This paper presents an end-to-end version of memory networks (Weston et al., 2015) such that the model doesn't train on the intermediate 'supporting facts' strong supervision of which input sentences are the best memory accesses, making it much more realistic. They also have multiple hops (computational steps) per output symbol. The tasks are Q&A and language modeling, and achieves strong results.

The paper is a useful extension of memNN because it removes the strong, unrealistic supervision requirement and still performs pretty competitively. The architecture is defined pretty cleanly and simply. The related work section is quite well-written, detailing the various similarities and differences with multiple streams of related work. The discussion about the model's connection to RNNs is also useful.

This paper from 2016 introduced a new k-mer based method to estimate isoform abundance from RNA-Seq data called kallisto.  The method provided a significant improvement in speed and memory usage compared to the previously used methods while yielding similar accuracy.   In fact, kallisto is able to quantify expression in a matter of minutes instead of hours.

The standard (previous) methods for quantifying expression rely on mapping, i.e. on the alignment of a transcriptome sequenced reads to a genome of reference.  Reads are assigned to a position in the genome and the gene or isoform expression values are derived by counting the number of reads overlapping the features of interest. 

The idea behind kallisto is to rely on a pseudoalignment which does not attempt to identify the positions of the reads in the transcripts, only the potential transcripts of origin. Thus,  it avoids doing an alignment of each read to a reference genome. In fact, kallisto only uses the transcriptome sequences (not the whole genome) in its first step which is the generation of  the kallisto index.  Kallisto builds a colored de Bruijn graph (T-DBG) from all the k-mers found in the transcriptome.  Each node of the graph corresponds to a k-mer (a short sequence of k nucleotides) and retains the information about the transcripts in which they can be found in the form of a color.  Linear stretches having the same coloring in the graph correspond to transcripts. Once the T-DBG is built, kallisto stores a hash table mapping each k-mer to its transcript(s) of origin along with the position within the transcript(s).  This step is done only once and is dependent on a provided annotation file (containing the sequences of all the transcripts in the transcriptome).  
  
Then for a given sequenced sample, kallisto decomposes each read into its k-mers and uses those k-mers to find a path covering in the T-DBG.  This path covering of the transcriptome graph, where a path corresponds to a transcript, generates k-compatibility classes for each k-mer, i.e. sets of potential transcripts of origin on the nodes.   The potential transcripts of origin for a read can be obtained using the intersection of its k-mers k-compatibility classes. To make the pseudoalignment faster, kallisto removes redundant k-mers since neighboring k-mers often belong to the same transcripts. Figure1, from the paper, summarizes these different steps.

https://i.imgur.com/eNH2kuO.png

**Figure1**. Overview of kallisto. The input consists of a reference transcriptome and reads from an RNA-seq experiment. (a) An example of a read (in black) and three overlapping transcripts with exonic regions as shown. (b) An index is constructed by creating the transcriptome de Bruijn Graph (T-DBG) where nodes (v1, v2, v3, ... ) are k-mers, each transcript corresponds to a colored path as shown and the path cover of the transcriptome induces a k-compatibility class for each k-mer. (c) Conceptually, the k-mers of a read are hashed (black nodes) to find the k-compatibility class of a read. (d) Skipping (black dashed lines) uses the information stored in the T-DBG to skip k-mers that are redundant because they have the same k-compatibility class. (e) The k-compatibility class of the read is determined by taking the intersection of the k-compatibility classes of its constituent k-mers.[From Bray et al. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology, 2016.]

Then, kallisto optimizes the following RNA-Seq likelihood function using the expectation-maximization (EM) algorithm.  

$$L(\alpha) \propto \prod_{f \in F} \sum_{t \in T} y_{f,t} \frac{\alpha_t}{l_t} = \prod_{e \in E}\left(  \sum_{t \in e} \frac{\alpha_t}{l_t} \right )^{c_e}$$

In this function,  $F$ is the set of fragments (or reads), $T$ is the set of transcripts, $l_t$ is the (effective) length of transcript $t$ and **y**$_{f,t}$ is a compatibility matrix defined as 1 if  fragment $f$ is compatible with $t$ and 0 otherwise.  The parameters $α_t$ are the probabilities of selecting reads from a transcript $t$.  These $α_t$ are the parameters of interest since they represent the isoforms abundances or relative expressions.

