相关论文: R-enum: Enumeration of Characteristic Substrings i…

We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input parameter, and tries to make the best use of it by splitting…

High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…

Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…

In this paper we revisit the classical regular expression matching problem, namely, given a regular expression $R$ and a string $Q$, decide if $Q$ matches one of the strings specified by $R$. Let $m$ and $n$ be the length of $R$ and $Q$,…

Animals ranging from rats to humans can demonstrate cognitive map capabilities. We evolved weights in a biologically plausible recurrent neural network (RNN) using an evolutionary algorithm to replicate the behavior and neural activity…

Future robotic systems operating in real-world environments will require on-board embodied intelligence without continuous cloud connection, balancing capabilities with constraints on computational power and memory. This work presents an…

Given a string $T$ of length $n$, a substring $u = T[i..j]$ of $T$ is called a shortest unique substring (SUS) for an interval $[s,t]$ if (a) $u$ occurs exactly once in $T$, (b) $u$ contains the interval $[s,t]$ (i.e. $i \leq s \leq t \leq…

The r largest order statistics approach is widely used in extreme value analysis because it may use more information from the data than just the block maxima. In practice, the choice of r is critical. If r is too large, bias can occur; if…

The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…

Binary Balanced Tree RvNNs (BBT-RvNNs) enforce sequence composition according to a preset balanced binary tree structure. Thus, their non-linear recursion depth is just $\log_2 n$ ($n$ being the sequence length). Such logarithmic scaling…

Recurrent neural networks (RNNs) have recently achieved remarkable successes in a number of applications. However, the huge sizes and computational burden of these models make it difficult for their deployment on edge devices. A practically…

We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…

The Burrows-Wheeler transform (BWT) is a string transformation that enhances string indexing and compressibility. Cotumaccio and Prezza [SODA '21] extended this transformation to nondeterministic finite automata (NFAs) through…

Linear regression is a widely used technique to fit linear models and finds widespread applications across different areas such as machine learning and statistics. In most real-world scenarios, however, linear regression problems are often…

We introduce a recurrent neural network language model (RNN-LM) with long short-term memory (LSTM) units that utilizes both character-level and word-level inputs. Our model has a gate that adaptively finds the optimal mixture of the…

Shannon's entropy is a definitive lower bound for statistical compression. Unfortunately, no such clear measure exists for the compressibility of repetitive strings. Thus, ad hoc measures are employed to estimate the repetitiveness of…

We investigate the computational complexity of various problems for simple recurrent neural networks (RNNs) as formal models for recognizing weighted languages. We focus on the single-layer, ReLU-activation, rational-weight RNNs with…

Learning intents and slot labels from user utterances is a fundamental step in all spoken language understanding (SLU) and dialog systems. State-of-the-art neural network based methods, after deployment, often suffer from performance…

A maximal repetition, or run, in a string, is a maximal periodic substring whose smallest period is at most half the length of the substring. In this paper, we consider runs that correspond to a path on a trie, or in other words, on a…

We revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results.…