I strongly suspect this is the case too! 

In fact, we might be able to speed up the learning of common features even further:

Pierre Peigné at SERIMATS has done some interesting work that looks at initialization schemes that speed up learning. If you initialize the autoencoders with a sample of datapoints (e.g. initialize the weights with a sample from the MLP activations dataset), each of which we assume to contain a linear combination of only a few of the ground truth features, then the initial phases of feature recovery is much faster*. We haven't had time to check, but it's presumably biased to recover the most common features first since they're the most likely to be in a given data point. 

*The ground truth feature recovery metric (MMCS) starts higher at the beginning of autoencoder training, but converges to full recovery at about the same time. 

No theoretical reason - The method we used in the Interim Report to combine the two losses into one metric was pretty cursed. It's probably just better to use L1 loss alone and reconstruction loss alone and then combine the findings. But having plots for both losses would have added more plots without much gain for the presentation. It also just seemed like the method that was hardest to discern the difference between full recovery and partial recovery because the differences were kind of subtle. In future work, some way to use the losses to measure feature recover will probably be re-introduced. It probably just won't be the way we used in the interim report.