A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Study on the structure of classifier boundaries in DNA sequencing.
Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model l…
The detection of rare variants is important for understanding the genetic heterogeneity in mixed samples. Recently, next-generation sequencing (NGS) technologies have enabled the identification of single nucleotide variants (SNVs) in mixed samples with high resolution. Yet, the noise inherent in the biological processe…
The emerging field of precision oncology relies on the accurate pinpointing of alterations in the molecular profile of a tumor to provide personalized targeted treatments. Current methodologies in the field commonly include the application of next generation sequencing technologies to a tumor sample, followed by the id…
Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Se…
Proposes PSCCA for estimating correlations and canonical correlations in sparse count data.
Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising method for this is through de novo peptide sequencing from m…
Scientific investigations that incorporate next generation sequencing involve analyses of high-dimensional data where the need to organize, collate and interpret the outcomes are pressingly important. Currently, data can be collected at the microbiome level leading to the possibility of personalized medicine whereby tr…
Next-generation sequencing (NGS) to profile temporal changes in living systems is gaining more attention for deriving better insights into the underlying biological mechanisms compared to traditional static sequencing experiments. Nonetheless, the majority of existing statistical tools for analyzing NGS data lack the c…
The purpose of this study is to introduce new design-criteria for next-generation hyperparameter optimization software. The criteria we propose include (1) define-by-run API that allows users to construct the parameter search space dynamically, (2) efficient implementation of both searching and pruning strategies, and …
New method infers centromere locations in yeast using Hi-C data.
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Due to the large volume of metagenomics datasets,…
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high dimensional genotype (next-generation sequencing) data. To overcome these limitations, we …
Machine learning accurately diagnoses cancer from whole genome sequencing data.
The genomic profile underlying an individual tumor can be highly informative in the creation of a personalized cancer treatment strategy for a given patient; a practice known as precision oncology. This involves next generation sequencing of a tumor sample and the subsequent identification of genomic aberrations, such …
Next-gen reservoir computers fail to predict complex processes, highlighting need for better architectures.
Understanding the nature of dark energy, the mysterious force driving the accelerated expansion of the Universe, is a major challenge of modern cosmology. The next generation of cosmological surveys, specifically designed to address this issue, rely on accurate measurements of the apparent shapes of distant galaxies. H…
We prove metric rigidity for complete manifolds supporting solutions of certain second order differential systems, thus extending classical works on a characterization of space-forms. In the route, we also discover new characterizations of space-forms. We next generalize results concerning metric rigidity via equations…
Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced genomes. A fundamental question is how to efficiently extract genomic and epigenomi…
Many biological data analysis processes like Cytometry or Next Generation Sequencing (NGS) produce massive amounts of data which needs to be processed in batches for down-stream analysis. Such datasets are prone to technical variations due to difference in handling the batches possibly at different times, by different …
Next-gen reservoir computing models dynamical systems from time-series data.
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads", which constitute a fundamentally discrete measure of the level of gene expression. A…
Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or on a dense grid and referred to as function-valued traits. Both physiological a…
High-dimensional data acquired from biological experiments such as next generation sequencing are subject to a number of confounding effects. These effects include both technical effects, such as variation across batches from instrument noise or sample processing, or institution-specific differences in sample acquisiti…
NGRC shows numerical instabilities with short lags and high-degree polynomials.
The Poisson distribution has been widely studied and used for modeling univariate count-valued data. Multivariate generalizations of the Poisson distribution that permit dependencies, however, have been far less popular. Yet, real-world high-dimensional count-valued data found in word counts, genomics, and crime statis…
"Mixed Data" comprising a large number of heterogeneous variables (e.g. count, binary, continuous, skewed continuous, among other data types) are prevalent in varied areas such as genomics and proteomics, imaging genetics, national security, social networking, and Internet advertising. There have been limited efforts a…
Matter-antimatter asymmetry is one of the major unsolved problems in physics that can be probed through precision measurements of charge-parity symmetry violation at current and next-generation neutrino oscillation experiments. In this work, we demonstrate the capability of variational autoencoders and normalizing flow…
LADaR framework calibrates machine learning models for instance-wise predictions.
Improves classification of microbiome data using mixture distributions.
The next generation of AI applications will continuously interact with the environment and learn from these interactions. These applications impose new and demanding systems requirements, both in terms of performance and flexibility. In this paper, we consider these requirements and present Ray---a distributed system t…
The tremendous boost in the next generation sequencing and in the omics technologies makes it possible to characterize human gut microbiome (the collective genomes of the microbial community that reside in our gastrointestinal tract). While some of these microorganisms are considered as essential regulators of our immu…
Bayesian method improves star location and flux estimation from coadded images.
A genetic algorithm improves multivariate kernel density estimation.
In the coming years, the satellite broadband market will experience significant increases in the service demand, especially for the mobility sector, where demand is burstier. Many of the next generation of satellites will be equipped with numerous degrees of freedom in power and bandwidth allocation capabilities, makin…
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run large genomic data mining analyses. Additional enhancements include integration wi…
Next generation deep neural networks for classification hosted on embedded platforms will rely on fast, efficient, and accurate learning algorithms. Initialization of weights in learning networks has a great impact on the classification accuracy. In this paper we focus on deriving good initial weights by modeling the e…
Developing a visual platform for faster astronomical source cataloging.
A new framework enhances binaural audio for moving talkers.
In this paper, we introduce an alternative approach, namely GEN (Genetic Evolution Network) Model, to the deep learning models. Instead of building one single deep model, GEN adopts a genetic-evolutionary learning strategy to build a group of unit models generations by generations. Significantly different from the well…
Quantitative finance has had a long tradition of a bottom-up approach to complex systems inference via multi-agent systems (MAS). These statistical tools are based on modelling agents trading via a centralised order book, in order to emulate complex and diverse market phenomena. These past financial models have all rel…
This paper provides a review and commentary on the past, present, and future of numerical optimization algorithms in the context of machine learning applications. Through case studies on text classification and the training of deep neural networks, we discuss how optimization problems arise in machine learning and what…
GraphBench creates a unified benchmark for graph learning tasks.
DiffObs predicts global precipitation with realistic wave modes and low frequency variations.
Alpha-GPT 2.0 integrates human insights into AI-driven investment research.
Paper proposes verifier engineering for improving foundation models.
Paper reviews the evolution of alpha from human insight to AI-powered systems.
Connected and autonomous vehicles (CAVs) will form the backbone of future next-generation intelligent transportation systems (ITS) providing travel comfort, road safety, along with a number of value-added services. Such a transformation---which will be fuelled by concomitant advances in technologies for machine learnin…