Related papers: FMtree: A fast locating algorithm of FM-indexes fo…
Document listing on string collections is the task of finding all documents where a pattern appears. It is regarded as the most fundamental document retrieval problem, and is useful in various applications. Many of the fastest-growing…
Levin Tree Search (LTS) (Orseau et al., 2018) is a search algorithm for deterministic environments that uses a user-specified policy to guide the search. It comes with a formal guarantee on the number of search steps (node visits) for…
We present a new compact representation to efficiently store and query large RDF datasets in main memory. Our proposal, called BMatrix, is based on the k2-tree, a data structure devised to represent binary matrices in a compressed way, and…
Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…
As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard…
The $k^2$-tree is a compact data structure designed to efficiently store sparse binary matrices by leveraging both sparsity and clustering of nonzero elements. This representation supports efficiently navigational operations and complex…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Applying machine learning algorithms to private data, such as financial or medical data, while preserving their confidentiality, is a difficult task. Homomorphic Encryption (HE) is acknowledged for its ability to allow computation on…
Path planning in dynamic environments remains a core challenge in robotics, especially as autonomous systems are deployed in unpredictable spaces such as warehouses and public roads. While algorithms like Fast Marching Tree (FMT$^{*}$)…
A search query consists of several words. In a proximity full-text search, we want to find documents that contain these words near each other. This task requires much time when the query consists of high-frequently occurring words. If we…
Autonomous driving holds promise for increased safety, optimized traffic management, and a new level of convenience in transportation. While model-based reinforcement learning approaches such as MuZero enables long-term planning, the…
Motif finding is an important step for the detection of rare events occurring in a set of DNA or protein sequences. Extraction of information about these rare events can lead to new biological discoveries. Motifs are some important patterns…
Tree ensembles are powerful models that achieve excellent predictive performances, but can grow to unwieldy sizes. These ensembles are often post-processed (pruned) to reduce memory footprint and improve interpretability. We present…
Retrosynthesis, the process of deconstructing a target molecule into simpler precursors, is crucial for computer-aided synthesis planning (CASP). Widely adopted tree-search methods often suffer from exponential computational complexity. In…
Smart energy performance monitoring and optimisation at the supplier and consumer levels is essential to realising smart cities. In order to implement a more sustainable energy management plan, it is crucial to conduct a better energy…
Suffix trees have emerged to be very fast for pattern searching yielding O (m) time, where m is the pattern size. Unfortunately their high memory requirements make it impractical to work with huge amounts of data. We present a memory…
Cartesian tree matching is the problem of finding all substrings in a given text which have the same Cartesian trees as that of a given pattern. In this paper, we deal with Cartesian tree matching for the case of multiple patterns. We…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
We propose an extension of tree-based space-partitioning indexing structures for data with low intrinsic dimensionality embedded in a high dimensional space. We call this extension an Angle Tree. Our extension can be applied to both…
A compressed full-text self-index occupies space close to that of the compressed text and simultaneously allows fast pattern matching and random access to the underlying text. Among the best compressed self-indexes, in theory and in…