To make things faster, the compatibility matrix is collapsed (factorized) into equivalence classes. An equivalent class consists of all the reads compatible with the same subsets of transcripts. The EM algorithm is applied to equivalence classes (not to reads).  Each $α_t$ will be optimized to maximise the likelihood of transcript abundances given observations of the equivalence classes. The speed of the method makes it possible to evaluate the uncertainty of the  abundance estimates for each RNA-Seq sample using a bootstrap technique.  For a given sample containing $N$ reads, a bootstrap sample is generated from the sampling of $N$ counts from a multinomial distribution over the equivalence classes derived from the original sample.  The EM algorithm is applied on those sampled equivalence class counts to estimate transcript abundances. The bootstrap information is then used in downstream analyses such as determining which genes are differentially expressed.

Practically, we can illustrate the different steps involved in kallisto using a small example.  Starting from a tiny genome with 3 transcripts, assume that the RNA-Seq experiment produced 4 reads as depicted in the image below.

https://i.imgur.com/5JDpQO8.png

The first step is to build the T-DBG graph and the kallisto index.  All transcript sequences are decomposed into k-mers (here k=5) to construct the colored de Bruijn graph. Not all nodes are represented in the following drawing.  The idea is that each different transcript will lead to a different path in the graph.  The strand is not taken into account, kallisto is strand-agnostic.

https://i.imgur.com/4oW72z0.png

Once the index is built, the four reads of the sequenced sample can be analysed.  They are decomposed into k-mers (k=5 here too) and the pre-built index is used to determine the k-compatibility class of each k-mer. Then, the k-compatibility class of each read is computed. For example, for read 1, the intersection of all the k-compatibility classes of its k-mers suggests that it might come from transcript 1 or transcript 2.

https://i.imgur.com/woektCH.png

This is done for the four reads enabling the construction of the compatibility matrix  **y**$_{f,t}$ which is part of the RNA-Seq likelihood function.  In this equation, the $α_t$ are the parameters that we want to estimate.

https://i.imgur.com/Hp5QJvH.png

The EM algorithm being too slow to be applied on millions of reads, the compatibility matrix **y**$_{f,t}$ is factorized into equivalence classes and a count is computed for each class (how many reads are represented by this equivalence class). The EM algorithm uses this collapsed information to maximize the new equivalent RNA-Seq likelihood function and optimize the $α_t$.

https://i.imgur.com/qzsEq8A.png

The EM algorithm stops when for every transcript $t$, $α_tN$ > 0.01 changes less than 1%, where $N$ is the total number of reads. 

# Summary

This paper presents state-of-the-art methods for both caption generation of images and visual question answering (VQA). The authors build on previous methods by adding what they call a "bottom-up" approach to previous "top-down" attention mechanisms. They show that using their approach they obtain SOTA on both Image captioning (MSCOCO) and the Visual Question and Answering (2017 VQA challenge). They propose a specific network configurations for each. Their biggest contribution is using Faster-R-CNN to retrieve the "important" parts of an image to focus on in both models.

## Top Down

Up until this paper, the traditional approach was to use a "top-down" approach, in which the last feature map layer of a CNN is used to obtain a latent representation of the given input image. These features, along with the context of the caption being generated, were used to generate attention weights that were used to predict the next sequence in the context of caption generation. The network would learn to focus its attention on regions of the feature map that matters most. This is the approach used in previous SOTA methods like [Show, Attend and Tell: Neural Image Caption Generation with Visual Attention](https://arxiv.org/abs/1502.03044).

