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…
On-device research index
arXiv research
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.
168,657 papers · 148 categories
Trend · papers per month
48 results for “DNA design”
A faster method for optimizing DNA and protein sequences using machine learning.
problem Designing DNA and protein sequences with improved function.
method Activation maximization with a straight-through approximation and adaptive entropy variable.
result Fast SeqProp achieves up to 100-fold faster convergence and improved fitness optima.
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 …
Paper uses transfer learning and Bayesian optimization to reduce DNA sequence design experiments.
problem Designing many similar DNA sequences for specific applications is expensive and time-consuming.
method Combines transfer learning with Bayesian optimization to reduce experiment count.
result Total number of experiments can be significantly reduced by sharing information between tasks.
An evolutionary algorithm separates mixed DNA profiles in forensic genetics.
problem Deconvolving mixed DNA profiles from crime samples.
method Multiple population evolutionary algorithm (MEA) with guided mutation.
result The MEA successfully deconvoluted DNA profiles from crime samples.
A novel framework refines diffusion models iteratively for better downstream reward optimization.
problem Optimizing reward functions during inference of diffusion models.
method Iterative refinement process with noising and reward-guided denoising steps.
result Superior empirical performance in protein and DNA design.
Genomic models learn DNA sequences to predict functions.
problem Understanding complex genetic interactions.
method Training LLMs on DNA sequences to predict functions.
result gLMs can predict functions of DNA elements.
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…
Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequencesq-bio.QM
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
problem Optimizing biological sequences for a black-box score function.
method Bootstrapped training of score-conditioned generator (BootGen) algorithm.
result Our method outperforms competitive baselines on biological sequential design tasks.
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…
This research adapts superpixels for Shapley value computation in DNA profile classification.
problem Efficiently computing Shapley values for large, multidimensional time-series data.
method Adapting the concept of superpixels to streamline Shapley value computation for time-series-like data.
result Realistic, accurate, and fast computation of Shapley values for DNA profile classification.
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 improves DNA methylation data analysis.
problem Analyzing DNA methylation data with complex distributions.
method Doubly non-central beta (DNCB) distribution for non-negative matrix factorization.
result Improves predictive performance and yields meaningful latent representations.
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.
problem Lack of interpretability in existing neural architecture search methods.
method DNAS disentangles the hidden representation of the controller into semantically meaningful concepts.
result DNAS achieves state-of-the-art performance and competitive architectures.
Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decodingcs.LG
New method optimizes diffusion models without fine-tuning, integrating soft value functions.
problem Optimizing natural design spaces of images, molecules, DNA, RNA, and protein sequences.
method Iterative sampling method integrating soft value functions into diffusion model inference.
result Directly utilizes non-differentiable features/reward feedback, applies to discrete diffusion models.
VSD efficiently learns conditional distributions for combinatorial designs.
problem Learning conditional distributions for rare combinatorial designs.
method Variational Search Distributions (VSD) using variational inference.
result VSD outperforms existing methods on real sequence-design problems.
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…
From tangle fractions to DNAmath.GT
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…
DNA Methylation Data to Predict Suicidal and Non-Suicidal Deaths: A Machine Learning Approachq-bio.GN
Study uses DNA methylation data to predict suicidal and non-suicidal deaths.
problem Predicting suicidal and non-suicidal deaths from DNA methylation data.
method Support Vector Machines (SVM) with dimensionality reduction using PCA and t-SNE.
result t-SNE outperforms PCA in reducing data dimensionality.
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 deep probabilistic model analyzes DNA-encoded library data for efficient screening.
problem Complex data from DNA-encoded library experiments mask underlying signals.
method Compositional deep probabilistic model of DEL data, modeling latent reactions between synthons.
result DEL-Compose model demonstrates strong performance and valuable insights.
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.
problem Identifying degraded DNA sequence data.
method Novel quality quantification based on intentional degradation effects.
result Quantified measures of degradation can be used for multiple purposes.
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…
New method disentangles hidden data structures using HSIC and supervision.
problem Tackles the challenge of interpreting high-dimensional data.
method Supervised Independent Subspace Principal Component Analysis (sisPCA) using HSIC.
result Identifies and separates hidden data structures effectively.
