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Transformers  powered by selfattention mechanisms  have been a paradigm shift in NLP, and are now the standard choice for training large language models. However, while transformers do have many benefits in terms of computational constraints  most saliently, that attention between tokens can be computed in parallel, rather than needing to be evaluated sequentially like in a RNN  a major downside is their memory (and, secondarily, computational) requirements. The baseline form of selfattention works by having every token attend to every other token, where "attend" here means that a query from each token A will take an inner product with each other token A, and then be elementwisemultiplied with the values of every other token A. This implies a O(N^2) memory and computation requirement, where N is your sequence length. So, the question this paper asks is: how do you get the benefits, or most of the benefits, of a fullattention network, while reducing the number of other tokens each token attends to. The authors' solution  Big Bird  has three components. First, they approach the problem of approximating the global graph as a graph theory problem, where each token attending to every other is "fully connected," and the goal is to try to sparsify the graph in a way that keeps shortest path between any two nodes low. They use the fact that in an ErdosRenyi graph  where very edge is simply chosen to be on or off with some fixed probability  the shortest path is known to be logN. In the context of aggregating information about a sequence, a short path between nodes means that the number of iterations, or layers, that it will take for information about any given node A to be part of the "receptive field" (so to speak) of node B, will be correspondingly short. Based on this, they propose having the foundation of their sparsified attention mechanism be simply a random graph, where each node attends to each other with probability k/N, where k is a tunable hyperparameter representing how many nodes each other node attends to on average. To supplement, the authors further note that sequence tasks of interest  particularly language  are very local in their information structure, and, while it's important to understand the global context of the full sequence, tokens close to a given token are most likely to be useful in constructing a representation of it. Given this, they propose supplementing their randomgraph attention with a block diagonal attention, where each token attends to w/2 tokens prior to and subsequent to itself. (Where, again, w is a tunable hyperparameter) However, the authors find that these components aren't enough, and so they add a final component: having some small set of tokens that attend to all tokens, and are attended to by all tokens. This allows them to theoretically prove that Big Bird can approximate full sequences, and is a universal Turing machine, both of which are true for full Transformers. I didn't follow the details of the proof, but, intuitively, my reading of this is that having a small number of these global tokens basically acts as a shortcut way for information to get between tokens in the sequence  if information is globally valuable, it can be "written" to one of these global aggregator nodes, and then all tokens will be able to "read" it from there. The authors do note that while their sparse model approximates the full transformer well in many settings, there are some problems  like needing to find the token in the sequence that a given token is farthest from in vector space  that a full attention mechanism could solve easily (since it directly calculates all pairwise comparisons) but that a sparse attention mechanism would require many layers to calculate. Empirically, Big Bird ETC (a version which adds on additional tokens for the global aggregators, rather than making existing tokens serve thhttps://i.imgur.com/ks86OgJ.pnge purpose) performs the best on a big language model training objective, has comparable performance to existing models on questionhttps://i.imgur.com/x0BdamC.png answering, and pretty dramatic performance improvements in document summarization. It makes sense for summarization to be a place where this model in particular shines, because it's explicitly designed to be able to integrate information from very large contexts (albeit in a randomly sampled way), where fullattention architectures must, for reasons of memory limitation, do some variant of a sliding window approach. 
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We want to find two matrices $W$ and $H$ such that $V = WH$. Often a goal is to determine underlying patterns in the relationships between the concepts represented by each row and column. $W$ is some $m$ by $n$ matrix and we want the inner dimension of the factorization to be $r$. So $$\underbrace{V}_{m \times n} = \underbrace{W}_{m \times r} \underbrace{H}_{r \times n}$$ Let's consider an example matrix where of three customers (as rows) are associated with three movies (the columns) by a rating value. $$ V = \left[\begin{array}{c c c} 5 & 4 & 1 \\\\ 4 & 5 & 1 \\\\ 2 & 1 & 5 \end{array}\right] $$ We can decompose this into two matrices with $r = 1$. First lets do this without any nonnegative constraint using an SVD reshaping matrices based on removing eigenvalues: $$ W = \left[\begin{array}{c c c} 0.656 \\\ 0.652 \\\ 0.379 \end{array}\right], H = \left[\begin{array}{c c c} 6.48 & 6.26 & 3.20\\\\ \end{array}\right] $$ We can also decompose this into two matrices with $r = 1$ subject to the constraint that $w_{ij} \ge 0$ and $h_{ij} \ge 0$. (Note: this is only possible when $v_{ij} \ge 0$): $$ W = \left[\begin{array}{c c c} 0.388 \\\\ 0.386 \\\\ 0.224 \end{array}\right], H = \left[\begin{array}{c c c} 11.22 & 10.57 & 5.41 \\\\ \end{array}\right] $$ Both of these $r=1$ factorizations reconstruct matrix $V$ with the same error. $$ V \approx WH = \left[\begin{array}{c c c} 4.36 & 4.11 & 2.10 \\\ 4.33 & 4.08 & 2.09 \\\ 2.52 & 2.37 & 1.21 \\\ \end{array}\right] $$ If they both yield the same reconstruction error then why is a nonnegativity constraint useful? We can see above that it is easy to observe patterns in both factorizations such as similar customers and similar movies. `TODO: motivate why NMF is better` #### Paper Contribution This paper discusses two approaches for iteratively creating a nonnegative $W$ and $H$ based on random initial matrices. The paper discusses a multiplicative update rule where the elements of $W$ and $H$ are iteratively transformed by scaling each value such that error is not increased. The multiplicative approach is discussed in contrast to an additive gradient decent based approach where small corrections are iteratively applied. The multiplicative approach can be reduced to this by setting the learning rate ($\eta$) to a ratio that represents the magnitude of the element in $H$ to the scaling factor of $W$ on $H$. ### Still a draft 
