J. R. Taylor

Maciej Sypetkowski, Morteza Rezanejad, Saber Saberian et al.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

Philipp Becker, Harit Pandya, Gregor Gebhardt et al.

In order to integrate uncertainty estimates into deep time-series modelling, Kalman Filters (KFs) (Kalman et al., 1960) have been integrated with deep learning models, however, such approaches typically rely on approximate inference techniques such as variational inference which makes learning more complex and often less scalable due to approximation errors. We propose a new deep approach to Kalman filtering which can be learned directly in an end-to-end manner using backpropagation without additional approximations. Our approach uses a high-dimensional factorized latent state representation for which the Kalman updates simplify to scalar operations and thus avoids hard to backpropagate, computationally heavy and potentially unstable matrix inversions. Moreover, we use locally linear dynamic models to efficiently propagate the latent state to the next time step. The resulting network architecture, which we call Recurrent Kalman Network (RKN), can be used for any time-series data, similar to a LSTM (Hochreiter & Schmidhuber, 1997) but uses an explicit representation of uncertainty. As shown by our experiments, the RKN obtains much more accurate uncertainty estimates than an LSTM or Gated Recurrent Units (GRUs) (Cho et al., 2014) while also showing a slightly improved prediction performance and outperforms various recent generative models on an image imputation task.