## Bottom-up

The authors argue that the feature map of a CNN is too generic and can be thought of operating on a uniform, grid-like feature map. In other words, there is no particular reason to think that the feature map of generated by a CNN would give optimal regions to attend to. Also, carefully choosing the dimensions of the feature map can be very arbitrary.

In order to fix this, the authors propose combining object detection methods in a *bottom-up* approach. To do so, the authors propose using Faster-R-CNN to identify regions of interest in an image. Given an input image, Faster-R-CNN will identify bounding boxes of the image that likely correspond to objects of a given category and simultaneously compute a feature vector of that bounding box. Figure 1 shows the difference between the Bottom-up and Top-Down approach.

![image](https://user-images.githubusercontent.com/18450628/61817263-2683cd00-ae1c-11e9-971a-d3b531dbbd98.png)

## Combining the two

In this paper, the authors suggest using the bottom-up approach to compute the salient regions of the image the network should focus on using Faster-R-CNN. FRCNN is carefully pretrained on both imagenet and the Visual Genome dataset. It is then frozen and only used to generate bounding boxes of regions with high confidence of being of interest. The top-down approach is then used on the features obtained from the bottom-up approach. In order to "enhance" the FRCNN performance, they initialize their FRCNN with a ResNet-101 pre-trained on imagenet. They train their FRCNN on the Visual Genome dataset, adding attributes to the loss function that are available from the Visual Genome dataset, attributes such as color (black, white, gold etc.),  state (open, close, dark, bright, etc.). A sample of FRCNN outputs are shown in figure 2. It is important to stress that only the feature representations and not the actual outputs (i.e. not the labels) are used in their model.

![image](https://user-images.githubusercontent.com/18450628/61817487-aca01380-ae1c-11e9-90fa-134033b95bb0.png)

## Caption Generation

Figure 3 provides a high-level overview of the model being used for caption generation for images. The image is first passed through FRCNN which produces a set of image features *V*. In their specific implementation, *V* consists of *k* vectors of size 1x2048. Their model consists of two LSTM blocks, one for attention and the other for language generation.

![image](https://user-images.githubusercontent.com/18450628/61818488-effb8180-ae1e-11e9-8ae4-14355115429a.png)

The first block of their model is a Top-Down Attention LSTM layer. It takes as input the mean-pooled features *V* , i.e. 1/k*sum(v_i), concatenated with the previous timestep's hidden representation of the language LSTM as well as the word embedding of the previously generated word. The word embedding is learned and not pretrained. 

The output of the first LSTM is used to compute the attention for each vector using an MLP and softmax:

![image](https://user-images.githubusercontent.com/18450628/61819982-21298100-ae22-11e9-80a9-99640896413d.png)

The attention weighted image feature is then used as an input to the language LSTM model, concatenated with the output from the top-down Attention LSTM and a softmax is used to predict the next word in the sequence. The loss function seeks to minimize the cross-entropy of the generated sentence. 

## VQA Model

The VQA task differs to the image generation in that a text-based question accompanies an input image and the network must produce an answer. The VQA model proposed is different to that of the caption generation model previously described, however they both use the same bottom-up approach to generate the feature vectors of the image based on the FRCNN architecture. A high-level overview of the architecture for the VQA model is presented in Figure 4.

![image](https://user-images.githubusercontent.com/18450628/61821988-8da67f00-ae26-11e9-8456-3c9e5ec60787.png)

Each word from the question is converted to a learned word embedding which is used as input to a GRU. The number of words for each question is limited to 14 for computational efficiency. The output from the GRU is concatenated with each of the *k* image features, and attention weights are computed for each *k*th feature using an MLP and softmax, similar to what is done in the attention for caption generation. The weighted sum of the feature vectors is then passed through an linear layer such that its shape is compatible with the gru output, and the Hadamard product (element-wise product) is computed over the GRU output and attention-weighted image feature representation. Finally, a tanh non-linear activation is used. This results in a "gated tanh", which have been shown empirically to outperform both ReLU and tanh. Finally, a softmax probability distribution is generated at the output which selects a candidate answer among all possible candidate answers.

