相关论文: NTRFINDER: A Software Tool to Find Nested Tandem R…

RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…

The typical problem in Data Science is creating a structure that encodes the occurrence frequency of unique elements in rows and relations between different rows of a data frame. We present the probability tree abstract data structure, an…

Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…

Pattern matching can be used to calculate the support of patterns, and is a key issue in sequential pattern mining (or sequence pattern mining). Nonoverlapping pattern matching means that two occurrences cannot use the same character in the…

Over the long history of machine learning, which dates back several decades, recurrent neural networks (RNNs) have been used mainly for sequential data and time series and generally with 1D information. Even in some rare studies on 2D…

The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured in ways that are otherwise inaccessible to observation. Here, we introduce the $n$-tangle method to directly compare two…

MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor…

Neural collaborative filtering (NCF) and recurrent recommender systems (RRN) have been successful in modeling user-item relational data. However, they are also limited in their assumption of static or sequential modeling of relational data…

Discovering the latent structure from many observed variables is an important yet challenging learning task. Existing approaches for discovering latent structures often require the unknown number of hidden states as an input. In this paper,…

Tensor ring (TR) decomposition is an efficient approach to discover the hidden low-rank patterns for higher-order tensors, and streaming tensors are becoming highly prevalent in real-world applications. In this paper, we investigate how to…

Current state-of-the-art models for named entity recognition (NER) are neural models with a conditional random field (CRF) as the final layer. Entities are represented as per-token labels with a special structure in order to decode them…

Python's dynamic typing system offers flexibility and expressiveness but can lead to type-related errors, prompting the need for automated type inference to enhance type hinting. While existing learning-based approaches show promising…

In the context of End-to-End testing of web applications, automated exploration techniques (a.k.a. crawling) are widely used to infer state-based models of the site under test. These models, in which states represent features of the web…

Named Entity Recognition and Disambiguation (NERD) systems have recently been widely researched to deal with the significant growth of the Web. NERD systems are crucial for several Natural Language Processing (NLP) tasks such as…

The Detection Transformer (DETR), by incorporating the Hungarian algorithm, has significantly simplified the matching process in object detection tasks. This algorithm facilitates optimal one-to-one matching of predicted bounding boxes to…

A novel graph-to-tree conversion mechanism called the deep-tree generation (DTG) algorithm is first proposed to predict text data represented by graphs. The DTG method can generate a richer and more accurate representation for nodes (or…

In this work, we present the tree tensor network Nystr\"om (TTNN), an algorithm that extends recent research on streamable tensor approximation, such as for Tucker and tensor-train formats, to the more general tree tensor network format,…

Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the…

Neural networks (NNs) and decision trees (DTs) are both popular models of machine learning, yet coming with mutually exclusive advantages and limitations. To bring the best of the two worlds, a variety of approaches are proposed to…

We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA…