GANs generate biological cell images capturing protein relationships.
problem Synthesize cells from fluorescence microscopy images.
method Adapted GANs with casual dependencies for multi-channel image generation.
result Demonstrated ability to predict temporal evolution from static images.
Corrects nuisance variation in cell image embeddings using Wasserstein distance.
problem Separating biological signal from domain-specific nuisance variation in cell images.
method Minimizing distances between marginal distributions (Wasserstein distance) to adjust embeddings.
result Transformed embeddings carry improved biological signal and less domain-specific information.
Study compares different superpixel methods for explaining CNNs in biological images.
problem Transparency of deep learning models in image classification.
method Compared Felzenszwalb, SLIC, and Compact-Watershed superpixel methods on explaining CNNs.
result Compact-Watershed method most closely matches human-referenced relevance areas.
Deep learning applied to biological data mining.
problem Mining complex biological data from diverse sources.
method Artificial neural networks, deep learning architectures.
result Deep learning techniques improve pattern recognition in biological data.
Hexnet framework enhances image processing with hexagonal structures.
problem Improve image processing systems with biological-inspired hexagonal structures.
method Develops a hexagonal deep learning framework (Hexnet) for image processing.
result Hexnet surpasses current hexagonal image processing systems and artificial neural networks.
Stem uses diffusion models to infer gene expression from H&E images.
problem Inference of gene expression from H&E stained images is time-consuming and expensive.
method Conditional diffusion generative model to infer gene expression.
result Stem achieves state-of-the-art performance in spatial gene expression prediction.
New method extracts biological concepts from cell microscopy images.
problem Extracting meaningful concepts from vision foundation models trained on cell microscopy images.
method Sparse dictionary learning (DL) combined with PCA whitening pre-processing.
result Successfully retrieved biologically meaningful concepts like cell types and genetic perturbations.
A new image completion method inspired by brain cells.
problem Image restoration from corrupted data.
method Biologically-inspired sub-Riemannian model with frequency and phase.
result Completion of two-dimensional images using cortical cell responses.
Efficient algorithm for cell detection and segmentation in crowded images.
problem Instance segmentation in biological images with overlapping cells.
method Column generation approach with exact optimization and odd set inequalities.
result Rapid and accurate instance segmentation on multiple datasets.
DCMIX learns channel importance for high content imaging.
problem Lack of channel importance information in deep learning-based image analysis.
method Image blending concepts with alpha compositing for arbitrary channels.
result DCMIX learns biologically relevant channel importance without sacrificing prediction performance.
Intratumor heterogeneity is often manifested by vascular compartments with distinct pharmacokinetics that cannot be resolved directly by in vivo dynamic imaging. We developed tissue-specific compartment modeling (TSCM), an unsupervised computational method of deconvolving dynamic imaging series from heterogeneous tumor…
Automated tests detect interactions in unstructured data.
problem Detecting interactions between latent variables in low-dimensional systems.
method Derive two interaction tests based on pairwise interventions and integrate them into an active learning pipeline.
result Tests can identify more known biological interactions than random search and standard active learning baselines.
LM-SNNs use lattice maps to classify and cluster images.
problem Image classification and clustering.
method Lattice map spiking neural networks with cooperative and competitive interactions, inhibition strategies, and biologically motivated learning rules.
result LM-SNNs effectively classify and cluster images using self-organized filters.
Combining insights from neural networks and neuroscience to understand complex tasks.
problem Understanding how biological and artificial neural networks learn and solve complex tasks.
method Review of data-analysis techniques from computational neuroscience applied to DNNs, and vice versa.
result Opportunities for synergy between machine learning and neuroscience to enhance understanding of neural representations.
New method trains neural networks with local error signals, outperforming global methods.
problem Training neural networks with global error signals.
method Layer-wise training with local error signals.
result Layer-wise training with local error signals can approach state-of-the-art performance.
A method predicts posterior PCs for faster uncertainty quantification in imaging.
problem Uncertainty visualization in image restoration models is limited by per-pixel variances.
method Neural Posterior Principal Components (NPPC) method for predicting PCs in a single forward pass.
result Orders of magnitude faster uncertainty quantification compared to posterior samplers.
