Refines Khovanov homology for knots with involution.
problem Detecting mutations in knots with an involution.
method Introduces a triply-graded theory with two filtrations.
result Shows the refinement can detect mutation.
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48 results for “mutation detection”
This paper gives an alternate definition of the Affine Index Polynomial (called the Wriggle Polynomial) using virtual linking numbers and explores applications of this polynomial. In particular, it proves the Cosmetic Crossing Change Conjecture for odd virtual knots and pure virtual knots. It also demonstrates that the…
Deep neural networks (DNN) have been shown to be useful in a wide range of applications. However, they are also known to be vulnerable to adversarial samples. By transforming a normal sample with some carefully crafted human imperceptible perturbations, even highly accurate DNN make wrong decisions. Multiple defense me…
SynGAN generates synthetic network attacks to improve NIDS effectiveness.
problem Low effectiveness of NIDS due to high false positives and lack of continuous testing.
method SynGAN uses GANs to generate adversarial network attacks based on real attack traffic.
result SynGAN-generated attacks improve NIDS detection rates compared to real attacks.
We describe a birational map between subvarieties in the character varieties of mutative 3-manifolds. By studying the birational map, one can decide in certain circumstances whether a mutation surface is detected by an ideal point of the character variety.
We illustrate from the viewpoint of braiding operations on WZNW conformal blocks how colored HOMFLY polynomials with multiplicity structure can detect mutations. As an example, we explicitly evaluate the (2,1)-colored HOMFLY polynomials that distinguish a famous mutant pair, Kinoshita-Terasaka and Conway knot.
In an earlier paper, we introduced a collection of graded Abelian groups $\HFKa(Y,K)$ associated to knots in a three-manifold. The aim of the present paper is to investigate these groups for several specific families of knots, including the Kinoshita-Terasaka knots and their ``Conway mutants''. These results show that …
Recently, it has been shown that deep neural networks (DNN) are subject to attacks through adversarial samples. Adversarial samples are often crafted through adversarial perturbation, i.e., manipulating the original sample with minor modifications so that the DNN model labels the sample incorrectly. Given that it is al…
Genus 2 mutation is the process of cutting a 3-manifold along an embedded closed genus 2 surface, twisting by the hyper-elliptic involution, and gluing back. This paper compares genus 2 mutation with the better-known Conway mutation in the context of knots in the 3-sphere. Despite the fact that any Conway mutation can …
Modeling correlated mutations in cancer for personalized treatment.
problem Identifying mutations for personalized cancer therapy in heterogeneous profiles.
method Proposed correlated zero-inflated negative binomial process with mixed beta-Bernoulli and variational inference.
result Identified biologically relevant correlations between somatic mutations.
Improved genetic programming by optimizing mutation operators for continuous program search.
problem Small syntactic mutations in genetic programming can lead to unpredictable behavioral shifts.
method Learned a compact trading-strategy DSL, created a block-factorized embedding, and designed geometry-compiled mutation operators.
result Geometry-compiled mutation operators discover strong strategies using fewer evaluations and achieve higher Sharpe ratios.
We define a link homology theory that is readily seen to be both isomorphic to reduced odd Khovanov homology and fully determined by data impervious to Conway mutation. This gives an elementary proof that odd Khovanov homology is mutation invariant, and therefore that mod 2 Khovanov homology is mutation invariant. We a…
Mutation Validation method assesses model fit using mutated training labels without validation sets.
problem Model selection and hyperparameter tuning accuracy in supervised learning.
method Mutation Validation (MV) method using mutated training labels to assess model fit.
result MV provides more accurate model selection and stable hyperparameter tuning results.
We give a new, elementary proof that Khovanov homology with --coefficients is invariant under Conway mutation. This proof also gives a strategy to prove Baldwin and Levine's conjecture that --graded knot Floer homology is mutation--invariant. Using the Clifford module structure on $\widetilde…
Mathematician summarizes protein geometry and mutation effects.
problem Understanding how proteins mutate and their structure-function relationship.
method Mathematical analysis of protein structures and functions, focusing on hydrogen bonds and secondary structure.
result Protein secondary structure regulates mutation by stabilizing or destabilizing regions.
