#### Motivation:

+ Take advantage of the fact that missing values can be very informative about the label.
+ Sampling a time series generates many missing values.

![Sampling](https://raw.githubusercontent.com/tiagotvv/ml-papers/master/clinical-data/images/Lipton2016_motivation.png?raw=true)


#### Model (indicator flag):

+ Indicator of occurrence of missing value.

![Indicator](https://raw.githubusercontent.com/tiagotvv/ml-papers/master/clinical-data/images/Lipton2016_indicator.png?raw=true)

+ An RNN can learn about missing values and their importance only by using the indicator function. The nonlinearity from this type of model helps capturing these dependencies.
+ If one wants to use a linear model, feature engineering is needed to overcome its limitations.
  + indicator for whether a variable was measured at all
  + mean and standard deviation of the indicator 
  + frequency with which a variable switches from measured to missing and vice-versa. 

#### Architecture:

+ RNN with target replication following the work "Learning to Diagnose with LSTM Recurrent Neural Networks" by the same authors.

![Architecture](https://raw.githubusercontent.com/tiagotvv/ml-papers/master/clinical-data/images/Lipton2016_architecture.png?raw=true)


#### Dataset:

+ Children's Hospital LA
+ Episode is a multivariate time series that describes the stay of one patient in the intensive care unit

Dataset properties  | Value 
---------|----------
Number of episodes | 10,401
Duration of episodes | From 12h to several months
Time series variables | Systolic blood pressure, Diastolic blood pressure,  Peripheral capillary refill rate, End tidal CO2, Fraction of inspired O2,  Glasgow coma scale,  Blood glucose,  Heart rate,  pH,  Respiratory rate, Blood O2 Saturation,  Body temperature,  Urine output.



#### Experiments and Results:

**Goal**
+ Predict 128 diagnoses.
+ Multilabel: patients can have more than one diagnose.

**Methodology**
+ Split: 80% training, 10% validation, 10% test.
+ Normalized data to be in the range [0,1].

+ LSTM RNN:
  + 2 hidden layers with 128 cells. Dropout = 0.5, L2-regularization: 1e-6
  + Training for 100 epochs. Parameters chosen correspond to the time that generated the smallest error in the validation dataset.
+ Baselines:
  + Logistic Regression (L2 regularization)
  + MLP with 3 hidden layers and 500 hidden neurons / layer (parameters chosen via validation set)
  + Tested with raw-features and hand-engineered features.
+ Strategies for missing values:
  + Zeroing
  + Impute via forward / backfilling
  + Impute with zeros and use indicator function
  + Impute via forward / backfilling and use indicator function
  + Use indicator function only

#### Results

+ Metrics:
  + Micro AUC, Micro F1: calculated by adding the TPs, FPs, TNs and FNs for the entire dataset and for all classes.
  + Macro AUC, Macro F1: Arithmetic mean of AUCs and F1 scores for each of the classes.
  + Precision at 10: Fraction of correct diagnostics among the top 10 predictions of the model.
    + The upper bound for precision at 10 is 0.2281 since in the test set there are on average 2.281 diagnoses per patient.

![Results](https://raw.githubusercontent.com/tiagotvv/ml-papers/master/clinical-data/images/Lipton2016_results.png?raw=true)


#### Discussion:

+ Predictive model based on data collected following a given routine. This routine can change if the model is put into practice. Will the model predictions in this new routine remain valid?

+ Missing values in a way give an indication of the type of treatment being followed.

+ Trade-off between complex models operating on raw features and very complex features operating on more interpretable models.

TLDR; The authors present an RNN-based variational autoencoder that can learn a  latent sentence representation while learning to decode. A linear layer that predicts the parameter of a Gaussian distribution is inserted between encoder and decoder. The loss is a combination of the reconstruction objective and the KL divergence with the prior (Gaussian) - similar to the "standard" VAE does. The authors evaluate the model on Language Modeling and Impution (Inserting Missing Words) tasks and also present a qualitative analysis of the latent space.