## Results and experiments

### Resnet Baseline

To demonstrate that their contribution of bottom-up mechanism actually improves on results, the authors use a ResNet trained on imagenet as a baseline for generating the image feature vectors (they resize the final CNN layers using bilinear interpolation when needed). They consistently obtain better results when using the bottom-up approach over the ResNet approach in both caption generation and VQA.

## MSCOCO

The authors demonstrate that they outperform all results on all metrics on the MSCOCO test server.

![image](https://user-images.githubusercontent.com/18450628/61824157-4f5f8e80-ae2b-11e9-8d90-657db453e26e.png)

They also show how using the bottom-up approach over ResNet consistently scores them higher on detecting instances of objects, attributes, relations, etc:

![image](https://user-images.githubusercontent.com/18450628/61824238-7fa72d00-ae2b-11e9-81b3-b5a7f80153f3.png)

The authors, like their predecessors, insist on demonstrating their network's frisbee ability:

![image](https://user-images.githubusercontent.com/18450628/61824344-bed57e00-ae2b-11e9-87cd-597568587e1d.png)

## VQA Results

They also demonstrate that the addition of bottom-up attention improves results over a ResNet baseline. 

![image](https://user-images.githubusercontent.com/18450628/61824500-28ee2300-ae2c-11e9-9016-2120a91917e4.png)

They also show that their model outperformed all other submissions on the VQA submission. They mention using an ensemble of 30 models for their submission. 

![image](https://user-images.githubusercontent.com/18450628/61824634-83877f00-ae2c-11e9-8d84-9589e0ea2be2.png)


A sample image of what is attended in an image given a proper answer is shown in figure 6.

![image](https://user-images.githubusercontent.com/18450628/61824608-736f9f80-ae2c-11e9-9d4e-8cb6bd0a1a92.png)


# Comments

The authors introduce a new way to select portions of the image on which to focus attention. The idea is very original and came at a time when object detection was making significant progress (i.e. FRCNN).

A few comments:

* This method might not generalize well to other types of data. It requires pre-training on larger datasets (visual genome, imagenet, etc.) which consist of categories that overlap with both the MSCOCO and VQA datasets (i.e. cars, people, etc.). It would be interesting to see an end-to-end model that does not rely on pre-training on other similar datasets.

* No insight is given to the computational complexity nor to the inference time or training time. I imagine that FRCNN is resource intensive, and having to do a forward pass of FRCNN for every pass of the network must be a computational bottleneck. Not to mention that they ensembled 30 of them!

**TL;DR**: Rearranging the terms in Maximum Mean Discrepancy yields a much better loss function for the discriminator of Generative Adversarial Nets.

**Keywords**: Generative adversarial nets, Maximum Mean Discrepancy, spectral normalization, convolutional neural networks, Gaussian kernel, local stability.

**Summary**

Generative adversarial nets (GANs) are widely used to learn the data sampling process and are notoriously difficult to train. The training of GANs may be improved from three aspects: loss function, network architecture, and training process.

This study focuses on a loss function called the Maximum Mean Discrepancy (MMD), defined as:
$$
MMD^2(P_X,P_G)=\mathbb{E}_{P_X}k_{D}(x,x')+\mathbb{E}_{P_G}k_{D}(y,y')-2\mathbb{E}_{P_X,P_G}k_{D}(x,y)
$$
where $G,D$ are the generator and discriminator networks, $x,x'$ are real samples, $y,y'$ are generated samples, $k_D=k\circ D$ is a learned kernel that calculates the similariy between two samples. Overall, MMD calculates the distance between the real and the generated sample distributions. Thus, traditionally, the generator is trained to minimize $L_G=MMD^2(P_X,P_G)$, while the discriminator minimizes $L_D=-MMD^2(P_X,P_G)$.

