Machine learning speeds up FLIM analysis in biomedical research.
problem Complex, slow, and computationally expensive FLIM analysis.
method Machine learning techniques for faster and smarter FLIM data extraction and interpretation.
result Higher accuracy in classifying and segmenting FLIM images compared to conventional methods.
Deep learning methods have shown extraordinary potential for analyzing very diverse biomedical data, but their dissemination beyond developers is hindered by important computational hurdles. We introduce ImJoy (https://imjoy.io/), a flexible and open-source browser-based platform designed to facilitate widespread reuse…
Deep learning has shown its great promise in various biomedical image segmentation tasks. Existing models are typically based on U-Net and rely on an encoder-decoder architecture with stacked local operators to aggregate long-range information gradually. However, only using the local operators limits the efficiency and…
Self-supervised method predicts clean signal and noise distribution from noisy images.
problem Blind denoising and noise estimation in biomedical images with limited clean data.
method Two neural networks jointly predict clean signal and noise distribution from noisy observations.
result Significantly outperforms state-of-the-art algorithms on six biomedical image datasets.
Adversarial examples mislead deep learning models in medical image segmentation.
problem Vulnerability of deep learning models to adversarial examples in medical image segmentation.
method Proposed Adaptive Segmentation Mask Attack (ASMA) to craft targeted adversarial examples.
result Demonstrated vulnerability of deep learning models to adversarial examples in medical image segmentation.
Proposes a novel method to identify complex effects in multi-view datasets.
problem Challenges in analyzing multi-view biomedical datasets with complex interactions.
method Generalized kernel machine approach considering marginal and joint effects of features from different views.
result Effective identification of higher-order composite effects in multi-view datasets.
In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping chromosomes. A segmentation solution that is fast and automated will enable scaling of co…
Novel unsupervised method for fast 3D image registration using cycle-consistent CNN.
problem Medical image registration for cancer diagnosis.
method Unsupervised deep learning using cycle-consistent CNN for deformable registration.
result Very precise 3D image registration within a few seconds, improving cancer size estimation.
Study improves LLMs for PPI analysis by addressing uncertainty.
problem Uncertainty in LLM predictions for PPIs.
method Fine-tuned LLaMA-3 and BioMedGPT models, LoRA ensembles, Bayesian LoRA for UQ.
result Competitive PPI identification performance across diverse disease contexts.
Enhancement attacks can falsely improve machine learning model performance in biomedical research.
problem The trustworthiness of machine learning in biomedical research is threatened by enhancement attacks.
method Developed two techniques to enhance prediction performance with minimal changes to features.
result Falsely improved classifiers' accuracy from 50% to almost 100% while maintaining high feature similarities.
Develops spatial uncertainty guarantees for image segmentation models.
problem Ensuring reliable segmentation predictions for biomedical images.
method Adapting conformal inference to imaging, using transformed logit scores and calibration datasets.
result Confidence sets provide spatial uncertainty guarantees with desired probability.
New method uses artificial data to improve biomedical text tagging.
problem Lack of labeled data for biomedical tasks.
method Fine-tuning a pre-trained encoder with additional artificial labeled instances.
result Achieved state-of-the-art performance in PICO annotation.
Imaging genetic research has essentially focused on discovering unique and co-association effects, but typically ignoring to identify outliers or atypical objects in genetic as well as non-genetics variables. Identifying significant outliers is an essential and challenging issue for imaging genetics and multiple source…
Locally sparse neural networks improve interpretability for biomedical tabular data.
problem Overfitting and lack of interpretability in neural networks for tabular biomedical data.
method Locally sparse neural network with a gating network to select relevant features.
result The method outperforms state-of-the-art models in synthetic and real-world biomedical datasets.
Efficiently clusters data with weak assumptions, robust to contamination.
problem General-shaped clustering under weak parametric assumptions with data contamination.
method Two-step hybrid robust clustering algorithm combining trimmed k-means and hierarchical agglomeration.
result Outperforms state-of-the-art methods in various applications.
