A very simple (but impractical) discrete model of subclonal evolution would include the following events:

* Division of a cell to create two cells:
    * **Mutation** at a location in the genome of the new cells
* Cell death at a new timestep
* Cell survival at a new timestep

Because measurements of mutations are usually taken at one time point, this is taken to be at the end of a time series of these events, where a tiny of subset of cells are observed and a **genotype matrix** $A$ is produced, in which mutations and cells are arbitrarily indexed such that $A_{i,j} = 1$ if mutation $j$ exists in cell $i$. What this matrix allows us to see is the proportion of cells which *both have mutation $j$*.

Unfortunately, I don't get to observe $A$, in practice $A$ has been corrupted by IID binary noise to produce $A'$. This paper focuses on difference inference problems given $A'$, including *inferring $A$*, which is referred to as **`noise_elimination`**. The other problems involve inferring only properties of the matrix $A$, which are referred to as:

* **`noise_inference`**: predict whether matrix $A$ would satisfy the *three gametes rule*, which asks if a given genotype matrix *does not describe a branching phylogeny* because a cell has inherited mutations from two different cells (which is usually assumed to be impossible under the infinite sites assumption). This can be computed exactly from $A$.
* **Branching Inference**: it's possible that all mutations are inherited between the cells observed; in which case there are *no branching events*. The paper states that this can be computed by searching over permutations of the rows and columns of $A$. The problem is to predict from $A'$ if this is the case.

In both problems inferring properties of $A$, the authors use fully connected networks with two hidden layers on simulated datasets of matrices. For **`noise_elimination`**, computing $A$ given $A'$, the authors use a network developed for neural machine translation called a [pointer network][pointer]. They also find it necessary to map $A'$ to a matrix $A''$, turning every element in $A'$ to a fixed length row containing the location, mutation status and false positive/false negative rate.

Unfortunately, reported results on real datasets are reported only for branching inference and are limited by the restriction on input dimension. The inferred branching probability reportedly matches that reported in the literature.

[pointer]: https://arxiv.org/abs/1409.0473

In this tutorial paper, Carl E. Rasmussen gives an introduction to Gaussian Process Regression focusing on the definition, the hyperparameter learning and future research directions.

A Gaussian Process is completely defined by its mean function $m(\pmb{x})$ and its covariance function (kernel) $k(\pmb{x},\pmb{x}')$. The mean function $m(\pmb{x})$ corresponds to the mean vector $\pmb{\mu}$ of a Gaussian distribution whereas the covariance function $k(\pmb{x}, \pmb{x}')$ corresponds to the covariance matrix $\pmb{\Sigma}$. Thus, a Gaussian Process $f \sim \mathcal{GP}\left(m(\pmb{x}), k(\pmb{x}, \pmb{x}')\right)$ is a generalization of a Gaussian distribution over vectors to a distribution over functions. A random function vector $\pmb{\mathrm{f}}$ can be generated by a Gaussian Process through the following procedure:

1. Compute the components $\mu_i$ of the mean vector $\pmb{\mu}$ for each input $\pmb{x}_i$ using the mean function $m(\pmb{x})$
2. Compute the components $\Sigma_{ij}$ of the covariance matrix $\pmb{\Sigma}$ using the covariance function $k(\pmb{x}, \pmb{x}')$
3. A function vector $\pmb{\mathrm{f}} = [f(\pmb{x}_1), \dots, f(\pmb{x}_n)]^T$ can be drawn from the Gaussian distribution $\pmb{\mathrm{f}} \sim \mathcal{N}\left(\pmb{\mu}, \pmb{\Sigma} \right)$

Applying this procedure to regression, means that the resulting function vector $\pmb{\mathrm{f}}$ shall be drawn in a way that a function vector $\pmb{\mathrm{f}}$ is rejected if it does not comply with the training data $\mathcal{D}$. This is achieved by conditioning the distribution on the training data $\mathcal{D}$ yielding the posterior Gaussian Process $f \rvert \mathcal{D} \sim \mathcal{GP}(m_D(\pmb{x}), k_D(\pmb{x},\pmb{x}'))$ for noise-free observations with the posterior mean function $m_D(\pmb{x}) = m(\pmb{x}) + \pmb{\Sigma}(\pmb{X},\pmb{x})^T \pmb{\Sigma}^{-1}(\pmb{\mathrm{f}} - \pmb{\mathrm{m}})$  and the posterior covariance function $k_D(\pmb{x},\pmb{x}')=k(\pmb{x},\pmb{x}') - \pmb{\Sigma}(\pmb{X}, \pmb{x}')$ with $\pmb{\Sigma}(\pmb{X},\pmb{x})$ being a vector of covariances between every training case of $\pmb{X}$ and $\pmb{x}$.

