Soft cells fill space without gaps, derived from minimal surfaces and deformed using edge bending.
problem Creating space-filling shapes without sharp corners.
method Edge bending algorithm to deform polyhedral tilings into soft tilings.
result Soft tilings derived from minimal surfaces can be continuously transformed into one another.
We posit that hippocampal place cells encode information about future locations under a transition distribution observed as an agent explores a given (physical or conceptual) space. The encoding of information about the current location, usually associated with place cells, then emerges as a necessary step to achieve t…
In this paper, we consider the problem of reducing the bit error rate of flash-based solid state drives (SSDs) when cells are subject to inter-cell interference (ICI). By observing that the outputs of adjacent victim cells can be correlated due to common aggressors, we propose a novel channel model to accurately repres…
New method extracts hidden phases in binary mixtures using tubular tilings.
problem Hidden phases in binary mixtures are difficult to observe.
method Introduce tubular tilings for discretizing binary mixtures on smooth manifolds.
result Recover topological information about hidden phases from observable phases and interfaces.
Electron Cryo-Tomography (ECT) enables 3D visualization of macromolecule structure inside single cells. Macromolecule classification approaches based on convolutional neural networks (CNN) were developed to separate millions of macromolecules captured from ECT systematically. However, given the fast accumulation of ECT…
Softens tilings in 3D space, proving conjectures about polyhedral tilings.
problem Proving that all locally polyhedral tilings in 3D space can be softened.
method Developed a new edge-bending algorithm to prove the statement.
result Proved conjectures about polyhedral tilings in 3D space and the plane.
Many applications in data analysis begin with a set of points in a Euclidean space that is partitioned into clusters. Common tasks then are to devise a classifier deciding which of the clusters a new point is associated to, finding outliers with respect to the clusters, or identifying the type of clustering used for th…
Lipid-bilayers are the fundamental constituents of the walls of most living cells and lipid vesicles, giving them shape and compartment. The formation and growing of pores in a lipid bilayer have attracted considerable attention from an energetic point of view in recent years. Such pores permit targeted delivery of dru…
Theory models nonlinear soft tissue elasticity and remodeling using extended Finsler geometry.
problem Understanding and predicting the behavior of nonlinear soft tissues, especially in biologic contexts.
method Formulated a continuum mechanical theory incorporating extended Finsler geometry to describe the complex behaviors of fibrous soft solids.
result The model quantifies residual strains from growth, remodeling, and degradation, and predicts equilibrium configurations.
Employers actively look for talents having not only specific hard skills but also various soft skills. To analyze the soft skill demands on the job market, it is important to be able to detect soft skill phrases from job advertisements automatically. However, a naive matching of soft skill phrases can lead to false pos…
Soft labeling impacts OOD detection in neural networks.
problem Impact of soft labeling on OOD detection in deep neural networks.
method Empirical analysis of how soft labeling affects OOD detection performance.
result Soft labeling can either improve or deteriorate OOD detection performance.
Developed a new thresholding method that connects soft and hard thresholding.
problem Connecting soft and hard thresholding methods in data analysis.
method Scaled soft thresholding method with empirical scaling values.
result Found two sources of over-fitting in the scaled soft thresholding method.
Maximum entropy deep reinforcement learning (RL) methods have been demonstrated on a range of challenging continuous tasks. However, existing methods either suffer from severe instability when training on large off-policy data or cannot scale to tasks with very high state and action dimensionality such as 3D humanoid l…
ASBART accelerates Soft BART for faster Bayesian regression.
problem Slow computation in Soft BART.
method Proposed ASBART, a variant of Soft BART.
result ASBART is about 10 times faster than Soft BART with similar accuracy.
New method improves stability of soft FQI for offline RL.
problem Stability issues in soft FQI under function approximation.
method Stationary reweighting to align operator norms.
result Local linear convergence proved under certain conditions.
Kernel testing compares cell states in single-cell data.
problem Comparing non-linear cell states in single-cell data.
method Kernel-based testing framework for non-linear distribution comparison.
result Identifies subtle population variations in cell states.
