This method is based on improving the speed of R-CNN \cite{conf/cvpr/GirshickDDM14}

1. Where R-CNN would have two different objective functions, Fast R-CNN combines localization and classification losses into a "multi-task loss" in order to speed up training.
2. It also uses a pooling method based on \cite{journals/pami/HeZR015} called the RoI pooling layer that scales the input so the images don't have to be scaled before being set an an input image to the CNN. "RoI max pooling works by dividing the $h \times w$ RoI window into an $H \times W$ grid of sub-windows of approximate size $h/H \times w/W$ and then max-pooling the values in each sub-window into the corresponding output grid cell."
3. Backprop is performed for the RoI pooling layer by taking the argmax of the incoming gradients that overlap the incoming values.

This method is further improved by the paper "Faster R-CNN" \cite{conf/nips/RenHGS15}

Deeper networks should never have a higher **training** error than smaller ones. In the worst case, the layers should "simply" learn identities. It seems as this is not so easy with conventional networks, as they get much worse with more layers. So the idea is to add identity functions which skip some layers. The network only has to learn the **residuals**. 

Advantages:

* Learning the identity becomes learning 0 which is simpler
* Loss in information flow in the forward pass is not a problem anymore
    * No vanishing / exploding gradient
* Identities don't have parameters to be learned

## Evaluation

The learning rate starts at 0.1 and is divided by 10 when the error plateaus. Weight decay of 0.0001 ($10^{-4}$), momentum of 0.9. They use mini-batches of size 128.

* ImageNet ILSVRC 2015: 3.57% (ensemble)
* CIFAR-10: 6.43%
* MS COCO: 59.0% mAp@0.5 (ensemble)
* PASCAL VOC 2007: 85.6% mAp@0.5
* PASCAL VOC 2012: 83.8% mAp@0.5

## See also

* [DenseNets](http://www.shortscience.org/paper?bibtexKey=journals/corr/1608.06993)

Large-scale transformers on unsupervised text data have been wildly successful in recent years; arguably, the most successful single idea in the last ~3 years of machine learning. Given that, it's understandable that different domains within ML want to take their shot at seeing whether the same formula will work for them as well. This paper applies the principles of (1) transformers and (2) large-scale unlabeled data to the problem of learning informative embeddings of molecular graphs. 

Labeling is a problem in much of machine learning - it's costly, and narrowly defined in terms of a certain task - but that problem is even more exacerbated when it comes to labeling properties of molecules, since they typically require wetlab chemistry to empirically measure. Given that, and also given the fact that we often want to predict new properties - like effectiveness against a new targetable drug receptor - that we don't yet have data for, finding a way to learn and transfer from unsupervised data has the potential to be quite valuable in the molecular learning sphere. 

There are two main conceptual parts to this paper and its method - named GROVER, in true-to-ML-form tortured acronym style. The first is the actual architecture of their model itself, which combines both a message-passing Graph Neural Network to aggregate local information, and a Transformer to aggregate global information. The paper was a bit vague here, but the way I understand it is: 

https://i.imgur.com/JY4vRdd.png
- There are parallel GNN + Transformer stacks for both edges and nodes, each of which outputs both a node and edge embedding, for four embeddings total. I'll describe the one for nodes, and the parallel for edges operates the same way, except that hidden states live on edges rather than nodes, and attention is conducted over edges rather than nodes
- In the NodeTransformer version, a message passing NN (of I'm not sure how many layers) performs neighborhood aggregation (aggregating the hidden states of neighboring nodes and edges, then weight-transforming them, then aggregating again) until each node has a representation that has "absorbed" in information from a few hops out of its surrounding neighborhood. My understanding is that there is a separate MPNN for queries, keys, and values, and so each nodes end up with three different vectors for these three things.
- Multi-headed attention is then performed over these node representations, in the normal way, where all keys and queries are dot-product-ed together, and put into a softmax to calculate a weighted average over the values
- We now have node-level representations that combine both local and global information. These node representations are then aggregated into both node and edge representations, and each is put into a MLP layer and Layer Norm before finally outputting a node-based node and edge representation. This is then joined by an edge-based node and edge representation from the parallel stack. These are aggregated on a full-graph level to predict graph-level properties

https://i.imgur.com/NNl6v4Y.png

The other component of the GROVER model is the way this architecture is actually trained - without explicit supervised labels. The authors use two tasks - one local, and one global. The local task constructs labels based on local contextual properties of a given atom - for example, the atom here has one double-bonded Nitrogen and one single-bonded Oxygen in its local environment - and tries to predict those labels given the representations of that atom (or node). The global task uses RDKit (an analytically constructed molecular analysis kit) to identify 85 different modifs or functional groups in the molecule, and encodes those into an 85-long one-hot vector that is being predicted on a graph level. 

