Related papers: Practical combinations of repetition-aware data st…
The Burrows-Wheeler-Transform (BWT) is a reversible string transformation which plays a central role in text compression and is fundamental in many modern bioinformatics applications. The BWT is a permutation of the characters, which is in…
Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…
The Burrows-Wheeler Transform (BWT) is often taught in undergraduate courses on algorithmic bioinformatics, because it underlies the FM-index and thus important tools such as Bowtie and BWA. Its admirers consider the BWT a thing of beauty…
Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…
Adaptations of features commonly applied in the field of visual computing, co-occurrence matrix (COM) and run-length matrix (RLM), are proposed for the similarity computation of strings in general (words, phrases, codes and texts). The…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
The Burrows-Wheeler Transform (BWT) has been an essential tool in text compression and indexing. First introduced in 1994, it went on to provide the backbone for the first encoding of the classic suffix tree data structure in space close to…
Large-scale verifiable prompts underpin the success of Reinforcement Learning with Verifiable Rewards (RLVR), but they contain many uninformative examples and are costly to expand further. Recent studies focus on better exploiting limited…
Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…
Domains like bioinformatics, version control systems, collaborative editing systems (wiki), and others, are producing huge data collections that are very repetitive. That is, there are few differences between the elements of the collection.…
A retrieval data structure stores a static function f : S -> {0,1}^r . For all x in S, it returns the r-bit value f(x), while for other inputs it may return an arbitrary result. The structure cannot answer membership queries, so it does not…
Complex information needs may involve set-compositional queries using conjunction, disjunction, and exclusion, yet it remains unclear whether current retrieval paradigms genuinely satisfy such constraints or exploit `semantic shortcuts'. We…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
Retrieval-Augmented Generation systems depend on retrieving semantically relevant document chunks to support accurate, grounded outputs from large language models. In structured and repetitive corpora such as regulatory filings, chunk…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
Advancements in additive manufacturing have enabled design and fabrication of materials and structures not previously realizable. In particular, the design space of composite materials and structures has vastly expanded, and the resulting…
Retrieval-augmented language models (LMs) have received much attention recently. However, typically the retriever is not trained jointly as a native component of the LM, but added post-hoc to an already-pretrained LM, which limits the…
A well-known fact in the field of lossless text compression is that high-order entropy is a weak model when the input contains long repetitions. Motivated by this, decades of research have generated myriads of so-called dictionary…