Generalizes soft noncommutative schemes to flag varieties.
problem Applying soft noncommutative schemes to flag varieties.
method Generalization via toric geometry and distinguished affine charts.
result Soft noncommutative schemes can be applied to flag varieties.
Paper proposes a new loss function for conditional models using soft targets.
problem Improving generalization performance of deep neural networks on supervised classification tasks.
method Introduces a new loss function compatible with soft targets, based on noise contrastive estimation.
result Soft target InfoNCE loss performs on par with cross-entropy baselines and outperforms other losses.
Introduces Soft-SVM for binary classification bridging logistic and SVM.
problem Data separability issues in binary classification.
method Soft-SVM regression using convex relaxation of hinge loss with softness and class-separation parameters.
result Soft-SVM performs well in classification and prediction errors.
Deep model learns from labeled and unlabeled data for industrial soft sensing.
problem Lack of data limits soft sensor development in industrial processes.
method Hierarchical, generative deep latent variable model for semi-supervised multi-unit soft sensing.
result Model outperforms current methods for soft sensing in industrial processes.
This study reviews and evaluates clustering methods for single-cell RNA-seq data.
problem Identifying and characterizing novel cell types from single-cell RNA-seq data.
method Review and performance comparison of clustering methods.
result Performance comparison experiments on two datasets.
Cell detection and cell type classification from biomedical images play an important role for high-throughput imaging and various clinical application. While classification of single cell sample can be performed with standard computer vision and machine learning methods, analysis of multi-label samples (region containi…
New method constructs Floer homologies without hard analysis.
problem Constructing homological invariants in infinite dimensions.
method Soft, finite-dimensional tools to avoid hard analysis.
result Demonstrates construction of Floer homologies without PDE.
This paper introduces TNTK to study infinite soft tree ensembles.
problem Understanding the behavior of infinite soft tree ensembles.
method Introduced Tree Neural Tangent Kernel (TNTK) to analyze infinite soft tree ensembles.
result Identified several non-trivial properties of infinite soft tree ensembles.
Forest Fire Clustering discovers cell types from single-cell data.
problem Discovering cell types from large-scale single-cell sequencing data.
method Iterative label propagation and parallelized Monte Carlo simulation.
result Forest Fire Clustering outperforms state-of-the-art methods on diverse benchmarks.
Improves deep neural networks using soft labels through alternating minimization.
problem Improving deep neural networks training with soft labels.
method Co-Learns DNNs and soft labels via Alternating Minimization of two objectives.
result COLAM achieves improved performance on many tasks with better testing classification accuracy.
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
problem Improving single-cell RNA sequencing clustering by incorporating cell-cell communication.
method Integrates cell-cell communication into a variational autoencoder framework.
result Empirical results show CCCVAE outperforms standard VAEs in clustering performance.
Matching cells over time has long been the most difficult step in cell tracking. In this paper, we approach this problem by recasting it as a classification problem. We construct a feature set for each cell, and compute a feature difference vector between a cell in the current frame and a cell in a previous frame. Then…
Improved GPLVM model for single-cell RNA-seq data.
problem Lack of effective scalable models for clustering cell types in large-scale single-cell RNA-seq data.
method Introduces amortized stochastic variational Bayesian GPLVM (BGPLVM) tailored for single-cell RNA-seq.
result Matches the performance of scVI on synthetic and real-world datasets and reveals more interpretable latent structures.
The paper develops a multi-unit soft sensing model for virtual flow meters that improves few-shot learning.
problem Improving soft sensor performance for new wells with limited data.
method Formulates a probabilistic, hierarchical model using a deep neural network for multi-unit soft sensing.
result Multi-unit models trained on many wells can perform well on new wells with just a few data points.
The study identifies all possible vector field structures on specific 2D shapes.
problem Optimal discrete gradient vector fields on surfaces with 1-2 critical cells.
method Analysis of discrete vector fields on 2D shapes with minimal critical cells.
result All possible structures of discrete Morse functions on specified shapes.
