Related papers: qPMS Sigma -- An Efficient and Exact Parallel Algo…
The extraction of $k$-mers is a fundamental component in many complex analyses of large next-generation sequencing datasets, including reads classification in genomics and the characterization of RNA-seq datasets. The extraction of all…
We introduce a pattern mining framework that operates on semi-structured datasets and exploits the dichotomy between outcomes. Our approach takes advantage of constraint reasoning to find sequential patterns that occur frequently and…
The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify variable…
In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional…
One fundamental problem in temporal graph analysis is to count the occurrences of small connected subgraph patterns (i.e., motifs), which benefits a broad range of real-world applications, such as anomaly detection, structure prediction,…
Since the adoption of large language models (LLMs) for text evaluation has become increasingly prevalent in the field of natural language processing (NLP), a series of existing works attempt to optimize the prompts for LLM evaluators to…
Since model quantization helps to reduce the model size and computation latency, it has been successfully applied in many applications of mobile phones, embedded devices and smart chips. The mixed-precision quantization model can match…
The widespread application of Large Language Models (LLMs) has motivated a growing interest in their capacity for processing dynamic graphs. Temporal motifs, as an elementary unit and important local property of dynamic graphs which can…
Inverse design of short single-stranded RNA and DNA sequences (aptamers) is the task of finding sequences that satisfy a set of desired criteria. Relevant criteria may be, for example, the presence of specific folding motifs, binding to…
Schema matching is the process of identifying correspondences between the elements of two given schemata, essential for database management systems, data integration, and data warehousing. For datasets across different scenarios, the…
The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures…
Few-shot segmentation is challenging because objects within the support and query images could significantly differ in appearance and pose. Using a single prototype acquired directly from the support image to segment the query image causes…
Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA.…
Various grammar compression algorithms have been proposed in the last decade. A grammar compression is a restricted CFG deriving the string deterministically. An efficient grammar compression develops a smaller CFG by finding duplicated…
As language models (LMs) deliver increasing performance on a range of NLP tasks, probing classifiers have become an indispensable technique in the effort to better understand their inner workings. A typical setup involves (1) defining an…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
Most of the current understanding of structure-property relations at the molecular and the supramolecular scales can be formulated in terms of the stability of and the interactions between a limited number of recurring structural motifs…
The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…
Motif counting plays a crucial role in understanding the structural properties of networks. By computing motif frequencies, researchers can draw key insights into the structural properties of the underlying network. As networks become…
Identifying frequent subgraphs, also called network motifs, is crucial in analyzing and predicting properties of real-world networks. However, finding large commonly-occurring motifs remains a challenging problem not only due to its NP-hard…