#### Key Points

- Training is tricky. Vanilla training results in the decoder ignoring the encoder and the KL error term becoming zero.
- Training Trick 1: KL Cost Annealing. During training, increase weight on the KL term of the cost to anneal from vanilla to VAE.
- Training Trick 2: Word dropout using a word keep rate hyperparameter. This forces the decoder to rely more on the global representation.
- Results on Language Modeling: Standard model (without cost annealing and word dropout) trails Vanilla RNNLM model, but not by much. KL cost term goes to zero in this setting. In an inputless decoder setting (word keep prob = 0) the VAE outperforms the RNNLM (obviously)
- Results on Imputing Missing Words: Benchmarked using an adversarial error classifier. VAE significantly outperforms RNNLM. However, the comparison is somewhat unfair since the RNNML has nothing to condition on and relies on unigram distribution for the first token.
- Qualitative: Can use higher word dropout to get more diverse sentences
- Qualitative: Can walk the latent space and get grammatical and meaningful sentences.

Sinha et al. introduce a variant of adversarial training based on distributional robust optimization. I strongly recommend reading the paper for understanding the introduced theoretical framework. The authors also provide guarantees on the obtained adversarial loss – and show experimentally that this guarantee is a realistic indicator. The adversarial training variant itself follows the general strategy of training on adversarially perturbed training samples in a min-max framework. In each iteration, an attacker crafts an adversarial examples which the network is trained on. In a nutshell, their approach differs from previous ones (apart from the theoretical framework) in the used attacker. Specifically, their attacker optimizes

$\arg\max_z l(\theta, z) - \gamma \|z – z^t\|_p^2$

where $z^t$ is a training sample chosen randomly during training.

On a side note, I also recommend reading the reviews of this paper: https://openreview.net/forum?id=Hk6kPgZA-

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

This is a paper where I keep being torn between the response of “this is so simple it’s brilliant; why haven’t people done it before,” and “this is so simple it’s almost tautological, and the results I’m seeing aren’t actually that surprising”. The basic observation this paper makes is one made frequently before, most recently to my memory by Geoff Hinton in his Capsule Net paper: sometimes the translation invariance of convolutional networks can be a bad thing, and lead to worse performance. In a lot of ways, translation invariance is one of the benefits of using a convolutional architecture in the first place: instead of having to learn separate feature detectors for “a frog in this corner” and “a frog in that corner,” we can instead use the same feature detector, and just move it over different areas of the image. However, this paper argues, this makes convolutional networks perform worse than might naively be expected at tasks that require them to remember or act in accordance with coordinates of elements within an image. 

For example, they find that normal convolutional networks take nearly an hour and 200K worth of parameters to learn to “predict” the one-hot encoding of a pixel, when given the (x,y) coordinates of that pixel as input, and only get up to about 80% accuracy. Similarly, trying to take an input image with only one pixel active, and predict the (x,y) coordinates as output, is something the network is able to do successfully, but only when the test points are sampled from the same spatial region as the training points: if the test points are from a held-out quadrant, the model can’t extrapolate to the (x, y) coordinates there, and totally falls apart. 

https://i.imgur.com/x6phN4p.png

The solution proposed by the authors is a really simple one: at one or more layers within the network, in addition to the feature channels sent up from the prior layer, add two addition channels: one with a with deterministic values going from -1 (left) to 1 (right), and the other going top to bottom. This essentially adds two fixed “features” to each pixel, which jointly carry information about where it is in space. Just by adding this small change, we give the network the ability to use spatial information or not, as it sees fit. If these features don’t prove useful, their weights will stay around their initialization values of expectation-zero, and the behavior should be much like a normal convolutional net. However, if it proves useful, convolution filters at the next layer can take position information into account. It’s easy to see how this would be useful for this paper’s toy problems: you can just create a feature detector for “if this pixel is active, pass forward information about it’s spatial position,” and predict the (x, y) coordinates out easily. You can also imagine this capability helping with more typical image classification problems, by having feature filters that carry with them not only content information, but information about where a pattern was found spatially.  