In this article supervised learning problems are solved using soft rule ensembles. We first review the importance sampling learning ensembles (ISLE) approach that is useful for generating hard rules. The soft rules are then obtained with logistic regression from the corresponding hard rules. In order to deal with the p…
Recently, deep learning becomes the main focus of machine learning research and has greatly impacted many important fields. However, deep learning is criticized for lack of interpretability. As a successful unsupervised model in deep learning, the autoencoder embraces a wide spectrum of applications, yet it suffers fro…
Proposes a new method for deep ensembles that improves accuracy and calibration.
problem Improving accuracy and calibration of deep ensembles.
method Estimates confusion matrices of ensemble members and weighs them according to their inferred performance.
result Empirically shows superiority of soft Dawid Skene over ensemble averaging.
New model identifies cell-specific genes for cancer prognosis.
problem No statistical model to integrate multiscale cancer data.
method Bayesian generalized promotion time cure models (GPTCMs).
result Improves cancer prognosis by identifying cell-specific genes.
MarkerMap selects key genes for cell type analysis in single-cell RNA-seq.
problem Selecting informative genes from large single-cell RNA-seq datasets is challenging and computationally intensive.
method MarkerMap is a generative model that identifies minimal gene sets explaining cell type variability.
result MarkerMap outperforms existing methods in both supervised and unsupervised marker selection.
Proposes CXNs for neural network computations on cell complexes.
problem Performing neural network computations on complex topological spaces.
method Introduces a message passing scheme and a unified encoder-decoder framework for cell complexes.
result Generalizes message passing to cell complexes and provides a cell2vec representation.
Bayesian neural networks update beliefs with soft evidence, improving accuracy and calibration.
problem Updating neural network weights with uncertain or soft evidence.
method Developed two algorithms to approximate Jeffrey's rule for updating neural network weights.
result Jeffrey-based methods outperform traditional approaches in accuracy and calibration, especially in noisy data.
A method for selecting pseudo-labeled data in semi-supervised learning using generalized Bayes and soft revision.
problem Selecting pseudo-labeled data for semi-supervised learning with robustness to uncertainty.
method Using credal sets and the Gamma-Maximin method with soft revision to update priors and select pseudo-labeled data.
result The Gamma-Maximin method with soft revision can achieve promising results, especially in scenarios with low labeled data proportions.
New metric scores perturbations across populations, not cells, improving model comparison.
problem Single-cell perturbation data overlaps, making per-cell accuracy unreliable.
method Average per-cell probability vectors over all cells of a perturbation to form a population profile and rank candidate perturbations.
result Classifier Discrimination Score (CDS) identifies true perturbation more reliably than pseudobulk-based scores.
Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of individual neurons and to categorize neurons based on their gene expression profil…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. Here, we suggest a set of …
Hippocampal dentate granule cells are among the few neuronal cell types generated throughout adult life in mammals. In the normal brain, new granule cells are generated from progenitors in the subgranular zone and integrate in a typical fashion. During the development of epilepsy, granule cell integration is profoundly…
NESS improves neighbor embedding for smooth cell-state transitions in single-cell data.
problem Challenges in extracting smooth, low-dimensional representations from noisy single-cell data.
method Builds on PCS framework to develop NESS, a stable machine learning approach.
result NESS consistently yields useful biological insights across diverse single-cell datasets.
New model clusters cells and individuals, revealing genetic influences on cell types.
problem Clustering nested data with group-level and observation-level variables.
method Nested Atoms Model (NAM), Bayesian nonparametric approach.
result Identifies clusters of genetically similar individuals with homogeneous cell-type profiles.
MSLG generates soft labels to improve DNN performance on noisy datasets.
problem Significant performance degradation of DNNs due to noisy labels.
method Meta-learning techniques to estimate optimal label distribution and iteratively update soft labels.
result MSLG outperforms state-of-the-art methods by a large margin on various datasets.
Cell-based NAS search spaces are redundant and lack novelty.
problem Redundancy and lack of novelty in cell-based neural architecture search.
method Empirical analysis of architectures from popular cell-based search spaces.
result Randomly sampled architectures can match or outperform state-of-the-art results.
New method classifies reticulocytes from red blood cells without labels.
problem Classifying reticulocytes from mature red blood cells without fluorescent labels.
method Unsupervised machine learning on morpho-rheological markers.
result Promising results in classifying reticulocytes from mature red blood cells.