Noisy observations $y(\pmb{x}) = f(\pmb{x}) + \epsilon$ with $\epsilon \sim \mathcal{N}(0,\sigma_n^2)$ can be taken into account with a second Gaussian Process with mean $m$ and covariance function $k$ resulting in $f \sim \mathcal{GP}(m,k)$ and $y \sim \mathcal{GP}(m, k + \sigma_n^2\delta_{ii'})$. The figure illustrates the cases of noisy observations (variance at training points) and of noise-free observationshttps://i.imgur.com/BWvsB7T.png (no variance at training points).

In the Machine Learning perspective, the mean and the covariance function are parametrised by hyperparameters and provide thus a way to include prior knowledge e.g. knowing that the mean function is a second order polynomial. To find the optimal hyperparameters $\pmb{\theta}$, 

1. determine the log marginal likelihood $L= \mathrm{log}(p(\pmb{y} \rvert \pmb{x}, \pmb{\theta}))$,
2. take the first partial derivatives of $L$ w.r.t. the hyperparameters, and
3. apply an optimization algorithm.

It should be noted that a regularization term is not necessary for the log marginal likelihood $L$ because it already contains a complexity penalty term. Also, the tradeoff between data-fit and penalty is performed automatically.

Gaussian Processes provide a very flexible way for finding a suitable regression model. However, they require the high computational complexity $\mathcal{O}(n^3)$ due to the inversion of the covariance matrix. In addition, the generalization of Gaussian Processes to non-Gaussian likelihoods remains complicated. 

This work expands on prior techniques for designing models that can both be stored using fewer parameters, and also execute using fewer operations and less memory, both of which are key desiderata for having trained machine learning models be usable on phones and other personal devices. 

The main contribution of the original MobileNets paper was to introduce the idea of using "factored" decompositions of Depthwise and Pointwise convolutions, which separate the procedures of "pull information from a spatial range" and "mix information across channels" into two distinct steps. In this paper, they continue to use this basic Depthwise infrastructure, but also add a new design element: the inverted-residual linear bottleneck. 

The reasoning behind this new layer type comes from the observation that, often, the set of relevant points in a high-dimensional space (such as the 'per-pixel' activations inside a conv net) actually lives on a lower-dimensional manifold. So, theoretically, and naively, one could just try to use lower dimensional internal representations to map the dimensionality of that assumed manifold. However, the authors argue that ReLU non-linearities kill information (because of the region where all inputs are mapped to zero), and so having layers contain only the number of dimensions needed for the manifold would mean that you end up with too-few dimensions after the ReLU information loss. However, you need to have non-linearities somewhere in the network in order to be able to learn complex, non-linear functions. 

So, the authors suggest a method to mostly use smaller-dimensional representations internally, but still maintain ReLus and the network's needed complexity. 

https://i.imgur.com/pN4d9Wi.png

- A lower-dimensional output is "projected up" into a higher dimensional output
- A ReLu is applied on this higher-dimensional layer
- That layer is then projected down into a smaller-dimensional layer, which uses a linear activation to avoid information loss
- A residual connection between the lower-dimensional output at the beginning and end of the expansion

This way, we still maintain the network's non-linearity, but also replace some of the network's higher-dimensional layers with lower-dimensional linear ones

## General Framework
Extends T-REX (see [summary](https://www.shortscience.org/paper?bibtexKey=journals/corr/1904.06387&a=muntermulehitch)) so that preferences (rankings) over demonstrations are generated automatically (back to the common IL/IRL setting where we only have access to a set of unlabeled demonstrations). Also derives some theoretical requirements and guarantees for better-than-demonstrator performance. 

## Motivations
* Preferences over demonstrations may be difficult to obtain in practice. 
* There is no theoretical understanding of the requirements that lead to outperforming demonstrator. 

