Transformer models have achieved state-of-the-art results across a diverse range of domains. However, concern over the cost of training the attention mechanism to learn complex dependencies between distant inputs continues to grow. In response, solutions that exploit the structure and sparsity of the learned attention matrix have blossomed. However, real-world applications that involve long sequences, such as biological sequence analysis, may fall short of meeting these assumptions, precluding exploration of these models. To address this challenge, we present a new Transformer architecture, Performer, based on Fast Attention Via Orthogonal Random features (FAVOR). Our mechanism scales linearly rather than quadratically in the number of tokens in the sequence, is characterized by sub-quadratic space complexity and does not incorporate any sparsity pattern priors. Furthermore, it provides strong theoretical guarantees: unbiased estimation of the attention matrix and uniform convergence. It is also backwards-compatible with pre-trained regular Transformers. We demonstrate its effectiveness on the challenging task of protein sequence modeling and provide detailed theoretical analysis.

The use of black-box optimization for the design of new biological sequences is an emerging research area with potentially revolutionary impact. The cost and latency of wet-lab experiments requires methods that find good sequences in few experimental rounds of large batches of sequences--a setting that off-the-shelf black-box optimization methods are ill-equipped to handle. We find that the performance of existing methods varies drastically across optimization tasks, posing a significant obstacle to real-world applications. To improve robustness, we propose Population-Based Black-Box Optimization (P3BO), which generates batches of sequences by sampling from an ensemble of methods. The number of sequences sampled from any method is proportional to the quality of sequences it previously proposed, allowing P3BO to combine the strengths of individual methods while hedging against their innate brittleness. Adapting the hyper-parameters of each of the methods online using evolutionary optimization further improves performance. Through extensive experiments on in-silico optimization tasks, we show that P3BO outperforms any single method in its population, proposing higher quality sequences as well as more diverse batches. As such, P3BO and Adaptive-P3BO are a crucial step towards deploying ML to real-world sequence design.

Current end-to-end machine reading and question answering (Q\&A) models are primarily based on recurrent neural networks (RNNs) with attention. Despite their success, these models are often slow for both training and inference due to the sequential nature of RNNs. We propose a new Q\&A architecture called QANet, which does not require recurrent networks: Its encoder consists exclusively of convolution and self-attention, where convolution models local interactions and self-attention models global interactions. On the SQuAD dataset, our model is 3x to 13x faster in training and 4x to 9x faster in inference, while achieving equivalent accuracy to recurrent models. The speed-up gain allows us to train the model with much more data. We hence combine our model with data generated by backtranslation from a neural machine translation model. On the SQuAD dataset, our single model, trained with augmented data, achieves 84.6 F1 score on the test set, which is significantly better than the best published F1 score of 81.8.