We study the effect of mutation on link concordance and 3-manifolds. We show that the set of links concordant to sublinks of homology boundary links is not closed under positive mutation. We show that mutation does not preserve homology cobordism classes of 3-manifolds. A significant consequence is that there exist 3-m…
Paper tackles cancer mutation data challenges by creating useful low-dimensional representations.
problem Challenges in analyzing and using cancer mutation data for classification and clustering.
method Flatsomatic: variational autoencoders (VAEs) to create latent representations of somatic profiles.
result VAE embeddings perform better than PCA for clustering and equally well for classification.
Khovanov homology invariant under Conway mutation.
problem Invariance of Khovanov homology under specific transformations.
method Strong geography restrictions and homological mirror symmetry.
result Classification of components of a Khovanov multicurve invariant.
Mutation graph of support τ-tilting modules over skew-gentle algebras is connected.
problem Understanding the structure of support τ-tilting modules over skew-gentle algebras.
method Introducing mutation of maximal rigid objects and using exchange triangles to define mutations of support τ-tilting modules.
result The mutation graph of support τ-tilting modules over a skew-gentle algebra is connected.
New invariant measures loop iterations in algebraic structures.
problem Measuring the asymptotic behavior of loop iterations in algebraic structures.
method Introduced sign stability and cluster stretch factor to measure loops.
result Cluster algebraic entropies match cluster stretch factor.
The paper studies alternating links in thickened surfaces using flow lattices and disc mutations.
problem Understanding alternating links in thickened surfaces and their invariants.
method Using integer flows on Tait graphs and disc mutations, the paper proves invariants and compares link properties.
result Found alternating knots with isometric flow lattices but different linking forms.
Paper tackles gene mutation prediction for HCC using multi-instance multi-label learning.
problem Gene mutation prediction in hepatocellular carcinoma for personalized treatments.
method Multi-instance multi-label learning with oversampling for data imbalance.
result Proposed approach shows superiority in gene mutation prediction.
We show that instanton knot homology is mutation-invariant, as a consequence of earlier work of the third author.
Study shows Conway mutation preserves a specific link invariant.
problem Investigating symmetry properties of peculiar modules.
method Analysis of Heegaard Floer invariants of 4-ended tangles.
result Conway mutation preserves the hat flavor of relatively δ-graded Heegaard Floer theory of links.
We construct finite volume hyperbolic manifolds with large symmetry groups. The construction makes use of the presentations of finite Coxeter groups provided by Barot and Marsh and involves mutations of quivers and diagrams defined in the theory of cluster algebras. We generalize our construction by assigning to every …
We prove that generalized mutation preserves several geometric invariants such as the volume and Goncharov invariant of Q-rank 1 locally symmetric spaces.
EDAs with matrix transpose improve Bayesian structure learning performance.
problem Improving Bayesian structure learning performance.
method Introducing a matrix transpose mutation operator for EDAs in Bayesian structure learning.
result EDAs with transpose mutation give markedly better performance than conventional EDAs.
The study explores properties and mutations in oriented matroids, proving new results on Euclidean and non-Euclidean structures.
problem Investigating the Euclidean and non-Euclidean properties of oriented matroids.
method Analyzing the minimum number of mutations, using lexicographic extensions, and mutation-flips to prove properties.
result For rank 4 uniform oriented matroids, the minimum number of mutations adjacent to an element is at most 3.
We show that the reduced sl(n) homology defined by Khovanov and Rozansky is invariant under component-preserving positive mutation when n is odd.
We prove that Khovanov homology and Lee homology with coefficients in are invariant under component-preserving link mutations.
We give a short topological proof for Rubermans Theorem about mutation and volume, using the Maskit combination theorem and the homology of the linear group.
