Related papers: Parametrized Stochastic Grammars for RNA Secondary…
Synchronous Context-Free Grammars (SCFGs), also known as syntax-directed translation schemata, are unlike context-free grammars in that they do not have a binary normal form. In general, parsing with SCFGs takes space and time polynomial in…
We study the problem of computing the probability that a given stochastic context-free grammar (SCFG), G, generates a string in a given regular language L(D) (given by a DFA, D). This basic problem has a number of applications in…
In past work (Onokpasa, Wild, Wong, DCC 2023), we showed that (a) for joint compression of RNA sequence and structure, stochastic context-free grammars are the best known compressors and (b) that grammars which have better compression…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
In this paper we introduce a novel, context-free grammar, {\it RNAFeatures$^*$}, capable of generating any RNA structure including pseudoknot structures (pk-structure). We represent pk-structures as orientable fatgraphs, which naturally…
Log-linear models provide a statistically sound framework for Stochastic ``Unification-Based'' Grammars (SUBGs) and stochastic versions of other kinds of grammars. We describe two computationally-tractable ways of estimating the parameters…
The aim of syntactic tracking is to classify spatio-temporal patterns of a target's motion using natural language processing models. In this paper, we generalize earlier work by considering a constrained stochastic context free grammar…
Traditional Linear Genetic Programming (LGP) algorithms are based only on the selection mechanism to guide the search. Genetic operators combine or mutate random portions of the individuals, without knowing if the result will lead to a…
We analyze the distribution of RNA secondary structures given by the Knudsen-Hein stochastic context-free grammar used in the prediction program Pfold. We prove that the distribution of base pairs, helices and various types of loops in RNA…
Neural QCFG is a grammar-based sequence-tosequence (seq2seq) model with strong inductive biases on hierarchical structures. It excels in interpretability and generalization but suffers from expensive inference. In this paper, we study two…
The problem of identifying a probabilistic context free grammar has two aspects: the first is determining the grammar's topology (the rules of the grammar) and the second is estimating probabilistic weights for each rule. Given the hardness…
Probabilistic context-free grammars (PCFGs) with neural parameterization have been shown to be effective in unsupervised phrase-structure grammar induction. However, due to the cubic computational complexity of PCFG representation and…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
The problem of identifying a probabilistic context free grammar has two aspects: the first is determining the grammar's topology (the rules of the grammar) and the second is estimating probabilistic weights for each rule. Given the hardness…
RNA secondary structure is modeled with the novel arbitrary-order hidden Markov model ({\alpha}-HMM). The {\alpha}-HMM extends over the traditional HMM with capability to model stochastic events that may be in influenced by historically…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
In this paper, we present a novel approach to natural language understanding that utilizes context-free grammars (CFGs) in conjunction with sequence-to-sequence (seq2seq) deep learning. Specifically, we take a CFG authored to generate…
Predicting protein secondary structure is a fundamental problem in protein structure prediction. Here we present a new supervised generative stochastic network (GSN) based method to predict local secondary structure with deep hierarchical…
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and…
The natural language generation (NLG) component of a spoken dialogue system (SDS) usually needs a substantial amount of handcrafting or a well-labeled dataset to be trained on. These limitations add significantly to development costs and…