Related papers: Parametrized Stochastic Grammars for RNA Secondary…

This paper presents a new approach of automatic text summarization which combines domain oriented text analysis (DoTA) and rhetorical structure theory (RST) in a grammar form: the attributed rhetorical structure grammar (ARSG), where the…

This paper proposes a hierarchical generative model with a multi-grained latent variable to synthesize expressive speech. In recent years, fine-grained latent variables are introduced into the text-to-speech synthesis that enable the fine…

Structured distributions, i.e. distributions over combinatorial spaces, are commonly used to learn latent probabilistic representations from observed data. However, scaling these models is bottlenecked by the high computational and memory…

Gene expression estimation from pathology images has the potential to reduce the RNA sequencing cost. Point-wise loss functions have been widely used to minimize the discrepancy between predicted and absolute gene expression values.…

We describe a generative probabilistic model of natural language, which we call HBG, that takes advantage of detailed linguistic information to resolve ambiguity. HBG incorporates lexical, syntactic, semantic, and structural information…

We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…

The goal of the present paper is to provide a systematic and comprehensive study of rational stochastic languages over a semiring K \in {Q, Q +, R, R+}. A rational stochastic language is a probability distribution over a free monoid…

We propose a neural language model capable of unsupervised syntactic structure induction. The model leverages the structure information to form better semantic representations and better language modeling. Standard recurrent neural networks…

Model structure and complexity selection remains a challenging problem in system identification, especially for parametric non-linear models. Many Evolutionary Algorithm (EA) based methods have been proposed in the literature for estimating…

State space models (SSMs) provide a flexible framework for modeling complex time series via a latent stochastic process. Inference for nonlinear, non-Gaussian SSMs is often tackled with particle methods that do not scale well to long time…

Inspired by the success of large language models (LLM) for DNA and proteins, several LLM for RNA have been developed recently. RNA-LLM uses large datasets of RNA sequences to learn, in a self-supervised way, how to represent each RNA base…

Sequence to sequence (seq2seq) models are often employed in settings where the target output is natural language. However, the syntactic properties of the language generated from these models are not well understood. We explore whether such…

We introduce the probabilistic sequential matrix factorization (PSMF) method for factorizing time-varying and non-stationary datasets consisting of high-dimensional time-series. In particular, we consider nonlinear Gaussian state-space…

Probabilistic context-free grammars (PCFGs) and dynamic Bayesian networks (DBNs) are widely used sequence models with complementary strengths and limitations. While PCFGs allow for nested hierarchical dependencies (tree structures), their…

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…

Learning useful information across long time lags is a critical and difficult problem for temporal neural models in tasks such as language modeling. Existing architectures that address the issue are often complex and costly to train. The…

Linear chain conditional random fields (CRFs) combined with contextual word embeddings have achieved state of the art performance on sequence labeling tasks. In many of these tasks, the identity of the neighboring words is often the most…

We introduce a novel training principle for probabilistic models that is an alternative to maximum likelihood. The proposed Generative Stochastic Networks (GSN) framework is based on learning the transition operator of a Markov chain whose…

Most state-of-the-art systems today produce morphological analysis based only on orthographic patterns. In contrast, we propose a model for unsupervised morphological analysis that integrates orthographic and semantic views of words. We…

Probabilistic analogues of regular and context-free grammars are well-known in computational linguistics, and currently the subject of intensive research. To date, however, no satisfactory probabilistic analogue of attribute-value grammars…