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.
Deep Bayesian neural networks improve somatic variant calling accuracy.
Deep neural network improves cancer mutation calls with confidence.
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown great promise in improving on these variant calls, but the input for these is still…
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutation…
Modeling correlated mutations in cancer for personalized treatment.
Paper tackles cancer mutation data challenges by creating useful low-dimensional representations.
High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history and population frequency of the subclonal lineages of tumor cells present in the sample can be reconstructed from…
Flatsomatic compresses cancer mutation data with VAEs, maintaining predictive power.
Sparse coding has been popularly used as an effective data representation method in various applications, such as computer vision, medical imaging and bioinformatics, etc. However, the conventional sparse coding algorithms and its manifold regularized variants (graph sparse coding and Laplacian sparse coding), learn th…
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…
In this paper, we introduce and study various kinds of decomposition complexity. First, we give a characterization of residually finite groups having finite decomposition complexity (FDC). Secondly, we introduce equi-variant straight FDC (sFDC), and prove that a group having equi-variant sFDC if and only if its box spa…
A new decision tree variant improves linear model performance.
This paper corrects errors in UMAP's derivation and explains its properties.
Stochastic gradient descent~(SGD) and its variants have become more and more popular in machine learning due to their efficiency and effectiveness. To handle large-scale problems, researchers have recently proposed several parallel SGD methods for multicore systems. However, existing parallel SGD methods cannot achieve…
We present a novel method for extracting cancer signatures by applying statistical risk models (http://ssrn.com/abstract=2732453) from quantitative finance to cancer genome data. Using 1389 whole genome sequenced samples from 14 cancers, we identify an "overall" mode of somatic mutational noise. We give a prescription …
Natural gradient learning improves synaptic plasticity in spiking neurons.
Novel CE-method variants reduce local minima convergence with fewer function evaluations.
A-StarGAN improves nonparallel voice conversion speed and realism.
New Muon and Momo variants improve neural network optimization robustness.
Proposes a neural framework to select subsets efficiently across different models.
As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and en…
Paper presents a new method to detect process differences at the trace level using mutual fingerprints.
The standard LSTM recurrent neural networks while very powerful in long-range dependency sequence applications have highly complex structure and relatively large (adaptive) parameters. In this work, we present empirical comparison between the standard LSTM recurrent neural network architecture and three new parameter-r…
Recent variants improve knowledge distillation performance.
Many contemporary statistical learning methods assume a Euclidean feature space. This paper presents a method for defining similarity based on hyperspherical geometry and shows that it often improves the performance of support vector machine compared to other competing similarity measures. Specifically, the idea of usi…
Unified framework for efficient Frank-Wolfe optimization of Dominant Set Clustering.
The Johnson filtration of the mapping class group of a compact, oriented surface is the descending series consisting of the kernels of the actions on the nilpotent quotients of the fundamental group of the surface. Each term of the Johnson filtration admits a Johnson homomorphism, whose kernel is the next term in the f…
We study primal-dual type stochastic optimization algorithms with non-uniform sampling. Our main theoretical contribution in this paper is to present a convergence analysis of Stochastic Primal Dual Coordinate (SPDC) Method with arbitrary sampling. Based on this theoretical framework, we propose Optimality Violation-ba…
We introduce a variant of the -nearest neighbor classifier in which is chosen adaptively for each query, rather than supplied as a parameter. The choice of depends on properties of each neighborhood, and therefore may significantly vary between different points. (For example, the algorithm will use larger $k…
A new gradient quantization scheme improves communication efficiency in distributed training.
In this paper, we briefly review the basic scheme of the pseudoinverse learning (PIL) algorithm and present some discussions on the PIL, as well as its variants. The PIL algorithm, first presented in 1995, is a non-gradient descent and non-iterative learning algorithm for multi-layer neural networks and has several adv…
The medical research facilitates to acquire a diverse type of data from the same individual for particular cancer. Recent studies show that utilizing such diverse data results in more accurate predictions. The major challenge faced is how to utilize such diverse data sets in an effective way. In this paper, we introduc…
Action recognition has attracted increasing attention from RGB input in computer vision partially due to potential applications on somatic simulation and statistics of sport such as virtual tennis game and tennis techniques and tactics analysis by video. Recently, deep learning based methods have achieved promising per…
This paper presents a novel deep learning based method for automatic malware signature generation and classification. The method uses a deep belief network (DBN), implemented with a deep stack of denoising autoencoders, generating an invariant compact representation of the malware behavior. While conventional signature…
The goal of this study is to explain and examine the statistical underpinnings of the Bollinger Band methodology. We start off by elucidating the rolling regression time series model and deriving its explicit relationship to Bollinger Bands. Next we illustrate the use of Bollinger Bands in pairs trading and prove the e…
Traditional Recurrent Neural Networks assume vectorized data as inputs. However many data from modern science and technology come in certain structures such as tensorial time series data. To apply the recurrent neural networks for this type of data, a vectorisation process is necessary, while such a vectorisation leads…
New random forest variants achieve optimal performance in high dimensions.
A new bandit problem where experiments can be interrupted if results are not promising.
Stochastic particle-optimization sampling (SPOS) is a recently-developed scalable Bayesian sampling framework that unifies stochastic gradient MCMC (SG-MCMC) and Stein variational gradient descent (SVGD) algorithms based on Wasserstein gradient flows. With a rigorous non-asymptotic convergence theory developed recently…
Graph spectral analysis can yield meaningful embeddings of graphs by providing insight into distributed features not directly accessible in nodal domain. Recent efforts in graph signal processing have proposed new decompositions-e.g., based on wavelets and Slepians-that can be applied to filter signals defined on the g…
We introduce a groupoid ${\mathbf{ΠMG}}}$, called the fundamental modular groupoid, which is a variant of Penner's mapping class groupoid. We study how it relates to the surface mapping class groups and Thompson's group . We also introduce larger groupoid , which is related to outer automorphis…
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…
New geometric variant of factorization homology for conformally flat manifolds.
A new NMF variant tackles underdetermined problems with sparse and separable assumptions.
This paper reviews recent advances in Bayesian nonparametric techniques for constructing and performing inference in infinite hidden Markov models. We focus on variants of Bayesian nonparametric hidden Markov models that enhance a posteriori state-persistence in particular. This paper also introduces a new Bayesian non…
In unsupervised outlier ensembles, the absence of ground truth makes the combination of base outlier detectors a challenging task. Specifically, existing parallel outlier ensembles lack a reliable way of selecting competent base detectors, affecting accuracy and stability, during model combination. In this paper, we pr…
Motivated by applications in Game Theory, Optimization, and Generative Adversarial Networks, recent work of Daskalakis et al \cite{DISZ17} and follow-up work of Liang and Stokes \cite{LiangS18} have established that a variant of the widely used Gradient Descent/Ascent procedure, called "Optimistic Gradient Descent/Asce…
Analyzing the temporal behavior of nodes in time-varying graphs is useful for many applications such as targeted advertising, community evolution and outlier detection. In this paper, we present a novel approach, STWalk, for learning trajectory representations of nodes in temporal graphs. The proposed framework makes u…