How noncoding DNA determines gene expression in different cell types is a major unsolved problem, and critical downstream applications in human genetics depend on improved solutions. Here, we report substantially improved gene expression prediction accuracy from DNA sequences through the use of a deep learning architecture, called Enformer, that is able to integrate information from long-range interactions (up to 100 kb away) in the genome. This improvement yielded more accurate variant effect predictions on gene expression for both natural genetic variants and saturation mutagenesis measured by massively parallel reporter assays. Furthermore, Enformer learned to predict enhancer–promoter interactions directly from the DNA sequence competitively with methods that take direct experimental data as input. We expect that these advances will enable more effective fine-mapping of human disease associations and provide a framework to interpret cis-regulatory evolution.

This work presents a scalable solution to open-vocabulary visual speech recognition. To achieve this, we constructed the largest existing visual speech recognition dataset, consisting of pairs of text and video clips of faces speaking (3,886 hours of video). In tandem, we designed and trained an integrated lipreading system, consisting of a video processing pipeline that maps raw video to stable videos of lips and sequences of phonemes, a scalable deep neural network that maps the lip videos to sequences of phoneme distributions, and a production-level speech decoder that outputs sequences of words. The proposed system achieves a word error rate (WER) of 40.9% as measured on a held-out set. In comparison, professional lipreaders achieve either 86.4% or 92.9% WER on the same dataset when having access to additional types of contextual information. Our approach significantly improves on other lipreading approaches, including variants of LipNet and of Watch, Attend, and Spell (WAS), which are only capable of 89.8% and 76.8% WER respectively. * These authors contributed equally to this work.

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Ancient history relies on disciplines such as epigraphy—the study of inscribed texts known as inscriptions—for evidence of the thought, language, society and history of past civilizations1. However, over the centuries, many inscriptions have been damaged to the point of illegibility, transported far from their original location and their date of writing is steeped in uncertainty. Here we present Ithaca, a deep neural network for the textual restoration, geographical attribution and chronological attribution of ancient Greek inscriptions. Ithaca is designed to assist and expand the historian’s workflow. The architecture of Ithaca focuses on collaboration, decision support and interpretability. While Ithaca alone achieves 62% accuracy when restoring damaged texts, the use of Ithaca by historians improved their accuracy from 25% to 72%, confirming the synergistic effect of this research tool. Ithaca can attribute inscriptions to their original location with an accuracy of 71% and can date them to less than 30 years of their ground-truth ranges, redating key texts of Classical Athens and contributing to topical debates in ancient history. This research shows how models such as Ithaca can unlock the cooperative potential between artificial intelligence and historians, transformationally impacting the way that we study and write about one of the most important periods in human history.