Related papers: Fast Exact String to D-Texts Alignments
DCAlign is a new alignment method able to cope with the conservation and the co-evolution signals that characterize the columns of multiple sequence alignments of homologous sequences. However, the pre-processing steps required to align a…
Sparse representation-based classifiers have shown outstanding accuracy and robustness in image classification tasks even with the presence of intense noise and occlusion. However, it has been discovered that the performance degrades…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
Many tasks in natural language processing, ranging from machine translation to question answering, can be reduced to the problem of matching two sentences or more generally two short texts. We propose a new approach to the problem, called…
Question Answering (QA) systems are used to provide proper responses to users' questions automatically. Sentence matching is an essential task in the QA systems and is usually reformulated as a Paraphrase Identification (PI) problem. Given…
We present a new efficient method for approximate search in electronic lexica. Given an input string (the pattern) and a similarity threshold, the algorithm retrieves all entries of the lexicon that are sufficiently similar to the pattern.…
Recently, end-to-end mispronunciation detection and diagnosis (MD&D) systems has become a popular alternative to greatly simplify the model-building process of conventional hybrid DNN-HMM systems by representing complicated modules with a…
Large language models (LLMs) offer a promising way to simulate human survey responses, potentially reducing the cost of large-scale data collection. However, existing zero-shot methods suffer from prompt sensitivity and low accuracy, while…
Continuously-growing data volumes lead to larger generic models. Specific use-cases are usually left out, since generic models tend to perform poorly in domain-specific cases. Our work addresses this gap with a method for selecting…
In the field of domain adaptation, a trade-off exists between the model performance and the number of target domain annotations. Active learning, maximizing model performance with few informative labeled data, comes in handy for such a…
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…
Efficient long-sequence generation is a critical challenge for Large Language Models. While recent sparse decoding methods improve efficiency, they suffer from KV cache misalignment, where approximation errors accumulate and degrade…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
We propose a new algorithm called DK-vec for aligning pairs of Asian/Indo-European noisy parallel texts without sentence boundaries. DK-vec improves on previous alignment algorithms in that it handles better the non-linear nature of noisy…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
Intersecting branes provide a useful mechanism to construct particle physics models from string theory with a wide variety of desirable characteristics. The landscape of such models can be enormous, and navigating towards regions which are…
In this paper we introduce a General Dynamic String-Averaging (GDSA) iterative scheme and investigate its convergence properties in the inconsistent case, that is, when the input operators don't have a common fixed point. The Dynamic…
In this paper, we present an adaptive bitextual alignment system called AIlign. This aligner relies on sentence embeddings to extract reliable anchor points that can guide the alignment path, even for texts whose parallelism is fragmentary…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…