13 papers · ranked by Valyu relevance
Niklas Brunn, Sonia Maria Krißmer, Maximilian Frosch, Markus Frick + 2 more
The single-cell literature catalogs cell states as validated marker-gene programs — a sparse, compositional prior. Conventional embedding methods do not leverage this prior and learn cell-state structure de novo from the expression matrix, producing dense dimensions needing post-hoc interpretation and batch correction.…
Pawel Pratyush, Callen Carrier, Suresh Pokharel, Hamid D. Ismail + 2 more
The mapping from codon to amino acid is surjective due to the high degeneracy of the codon alphabet, suggesting that codon space might harbor higher information content. Embeddings from the codon language model have recently demonstrated success in various downstream tasks. However, predictive models for…
Rachel D. Melamed
The electronic health record is a rising resource for quantifying medical practice and discovering adverse effects of drugs. One of the challenges of applying these methods to health care data is the high dimensionality of the health record. Methods to discover effects of drugs in health data must account for tens of…
Yun-Fei Liu, Marina Bedny
Programming is a cornerstone of modern society, yet its cognitive and neural basis remains poorly understood. In this study, we test the hypothesis that programming “recycles” pre-existing neural mechanisms and representations in fronto-parietal reasoning networks. Using fMRI, we scanned programming-naïve…
Wenshuo Liu, Karandeep Singh, Andrew M. Ryan, Devraj Sukul + 5 more
Reducing unplanned readmissions is a major focus of current hospital quality efforts. In order to avoid unfair penalization, administrators and policymakers use prediction models to adjust for the performance of hospitals from healthcare claims data. Regression-based models are a commonly utilized method for such…
Melissa Franch, Elizabeth A. Mickiewicz, James L. Belanger, Assia Chericoni + 10 more
As we listen to speech, our brains actively compute the meaning of individual words. Inspired by the success of large language models (LLMs), we hypothesized that the brain employs vectorial coding principles, such that meaning is reflected in distributed activity of single neurons. We recorded responses of hundreds of…
Dawei Shen, Yao-zhong Zhang, Seiya Imoto
Whole Slide Images (WSIs) are gigapixel, high-resolution digital scans of microscope slides, providing detailed tissue profiles for pathological analysis. Due to their gigapixel size and lack of detailed annotations, Multiple Instance Learning (MIL) becomes the primary technique for WSI analysis. However, current MIL…
Zhe Liu, Yihang Bao, Wenhao Li, Weihao Li + 1 more
Non-coding single nucleotide polymorphisms (SNPs) are critical drivers of gene regulation and disease susceptibility, yet predicting their functional impact remains a challenging task. A variety of methods exist for encoding non-coding SNPs, such as direct base encoding or using pre-trained models to obtain embeddings.…
Raphael Kirchgaessner, Kaya Keutler, Layaa Sivakumar, Xubo Song + 1 more
AI based embeddings offer the possibilities of encoding complex biological data into low dimensional spaces, called embedding spaces, that maintain the relationships between entities. There is an open question about the compatibility of embedding spaces that are created without any coordination. It has been assumed…
Ian Holmes
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by interleaving watermark and periodic marker signals; conversion from binary to…
Zhi Ping, Haoling Zhang, Shihong Chen, Qianlong Zhuang + 2 more
Chamaeleo is currently the only collection library that focuses on adapting multiple well-established coding schemes for DNA storage. It provides a tool for researchers to study various coding schemes and apply them in practice. Chamaeleo adheres to the concept of high aggregation and low coupling for software design…
Inbal Preuss, Michael Rosenberg, Zohar Yakhini, Leon Anavy
With the world generating digital data at an exponential rate, DNA has emerged as a promising archival medium. It offers a more efficient and long-lasting digital storage solution due to its durability, physical density, and high information capacity. Research in the field includes the development of encoding schemes…
Y. Liu, J. Kim, C. Wilson, M. Bedny
Despite the importance of programming to modern society, the cognitive and neural bases of code comprehension are largely unknown. Programming languages might ‘recycle’ neurocognitive mechanisms originally used for natural languages. Alternatively, comprehension of code could depend on fronto-parietal networks shared…