27 papers · ranked by Valyu relevance
Cao, Kai, Duan, Yucong + 2 more
Incorporating utility into targeted pattern mining can address the practical limitations of traditional frequencybased approaches. However, utility-based methods often suffer from generating a large number of long and complicated sequences. To improve pattern relevance and interpretability, average utility provides a…
Hao Xuan, Hongyang Sun, Xiangtao Liu, Hanyuan Zhang + 2 more
Sequence alignment underpins nearly every facet of modern genomics, from genetic testing and cancer profiling to functional genome annotation. Yet, despite decades of algorithmic innovation, most existing aligners remain narrowly optimized for specific tasks, fragmenting analytical workflows and limiting…
Donald R Campbell, Timothee Cezard, Sveinung Gundersen, Andrew D. Yates + 8 more
Reference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for comparison. To address this, we introduce the GA4GH refget Sequence Collections (seqcol) standard. Refget seqcol is a framework…
Chunkai Zhang, Jiarui Deng, Maohua Lyu, Wensheng Gan + 1 more
—Within the domain of data mining, one critical objective is the discovery of sequential rules with high utility. The goal is to discover sequential rules that exhibit both high utility and strong confidence, which are valuable in real-world applications. However, existing high-utility sequential rule mining algorithms…
Donald R Campbell Jr, Timothee Cezard, Sveinung Gundersen, Andrew D. Yates + 8 more
Reference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for comparison. To address this, we introduce the GA4GH refget Sequence Collections (seqcol) standard. Refget seqcol is a framework…
Noam Teyssier, Alexander Dobin, Stephan Schiffels
Modern genomics produces billions of sequencing records per run, which are typically stored as gzip-compressed FASTQ files. While this format is widely used, it is not optimal for high-throughput processing due to its reliance on single-threaded decompression and sequential parsing of irregularly sized records. This…
Rick den Otter, Anna Dame, Sjoerd Stuit, Leendert van Maanen + 1 more
Theories of dual-task interference assume that the same cognitive operations underlie multitasking regardless of stimulus timing, yet this core assumption has remained untested due to methodological limitations of behavioral averaging. Here, we combine hidden multivariate pattern (HMP) analysis with deep spatiotemporal…
Tessa Alexanian, Jacob Beal, Craig Bartling, Jens Berlips + 20 more
Readily available nucleic acid synthesis is both critical for the bioeconomy and an increasingly pressing security concern due to the potential for accidental or deliberate misuse. While biosecurity experts broadly agree that nucleic acid providers should screen orders for potential “sequences of concern,” there has…
Maike Hille, Elisabeth Wenger, Eleftheria Papadaki, Yana Fandakova
Humans possess an astounding ability to acquire complex movement sequences with limited practice. Motor sequence learning engages a distributed network of brain regions that show distinct learning-related changes, often characterized by predominant involvement of the prefrontal cortex (PFC) early in learning and…
Zhu, Jian, Lin, Zhidong + 8 more
—Discovering valuable insights from rich data is a crucial task for exploratory data analysis. Sequential pattern mining (SPM) has found widespread applications across various domains. In recent years, low-utility sequential pattern mining (LUSPM) has shown strong potential in applications such as intrusion detection…
Li-Ann Leow, Jarrad Lum, Sara Johnson, Emily Corti + 1 more
Musicians demonstrate advantages in acquiring motor sequences, showing faster learning and better explicit sequence knowledge than non-musicians. However, it is unclear whether this advantage extends beyond acquisition to the consolidation phase, which is when newly learned skills stabilize and become resistant to…
Mikhail Karasikov, Harun Mustafa, Daniel Danciu, Oleksandr Kulkov + 4 more
The amount of biological sequencing data available in public repositories is growing rapidly, forming a critical resource for biomedicine. However, making these data efficiently and accurately full-text searchable remains challenging. Here we build on efficient data structures and algorithms for representing large…
Asad Khan, Michael Burke, Erhan Genc, Min-Fang Kuo + 1 more