TUNet improves protein classification in cell images.
problem Classifying specific proteins in human cells using microscopy images.
method TUNet model incorporating segmentation maps for improved classification.
result TUNet achieves competitive performance in protein classification.
Study adapts AI research methods to analyze image augmentation impacts on neural network operations.
problem Understanding how image augmentation affects neural network performance and sensitivity.
method Adapted treatment-control paradigm, uses variance decomposition, Sobol indices, and Shapley values for sensitivity analysis.
result Visualizes and quantifies sensitivity to different image augmentation parameters.
Graph Spectral Regularization makes neural network layers more interpretable.
problem Making neural network layers more interpretable without sacrificing performance.
method Using a graph Laplacian penalty to structure hidden layer activations.
result Encourages smooth activations within hidden layers, leading to better interpretability.
New learning rules from information bottleneck improve deep learning without precise labels.
problem Training deep neural networks with backpropagation is biologically implausible.
method Kernelized information bottleneck principle with 3-factor Hebbian structure.
result The new learning rules perform nearly as well as backpropagation on image classification tasks.
Deep CNN model predicts neuronal cell health from images.
problem Predicting the biological activity of chemical compounds on neuronal cells.
method Deep convolutional neural network (CNN) with residual connections.
result Achieved 99.6% accuracy in distinguishing treated from untreated cells.
C2G-Net improves image classification of similar objects like cells.
problem Classifying images with many similar objects efficiently and interpretably.
method Combines image compression and a CNN with reduced parameters.
result C2G-Net achieves similar accuracy to conventional CNNs but with reduced training time and improved interpretability.
Proposes VPF for efficient training of DBMs without Gibbs sampling or feedback phases.
problem Efficient training of deep neural networks with biological plausibility.
method Variational Probability Flow (VPF) for binary Deep Boltzmann Machines (DBMs).
result VPF learns features quickly and generates high-likelihood samples.
Develops statistical guarantees for image-to-image regression models.
problem Current image-to-image regression models lack statistical guarantees for model mistakes and hallucinations.
method Uncertainty quantification techniques with rigorous statistical guarantees for image-to-image regression problems.
result Derives uncertainty intervals around each pixel with formal mathematical guarantees.
New metric compares noisy neural trajectories using optimal transport.
problem Existing metrics fail to capture differences in noisy, dynamic neural responses.
method Proposed an optimal transport distance metric for Gaussian processes.
result Metric effectively compares neural dynamics in different systems.
NestedVAE isolates common factors from paired images without additional supervision.
problem Reduction of data-driven biases in machine learning models.
method Combines deep latent variable models with information bottleneck theory.
result NestedVAE significantly outperforms alternative methods in various tasks.
Spiking neural networks perform similarly to deep networks on occluded images.
problem Robust object recognition in partially occluded images.
method Developed a two-layer spiking neural network trained on natural scenes with a biologically plausible learning rule, compared to deep convolutional networks.
result Spiking neural networks achieve good accuracy and robustness on stepwise pixel erasement tasks.
Deep learning and reinforcement learning improve data analysis in biology.
problem Mining biological data from large and complex datasets.
method Application of deep learning, reinforcement learning, and their combination to biological data.
result Techniques improve performance on previously intractable datasets.
Olshausen and Field (OF) proposed that neural computations in the primary visual cortex (V1) can be partially modeled by sparse dictionary learning. By minimizing the regularized representation error they derived an online algorithm, which learns Gabor-filter receptive fields from a natural image ensemble in agreement …
New algorithms for deep learning mimic brain's learning but struggle with complex images.
problem Evaluating biologically inspired deep learning algorithms on complex image datasets.
method Implemented and compared various biologically inspired algorithms (TP, FA, DTP) on MNIST, CIFAR-10, and ImageNet.
result Biologically inspired algorithms perform well on MNIST but poorly on CIFAR and ImageNet, suggesting new architectures or algorithms are needed.
Method estimates section thickness and XY anisotropy in ssEM images.
problem Accurate 3D reconstructions require precise section thickness and XY anisotropy estimates.
method Non-parametric Bayesian regression of image statistics.
result Method has lower estimation error compared to existing methods.
Enhances high-throughput imaging of microtubule networks, improving clarity and consistency.
problem Fluorescence noise obscures microtubule structures in high-throughput imaging.
method CycleGAN learning to enhance low-resolution images of microtubule networks.
result CycleGAN effectively identifies microtubules with high accuracy (0.93+ AUC-ROC).