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This is a nice little empirical paper that does some investigation into which features get learned during the course of neural network training. To look at this, it uses a notion of "decodability", defined as the accuracy to which you can train a linear model to predict a given conceptual feature on top of the activations/learned features at a particular layer. This idea captures the amount of information about a conceptual feature that can be extracted from a given set of activations. They work with two synthetic datasets. 1. Trifeature: Generated images with a color, shape, and texture, which can be engineered to be either entirely uncorrelated or correlated with each other to varying degrees. 2. Navon: Generated images that are letters on the level of shape, and are also composed of letters on the level of texture The first thing the authors investigate is: to what extent are the different properties of these images decodable from their representations, and how does that change during training? In general, decodability is highest in lower layers, and lowest in higher layers, which makes sense from the perspective of the Information Processing Inequality, since all the information is present in the pixels, and can only be lost in the course of training, not gained. They find that decodability of color is high, even in the later layers untrained networks, and that the decodability of texture and shape, while much less high, is still above chance. When the network is trained to predict one of the three features attached to an image, you see the decodability of that feature go up (as expected), but you also see the decodability of the other features go down, suggesting that training doesn't just involve amplifying predictive features, but also suppressing unpredictive ones. This effect is strongest in the Trifeature case when training for shape or color; when training for texture, the dampening effect on color is strong, but on shape is less pronounced. https://i.imgur.com/o45KHOM.png The authors also performed some experiments on cases where features are engineered to be correlated to various degrees, to see which of the predictive features the network will represent more strongly. In the case where two features are perfectly correlated (and thus both perfectly predict the label), the network will focus decoding power on whichever feature had highest decodability in the untrained network, and, interestingly, will reduce decodability of the other feature (not just have it be lower than the chosen feature, but decrease it in the course of training), even though it is equally as predictive. https://i.imgur.com/NFx0h8b.png Similarly, the network will choose the "easy" feature (the one more easily decodable at the beginning of training) even if there's another feature that is slightly *more* predictive available. This seems quite consistent with the results of another recent paper, Shah et al, on the Pitfalls of Simplicity Bias in neural networks. The overall message of both of these experiments is that networks generally 'put all their eggs in one basket,' so to speak, rather than splitting representational power across multiple features. There were a few other experiments in the paper, and I'd recommend reading it in full  it's quite well written  but I think those convey most of the key insights for me. 
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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 
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When humans classify images, we tend to use highlevel information about the shape and position of the object. However, when convolutional neural networks classify images,, they tend to use lowlevel, or textural, information more than highlevel shape information. This paper tries to understand what factors lead to higher shape bias or texture bias. To investigate this, the authors look at three datasets with disagreeing shape and texture labels. The first is GST, or Geirhos Style Transfer. In this dataset, style transfer is used to render the content of one class in the style of another (for example, a cat shape in the texture of an elephant). In the Navon dataset, a largescale letter is rendered by tiling smaller letters. And, in the ImageNetC dataset, a given class is rendered with a particular kind of distortion; here the distortion is considered to be the "texture label". In the rest of the paper, "shape bias" refers to the extent to which a model trained on normal images will predict the shape label rather than the texture label associated with a GST image. The other datasets are used in experiments where a model explicitly tries to learn either shape or texture. https://i.imgur.com/aw1MThL.png To start off, the authors try to understand whether CNNs are inherently more capable of learning texture information rather than shape information. To do this, they train models on either the shape or the textural label on each of the three aforementioned datasets. On GST and Navon, shape labels can be learned faster and more efficiently than texture ones. On ImageNetC (i.e. distorted ImageNet), it seems to be easier to learn texture than texture, but recall here that texture corresponds to the type of noise, and I imagine that the cardinality of noise types is far smaller than that of ImageNet images, so I'm not sure how informative this comparison is. Overall, this experiment suggests that CNNs are able to learn from shape alone without lowlevel texture as a clue, in cases where the two sources of information disagree The paper moves on to try to understand what factors about a normal ImageNet model give it higher or lower shape bias  that is, a higher or lower likelihood of classifying a GST image according to its shape rather than texture. Predictably, data augmentations have an effect here. When data is augmented with aggressive random cropping, this increases texture bias relative to shape bias, presumably because when large chunks of an object are cropped away, its overall shape becomes a less useful feature. Center cropping is better for shape bias, probably because objects are likely to be at the center of the image, so center cropping has less of a chance of distorting them. On the other hand, more "naturalistic" augmentations like adding Gaussian noise or distorting colors lead to a higher shape bias in the resulting networks, up to 60% with all the modifications. However, the authors also find that pushing the shape bias up has the result of dropping final test accuracy. https://i.imgur.com/Lb6RMJy.png Interestingly, while the techniques that increase shape bias seem to also harm performance, the authors also find that higherperforming models tend to have higher shape bias (though with texture bias still outweighing shape) suggesting that stronger models learn how to use shape more effectively, but also that handicapping models' ability to use texture in order to incentivize them to use shape tends to hurt performance overall. Overall, my take from this paper is that texturelevel data is actually statistically informative and useful for classification  even in terms of generalization  even if is too highresolution to be useful as a visual feature for humans. CNNs don't seem inherently incapable of learning from shape, but removing their ability to rely on texture seems to lead to a notable drop in accuracy, suggesting there was real signal there that we're losing out on.
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