Related papers: qPMS Sigma -- An Efficient and Exact Parallel Algo…
Let $t$ be a permutation (that shall play the role of the {\em text}) on $[n]$ and a pattern $p$ be a sequence of $m$ distinct integer(s) of $[n]$, $m\leq n$. The pattern $p$ occurs in $t$ in position $i$ if and only if $p_1... p_m$ is…
We consider a statistical model for the problem of finding subgraphs with specified topology in an otherwise random graph. This task plays an important role in the analysis of social and biological networks. In these types of networks,…
Probing Pre-trained Language Models (PLMs) using prompts has indirectly implied that language models (LMs) can be treated as knowledge bases. To this end, this phenomena has been effective especially when these LMs are fine-tuned towards…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
We present MEDUSA, an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data. We use a modern large-margin machine learning approach, based on boosting,…
Distributed algorithms for solving coupled semidefinite programs (SDPs) commonly require many iterations to converge. They also put high computational demand on the computational agents. In this paper we show that in case the coupled…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
We address the problem of summarizing embedded tree patterns extracted from large data trees. We do so by defining and mining closed and maximal embedded unordered tree patterns from a single large data tree. We design an embedded frequent…
Researchers and practitioners in natural language processing and computational linguistics frequently observe and analyze the real language usage in large-scale corpora. For that purpose, they often employ off-the-shelf pattern-matching…
Large language models (LLMs) have demonstrated remarkable capabilities in code generation and structured reasoning; however, their performance often degrades on complex tasks that require consistent multi-step planning. Recent work has…
RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these patterns is of fundamental importance for assessing the statistical significance of matches…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Utilizing large language models (LLMs) for zero-shot document ranking is done in one of two ways: (1) prompt-based re-ranking methods, which require no further training but are only feasible for re-ranking a handful of candidate documents…
The quantity of event logs available is increasing rapidly, be they produced by industrial processes, computing systems, or life tracking, for instance. It is thus important to design effective ways to uncover the information they contain.…
The GRAPH MOTIF problem asks whether a given multiset of colors appears on a connected subgraph of a vertex-colored graph. The fastest known parameterized algorithm for this problem is based on a reduction to the $k$-Multilinear Detection…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
Time Series Motif Discovery (TSMD), which aims at finding recurring patterns in time series, is an important task in numerous application domains, and many methods for this task exist. These methods are usually evaluated qualitatively. A…
Longest Common Subsequence ($LCS$) deals with the problem of measuring similarity of two strings. While this problem has been analyzed for decades, the recent interest stems from a practical observation that considering single characters is…
This paper addresses the Restricted Longest Common Subsequence (RLCS) problem, an extension of the well-known Longest Common Subsequence (LCS) problem. This problem has significant applications in bioinformatics, particularly for…
Recently, two new parallel algorithms for on-the-fly model checking of LTL properties were presented at the same conference: Automated Technology for Verification and Analysis, 2011. Both approaches extend Swarmed NDFS, which runs several…