system can perform classification young these examples with or without the need of additional training.

In general, in few shot classification four terminologies (N way, K shot, support set, and query set) are used.

  1. N way: It means that there will be total N classes which we will be using for training/testing, like 5 classes in above example.
  2. K shot: Here, K means we have only K example images available for each classes during training/testing.
  3. Support set: It represents a collection of all available K examples images from each classes. Therefore, in support set we have total N*K images.
  4. Query set: This set will have all the images for which we want to predict the respective classes.

At this point, someone new to this concept will have doubt regarding the need of support and query set. So, let’s understand it intuitively. Whenever humans sees any object for the first time, we get the rough idea about that object. Now, in future if we see the same object second time then we will compare it with the image stored in memory from the when we see it for the first time. This applied to all of our surroundings things whether we see, read, or hear. Similarly, to recognise new images from query set, we will provide our model a set of examples i.e., support set to compare.

And this is the basic concept behind Relation Network as well. In next sections, I will be giving the rough idea behind Relation Network and I will be performing different experiments on 102-flower dataset.

About Relation Network

The Core idea behind Relation Network is to learn the generalized image representations for each classes using support set such that we can compare lower dimensional representation of query images with each of the class representations. And based on this comparison decide the class of each query images. Relation Network has two modules which allows us to perform above two tasks:

  1. Embedding module: This module will extract the required underlying representations from each input images irrespective of the their classes.
  2. Relation Module: This module will score the relation of embedding of query image with each class embedding.

Training/Testing procedure:

We can define the whole procedure in just 5 steps.

  1. Use the support set and get underlying representations of each images using embedding module.
  2. Take the average of between each class images and get the single underlying representation for each class.
  3. Then get the embedding for each query images and concatenate them with each class’ embedding.
  4. Use the relation module to get the scores. And class with highest score will be the label of respective query image.
  5. [Only during training] Use MSE loss functions to train both (embedding + relation) modules.

Few things to know during the training is that we will use only images from the set of selective class, and during the testing, we will be using images from unseen classes. For example, from the 102-flower dataset, we will use 50% classes for training, and rest will be used for validation and testing. Moreover, in each episode, we will randomly select 5 classes to create the support and query set and follow the above 5 steps.

That is all need to know about the implementation point of view. Although the whole process is simple and easy to understand, I’ll recommend reading the published research paper, Learning to Compare: Relation Network for Few-Shot Learning, for better understanding.

#deep-learning #few-shot-learning #computer-vision #machine-learning #deep learning #deep learning

Medical Report Generation Using Deep Learning

1. Introduction

Image Captioning is a challenging artificial intelligence problem which refers to the process of generating textual description from an image based on the image contents. For instance, look at the picture below:

Image for post

A common answer would be “A woman playing a guitar”. We as humans can look at a picture and describe whatever it is in it, in an appropriate language. This is easy. Let me show you another one:

Image for post

Well, how would you describe this one?

For all of us ‘non-radiologists’, a common answer would be _“a chest x-ray”. _Well, we are not wrong but a radiologist might have some different interpretations. They write textual reports to narrate the findings regarding each area of the body examined in the imaging study, specifically whether each area was found to be normal, abnormal or potentially abnormal. They can derive such valuable information and make medical reports from one such image.

For less-experienced radiologists and pathologists, especially those working in the rural areas where the quality of healthcare is relatively low, writing medical-imaging reports is demanding or on the other hand for experienced radiologists and pathologists, writing imaging reports can be tedious and time consuming.

So, to address all these matters, wouldn’t it be great if a computer can take a chest x-ray like the one above as input and output the findings as text just like how a radiologist would do?

Image for post

Image by the Author | Are we asking a machine to be a doctor now?!!

But, can you indeed write such a computer program? Well, if the answer was ‘no’, you wouldn’t be reading this story.

2. Prerequisites

This work assumes some deep learning familiarity with topics like Neural Nets, CNNs, RNNs, Transfer Learning, Python programming and Keras library. The two below mentioned models will be used for our problem, which will be explained briefly later in this blog itself:

  1. Encoder-Decoder Model
  2. Attention-Mechanism

Decent knowledge about them will help you understand the models better.

3. Data

You can obtain the data needed for this problem from the below links:

  • Images**_- _**Contains all the chest X-rays.
  • Reports**_- _**Contains the corresponding reports for the above images.

The image dataset contains multiple chest x-rays of a single person. For instance: side-view of the x-ray, multiple frontal views etc. Just as a radiologist uses all these images to write the findings, the models will also use all these images together to generate the corresponding findings. There are 3955 reports present in the dataset, with each report having one or more images associated with it.

3.1. Extracting the Required Data From the XML files

The reports in the dataset are XML files where each file corresponds to an individual. The image IDs and the corresponding findings associated with that person is contained in these files. An example is shown below:

Image for post

Image for post

The left image shows the ‘findings’ in the file whereas the right image shows the given image IDs of the same file

The highlighted info are the things that you need to extract from these files. This can be done with the help of python’s XML library.

**NOTE: **The findings will be also referred to as reports. They will be used interchangeably in the rest of the blog.

Extracting Findings and Reports from the XML file

4. Obtaining Structured Data

After extracting the required data from the XML files, the data is converted into a structured format for easy understanding and accessibility. As mentioned before, there are multiple images associated with a single report. Therefore, our model also needs to see these images while generating reports. But some reports have only 1 image associated with it, while some have 2 and the maximum being 4.