SODA optimizes data augmentation allocation for deep learning models.
problem Inefficient allocation of data augmentation budget in deep neural networks.
method Online learning to dynamically allocate data augmentation budget during training.
result Optimized data augmentation can save computation time and promote greener machine learning.
A framework uses variational Bayes for solving inverse problems efficiently.
problem Solving inverse problems in various dimensions with flexibility and accuracy.
method Variational Bayes approximations with message passing and factor graph approach.
result Efficient algorithm updates for higher dimensions and computational advantage over MCMC.
This paper shows feature importance remains valid even in low-performing models.
problem Feature importance validity in low-performing machine learning models for biomedical data.
method Experiments with synthetic and real biomedical datasets to compare feature rank stability under different data reductions.
result Feature importance can be maintained even at low performance levels if data size is adequate.
SMM improves signal recovery from noisy data.
problem Estimating signals from noisy and scaled observations.
method Spiked mixture model (SMM) with EM algorithm.
result SMM outperforms GMM in signal recovery.
This study evaluates data pre-processing techniques for class imbalance in biomedical data.
problem Class imbalance in biomedical datasets affects model performance.
method Resampling and feature selection techniques evaluated using SVM, C4.5, LDA, and KNN classifiers.
result Feature Selection outperforms other methods in most cases, especially with SVM.
We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type and cell type that are associated …
Designs CNNs for better image reconstruction.
problem Image reconstruction from limited data.
method Parseval convolution operators and chaining of elementary modules.
result CNN-based algorithm yields better results than sparsity-based methods.
The growing use of neuroimaging technologies generates a massive amount of biomedical data that exhibit high dimensionality. Tensor-based analysis of brain imaging data has been proved quite effective in exploiting their multiway nature. The advantages of tensorial methods over matrix-based approaches have also been de…
Framework for causal discovery using multi-modal data.
problem Failure of representation learning in causal tasks.
method Statistical and computational framework combining representation learning and causal inference.
result Effective use of observational and perturbational data for causal discovery.
Linear problems appear in a variety of disciplines and their application for the transmission matrix recovery is one of the most stimulating challenges in biomedical imaging. Its knowledge turns any random media into an optical tool that can focus or transmit an image through disorder. Here, converting an input-output …
Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network models for BioNER to free experts from manual feature engineering, the performan…
Optimal Transport CycleGAN improves unsupervised learning in imaging problems.
problem Improving unsupervised learning in inverse problems using generative models.
method Developed an OT-cycleGAN architecture using a PLS cost with deep learning-based inverse path penalty.
result Distinct variations of cycleGAN architecture can be derived based on forward problem knowledge.
This work abstracts deep neural networks into concept graphs for better interpretability in medical tasks.
problem Lack of interpretability in deep learning models, especially in medical domains.
method Developed a graphical representation of medical image processing models to understand concept-based reasoning.
result Extracted a concept-level graph that reveals the decision-making process of deep learning models.
At this moment, databanks worldwide contain brain images of previously unimaginable numbers. Combined with developments in data science, these massive data provide the potential to better understand the genetic underpinnings of brain diseases. However, different datasets, which are stored at different institutions, can…
Paper tackles image reconstruction from limited data using polyhedral norms and convex regularizers.
problem Learning convex regularizers for image reconstruction from limited data.
method Imposes amplitude-equivariance, approximates functionals with polyhedral norms, identifies synthesis and analysis forms, proposes a trainable tight frame architecture.
result Proposed framework outperforms sparsity-based methods in denoising and biomedical image reconstruction.
A rigorous ML pipeline for binary classification in biomedical studies, focusing on pancreatic cancer.
problem Handling bias in ML models for complex biomedical data.
method Customizable ML analysis pipeline with 9 algorithms, hyperparameter optimization, and thorough evaluation.
result Comparison of ML algorithms to ExSTraCS, highlighting interpretability and bias handling.
M3E2 neural network estimates multiple treatment effects.
problem Estimating effects of multiple treatments simultaneously.
method Multi-task learning neural network model for multiple treatments, continuous and binary.
result M3E2 outperforms baselines in synthetic datasets.