Detecting a change point is a crucial task in statistics that has been recently extended to the quantum realm. A source state generator that emits a series of single photons in a default state suffers an alteration at some point and starts to emit photons in a mutated state. The problem consists in identifying the poin…
Deep learning improves tumor type classification accuracy.
problem Classifying cancer types based on DNA mutations is challenging.
method Deep transfer learning and fine-tuning of gene expression data.
result Significantly improved tumor type classification accuracy (78.3%) using DNA point mutations.
In this paper, we explicitly construct large classes of incommensurable hyperbolic knot complements with the same volume and the same initial (complex) length spectrum. Furthermore, we show that these knot complements are the only knot complements in their respective commensurabiltiy classes by analyzing their cusp sha…
For the alternating knots or links, mutations do not change the arc index. In the case of nonalternating knots, some semi-alternating knots or links have this property. We mainly focus on the problem of mutation invariance of the arc index for nonalternating knots which are not semi-alternating. In this paper, we found…
Motivation: HIV is difficult to treat because its virus mutates at a high rate and mutated viruses easily develop resistance to existing drugs. If the relationships between mutations and drug resistances can be determined from historical data, patients can be provided personalized treatment according to their own mutat…
Morsifications and mutationsmath.GT
We describe and investigate a connection between the topology of isolated singularities of plane curves and the mutation equivalence, in the sense of cluster algebra theory, of the quivers associated with their morsifications.
Given a hyperbolic knot, we prove that the Reidemeister torsion of any lift of the holonomy to SL(2,C) is invariant under mutation along a Conway sphere.
Mutation is an operation on 3-manifolds containing an embedded surface of genus 2. It is defined by cutting along the surface and regluing using the `hyperelliptic' involution, and is known to preserve many 3-manifold invariants. I show that mutation of a homology 3-sphere preserves its (instanton) Floer homology, and …
MutaGAN predicts mutations of evolving protein populations using GANs.
problem Predicting mutations in evolving protein populations.
method Generative adversarial networks (GANs) with recurrent neural networks (RNNs).
result MutaGAN generates complete protein sequences with mutations.
Deep neural network improves cancer mutation calls with confidence.
problem Improving accuracy and confidence in somatic variant calls from cancer sequencing.
method Deep Bayesian Recurrent Neural Network (RNN) with flexible priors.
result Enhanced confidence in mutation calls without performance degradation.
PANDA: Predicting the change in proteins binding affinity upon mutations using sequence informationq-bio.BM
PANDA predicts protein binding affinity changes from sequences, outperforming existing methods.
problem Accurately predicting changes in protein binding affinity due to mutations.
method Sequence-based machine learning approach using protein sequence information.
result PANDA achieves higher Pearson correlation coefficients than existing methods.
Mutations and faces of the Thurston norm ball dynamically represented by multiple distinct flowsmath.GT
New flows represent Thurston norm ball faces, differing by veering mutations.
problem Dynamic representation of Thurston norm ball faces by distinct flows.
method Combining veering triangulations and mutations to represent faces by multiple flows.
result Non-fibered faces can be represented by two distinct flows differing by veering mutations.
It is conjectured that the Khovanov homology of a knot is invariant under mutation. In this paper, we review the spanning tree complex for Khovanov homology, and reformulate this conjecture using a matroid obtained from the Tait graph (checkerboard graph) G of a knot diagram K. The spanning trees of G provide a filtrat…
This paper establishes that sutured annular Khovanov homology is not invariant for braid closures under axis-preserving mutations. This follows from an explicit relationship between sutured annular Khovanov homology and the classical Burau representation for braid closures.
For any quiver mutation sequence, we define a pair of matrices that describe a fixed point equation of a cluster transformation determined from the mutation sequence. We give an explicit relationship between this pair of matrices and the Jacobian matrix of the cluster transformation. Furthermore, we show that this rela…
We construct a family of hyperbolic link complements by gluing tangles along totally geodesic four-punctured spheres, then investigate the commensurability relation among its members. Those with different volume are incommensurable, distinguished by their scissors congruence classes. Mutation produces arbitrarily large…
In this paper, we prove that the Reidemeister torsion twisted by the adjoint representation, which is considered as a 1-form, on the SU(2)-character variety of a knot exterior is invariant under mutation along a Conway sphere.