## Contributions
* Theoretical results (with linear reward function) on when better-than-demonstrator performance is possible: 1- the demonstrator must be suboptimal (room for improvement, obviously), 2- the learned reward must be close enough to the reward that the demonstrator is suboptimally optimizing for (be able to accurately capture the intent of the demonstrator), 3- the learned policy (optimal wrt the learned reward) must be close enough to the optimal policy (wrt to the ground truth reward). Obviously if we have 2- and a good enough RL algorithm we should have 3-, so it might be interesting to see if one can derive a requirement from only 1- and 2- (and possibly a good enough RL algo). 
* Theoretical results (with linear reward function) showing that pairwise preferences over demonstrations reduce the error and ambiguity of the reward learning. They show that without rankings two policies might have equal performance under a learned reward (that makes expert's demonstrations optimal) but very different performance under the true reward (that makes the expert optimal everywhere). Indeed, the expert's demonstration may reveal very little information about the reward of (suboptimal or not) unseen regions which may hurt very much the generalizations (even with RL as it would try to generalize to new states under a totally wrong reward). They also show that pairwise preferences over trajectories effectively give half-space constraints on the feasible reward function domain and thus may decrease exponentially the reward function ambiguity. 
* Propose a practical way to generate as many ranked demos as desired.

## Additional Assumption
Very mild, assumes that a Behavioral Cloning (BC) policy trained on the provided demonstrations is better than a uniform random policy. 

## Disturbance-based Reward Extrapolation (D-REX)

![](https://i.imgur.com/9g6tOrF.png)

![](https://i.imgur.com/zSRlDcr.png)

They also show that the more noise added to the BC policy the lower the performance of the generated trajs. 

## Results
Pretty much like T-REX.

Disclaimer: I am an author

# Intro

Experience replay (ER) and generative replay (GEN) are two effective continual learning strategies. In the former, samples from a stored memory are replayed to the continual learner to reduce forgetting. In the latter, old data is compressed with a generative model and generated data is replayed to the continual learner. Both of these strategies assume a random sampling of the memories. But learning a new task doesn't cause **equal** interference (forgetting) on the previous tasks!  

In this work, we propose a controlled sampling of the replays. Specifically, we retrieve the samples which are most interfered, i.e. whose prediction will be most negatively impacted by the foreseen parameters update. The method is called Maximally Interfered Retrieval (MIR).

## Cartoon for explanation

https://i.imgur.com/5F3jT36.png

Learning about dogs and horses might cause more interference on lions and zebras than on cars and oranges. Thus, replaying lions and zebras would be a more efficient strategy.

# Method

1) incoming data: $(X_t,Y_t)$

2) foreseen parameter update: $\theta^v= \theta-\alpha\nabla\mathcal{L}(f_\theta(X_t),Y_t)$

### applied to ER (ER-MIR)
3) Search for the top-$k$ values $x$ in the stored memories using the criterion $$s_{MI}(x) = \mathcal{L}(f_{\theta^v}(x),y) -\mathcal{L}(f_{\theta}(x),y)$$

### or applied to GEN (GEN-MIR)
3)   
$$
     \underset{Z}{\max} \, \mathcal{L}\big(f_{\theta^v}(g_\gamma(Z)),Y^*\big) -\mathcal{L}\big(f_{\theta}(g_\gamma(Z)),Y^*\big)
$$
$$
         \text{s.t.}   \quad ||z_i-z_j||_2^2 > \epsilon \forall  z_i,z_j \in Z \,\text{with} \, z_i\neq z_j
$$
i.e. search in the latent space of a generative model $g_\gamma$ for samples that are the most forgotten given the foreseen update.

4) Then add theses memories to incoming data $X_t$ and train $f_\theta$

# Results

### qualitative
https://i.imgur.com/ZRNTWXe.png

Whilst learning 8s and 9s (first row), GEN-MIR mainly retrieves 3s and 4s (bottom two rows) which are similar to 8s and 9s respectively.

### quantitative 

GEN-MIR was tested on MNIST SPLIT and Permuted MNIST, outperforming the baselines in both cases.

ER-MIR was tested on MNIST SPLIT, Permuted MNIST and Split CIFAR-10, outperforming the baselines in all cases.


# Other stuff
### (for avid readers)

We propose a hybrid method (AE-MIR) in which the generative model is replaced with an autoencoder to facilitate the compression of harder dataset like e.g. CIFAR-10.