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.

Learning with recurrent neural networks (RNNs) on long sequences is a notoriously difficult task. There are three major challenges: 1) complex dependencies, 2) vanishing and exploding gradients, and 3) efficient parallelization. In this paper, we introduce a simple yet effective RNN connection structure, the DilatedRNN, which simultaneously tackles all of these challenges. The proposed architecture is characterized by multi-resolution dilated recurrent skip connections and can be combined flexibly with diverse RNN cells. Moreover, the DilatedRNN reduces the number of parameters needed and enhances training efficiency significantly, while matching state-of-the-art performance (even with standard RNN cells) in tasks involving very long-term dependencies. To provide a theory-based quantification of the architecture's advantages, we introduce a memory capacity measure, the mean recurrent length, which is more suitable for RNNs with long skip connections than existing measures. We rigorously prove the advantages of the DilatedRNN over other recurrent neural architectures.

In many applications such as advertisement placement or automated dialog systems, an intelligent system optimizes performance over a sequence of interactions with each user. Such tasks often involve many states and potentially time-dependent transition dynamics, and can be modeled well as episodic Markov decision processes (MDPs). In this paper, we present a PAC algorithm for reinforcement learning in episodic finite MDPs with time-dependent transitions that acts epsilon-optimal in all but O(S A H^3 / epsilon^2 log(1 / delta)) episodes. Our algorithm has a polynomial computational complexity, and our sample complexity bound accounts for the fact that we may only be able to approximately solve the internal planning problems. In addition, our PAC sample complexity bound has only linear dependency on the number of states S and actions A and strictly improves previous bounds with S^2 dependency in this setting. Compared against other methods for infinite horizon reinforcement learning with linear state space sample complexity our method has much lower dependency on the (effective) horizon. Indeed, our bound is optimal up to a factor of H.

Bounding the generalization error of learning algorithms has a long history, which yet falls short in explaining various generalization successes including those of deep learning. Two important difficulties are (i) exploiting the dependencies between the hypotheses, (ii) exploiting the dependence between the algorithm's input and output. Progress on the first point was made with the chaining method, originating from the work of Kolmogorov, and used in the VC-dimension bound. More recently, progress on the second point was made with the mutual information method by Russo and Zou '15. Yet, these two methods are currently disjoint. In this paper, we introduce a technique to combine chaining and mutual information methods, to obtain a generalization bound that is both algorithm-dependent and that exploits the dependencies between the hypotheses. We provide an example in which our bound significantly outperforms both the chaining and the mutual information bounds. As a corollary, we tighten Dudley's inequality when the learning algorithm chooses its output from a small subset of hypotheses with high probability.

We use the discrete variablezd,t to represent the topic that thetth word is generated from.

We also study the more general case of an additional entropy regularizer.

Code is at this URL.