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.
Improved genetic programming by optimizing mutation operators for continuous program search.
VEGN uses graph neural networks to predict disease-causing mutations from genetic variants.
Genetic algorithms have been widely used in many practical optimization problems. Inspired by natural selection, operators, including mutation, crossover and selection, provide effective heuristics for search and black-box optimization. However, they have not been shown useful for deep reinforcement learning, possibly …
This paper presents details of our winning solutions to the task IV of NIPS 2017 Competition Track entitled Classifying Clinically Actionable Genetic Mutations. The machine learning task aims to classify genetic mutations based on text evidence from clinical literature with promising performance. We develop a novel mul…
New method resolves time order in genetic mutation models.
An evolutionary algorithm separates mixed DNA profiles in forensic genetics.
A genetic algorithm improves multivariate kernel density estimation.
Optimizing a neural network's performance is a tedious and time taking process, this iterative process does not have any defined solution which can work for all the problems. Optimization can be roughly categorized into - Architecture and Hyperparameter optimization. Many algorithms have been devised to address this pr…
The Interaction-Transformation (IT) is a new representation for Symbolic Regression that restricts the search space into simpler, but expressive, function forms. This representation has the advantage of creating a smoother search space unlike the space generated by Expression Trees, the common representation used in Ge…
Zoetrope Genetic Programming improves symbolic regression performance.
Traditional Linear Genetic Programming (LGP) algorithms are based only on the selection mechanism to guide the search. Genetic operators combine or mutate random portions of the individuals, without knowing if the result will lead to a fitter individual. Probabilistic Model Building Genetic Programming (PMB-GP) methods…
Evolution and learning are two of the fundamental mechanisms by which life adapts in order to survive and to transcend limitations. These biological phenomena inspired successful computational methods such as evolutionary algorithms and deep learning. Evolution relies on random mutations and on random genetic recombina…
New RL approach builds short ancestral recombination graphs.
Genetic sequence data are well described by hidden Markov models (HMMs) in which latent states correspond to clusters of similar mutation patterns. Theory from statistical genetics suggests that these HMMs are nonhomogeneous (their transition probabilities vary along the chromosome) and have large support for self tran…
ESAC combines genetic methods with RL to improve scalability and efficiency.
MutaGAN predicts mutations of evolving protein populations using GANs.
Proposes Genetic Thompson Sampling for multi-armed bandits, improving performance in nonstationary settings.
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects. While recent models have relaxed this constraint to also account for pairwise in…
Gradient boosting enhances existing Mendelian models for genetic disease risk prediction.
Study investigates how preprocessing, feature selection, and model selection affect performance on imbalanced genetic data.
One primary task of population health analysis is the identification of risk factors that, for some subpopulation, have a significant association with some health condition. Examples include finding lifestyle factors associated with chronic diseases and finding genetic mutations associated with diseases in precision he…
The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model the order of accumulation of such mutations during the progression, which eventual…
Selective deconfounding improves ATE estimation with less data.
Sparse GFA identifies disease factors in FTD subgroups.
As the complexity of neural network models has grown, it has become increasingly important to optimize their design automatically through metalearning. Methods for discovering hyperparameters, topologies, and learning rate schedules have lead to significant increases in performance. This paper shows that loss functions…
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 …
In this paper, we develop a convolutional neural network model to predict the mechanical properties of a two-dimensional checkerboard composite quantitatively. The checkerboard composite possesses two phases, one phase is soft and ductile while the other is stiff and brittle. The ground-truth data used in the training …
Transposable Elements (TEs) or jumping genes are the DNA sequences that have an intrinsic capability to move within a host genome from one genomic location to another. Studies show that the presence of a TE within or adjacent to a functional gene may alter its expression. TEs can also cause an increase in the rate of m…
Modeling correlated mutations in cancer for personalized treatment.
Drug resistance is still a major challenge in cancer therapy. Drug combination is expected to overcome drug resistance. However, the number of possible drug combinations is enormous, and thus it is infeasible to experimentally screen all effective drug combinations considering the limited resources. Therefore, computat…
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…
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.
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…
Khovanov homology invariant under Conway mutation.
Mutation graph of support τ-tilting modules over skew-gentle algebras is connected.
The paper studies alternating links in thickened surfaces using flow lattices and disc mutations.
Paper tackles gene mutation prediction for HCC using multi-instance multi-label learning.
We introduce a property of mutation loops, called the sign stability, with a focus on an asymptotic behavior of the iteration of the tropical -transformation. A sign-stable mutation loop has a numerical invariant which we call the cluster stretch factor, in analogy with that of a pseudo-Anosov mapping clas…
We show that instanton knot homology is mutation-invariant, as a consequence of earlier work of the third author.
The recent adoption of Electronic Health Records (EHRs) by health care providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in combination with machine learning and statistical approaches, generate new opport…
We introduce an exploratory study on Mutation Validation (MV), a model validation method using mutated training labels for supervised learning. MV mutates training data labels, retrains the model against the mutated data, then uses the metamorphic relation that captures the consequent training performance changes to as…
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 …
Unified pipeline detects multi-turn deception using geometric signals.
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.
Analysis of somatic mutation profiles from cancer patients is essential in the development of cancer research. However, the low frequency of most mutations and the varying rates of mutations across patients makes the data extremely challenging to statistically analyze as well as difficult to use in classification probl…
The study explores properties and mutations in oriented matroids, proving new results on Euclidean and non-Euclidean structures.