The authors do indeed find comparable performance or small benefits to ImageNet, MNIST, and Atari RL, when applying their layers in lieu of normal convolutional layer. On GANs in particular, they find less mode collapse, though I don’t yet 100% follow the intuition of why this would be the case. 
https://i.imgur.com/wu7wQZr.png

#### Introduction

* Introduces a new global log-bilinear regression model which combines the benefits of both global matrix factorization and local context window methods.


#### Global Matrix Factorization Methods

* Decompose large matrices into low-rank approximations.
* eg - Latent Semantic Analysis (LSA)

##### Limitations

* Poor performance on word analogy task
* Frequent words contribute disproportionately high to the similarity measure.

#### Shallow, Local Context-Based Window Methods

* Learn word representations using adjacent words.
* eg - Continous bag-of-words (CBOW) model and skip-gram model.

##### Limitations

* Since they do not operate directly on the global co-occurrence counts, they can not utilise the statistics of the corpus effectively.


#### GloVe Model

* To capture the relationship between words $i$ and $j$, word vector models should use ratios of co-occurene probabilites (with other words $k$) instead of using raw probabilites themselves.
* In most general form:
     * $F(w_{i}, w_{j}, w_{k}^{~} ) = P_{ik}/P_{jk}$
* We want $F$ to encode information in the vector space (which have a linear structure), so we can restrict to the difference of $w_{i}$ and $w_{j}$
    * $F(w_{i} - w_{j}, w_{k}^{~} ) = P_{ik}/P_{jk}$
* Since right hand side is a scalar and left hand side is a vector, we take dot product of the arguments.
    * $F( (w_{i} - w_{j})^{T}, w_{k}^{~} ) = P_{ik}/P_{jk}$
* *F* should be invariant to order of the word pair $i$ and $j$.
    * $F(w_{i}^{T}w_{k}^{~}) = P_{ik}$
* Doing further simplifications and optimisations (refer paper), we get cost function, 
    * $J = \sum_{\text{over all i, j pairs in the vocabulary}}[w_{i}^{T}w_{k}^{~} + b_{i} + b_{k}^{~} - log(X_{ik})]^{2}$
    * $f$ is a weighing function.
    * $f(x) = min((x/x_{max})^{\alpha}, 1)$
    * Typical values, $x_{\max} = 100$ and $\alpha = 3/4$
    * *b* are the bias terms.

##### Complexity

* Depends on a number of non-zero elements in the input matrix.
* Upper bound by the square of vocabulary size
* Since for shallow window-based approaches, complexity depends on $|C|$ (size of the corpus), tighter bounds are needed.
* By modelling number of co-occurrences of words as power law function of frequency rank, the complexity can be shown to be proportional to $|C|^{0.8}$

#### Evaluation

##### Tasks

* Word Analogies
    * a is to b as c is to ___?
    * Both semantic and syntactic pairs
    * Find closest d to $w_{b} - w_{c} + w_{a}$ (using cosine similarity)

* Word Similarity
* Named Entity Recognition

##### Datasets

* Wikipedia Dumps - 2010 and 2014
* Gigaword5
* Combination of Gigaword5 and Wikipedia2014
* CommonCrawl
* 400,000 most frequent words considered from the corpus.

##### Hyperparameters

* Size of context window.
* Whether to distinguish left context from right context.
* $f$ - Word pairs that are $d$ words apart contribute $1/d$ to the total count.
* $xmax = 100$
* $\alpha = 3/4$
* AdaGrad update

##### Models Compared With

* Singular Value Decomposition
* Continous Bag-Of-Words
* Skip-Gram

##### Results

* Glove outperforms all other models significantly.
* Diminishing returns for vectors larger than 200 dimensions.
* Small and asymmetric context windows (context window only to the left) works better for syntactic tasks.
* Long and symmetric context windows (context window to both the sides) works better for semantic tasks.
* Syntactic task benefited from larger corpus though semantic task performed better with Wikipedia instead of Gigaword5 probably due to the comprehensiveness of Wikipedia and slightly outdated nature of Gigaword5.
* Word2vec’s performance decreases if the number of negative samples increases beyond about 10.
* For the same corpus, vocabulary, and window size GloVe consistently achieves better results, faster.