This study makes three contributions:
-  It argues that $L_D$ encourages the discriminator to ignores the fine details in real data. By minimizing $L_D$, $D$ attempts to maximize $\mathbb{E}_{P_X}k_{D}(x,x')$, the similarity between real samples scores. Thus, $D$ has to focus on common features shared by real samples rather than fine details that separate them. This may slow down training. Instead, a repulsive loss is proposed, with no additional computational cost to MMD:
$$
L_D^{rep}=\mathbb{E}_{P_X}k_{D}(x,x')-\mathbb{E}_{P_G}k_{D}(y,y')
$$
- Inspired by the hinge loss, this study proposes a bounded Gaussian kernel for the discriminator to facilitate stable training of MMD-GAN.
- The spectral normalization method divides the weight matrix at each layer by its spectral norm to enforce that each layer is Lipschitz continuous. This study proposes a simple method to calculate the spectral norm of a convolutional kernel.

The results show the efficiency of proposed methods on CIFAR-10, STL-10, CelebA and LSUN-bedroom datasets. In Appendix, we prove that MMD-GAN training using gradient method is locally exponentially stable (a property that the Wasserstein loss does not have), and show that the repulsive loss works well with gradient penalty. 

The paper has been accepted at ICLR 2019 ([OpenReview link](https://openreview.net/forum?id=HygjqjR9Km)). The code is available at [GitHub link](https://github.com/richardwth/MMD-GAN). 

Lee et al. propose a regularizer to increase the size of linear regions of rectified deep networks around training and test points. Specifically, they assume piece-wise linear networks, in its most simplistic form consisting of linear layers (fully connected layers, convolutional layers) and ReLU activation functions. In these networks, linear regions are determined by activation patterns, i.e., a pattern indicating which neurons have value greater than zero. Then, the goal is to compute, and later to increase, the size $\epsilon$ such that the $L_p$-ball of radius $\epsilon$ around a sample $x$, denoted $B_{\epsilon,p}(x)$ is contained within one linear region (corresponding to one activation pattern). Formally, letting $S(x)$ denote the set of feasible inputs $x$ for a given activation pattern, the task is to determine

$\hat{\epsilon}_{x,p} = \max_{\epsilon \geq 0, B_{\epsilon,p}(x) \subset S(x)} \epsilon$.

For $p = 1, 2, \infty$, the authors show how $\hat{\epsilon}_{x,p}$ can be computed efficiently. For $p = 2$, for example, it results in

$\hat{\epsilon}_{x,p} = \min_{(i,j) \in I} \frac{|z_j^i|}{\|\nabla_x z_j^i\|_2}$.

Here, $z_j^i$ corresponds to the $j$th neuron in the $i$th layer of a multi-layer perceptron with ReLU activations; and $I$ contains all the indices of hidden neurons. This analytical form can then used to add a regularizer to encourage the network to learn larger linear regions:

$\min_\theta \sum_{(x,y) \in D} \left[\mathcal{L}(f_\theta(x), y) - \lambda \min_{(i,j) \in I} \frac{|z_j^i|}{\|\nabla_x z_j^i\|_2}\right]$

where $f_\theta$ is the neural network with paramters $\theta$. In the remainder of the paper, the authors propose a relaxed version of this training procedure that resembles a max-margin formulation and discuss efficient computation of the involved derivatives $\nabla_x z_j^i$ without too many additional forward/backward passes.

https://i.imgur.com/jSc9zbw.jpg
Figure 1: Visualization of locally linear regions for three different models on toy 2D data.

On toy data and datasets such as MNIST and CalTech-256, it is shown that the training procedure is effective in the sense that larger linear regions around training and test points are learned. For example, on a 2D toy dataset, Figure 1 visualizes the linear regions for the optimal regularizer as well as the proposed relaxed version.

Also find this summary at [davidstutz.de](https://davidstutz.de/category/reading/).