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.
An evolutionary algorithm separates mixed DNA profiles in forensic genetics.
This research adapts superpixels for Shapley value computation in DNA profile classification.
An important problem in forensic analyses is identifying the provenance of materials at a crime scene, such as biological material on a piece of clothing. This procedure, known as geolocation, is conventionally guided by expert knowledge of the biological evidence and therefore tends to be application-specific, labor-i…
Recently the GAN generated face images are more and more realistic with high-quality, even hard for human eyes to detect. On the other hand, the forensics community keeps on developing methods to detect these generated fake images and try to guarantee the credibility of visual contents. Although researchers have develo…
Bayesian neural networks improve reliability in multimedia forensics.
Recently, image forensics community has paied attention to the research on the design of effective algorithms based on deep learning technology and facts proved that combining the domain knowledge of image forensics and deep learning would achieve more robust and better performance than the traditional schemes. Instead…
We introduce a Bayesian solution for the problem in forensic speaker recognition, where there may be very little background material for estimating score calibration parameters. We work within the Bayesian paradigm of evidence reporting and develop a principled probabilistic treatment of the problem, which results in a…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in the context of CpG (cytosine and guanine bases linked by phosphate backbone) dinu…
Deep learning improves forensic matching of casings.
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary DNA sequence, though the interaction is not yet fully understood. In this paper we…
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish different subtypes of the tumor. However, the conventional statistical methods …
We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize t…
New model helps identify suspect footwear from crime scene prints.
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of the activation maximization ("deep dream") design method; and a joint procedure wh…
New model improves DNA methylation data analysis.
The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into another knot is normally mathematically modeled by band surgery. Band surgeries on a 2-bridge knot N((4mn-1)/(2m)) yielding a (2,2k)-torus link are characterized. We apply this and other rational tangl…
DNAS disentangles neural architecture search for better interpretability and performance.
Genomic models learn DNA sequences to predict functions.
In this paper, we consider recommender systems with side information in the form of graphs. Existing collaborative filtering algorithms mainly utilize only immediate neighborhood information and have a hard time taking advantage of deeper neighborhoods beyond 1-2 hops. The main caveat of exploiting deeper graph informa…
This paper is an introduction to rational tangles, rational knots and links and their applications to DNA. The paper can be read as an introduction to our more technical papers on rational tangles (math.GT/0311499) and on rational knots (math.GT/0212011). The present paper includes a self-contained account of the tangl…
Study uses DNA methylation data to predict suicidal and non-suicidal deaths.
We study two systems of tangle equations that arise when modeling the action of the Integrase family of proteins on DNA. These two systems--direct and inverted repeats--correspond to two different possibilities for the initial DNA sequence. We present one new class of solutions to the tangle equations. In the case of i…
A faster method for optimizing DNA and protein sequences using machine learning.
A deep probabilistic model analyzes DNA-encoded library data for efficient screening.
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer. DNA methylation is a…
Measures DNA quality degradation effects.
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently, externally learned memory models have proven to be effective methods for reasoning ov…
Paper uses transfer learning and Bayesian optimization to reduce DNA sequence design experiments.
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional conformation. In order to study long-distance dependencies, we develop and release …
We consider learning parameters of Binomial Hidden Markov Models, which may be used to model DNA methylation data. The standard algorithm for the problem is EM, which is computationally expensive for sequences of the scale of the mammalian genome. Recently developed spectral algorithms can learn parameters of latent va…
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms fo…
Study on the structure of classifier boundaries in DNA sequencing.
Study of Betti numbers in prodsimplicial complexes for directed graphs, focusing on DNA recombination.
Electrical network frequency (ENF) is the signature of a power distribution grid which represents the nominal frequency (50 or 60 Hz) of a power system network. Due to load variations in a power grid, ENF sequences experience fluctuations. These ENF variations are inherently located in a multimedia signal which is reco…
Integrase proteins acting on circular double-stranded DNA often change its topology by transforming unknotted circles into torus knots and links. Two systems of tangle equations--corresponding to the two initial DNA sequences--arise when modelling this transformation: direct and inverted. With no a priori assumptions o…
We categorise coherent band (aka nullification) pathways between knots and 2-component links. Additionally, we characterise the minimal coherent band pathways (with intermediates) between any two knots or 2-component links with small crossing number. We demonstrate these band surgeries for knots and links with small cr…
We propose a dynamic neighborhood aggregation (DNA) procedure guided by (multi-head) attention for representation learning on graphs. In contrast to current graph neural networks which follow a simple neighborhood aggregation scheme, our DNA procedure allows for a selective and node-adaptive aggregation of neighboring …
A novel framework refines diffusion models iteratively for better downstream reward optimization.
Graph Canonical Correlation Analysis improves CCA for multiomics datasets.
Chirality affects the curvature of molecular networks, influencing their shape and stability.
In this paper, we study a geometric/topological measure of knots and links called the nullification number. The nullification of knots/links is believed to be biologically relevant. For example, in DNA topology, one can intuitively regard it as a way to measure how easily a knotted circular DNA can unknot itself throug…
Matrix-variate distributions can intuitively model the dependence structure of matrix-valued observations that arise in applications with multivariate time series, spatio-temporal or repeated measures. This paper develops an Expectation-Maximization algorithm for discriminant analysis and classification with matrix-var…
Study surgeries between lens spaces using Heegaard Floer d-invariant.
The research reported in this paper identifies the epigenetic biomarker (methylation beta pattern) of breast cancer. Many cancers are triggered by abnormal gene expression levels caused by aberrant methylation of CpG sites in the DNA. In order to develop early diagnostics of cancer-causing methylations and to develop a…
Authorship verification (AV) is a research subject in the field of digital text forensics that concerns itself with the question, whether two documents have been written by the same person. During the past two decades, an increasing number of proposed AV approaches can be observed. However, a closer look at the respect…
The paper studies pseudo links in genus g handlebodies, generalizing knot theory.
Novel U-learning method for predicting continuous outcomes from high-dimensional data.
Network analysis detects insider trading by flagging coordinated trades.