ECLAIR improves lineage reconstruction from single-cell data with uncertainty estimates.
problem Uncertainty in cell lineage reconstruction from high-dimensional single-cell data.
method ECLAIR uses an ensemble approach to improve robustness and provide uncertainty estimates.
result ECLAIR successfully reconstructs known lineage relationships and improves robustness of predictions.
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…
Super-OT combines GANs and optimal transport for lineage tracing.
problem Lineage tracing in single-cell RNA-seq data.
method Supervised learning framework with GANs for optimal transport.
result Super-OT outperforms Waddington-OT in predicting cell differentiation outcomes.
Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the …
SDSR reconstructs species trees from genetic markers efficiently.
problem Challenges in reconstructing species trees from genetic data.
method Spectral divide-and-conquer approach based on graph theory.
result SDSR achieves up to 10-fold faster runtime with comparable accuracy.
SNJ recovers latent tree models from similarity matrices.
problem Reconstructing latent tree models from observed data.
method Spectral Neighbor Joining (SNJ) method.
result SNJ is consistent and requires fewer samples for accurate tree recovery.
This paper corrects ReLU attribution and compares activation functions in deep learning.
problem Historical misattribution and performance comparison of activation functions.
method Historical tracing and empirical comparison of ReLU, Tanh, and Sigmoid across tasks.
result ReLU outperforms Sigmoid and Tanh in deep learning tasks.
Recent work extends Turaev's modular categories to non-semisimple settings.
problem Building TQFTs beyond semisimplicity.
method Generalized modular categories.
result Success in extending Turaev's construction to non-semisimple settings.
The paper defines a new knot relation and explores fertile knots with many descendants.
problem Understanding the structure and properties of knot descendants.
method Introducing and studying the descendant relation between knots, focusing on fertile knots.
result Fertile knots have a large number of descendants.
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks …
The CAP slope is Bayes' theorem in cumulative coordinates, unlocking the weight of evidence, Somers' D, and Gini coefficient.
problem Calibration and weight of evidence
method Identifying the CAP slope as Bayes' theorem
result Revealing the CAP slope as Bayes' theorem
Evolutionary methods improve understanding of LLMs and their relationships.
problem Improving understanding of LLMs and their relationships.
method Relating weights to genotypes and output text to phenotypes using evolutionary methods.
result Estimated evolutionary trees reliably recover the topology of the ground-truth training tree.
New algorithm samples from complex non-convex distributions.
problem Sampling from non-convex, non-smooth distributions with superlinear gradients.
method Subgradient Tamed Unadjusted Langevin Algorithm (SG-TULA)
result Non-asymptotic convergence bounds in Wasserstein-2 distance for SG-TULA.
New methods for signal reconstruction using guiding sets and frame-less pathways.
problem Signal reconstruction in Hilbert spaces with specified properties.
method Axiomatic approach involving sample consistent and guiding sets, with reconstruction set defined as a shortest pathway.
result Existence and uniqueness of reconstruction set in Hilbert space, with derived stability and error bounds.
Efficiently models tree-like data with coupled branches using HMMs.
problem Modeling sequential data with coupled branches in biological systems.
method Developed a dynamic programming algorithm for tree-based HMMs with coupled branches.
result Efficiently solves likelihood, decoding, and parameter learning problems for tree-based HMMs with coupled branches.
Generative adversarial network improves signal reconstruction from magnitude spectrograms.
problem Reconstructing a time-domain signal from a magnitude spectrogram.
method Deep neural network and generative adversarial network approach.
result Our method reconstructs signals faster with higher quality than the Griffin-Lim method.
XPDNet wins MRI reconstruction challenge with neural network.
problem MRI reconstruction from under-sampled data.
method Inspired by MRI and computer vision best practices, XPDNet uses a neural network.
result XPDNet achieved state-of-the-art results in the 2020 fastMRI challenge.
CoRAS adapts image acquisition rates for accurate reconstruction.
problem Determining when enough measurements are collected for accurate image reconstruction.
method Adaptive acquisition rate selection based on reconstruction error probability.
result CoRAS achieves target stopping-time coverage with fewer measurements.