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 present a probabilistic modeling framework and adaptive sampling algorithm wherein unsupervised generative models are combined with black box predictive models to tackle the problem of input design. In input design, one is given one or more stochastic "oracle" predictive functions, each of which maps from the input …
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.
problem Understanding the structure of boundaries in a Bayes classifier for DNA sequencing.
method Examined the structure of the boundary in a Bayes classifier applied to DNA sequencing data. Introduced a new measure of uncertainty, Neighbor Similarity.
result The boundary is large and complex, and Neighbor Similarity effectively measures classifier uncertainty.
Betti Numbers of Prodsimplicial Complexes for Directed Graphs with Applications to Word Reductionsmath.CO
Study of Betti numbers in prodsimplicial complexes for directed graphs, focusing on DNA recombination.
problem Analyzing Betti numbers in directed graphs for DNA recombination.
method Custom prodsimplicial complexes for acyclic directed graphs, investigating Betti numbers.
result Investigated Betti numbers and cycles in prodsimplicial complexes for DNA recombination.
Classification of Tangle Solutions for Integrases, A Protein Family that Changes DNA Topologymath.GT
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 develop an algorithm for minimizing a function using batched function value measurements at each of rounds by using classifiers to identify a function's sublevel set. We show that sufficiently accurate classifiers can achieve linear convergence rates, and show that the convergence rate is tied to the difficu…
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 …
Graph Canonical Correlation Analysis improves CCA for multiomics datasets.
problem Limited ability of conventional CCA methods to incorporate structured patterns in cross-correlation matrices.
method Graph Canonical Correlation Analysis (gCCA) calculates canonical correlations based on the graph structure of cross-correlation matrices.
result gCCA outperforms competing CCA methods in simulations and multiomics dataset analysis.
Chirality Effects in Molecular Chainmailcond-mat.soft
Chirality affects the curvature of molecular networks, influencing their shape and stability.
problem Understanding how chirality influences the curvature of molecular networks.
method Langevin dynamics simulations and constrained gradient optimization of square lattice networks.
result Linking chirality dictates the sign of Gaussian curvature in molecular chainmail networks.
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…
Study surgeries between lens spaces using Heegaard Floer d-invariant.
problem Classify surgeries between lens spaces of type .
method Developed a -invariant surgery formula for -space knots.
result Classified distance one surgeries between lens spaces of the form .
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…
Pseudo links in handlebodiesmath.GT
The paper studies pseudo links in genus g handlebodies, generalizing knot theory.
problem Modeling DNA knots with missing crossing information.
method Introducing pseudo links as mixed pseudo links in S^3, generalizing Kauffman bracket polynomial and Alexander theorem.
result The theory of pseudo links is closely related to singular links and can be applied to study singular links in genus g handlebodies.
GIDS reduces high-dimensional response and predictor spaces, improving interpretability and computational efficiency.
problem Challenges in modeling interactions among high-dimensional multimodal data.
method Graph Independence Dual Screening (GIDS) framework that reduces both response and predictor dimensions.
result GIDS reduces feature space to 9,000 CpGs and 2,000 transcripts, revealing coordinated regulatory mechanisms.
A new framework scales active search for large datasets.
problem Scaling active search for large, high-dimensional data sets.
method Hierarchical Batch Bandit Search (HBBS) framework.
result HBBS improves performance and scalability for batch search.
New algorithm estimates intrinsic dimension of discrete datasets.
problem Inaccuracies in using continuous methods for discrete datasets.
method Introduced an algorithm to infer intrinsic dimension of discrete spaces.
result Demonstrated accuracy on benchmark datasets and found a small intrinsic dimension in a metagenomic dataset.
Novel U-learning method for predicting continuous outcomes from high-dimensional data.
problem Challenges in making valid inferences on predictions from high-dimensional inputs.
method U-learning via combinatory multi-subsampling for ensemble predictions and confidence intervals.
result Valid inferences on predictions from Lasso and neural networks.
Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to analyze. Typical challenges include a large number of possibly correlated featur…
Avian Influenza breakouts cause millions of dollars in damage each year globally, especially in Asian countries such as China and South Korea. The impact magnitude of a breakout directly correlates to time required to fully understand the influenza virus, particularly the interspecies pathogenicity. The procedure requi…