Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis. We introduce ProteinBERT, a deep language model specifically designed for proteins. Our pretraining scheme combines language modeling with a novel task of Gene Ontology (GO) annotation prediction. We introduce novel architectural elements that make the model highly efficient and flexible to long sequences. The architecture of ProteinBERT consists of both local and global representations, allowing end-to-end processing of these types of inputs and outputs. ProteinBERT obtains near state-of-the-art performance, and sometimes exceeds it, on multiple benchmarks covering diverse protein properties (including protein structure, post translational modifications and biophysical attributes), despite using a far smaller and faster model than competing deep-learning methods. Overall, ProteinBERT provides an efficient framework for rapidly training protein predictors, even with limited labeled data. Code and pretrained model weights are available at https://github.com/nadavbra/protein_bert.

Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis. We introduce ProteinBERT, a deep language model specifically designed for proteins. Our pretraining scheme consists of masked language modeling combined with a novel task of Gene Ontology (GO) annotation prediction. We introduce novel architectural elements that make the model highly efficient and flexible to very large sequence lengths. The architecture of ProteinBERT consists of both local and global representations, allowing end-to-end processing of these types of inputs and outputs. ProteinBERT obtains state-of-the-art performance on multiple benchmarks covering diverse protein properties (including protein structure, post translational modifications and biophysical attributes), despite using a far smaller model than competing deep-learning methods. Overall, ProteinBERT provides an efficient framework for rapidly training protein predictors, even with limited labeled data. Code and pretrained model weights are available at https://github.com/nadavbra/protein_bert.

In a previous paper, we introduced a deep learning neural network that should be able to detect the existence of very shallow periodic planetary transits in the presence of red noise. The network in that feasibility study would not provide any further details about the detected transits. The current paper completes this missing part. We present a neural network that tags samples that were obtained during transits. This is essentially similar to the task of identifying the semantic context of each pixel in an image—an important task in computer vision, called “semantic segmentation,” which is often performed by deep neural networks. The neural network we present makes use of novel deep learning concepts such as U-Nets, Generative Adversarial Networks, and adversarial loss. The resulting segmentation should allow further studies of the light curves that are tagged as containing transits. This approach toward the detection and study of very shallow transits is bound to play a significant role in future space-based transit surveys such as PLATO, which are specifically aimed to detect those extremely difficult cases of long-period shallow transits. Our segmentation network also adds to the growing toolbox of deep learning approaches that are being increasingly used in the study of exoplanets; but, so far mainly for vetting transits, rather than their initial detection.

No abstract