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

With these two components, GROVER is pretrained on 10 million unlabeled molecules, and then evaluated in transfer settings where its representations are fine-tuned on small amounts of labeled data. The results are pretty impressive - it achieves new SOTA performance by relatively large amounts on all tasks, even relative to exist semi-supervised pretraining methods that similarly have access to more data. The authors perform ablations to show that it's important to do the graph-aggregation step before a transformer (the alternative being just doing a transformer on raw node and edge features), and also show that their architecture without pretraining (just used directly in downstream tasks) also performs worse. One thing I wish they'd directly ablated was the value-add of the local (also referred to as "contextual") and global semi-supervised tasks. Naively, I'd guess that most of the performance gain came from the global task, but it's hard to know without them having done the test directly.

This paper explores the use of convolutional (PixelCNN) and recurrent units (PixelRNN) for modeling the distribution of images, in the framework of autoregression distribution estimation. In this framework, the input distribution $p(x)$ is factorized into a product of conditionals $\Pi p(x_i | x_i-1)$. Previous work has shown that very good models can be obtained by using a neural network parametrization of the conditionals (e.g. see our work on NADE \cite{journals/jmlr/LarochelleM11}). Moreover, unlike other approaches based on latent stochastic units that are directed or undirected, the autoregressive approach is able to compute log-probabilities tractably. 

So in this paper, by considering the specific case of x being an image, they exploit the topology of pixels and investigate appropriate architectures for this.

Among the paper's contributions are:

1. They propose Diagonal BiLSTM units for the PixelRNN, which are efficient (thanks to the use of convolutions) while making it possible to, in effect, condition a pixel's distribution on all the pixels above it (see Figure 2 for an illustration).

2. They demonstrate that the use of residual connections (a form of skip connections, from hidden layer i-1 to layer $i+1$) are very effective at learning very deep distribution estimators (they go as deep as 12 layers).

3. They show that it is possible to successfully model the distribution over the pixel intensities (effectively an integer between 0 and 255) using a softmax of 256 units.

4. They propose a multi-scale extension of their model, that they apply to larger 64x64 images.

The experiments show that the PixelRNN model based on Diagonal BiLSTM units achieves state-of-the-art performance on the binarized MNIST benchmark, in terms of log-likelihood. They also report excellent log-likelihood on the CIFAR-10 dataset, comparing to previous work based on real-valued density models. Finally, they show that their model is able to generate high quality image samples.

# Object detection system overview.

https://i.imgur.com/vd2YUy3.png
 
1.	takes an input image,
2.	extracts around 2000 bottom-up region proposals, 
3.	computes features for each proposal using a large convolutional neural network (CNN), and then
4.	classifies each region using class-specific linear SVMs.
* R-CNN achieves a mean average precision (mAP) of 53.7% on PASCAL VOC 2010.
* On the 200-class ILSVRC2013 detection dataset, R-CNN’s mAP is 31.4%, a large improvement over OverFeat , which had the previous best result at 24.3%.

## There is a 2 challenges faced in object detection 
1.	localization problem
2.	labeling the data

1 localization problem :
*  One approach frames localization as a regression problem.  they report a mAP of 30.5% on VOC 2007 compared to the 58.5% achieved by our method.
* An alternative is to build a sliding-window detector.  considered adopting a sliding-window approach increases the number of convolutional layers to 5, have very large receptive fields (195 x 195 pixels) and strides (32x32 pixels) in the input image, which makes precise localization within the sliding-window paradigm.

2 labeling the data:
* The conventional solution to this problem is to use unsupervised pre-training, followed by supervise fine-tuning 
* supervised pre-training on a large auxiliary dataset (ILSVRC), followed by domain specific fine-tuning on a small dataset (PASCAL),
* fine-tuning for detection improves mAP performance by 8 percentage points. 
* Stochastic gradient descent via back propagation was used to  effective for training convolutional neural networks (CNNs)
 
##  Object detection with R-CNN
This  system consists of three modules
* The first generates category-independent region proposals. These proposals define the set of candidate detections available to our detector.
*  The second module is a large convolutional neural network that extracts a fixed-length feature vector from each region.
* The third module is a set of class specific linear SVMs.

