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Several variants of recurrent neural networks (RNNs) with orthogonal or unitary recurrent matrices have recently been developed to mitigate the vanishing/exploding gradient problem and to model long-term dependencies of sequences. However, with the eigenvalues of the recurrent matrix on the unit circle, the recurrent state retains all input information which may unnecessarily consume model capacity. In this paper, we address this issue by proposing an architecture that expands upon an orthogonal/unitary RNN with a state that is generated by a recurrent matrix with eigenvalues in the unit disc. Any input to this state dissipates in time and is replaced with new inputs, simulating short-term memory. A gradient descent algorithm is derived for learning such a recurrent matrix. The resulting method, called the Eigenvalue Normalized RNN (ENRNN), is shown to be highly competitive in several experiments. 

Abstract The problem of determining which nucleotides of an RNA sequence are paired or unpaired in the secondary structure of an RNA, which we call RNA state inference, can be studied by different machine learning techniques. Successful state inference of RNA sequences can be used to generate auxiliary information for data-directed RNA secondary structure prediction. Typical tools for state inference, such as hidden Markov models, exhibit poor performance in RNA state inference, owing in part to their inability to recognize nonlocal dependencies. Bidirectional long short-term memory (LSTM) neural networks have emerged as a powerful tool that can model global nonlinear sequence dependencies and have achieved state-of-the-art performances on many different classification problems. This paper presents a practical approach to RNA secondary structure inference centered around a deep learning method for state inference. State predictions from a deep bidirectional LSTM are used to generate synthetic SHAPE data that can be incorporated into RNA secondary structure prediction via the Nearest Neighbor Thermodynamic Model (NNTM). This method produces predicted secondary structures for a diverse test set of 16S ribosomal RNA that are, on average, 25 percentage points more accurate than undirected MFE structures. Accuracy is highly dependent on the success of our state inference method, and investigating the global features of our state predictions reveals that accuracy of both our state inference and structure inference methods are highly dependent on the similarity of pairing patterns of the sequence to the training dataset. Availability of a large training dataset is critical to the success of this approach. Code available at https://github.com/dwillmott/rna-state-inf . 

Recurrent neural networks (RNNs) have been successfully used on a wide range of sequential data problems. A well known difficulty in using RNNs is the vanishing or exploding gradient problem. Recently, there have been several different RNN architectures that try to mitigate this issue by maintaining an orthogonal or unitary recurrent weight matrix. One such architecture is the scaled Cayley orthogonal recurrent neural network (scoRNN) which parameterizes the orthogonal recurrent weight matrix through a scaled Cayley transform. This parametrization contains a diagonal scaling matrix consisting of positive or negative one entries that can not be optimized by gradient descent. Thus the scaling matrix is fixed before training and a hyperparameter is introduced to tune the matrix for each particular task. In this paper, we develop a unitary RNN architecture based on a complex scaled Cayley transform. Unlike the real orthogonal case, the transformation uses a diagonal scaling matrix consisting of entries on the complex unit circle which can be optimized using gradient descent and no longer requires the tuning of a hyperparameter. We also provide an analysis of a potential issue of the modReLU activiation function which is used in our work and several other unitary RNNs. In the experiments conducted, the scaled Cayley unitary recurrent neural network (scuRNN) achieves comparable or better results than scoRNN and other unitary RNNs without fixing the scaling matrix.