**Background:** The goal of this work is to indicate image features which are relevant to the prediction of a neural network and convey that information to the user by displaying a counterfactual image animation.

**The Latent Shift Method:** This method works on any pretrained encoder/decoder and classifier which is differentiable. No special considerations are needed during model training. With this approach they want the exact opposite of an adversarial attack but it is using the same idea. They want to perturb the input image so that the classifier reduces its prediction. If they just compute $\frac{\partial f}{\partial x}$ and move the pixels directly then they will get an imperceivable difference like an adversarial attack. Using a decoder they can regularize the transformation so it will only yield value images.

The encoder takes the input image and encodes it into a latent representation $z$. Then the decoder reconstructs the image and feeds this image into the classifier. The gradient is computed from the output of the classifier with respect to $z$. Subtracting the gradient from z and reconstructing the image generates a counterfactual.

https://i.imgur.com/iuZGUTH.gif

They found that if they change the prediction by -30% the images come out pretty good. So an iterative search along the vector defined by the gradient in the latent space until the prediction is reduced by 30%.

From this sequence a 2D image can be reconstructed which is similar to a traditional attribution map by taking the maximum pixel wise difference between every image and the unperturbed reconstruction.

https://i.imgur.com/V3PCgXZ.png

The results look great!

https://i.imgur.com/DBki84c.gif

https://i.imgur.com/kFfQNKD.gif

In order to validate if this approach can help spot false positive predictions, two radiologists to evaluate how confident they were in a models predictions. For each image, radiologists viewed the prediction in two ways, using traditional methods or the Latent Shift images. Traditional methods includes the image gradient, guided backprop, and integrated gradients. The Latent Shift Counterfactual includes the animation as well as the 2D version.

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

What they would like to see, that for true positives, the results are all 5 and for false positives they are all 1. 
What they observe however, is that many false positives still cause high confidence in the model predictions but not as much as the true positives. Between these two methods they find for true positives that the latent shift counterfactuals show a significant increase in confidence which is good.

> 0.15±0.95 confidence increase using the Latent Shift method  (p=0.01).

For false positives they find an increase in confidence but it is not significant. 

> 0.04±1.06 increase which is not significant (p=0.57)

**Conclusions:**
 - Latent Shift's ability to generate counterfactuals is pretty good!
 - Vanilla autoencoders are sufficient for some pathologies.
 - StyleGAN and higher quality models should improve performance.
 - IoU analysis may not be the best fit.
 - Explainable AI methods can have an impact on the user confidence in the model.

(Disclaimer: I am the author of this work)

Project Website: https://mlmed.org/gifsplanation/

Keypoint detection is an important step in various tasks such as SLAM, panorama stitching, camera calibration, and more. Efficient keypoint detectors, FAST (Features from Accelerated and Segments Test) for example, would detect keypoints where a relatively high brightness change is observed in relation to surrounding pixels. Most probably, the keypoints would be located on edges, as shown below:
https://i.imgur.com/ylC4BM3.jpg
Let's consider another image shown below. Here, while the detector is capable of detecting many keypoints, they are mostly located on trees (see subfigure (a) below). This causes redundancy and this paper focuses on solving it by selecting locally strong keypoints that are well distributed all over the image (subfigure (c)).

https://i.imgur.com/1MqZhmT.png


The algorithm requires input keypoints to be sorted in decreasing order of strength. The keypoints are then processed in that order and points that fall within the suppression range of a current keypoint are removed from the consideration. The process is repeated for the next unsuppressed keypoint in the sorted order. The process continues until no points remain. If the number of filtered points is not close enough to what we require, the suppression range is modified and the process is repeated. The suppression range is modified using binary search.

