The past decade has seen a revolution in genomic technologies that enabled a flood of genome-wide profiling of chromatin marks. Recent literature tried to understand gene regulation by predicting gene expression from large-scale chromatin measurements. Two fundamental challenges exist for such learning tasks: (1) genome-wide chromatin signals are spatially structured, high-dimensional and highly modular; and (2) the core aim is to understand what are the relevant factors and how they work together. Previous studies either failed to model complex dependencies among input signals or relied on separate feature analysis to explain the decisions. This paper presents an attention-based deep learning approach; AttentiveChrome, that uses a unified architecture to model and to interpret dependencies among chromatin factors for controlling gene regulation. AttentiveChrome uses a hierarchy of multiple Long Short-Term Memory (LSTM) modules to encode the input signals and to model how various chromatin marks cooperate automatically. AttentiveChrome trains two levels of attention jointly with the target prediction, enabling it to attend differentially to relevant marks and to locate important positions per mark. We evaluate the model across 56 different cell types (tasks) in human. Not only is the proposed architecture more accurate, but its attention scores also provide a better interpretation than state-of-the-art feature visualization methods such as saliency map.

Given this wide prevalence of (networks of) oscillators in nature and man-made devices, it is not surprising that oscillators have inspired various machine learning architectures in recent years.

To fix ideas, consider ECG recordings from healthy patients during rest.

LSTMs are designed to help alleviate the issue of vanishing and exploding gradients commonly associatedwithtrainingRNNs[5].

We present a neural analysis and synthesis (NANSY) framework that can manipulate the voice, pitch, and speed of an arbitrary speech signal. Most of the previous works have focused on using information bottleneck to disentangle analysis features for controllable synthesis, which usually results in poor reconstruction quality. We address this issue by proposing a novel training strategy based on information perturbation. The idea is to perturb information in the original input signal (e.g., formant, pitch, and frequency response), thereby letting synthesis networks selectively take essential attributes to reconstruct the input signal. Because NANSY does not need any bottleneck structures, it enjoys both high reconstruction quality and controllability. Furthermore, NANSY does not require any labels associated with speech data such as text and speaker information, but rather uses a new set of analysis features, i.e., wav2vec feature and newly proposed pitch feature, Yingram, which allows for fully self-supervised training. Taking advantage of fully self-supervised training, NANSY can be easily extended to a multilingual setting by simply training it with a multilingual dataset. The experiments show that NANSY can achieve significant improvement in performance in several applications such as zero-shot voice conversion, pitch shift, and time-scale modification.