Module design

1 Region proposals 
* which detect mitotic cells by applying a CNN to regularly-spaced square crops.
* use selective search method in fast mode (Capture All Scales, Diversification, Fast to Compute).
* the time spent computing region proposals and features (13s/image on a GPU or 53s/image on a CPU)

2 Feature extraction.
* extract a 4096-dimensional feature vector from each region proposal using the Caffe  implementation of the CNN 
* Features are computed by forward propagating a mean-subtracted 227x227 RGB image through five convolutional layers and two fully connected layers.
* warp all pixels in a tight bounding box around it to the required size
* The feature matrix is typically 2000x4096 

3 Test time detection
* At test time, run selective search on the test image to extract around 2000 region proposals (we use selective search’s “fast mode” in all experiments).
*  warp each proposal and forward propagate it through the CNN in order to compute features. Then, for each class, we score each extracted feature vector using the SVM trained for that class.
* Given all scored regions in an image, we apply a greedy non-maximum suppression (for each class independently) that rejects a region if it has an intersection-over union (IoU) overlap with a higher scoring selected region larger than a learned threshold.
## Training

1 Supervised pre-training:
 * pre-trained the CNN on a large auxiliary dataset (ILSVRC2012 classification)  using image-level annotations only (bounding box labels are not available for this data)

2  Domain-specific fine-tuning.
* use the stochastic gradient descent (SGD) training of the CNN parameters using only warped region proposals with  learning rate of 0.001.

3  Object category classifiers.
*   use intersection-over union (IoU) overlap threshold method  to label a region with The overlap threshold of 0.3.
* Once features are extracted and training labels are applied, we optimize one linear SVM per class.
* adopt the standard hard negative mining method to fit large training data in memory.

### Results on PASCAL VOC 201012

1  VOC 2010
* compared against four strong baselines including SegDPM, DPM, UVA, Regionlets. 
* Achieve a large improvement in mAP, from 35.1% to 53.7% mAP,  while also being much faster
 https://i.imgur.com/0dGX9b7.png
2 ILSVRC2013 detection.
* ran R-CNN on the 200-class ILSVRC2013 detection dataset
* R-CNN achieves a mAP of 31.4%
https://i.imgur.com/GFbULx3.png
#### Performance layer-by-layer, without fine-tuning
1 pool5 layer 
* which is the max pooled output of the network’s fifth and final convolutional layer.
*The pool5 feature map is 6 x6 x 256 = 9216 dimensional
* each pool5 unit has a receptive field of 195x195 pixels in the original 227x227 pixel input

2 Layer fc6
* fully connected to pool5
*  it multiplies a 4096x9216 weight matrix by the pool5 feature map (reshaped as a 9216-dimensional vector) and then adds a vector of biases

3 Layer fc7
* It is implemented by multiplying the features computed by fc6 by a 4096 x 4096 weight matrix, and similarly adding a vector of biases and applying half-wave rectification
#### Performance layer-by-layer, with fine-tuning
* CNN’s parameters  fine-tuned on PASCAL.
* fine-tuning increases mAP by 8.0 % points to 54.2%

### Network architectures
* 16-layer deep network, consisting of 13 layers of 3 _ 3 convolution kernels, with five max pooling layers interspersed, and topped with three fully-connected layers. We refer to this network as “O-Net” for OxfordNet and the baseline as “T-Net” for TorontoNet.
* RCNN with O-Net substantially outperforms R-CNN with TNet, increasing mAP from 58.5% to 66.0%
* drawback in terms of compute time, with in terms of compute time, with than T-Net.

1 The ILSVRC2013 detection dataset
* dataset is split into three sets: train (395,918), val (20,121), and test (40,152) 

#### CNN features for segmentation.
* full R-CNN: The first strategy (full) ignores the re region’s shape and computes CNN features directly on the warped window. Two regions might have very similar bounding boxes while having very little overlap. 
* fg R-CNN: the second strategy (fg) computes CNN features only on a region’s foreground mask. We replace the background with the mean input so that background regions are zero after mean subtraction.
* full+fg R-CNN: The third strategy (full+fg) simply concatenates the full and fg features
 https://i.imgur.com/n1bhmKo.png