14 papers · ranked by Valyu relevance
Zihui Yan, Guanjin Qu, Xin Chen, Gang Zheng + 1 more
DNA-based data storage is a promising solution to the challenges of large-scale data storage. However, the low throughput of the mainstream inkjet-based DNA synthesis method has hindered its widespread adoption. In contrast, high-throughput electrochemical synthesis provides higher throughput but with more nucleotide…
Joshua P. Chu, Michael E. Coulter, Eric L. Denovellis, Trevor T. K. Nguyen + 5 more
Decoding algorithms provide a powerful tool for understanding the firing patterns that underlie cognitive processes such as motor control, learning, and recall. When implemented in the context of a real-time system, decoders also make it possible to deliver feedback based on the representational content of ongoing…
Kevin D. Volkel, Paul W. Hook, Albert Keung, Winston Timp + 1 more
As nanopore technology reaches ever higher throughput and accuracy, it becomes an increasingly viable candidate for reading out DNA data storage. Nanopore sequencing offers considerable flexibility by allowing long reads, real-time signal analysis, and the ability to read both DNA and RNA. We need flexible and…
Ramy Khabbaz, Jérémy Mateos, Marc Antonini, Serge Kas Hanna
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level dropouts, occur and pose major challenges for reliable data retrieval. Here we introduce…
Kimonas Provatas, Aris Karatzikos, Charalampos Koilakos, Michail Patsakis + 5 more
Genomic and protein foundation models (GFMs and PFMs) have demonstrated strong performance in learning the language of DNA and proteins, but their use in large-scale sequence generation is limited by the latency of autoregressive decoding. Because every token triggers a forward pass of a large Transformer, whose…
Kang Li, Mikiko Kadohisa, Makoto Kusunoki, John Duncan + 2 more
Serial and parallel processing in visual search have been long debated in psychology but the processing mechanism remains an open issue. Serial processing allows only one object at a time to be processed, whereas parallel processing assumes that various objects are processed simultaneously. Here we present novel neural…
Rob Patro, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal + 2 more
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compressed fastq.gz files has become a substantial scalability bottleneck in the modern world of fast and massively parallel…
Hao Ding, Nannan Wu, Tianyi Qiu
DNA foundation models such as Evo2 7B adopt hybrid Hyena/attention architectures (Striped-Hyena2) whose single-stream autoregressive decoding is bounded by weight bandwidth at ∼45 tok/s. Speculative decoding on such hybrids faces a systems problem that prior SSM work solves only partially: after a draft is verified…
Ethan M. Meyers
Neural decoding is a powerful method to analyze neural activity. However, the code needed to run a decoding analysis can be complex, which can present a barrier to using the method. In this paper we introduce a package that makes it easy to perform decoding analyses in the R programing language. We describe how the…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Puti Wen, Michael S. Landy, Bas Rokers
Accurate motion perception requires that the visual system integrate the retinal motion signals received by the two eyes into a single representation of 3D (i.e., world) motion. However, most experimental paradigms limit the motion stimuli to the fronto-parallel plane (i.e., 2D motion) and are thus unable to dissociate…
Lorenzo Posani
Neural decoding is a powerful approach for inferring which variables are represented in the activity of a population of neurons, with broad applications ranging from basic neuroscience to clinical settings such as brain-computer interfaces. More recently, decoding has also been used as a cross-validated tool for…
Alexey Zabelkin, Yulia Yakovleva, Olga Bochkareva, Nikita Alexeev
High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation.…
Nima Maleki, Hamid Karimi-Rouzbahani
Sensory neural coding, the brain’s process of transforming inputs into informative patterns of neural activity, generates complex and multiplexed neural codes which are hard to interpret. Although decoding methods have facilitated the interpretation of these codes, the specific features of neural activity that…