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

Binary search requires lower and upper bounds to operate. Naive initialization would be setting lower bound to 1 pixel, while upper bound - image width or height. On the other hand, this paper proposes better initialization of the suppression range that is dependent on image height $H_I$, width $W_I$, number of input keypoints $n$ as well as the number of output keypoints $m$.
* Upper bound: $\frac{H_I + W_I + 2m - \sqrt{\Delta}}{2m - 1}$ (see paper for more details)
* Lower bound: $\frac{1}{2}\sqrt{\frac{n}{m}}$

This initializing helps to decrease the number of iterations to convergence by a factor of three:

https://i.imgur.com/7NCpgbi.png

Homogenous location of keypoints is beneficial for SLAM algorithm and reduce translational and rotational errors compared to naive filtering when evaluated on KITTI:

https://i.imgur.com/4wq0kLK.png

Overall, this paper proposes a fast, efficient, and effective method to post-process noisy and redundant keypoint detections with a clear benefit to SLAM. The codes are publically available in multiple languages: C++, Python, Java, and Matlab. See https://github.com/BAILOOL/ANMS-Codes

In January of this year (2020), DeepMind released a model called AlphaFold, which uses convolutional networks atop sequence-based and evolutionary features to predict protein folding structure. In particular, their model was designed to predict a distribution for how far away each pair of amino acids will be from one another in the final folded structure. Given such a trained model, you can score a candidate structure according to how likely it is under the model, and - if your process for generating candidates is differentiable, as it is in this case - you can directly optimize the structure to increase its probability.  

https://i.imgur.com/9ZBhqRo.png

The distance-prediction model takes as input two main categories of feature: 

1. Per-residue features characterizing which amino acid that residue is based on different techniques that produce one-hot amino acid type, or a distribution over amino acids. 
2. Residue pair features based on parameters of Multiple Sequence Alignment (MSA) models. I don't deeply understand the details of how the specific models here work, but at a high level: MSA features are based on the evolutionary intuition that residues that make contact within  a protein will likely evolve in a correlation with one another, and that you can simulate these evolutionary timestep correlations by comparing highly similar proteins (which were likely close in evolutionary time). 

https://i.imgur.com/h16lPwU.png

These features are stacked in a LxL grid, with the per-residue-pair features differing at each point in the grid, and the per-residue features staying constant for a full row or column (since they correspond to a given i for all j). One relevant note here is that proteins can be hundreds or thousands of residues long, and, so you can't actually construct a full LxL matrix, either on the input or output end. Instead, the notional full LxL grid is subdivided into a courser grid of 64-residue square regions, and a single one of these 64x64 regions (which could be either adjacent or far away in the protein) is passed into the model at a time. 

Given these 64x64x<features> input, the model performs several layers of dilated convolutions - which allow features at a given point in the grid to be informed by information farther away - still in a 2D arrangement. The model then outputs a 64x64 grid (one element for each [i, j] amino acid pair), where each element in the grid is a 64-deep discretized probability distribution over the distance between those two residues. When I say "discretized probability distribution," what I actually mean is "histogram". This discretization of an output distribution, where you predict how much probability mass will be in each possible distance bin, allows for flexible and finer-grained predicted distributions than, for example, you could get with a continuous Gaussian model centered around a single point. Amusingly, because the model predicts distance histograms for each residue pair, the authors term the output a "distogram". During training, the next-to-last layer of the model is also used to predict per-residue auxiliary features: the accessible surface area of the residue in the folded structure, and the secondary structure type (helix, strand, etc) that the residue will be a part of. However, these are just used to provide more signal during training, and aren't used for either protein structure optimization or calculation of test scores. 

To actually generated predicted fold structures, the authors construct a generative model of fold structure where each amino acid is assigned two torsion angles that govern its connection to its neighbor. By setting these torsion angles to different values, you can twist and reshape the protein as a whole. Given this generative model, things proceed as you might suspect: you generate a candidate, calculate the resulting inter-residue distances, calculate a likelihood of those distances under the model you've learned, and send back a gradient to change your torsion angles to make that likelihood higher. 

Empirically, the Deepmind authors evaluated on a competition dataset, and specifically compared themselves against other approaches that (like theirs) didn't make predictions for a new protein by comparing against similar templates (Template Modeling, or TM) but instead modeled from raw features (Free Modeling, or FM). AlphaFold was able to achieve high accuracy on 24 out of the 43 test domains (where a domain is a cluster of highly related proteins) compared to the next best method, which only got 14 out of the 43. Definitely still not perfect, since almost half of the test proteins were out of its reach, but fairly compelling evidence that there's value to DeepMind's approach.

This is an interesting paper, investigating (with a team that includes the original authors of the Lottery Ticket paper) whether the initializations that result from BERT pretraining have Lottery Ticket-esque properties with respect to their role as initializations for downstream transfer tasks. 

