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We address the question of whether or not assembly bias arises in the absence of highly non-linear effects such as tidal stripping of halos near larger mass concentrations. Therefore, we use a simplified dynamical scheme where these effects…
Synthetic polymeric materials underpin fundamental technologies in the energy, electronics, consumer goods, and medical sectors, yet their development still suffers from prolonged design timelines. Although polymer informatics tools have…
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…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
The significant advancements of Large Language Models (LLMs) in generative tasks have led to a growing body of work exploring LLM-based embedding models. While these models, employing different pooling and attention strategies, have…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Halo assembly bias is a phenomenon whereby the clustering of dark matter halos is dependent on halo properties, such as age, at fixed mass. Understanding the origin of assembly bias is important for interpreting the clustering of galaxies…
Backpropagation (BP) is the cornerstone of today's deep learning algorithms, but it is inefficient partially because of backward locking, which means updating the weights of one layer locks the weight updates in the other layers.…
High-Level Synthesis (HLS) tools are widely adopted in FPGA-based domain-specific accelerator design. However, existing tools rely on fixed optimization strategies inherited from software compilations, limiting their effectiveness.…
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Logical reasoning of text is an important ability that requires understanding the information present in the text, their interconnections, and then reasoning through them to infer new conclusions. Prior works on improving the logical…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
Despite recent success in large language model (LLM) reasoning, LLMs struggle with hierarchical multi-step reasoning tasks like generating complex programs. For these tasks, humans often start with a high-level algorithmic design and…
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…
We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…
A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method that will enhance the quality of draft genomes by identifying and removing misassembly errors using paired…
Chromosome analysis is a fundamental step in the diagnosis of genetic diseases, but the manual karyotyping workflow is time-consuming and heavily dependent on expert specialists, often requiring several days per patient. Although Deep…