Image for post

Image by the Author | Graph showing the number of Images associated per report

So the question arises, how many images should we feed into the model at a time to generate a report? To make the model-input consistent, pairs of images i.e two images were chosen at a time as input. If a report only had 1 image, the same image would be replicated as the second input.

Image for post

A glance on how the structured data would look like

Now we have a proper and understandable structured data to work with. The images are saved by the names of their absolute address. This will be helpful while loading the data.

5. Prepare Text Data

After obtaining the findings from the XML file, they should be properly cleaned and prepared before we feed it into the model. Below image shows a few examples of how findings would look like before its cleaned.

Image for post

Example Findings before they are cleaned

We will clean the text in the following ways:

  1. Convert all characters into lowercase.
  2. Perform basic decontractions i.e words like won’t, can’t and so on will be converted to will not, cannot and so on respectively.
  3. Remove punctuation from text. Note that full stop will not be removed because the findings contain multiple sentences, so we need the model to generate reports in a similar way by identifying sentences.
  4. Remove all numbers from the text.
  5. Remove all words with length less than or equal to 2. For example, ‘is’, ‘to’ etc are removed. These words don’t provide much information. But the word ‘no’ will not be removed since it adds value. Adding ‘no’ to a sentence changes its meaning entirely. So we have to be careful while performing these kind of cleaning steps. You need to identify which words to keep and which ones to avoid.
  6. It was also found that some texts contain multiple full stops or spaces or ‘X’ repeated multiple times. Such characters are also removed.

The model we will develop will generate a report given a combination of two images, and the report will be generated one word at a time. The sequence of previously generated words will be provided as input. Therefore, we will need a ‘first word’ to kick-off the generation process and a ‘last word’ to signal the end of the report. We will use the strings ‘startseq’ and ‘endseq’ for this purpose. These strings are added to our findings. It is important to do this now because when we encode the text, we need these strings to be encoded correctly.

The major step in encoding text is to create a consistent mapping from words to unique integer values known as tokenization. In order to get our computer to understand any text, we need to break that word or sentence down in a way that our machine can understand. We can’t work with text data if we don’t perform tokenization. Tokenization is a way of separating a piece of text into smaller units called tokens. Tokens can be either words or characters but in our case it’ll be words. Keras provides an inbuilt library for this purpose.

from tensorflow.keras.preprocessing.text import Tokenizer
tokenizer = Tokenizer(filters='!"#$%&()*+,-/:;<=>?@[\\]^_`{|}~\t\n')
tokenizer.fit_on_texts(reports)

Now the text that we have are properly cleaned and tokenized for future use. The full code for all this is available in my GitHub account whose link is provided at the end of this story.

#encoder-decoder #deep-learning #image-captioning #attention-mechanism #artificial-intelligence #deep learning

Tia  Gottlieb

Tia Gottlieb

1595573880

Deep Reinforcement Learning for Video Games Made Easy

In this post, we will investigate how easily we can train a Deep Q-Network (DQN) agent (Mnih et al., 2015) for Atari 2600 games using the Google reinforcement learning library Dopamine. While many RL libraries exist, this library is specifically designed with four essential features in mind:

  • Easy experimentation
  • Flexible development
  • Compact and reliable
  • Reproducible

_We believe these principles makes __Dopamine _one of the best RL learning environment available today. Additionally, we even got the library to work on Windows, which we think is quite a feat!

In my view, the visualization of any trained RL agent is an absolute must in reinforcement learning! Therefore, we will (of course) include this for our own trained agent at the very end!

We will go through all the pieces of code required (which is** minimal compared to other libraries**), but you can also find all scripts needed in the following Github repo.

1. Brief Introduction to Reinforcement Learning and Deep Q-Learning

The general premise of deep reinforcement learning is to

“derive efficient representations of the environment from high-dimensional sensory inputs, and use these to generalize past experience to new situations.”

  • Mnih et al. (2015)

As stated earlier, we will implement the DQN model by Deepmind, which only uses raw pixels and game score as input. The raw pixels are processed using convolutional neural networks similar to image classification. The primary difference lies in the objective function, which for the DQN agent is called the optimal action-value function

Image for post

where_ rₜ is the maximum sum of rewards at time t discounted by γ, obtained using a behavior policy π = P(a_∣_s)_ for each observation-action pair.

There are relatively many details to Deep Q-Learning, such as Experience Replay (Lin, 1993) and an _iterative update rule. _Thus, we refer the reader to the original paper for an excellent walk-through of the mathematical details.

One key benefit of DQN compared to previous approaches at the time (2015) was the ability to outperform existing methods for Atari 2600 games using the same set of hyperparameters and only pixel values and game score as input, clearly a tremendous achievement.

2. Installation

This post does not include instructions for installing Tensorflow, but we do want to stress that you can use both the CPU and GPU versions.

Nevertheless, assuming you are using Python 3.7.x, these are the libraries you need to install (which can all be installed via pip):

tensorflow-gpu=1.15   (or tensorflow==1.15  for CPU version)
cmake
dopamine-rl
atari-py
matplotlib
pygame
seaborn
pandas

#reinforcement-learning #q-learning #games #machine-learning #deep-learning #deep learning