Motor sequence learning (MSL) underlies the acquisition of everyday skilled movements, and transcranial direct current stimulation (tDCS) has shown promise for enhancing it, although reported effects vary considerably. Before such interventions can be applied and interpreted reliably, the behavioural and neural…
Aidan Bennett, Curtis Bright, Paul Colinot, Ashwin Nayak
A finite sequence of numbers is perfect if it has zero periodic autocorrelation after a nontrivial cyclic shift. In this work, we study quaternionic perfect sequences having a one-to-one correspondence with the binary sequences arising in Williamson's construction of quaterniontype Hadamard matrices. Using this…
Yanming Wei, Zhaoyang Huang, Pinglu Zhang, Yizheng Wang + 3 more
Multiple sequence alignment (MSA) is a fundamental problem in bioinformatics. The quality of sequence alignment significantly impacts biological sequence analysis, especially that in next-generation sequencing . MSA results are widely used in various applications, including de novo genome assembly , detection of…
Authors not listed
Building on prior mathematical formulations of the periodic law, this paper demonstrates that the algebraic formula S(k) = 2 * (floor(k/2) + 1)^2 accurately predicts the period lengths (2, 8, 8, 18, 18, 32, ...) of the periodic table. This pattern is not a numerical coincidence but a direct consequence of the…
Changqing Wang, Matthew E. Ritchie, Nadia M. Davidson
Visualizing and troubleshooting long-read sequencing data is a common task when analyzing novel protocols, but identifying several primer sequences from reads exceeding 2 kb with fuzzy matching is challenging for the human eye. Here, we present seqsizzle, a cross-platform terminal user interface (TUI) based tool for…
Authors not listed
Perovskite solar cell performance depends on the joint configuration of materials, interfaces, and layer-specific physical parameters, forming a structured design space that is naturally sequential but rarely modeled as such. This work introduces PervoTransformer, a transformer-based framework that represents complete…
Michael X Wang, Bryce Kille, Michael G Nute, Siyi Zhou + 2 more
For each low-penalty subgraph (a set of connected minimizer nodes from the graph), a representative minimizer ordering is determined and the corresponding genomic sequence is output as a candidate signature. The procedure involves (1) finding the maximal consecutive occurrence of the subgraph’s minimizers in each…
Authors not listed
The recognition that many periodic trends recur in groups of eight dates back to New- lands’ 1866 Law of Octaves.Newlands [1866] In the mid-20th century, Robert L. Lehrman introduced the octave–decade mnemonic as a pedagogical device for the observed period- length pattern 8–8–18–18–32. These earlier formulations were…
Qin Yuan, Chunlei Li, Xiangyong Zeng
Constant amplitude zero auto-correlation (CAZAC) sequences are widely applied in waveforms for radar and communication systems. Motivated by a recent work [Berggren and Popović, IEEE Trans. Inf. Theory 70(8), 6068-6075 (2024)], this paper further investigates the approach to generating CAZAC sequences by interleaving…
Authors not listed
Atomic electrons exist under the central Coulomb potential of the nucleus, a constraint that mandates their wave functions be described by spherical harmonics. While standard quantum mechanics treats these functions as static geometric solutions, the empirical structure of the periodic table (2, 8, 8, 18, 18, ...)…
Ahsan Sanaullah, Nathaniel K Brown, Pramesh Shakya, Arun Deegutla + 4 more
Although the traditional definition of a disjoint interval sequence is an ordered list of r pairs of integers in [1, n], $(p_{i},f(p_{i}))$ where $[p_{i},p_{(i+1)}-1]$ is a conserved interval (define $(p_{(r+1)}=n+1)$), we define disjoint interval permutation, a closely related definition that may be more useful in…
Isabel Tardón, Pablo Martín-Santamaría
Barraqu´e's proliferating series give an interesting turn on the concept of classic serialism by creating a new invariant when it comes to constructing the series: rather than the intervals between consecutive notes, what remains unaltered during the construction of the proliferations of the given base series is the…
Collier Gaiser, Paul Horn
A sequence of positive integers $(a_1,a_2,\ldots,a_k)$ is called $\ell$-additive if $a_1+a_2+\cdots+a_k=\ell a_1$ or $\ell a_k$. In this paper, we prove that for all $k\geq3$, if $n$ is sufficiently large, then every permutation of $\{1,2,\ldots,n\}$ has a 2-additive subsequence of length $k$. We also provide…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…