We focus on an interpolation method referred to Bayesian reconstruction in this paper. Whereas in standard interpolation methods missing data are interpolated deterministically, in Bayesian reconstruction, missing data are interpolated probabilistically using a Bayesian treatment. In this paper, we address the framewor…
New method reconstructs moving parts of proteins in cryo-EM.
problem Reconstructing non-rigid molecules with moving parts in cryo-EM.
method Graph Laplacian construction from multiple projection images, followed by spectral volume expansion.
result High-resolution visualization of molecular dynamics using spectral volumes.
Deep learning improves ROI reconstruction in low-dose CT.
problem Severe cupping artifacts in standard analytic reconstruction.
method Proposes a deep learning architecture to remove null space signals from FBP reconstruction.
result Near-perfect reconstruction with 7-10 dB improvement in PSNR.
The paper discusses algorithms for reconstructing curves with given Euclidean or affine curvatures.
problem Reconstructing planar curves with specified Euclidean or affine curvatures.
method The paper presents algorithms for curve reconstruction under the special Euclidean and equi-affine groups.
result The reconstructed curves are close to the original curves in terms of the specified curvatures.
New method reconstructs signals and images from periodic nonlinearities.
problem Reconstructing signals and images from periodic nonlinearities.
method Design of measurement scheme for efficient reconstruction, adaptable to compressive sensing.
result Effective reduction in measurement complexity for HDR imaging with minimal quality loss.
IAGAN method improves medical image reconstruction by incorporating adaptive GAN priors.
problem Reconstructing high-fidelity medical images from incomplete data.
method Image-adaptive GAN-based reconstruction method (IAGAN).
result IAGAN can recover fine structures relevant for medical diagnosis.
Algorithm reconstructs conserved networks from flow data.
problem Network reconstruction from flow data.
method Polynomial time algorithm exploiting graph theoretic properties and learning techniques.
result Exact network reconstruction possible for arborescence networks.
Paper addresses data reconstruction from privacy-protected templates using STCA.
problem Reconstructing privacy-sensitive data from protected templates.
method Sparse ternary coding with ambiguization (STCA) for privacy preservation.
result STCA maintains theoretical performance against deep reconstruction attacks for synthetic data but requires special measures for real images.
This work improves understanding of neural network reconstruction attacks and distillation.
problem Understanding and mitigating reconstruction attacks on neural networks.
method Developed a stronger dataset reconstruction attack and studied its characteristics.
result Reconstruction attacks can recover entire training sets in the infinite width regime.
Sparse elasticity reconstruction from local displacements reduces error.
problem Reconstructing elasticity from limited data.
method Sparse elasticity reconstruction theory, local clustering, alternating optimization.
result Higher spatial resolution elasticity distribution estimation.
PC-RNN reconstructs MRI images from undersampled data with more details.
problem Recovering fine details from undersampled MRI data.
method Pyramid Convolutional RNN (PC-RNN) with three ConvRNN modules for multi-scale reconstruction.
result PC-RNN outperforms other methods in recovering more details from MRI images.
GCVAE improves disentanglement in VAEs while balancing reconstruction error.
problem Improving disentanglement in VAEs while maintaining low reconstruction error.
method Introduces three controllable Lagrangian hyperparameters to optimize reconstruction and KL divergence loss.
result GCVAE outperforms state-of-the-art models in disentanglement while balancing reconstruction.
Paper proposes RAN for better anomaly detection in time series data.
problem Anomaly detection algorithms often fail to accurately detect anomalies due to incomplete reconstruction of anomaly data.
method RAN uses adversarial learning and latent vector-constrained Autoencoder to ensure consistent reconstruction of anomaly data.
result RAN outperforms other algorithms in detecting meaningful anomalies with higher AUC-ROC scores.
This work improves data reconstruction methods by ensuring unique solutions and refining optimization.
problem Ensuring unique solutions and optimizing reconstruction from KKT conditions.
method Discussion of sufficient conditions for unique solutions and introduction of sample splitting for optimization.
result Sample splitting improves reconstruction performance across various methods.
Paper presents a method for robust surface reconstruction from noisy gradients using adaptive dictionary learning.
problem Reconstructing surfaces from noisy photometric stereo normal vector maps.
method Adaptive dictionary learning to sparsely represent spatial patches of the surface, enforcing smoothness constraints.
result The method effectively learns the underlying surface structure and is robust to noise.