As background context, the Lottery Ticket Hypothesis came out of an observation that trained networks could be pruned to remove low-magnitude weights (according to a particular iterative pruning strategy that is a bit more complex than just "prune everything at the end of training"), down to high levels of sparsity (5-40% of original weights, and that those pruned networks not only perform well at the end of training, but also can be "rewound" back to their initialization values (or, in some cases, values from early in training) and retrained in isolation, with the weights you pruned out of the trained network still set to 0, to a comparable level of accuracy. This is thought of as a "winning ticket" because the hypothesis Frankle and Carbin generated is that the reason we benefit from massively overparametrized neural networks is that we are essentially sampling a large number of small subnetworks within the larger ones, and that the more samples we get, the likelier it is we find a "winning ticket" that starts our optimization in a place conducive to further training. 

In this particular work, the authors investigate a slightly odd variant of the LTH. Instead of looking at training runs that start from random initializations, they look at transfer tasks that start their learning from a massively-pretrained BERT language model. They try to find out: 

1) Whether you can find "winning tickets" as subsets of the BERT initialization for a given downstream task

2) Whether those winning tickets generalize, i.e. whether a ticket/pruning mask for one downstream task can also have high performance on another. If that were the case, it would indicate that much of the value of a BERT initialization for transfer tasks could be captured by transferring only a small percentage of BERT's (many) weights, which would be beneficial for compression and mobile applications 

An interesting wrinkle in the LTH literature is the question of whether true "winning tickets" can be found (in the sense of the network being able to retrain purely from the masked random initializations), or whether it can only retrain to a comparable accuracy by rewinding to an early stage in training, but not the absolute beginning of training. Historically, the former has been difficult and sometimes not possible to find in more complex tasks and networks. 

https://i.imgur.com/pAF08H3.png

One finding of this paper is that, when your starting point is BERT initialization, you can indeed find "winning tickets" in the first sense of being able to rewind the full way back to the beginning of (downstream task) training, and retrain from there. (You can see this above with the results for IMP, Iterative Magnitude Pruning, rolling back to theta-0). This is a bit of an odd finding to parse, since it's not like BERT really is a random initialization itself, but it does suggest that part of the value of BERT is that it contains subnetworks that, from the start of training, are in notional optimization basins that facilitate future training. 

A negative result in this paper is that, by and large, winning tickets on downstream tasks don't transfer from one to another, and, to the extent that they do transfer, it mostly seems to be according to which tasks had more training samples used in the downstream mask-finding process, rather than any qualitative properties of the task. The one exception to this was if you did further training of the original BERT objective, Masked Language Modeling, as a "downstream task", and took the winning ticket mask from that training, which then transferred to other tasks. This is some validation of the premise that MLM is an unusually good training task in terms of its transfer properties. 

An important thing to note here is that, even though this hypothesis is intriguing, it's currently quite computationally expensive to find "winning tickets", requiring an iterative pruning and retraining process that takes far longer than an original training run would have. The real goal here, which this is another small step in the hopeful direction of, is being able to analytically specify subnetworks with valuable optimization properties, without having to learn them from data each time (which somewhat defeats the point, if they're only applicable for the task they're trained on, though is potentially useful is they do transfer to some other tasks, as has been shown within a set of image-prediction tasks).

### Key points

- Instead of just focusing on supervised learning, a self-critique and adapt network provides a unsupervised learning approach in improving the overall generalization. It does this via transductive learning by learning a label-free loss function from the validation set to improve the base model.
- The SCA framework helps a learning algorithm be more robust by learning more relevant features and improve during the training phase.

### Ideas

1. Combine deep learning models with SCA that help improve genearlization when we data is fed into these large networks.
2. Build a SCA that focuses not on learning a label-free loss function but on learning quality of a concept.

### Review

Overall, the paper present a novel idea that offers a unsupervised learning method to assist a supervised learning model to improve its performance. Implementation of this SCA framework is straightforward and demonstrates promising results. This approach is finally contributing to the actual theory of meta-learning and learning to learn research field. SCA framework is a new step towards self-adaptive learning systems. Unfortunately, the experimentation is insufficient and provided little insight into how this framework can help in cases where task domains vary in distribution or in concept.