Graph matching is a challenging problem with very important applications in a wide range of fields, from image and video analysis to biological and biomedical problems. We propose a robust graph matching algorithm inspired in sparsity-related techniques. We cast the problem, resembling group or collaborative sparsity f…
DISCoVeR learns disentangled representations by separating shared and condition-specific factors.
problem Learning disentangled representations for multi-condition data.
method Dual-latent architecture, parallel reconstructions, max-min objective.
result DISCoVeR achieves improved disentanglement on various datasets.
Bayesian variational inference improves medical image segmentation confidence.
problem Improving interpretability and confidence in deep learning models for medical image segmentation.
method Encoder-decoder architecture based on variational inference for segmenting brain tumor images.
result The model segments brain tumors with both aleatoric and epistemic uncertainty.
Estimates statistical power for cluster analysis in biomedical research.
problem Lack of established methods to compute a priori statistical power for cluster analysis.
method Simulation studies varying subgroup size, number, separation, and covariance structure.
result Sufficient statistical power achieved with small samples (N=20-30) for large effect sizes.
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been propos…
Extracts roles of authors from biomedical papers.
problem Lack of machine-readable author roles in biomedical papers.
method Statistical analysis of roles, Open Information Extraction, Naïve Bayes approach.
result Extracts roles with precision of 0.68, recall of 0.48, and F1 of 0.57.
Smile-GANs clusters brain MRI scans to reveal disease subtypes and progression.
problem Understanding disease heterogeneity in brain MRI scans.
method Generative Adversarial Networks (GANs) for semi-supervised clustering.
result Discovered four subtypes of Alzheimer's and prodromal phases, with two progressive pathways.
VICatMix clusters categorical biomedical data efficiently and selects relevant variables.
problem Efficient clustering of high-dimensional categorical biomedical data.
method Variational Bayesian finite mixture model with variational inference.
result Improves clustering accuracy and variable selection on noisy, high-dimensional data.
High-dimensional tensors or multi-way data are becoming prevalent in areas such as biomedical imaging, chemometrics, networking and bibliometrics. Traditional approaches to finding lower dimensional representations of tensor data include flattening the data and applying matrix factorizations such as principal component…
A new landmark sampling method improves TDA performance on biomedical data.
problem Improving landmark samplers for pseudometric spaces with varying density and multiplicities.
method Proposes 'lastfirst' procedure based on ranked distances, proving landmarks have desired properties.
result lastfirst outperforms maxmin on homology detection tasks and comparable on prediction tasks.
Quantum neural networks improve causal inference in biomedical studies, especially for small samples.
problem Addressing selection bias in comparing surgical techniques using observational data.
method Developed QNN-based propensity score models focusing on four key covariates (Age, Sex, Stage, BMI). Employed a linear ZFeatureMap for data encoding, SummedPaulis for predictions, and CMA-ES for optimization. Integrated noise modeling to enhance predictive stability.
result QNNs, particularly with noise-aware strategies, outperformed classical models in small samples, achieving AUC up to 0.750 for n=100.
New methods for selecting variables in complex biomedical data.
problem Selecting important variables in multivariate, functional, and complex biomedical data.
method Optimization-based variable selection methods for various regression models.
result Outperforms state-of-the-art methods in accuracy and speed.
Study compares DL models for medical image segmentation, finds synergistic ensemble strategies improve performance.
problem Improving DL models for specialized medical image segmentation using transfer learning.
method Detailed comparisons of TII and LMI models for binary segmentation of medical images.
result Ensemble strategies improve performance by 10% in certain scenarios.
Framework detects and classifies multi-label RBC images from microscopic images.
problem Challenges in separating touching or overlapping cells for classification.
method Region proposal model + CNN feature extraction + multi-label prediction networks.
result Framework achieves good performance in automatic cell detection and classification.
We propose UOLO, a novel framework for the simultaneous detection and segmentation of structures of interest in medical images. UOLO consists of an object segmentation module which intermediate abstract representations are processed and used as input for object detection. The resulting system is optimized simultaneousl…
Measurement noise limits the advantage of nonlinear models over linear models in biomedical prediction
problem Nonlinear models vs. linear models in biomedical prediction
method Measurement reliability
result Measurement noise blurs the population-optimal predictor