A new dataset for denoising real fluorescence microscopy images.
problem Noisy real fluorescence microscopy images.
method Constructed a dataset of 12,000 real fluorescence microscopy images with different noise levels.
result Deep learning methods perform best on the denoising of the FMD dataset.
Optimal algorithm selects biological models without prior info.
problem Determining the correct biological model without prior knowledge.
method Systems biology models and likelihood-free inference.
result Improved model selection performance over conventional methods.
We present a model for the joint estimation of disparity and motion. The model is based on learning about the interrelations between images from multiple cameras, multiple frames in a video, or the combination of both. We show that learning depth and motion cues, as well as their combinations, from data is possible wit…
New method recovers relative rates in spatial compositional data from IMS.
problem Challenges in analyzing spatial data from IMS due to competitive sampling.
method Hierarchical Variational Graph Fused Lasso using heavy-tailed graphical lasso prior and automatic differentiation variational inference.
result Our method outperforms state-of-the-practice point estimate methodologies in IMS and has superior posterior coverage.
Study uses Bayesian networks to infer causal relationships from observational biological data.
problem Understanding causal interactions in biological systems from observational data.
method Bayesian networks applied to small simulated and real biological networks.
result Bayesian networks can reveal causal information flow in gene expression data.
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
problem Challenges in applying machine learning to biological sequences, including unreliable methods.
method Theoretical analysis and development of modified kernels to ensure reliability and accuracy.
result Developed kernels that are universal, characteristic, and metrize the space of distributions for biological sequences.
Skip connections improve biologically-inspired learning rules.
problem Biologically-inspired learning rules often underperform compared to backpropagation.
method Introduced skip connections between intermediate layers in biologically-motivated learning rules.
result Skip connections can match the performance of backpropagation and are robust to hyper-parameters.
Enhances SSL methods with depth cues for better image understanding.
problem Lack of depth cues in 2D image pixel maps limits SSL performance.
method Integrates depth signals from a pretrained monocular RGB-to-depth model into contrastive learning frameworks.
result Improves SSL methods' robustness and generalization with depth signals.
New learning algorithm mimics biological neural networks.
problem Biologically implausible backpropagation for directed neural networks.
method Introduces new neuronal dynamics and learning rule for arbitrary architectures, sparsity-inducing pruning method, and dynamical-systems characterization.
result Prunes irrelevant connections and improves learning efficiency.
Quadratic autoencoder improves low-dose CT image denoising.
problem Low-dose CT image denoising.
method Quadratic autoencoder architecture applied to CT denoising.
result Quadratic autoencoder achieves superior denoising performance and efficiency.
Spatially positioned neurons in neural networks mimic biological systems.
problem Creating neural networks that can perform multiple tasks efficiently.
method Added spatial positions and proximity penalties to artificial neurons.
result Neurons naturally cluster, each responsible for a specific task.
One-dimensional CNNs improve signal recovery from sparse measurements.
problem Recovering signals from limited data.
method One-dimensional Deep Image Prior (DIP) using CNNs with regularization.
result One-dimensional CNNs outperform traditional methods in signal recovery.
Extracts biological context from biomedical texts to associate with events.
problem Identifying biological context and associating it with biochemical events in texts.
method Analyzed an annotated corpus and developed classifiers using syntactic, distance, and frequency features.
result Developed and evaluated classifiers for context-event association.
SENA-discrepancy-VAE interprets latent causal factors in biological pathways.
problem Interpreting latent causal factors in biological pathways.
method SENA-discrepancy-VAE, a model based on discrepancy-VAE, that produces interpretable latent causal factors.
result Sena-discrepancy-VAE achieves comparable predictive performance with non-interpretable counterparts while providing biologically meaningful causal factors.
The paper models retirement spending using biological age instead of chronological age.
problem Retirement spending varies at the same chronological age.
method Developed a stochastic mortality model to adjust for biological age.
result Optimal consumption rates derived using biological age.
This workshop explores the interface between cognitive neuroscience and recent advances in AI fields that aim to reproduce human performance such as natural language processing and computer vision, and specifically deep learning approaches to such problems. When studying the cognitive capabilities of the brain, scienti…