Generative Distribution Embeddings learn multiscale representations of distributions.
problem Learning representations of entire distributions for multiscale reasoning.
method Introducing GDE framework that lifts autoencoders to the space of distributions, using conditional generative models and distributional invariance.
result GDEs learn predictive sufficient statistics embedded in Wasserstein space, recovering distances and trajectories for Gaussian and Gaussian mixture distributions.
DCAE learns compact latent representations for one-class novelty detection.
problem Learning compact latent representations for one-class novelty detection.
method DCAE learns compact and collapse-free latent representations through internal discriminative layers of GANs, reconstructing in-class data finely and exclusively.
result DCAE achieves state-of-the-art performance on novelty and adversarial example detection.
New condition for reconstructing Morse functions on 3D manifolds.
problem Reconstructing Morse functions with specific level sets.
method Studied a necessary and sufficient condition for reconstruction.
result New condition strengthens previous sufficient conditions.
Graph filtering improves data reconstruction performance.
problem Data reconstruction and dimensionality reduction.
method Formulate data tasks as graph filtering operations, optimize mean-square error cost involving adjacency matrix, update filters via gradient descent.
result Better reconstruction performance of novel method compared to PCA.
A hybrid network improves MRI reconstruction from undersampled data.
problem Reducing MRI acquisition time while maintaining image quality.
method Hybrid architecture combining k-space and image domains using complex-valued and real-valued U-nets.
result Hybrid approach outperformed image-only deep learning methods in hard-to-reconstruct regions.
Noise2Filter improves 3D tomography reconstruction efficiency and accuracy.
problem Efficiently reconstructing 3D tomographic images in real-time with limited data.
method Self-supervised learning and a learned filter method.
result Noise2Filter achieves real-time reconstruction with limited loss of accuracy.
Deep learning enhances optical microscopy and image reconstruction.
problem Improving image data transformations in optical microscopy.
method Application of deep learning methods on optical microscopy and image reconstruction.
result Deep learning enables new transformations among different modes and modalities of microscopic imaging.
New method reconstructs CT images from limited angles using neural networks.
problem High artifact reconstructions from limited angle CT scans.
method Implicit sinogram completion with 1D and 2D CNNs.
result Combined strategy outperforms competitive baselines.
Single linear solve combines surface reconstruction and uncertainty quantification.
problem Reconstructing surfaces from partial point clouds with uncertainty.
method Geometric Gaussian processes for stochastic surface reconstruction.
result Single linear solve for surface reconstruction with probabilistic capabilities.
Unified theory explains and mitigates double descent in data reconstruction.
problem Understanding and mitigating double descent in reduced order modeling.
method Data-Noise Averaging theory, sufficient criteria, detailed risk curve prediction, regularization mechanisms.
result Detailed risk curves predicted at reduced computational cost, instability traced to individual sensors.
Paper tackles model vulnerabilities by reconstructing training data.
problem Reconstructing training data from model parameters poses a security risk.
method Developed a mathematical framework and score matching method for both Bayesian and non-Bayesian models.
result First score matching framework for reconstructing data in Bayesian models.
DEER network improves few-view breast CT image reconstruction efficiency and quality.
problem Efficient and high-quality few-view breast CT image reconstruction.
method Deep Efficient End-to-end Reconstruction (DEER) network with low model complexity.
result DEER network achieves competitive image quality with significantly fewer parameters compared to state-of-the-art methods.
Study shows how numerical discretization affects reconstructions and parameter distributions in nano metrology.
problem Impact of numerical discretization on parameter reconstructions and model parameter distributions.
method Bayesian target vector optimization, finite element model, Gaussian process, stochastic machine learning surrogate models, Markov chain Monte Carlo sampler.
result Numerical discretization parameters impact the accuracy and distribution of reconstructed model parameters.
This paper combines deep learning with medical imaging models to improve reconstruction speed and reduce radiation.
problem Medical imaging issues like slow MRI, radiation injury in CT and PET.
method Combining deep learning with model-based reconstruction.
result Improves reconstruction speed and reduces radiation in medical imaging.
TRex framework improves sparse view X-ray tomography reconstruction.
problem Sparse view X-ray tomography reconstruction challenges.
method Flexible Tomographic Reconstruction framework using proximal algorithms.
result Superior reconstruction quality compared to state-of-the-art methods.