Study examines how body segments respond to random vibrations.
problem Understanding human body responses to random vibrations.
method 35 participants were tested with random noise signals. Multiple linear regression models were created to determine influential predictors of peak translational gains.
result Multiple predictors, including motion direction and body segment, significantly influence peak translational gains.
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.
Machine learning improves concussion diagnosis in female athletes.
problem Limited effectiveness of traditional concussion diagnosis methods for female athletes.
method Advanced neuroinformatics and machine learning models.
result Improved understanding of concussion mechanisms in female athletes.
Background. Real-world data show that approximately 50% of psoriasis patients treated with a biologic agent will discontinue the drug because of loss of efficacy. History of previous therapy with another biologic, female sex and obesity were identified as predictors of drug discontinuations, but their individual predic…
Accurate diagnosis is crucial for preventing the progression of Parkinson's, as well as improving the quality of life with individuals with Parkinson's disease. In this paper, we develop a sex-specific and age-dependent classification method to diagnose the Parkinson's disease using the online handwriting recorded from…
We present two related methods for deriving connectivity-based brain atlases from individual connectomes. The proposed methods exploit a previously proposed dense connectivity representation, termed continuous connectivity, by first performing graph-based hierarchical clustering of individual brains, and subsequently a…
Data obtained from Flow Cytometry present pronounced variability due to biological and technical reasons. Biological variability is a well-known phenomenon produced by measurements on different individuals, with different characteristics such as illness, age, sex, etc. The use of different settings for measurement, the…
MRI image quality affects statistical and predictive analysis of brain morphology.
problem Impact of MRI image quality on statistical and predictive analysis of brain morphology.
method Systematic testing of image quality on univariate statistics and machine learning classification using three large datasets.
result Low-quality MRI data significantly affects detecting significant sex/gender differences in smaller samples, but not in larger ones.
Sex trafficking is a global epidemic. Escort websites are a primary vehicle for selling the services of such trafficking victims and thus a major driver of trafficker revenue. Many law enforcement agencies do not have the resources to manually identify leads from the millions of escort ads posted across dozens of publi…
Develops GIN for fMRI sex classification, explaining results.
problem Difficulty in explaining GNN classification results in neuroscientific terms.
method Develops Graph Isomorphism Network (GIN) for fMRI data, leveraging CNN saliency maps.
result GIN enables visualization of brain regions important for sex classification.
This article applies a long short-term memory recurrent neural network to mortality rate forecasting. The model can be trained jointly on the mortality rate history of different countries, ages, and sexes. The RNN-based method seems to outperform the popular Lee-Carter model.
Intelligent control for greenhouses using deep reinforcement learning.
problem Uncertain nonlinear system of greenhouse environment control.
method Model Embedded Deep Reinforcement Learning (MEDRL) with computer vision and crop growth models.
result Precision and convenience in precise control of greenhouse environment.
Two new models forecast multiple subpopulations' mortality, outperforming existing methods.
problem Modeling mortality patterns and trajectories in related populations.
method Adapted multivariate functional principal component analysis techniques.
result The second proposed model outperforms existing methods in forecast accuracy.
DynDepNet learns dynamic brain graphs from fMRI data for better prediction performance.
problem Static brain graphs from fMRI data lead to poor GNN performance.
method Dynamic Graph Structure Learning for time-varying brain connectivity.
result DynDepNet achieves state-of-the-art sex classification accuracy on real-world fMRI data.
Study removes bias from chest X-ray embeddings using orthogonalization.
problem Reduces bias in chest X-ray embeddings due to protected features.
method Orthogonalization technique to remove protected feature effects.
result Orthogonalization removes bias and makes predictions of protected attributes infeasible.
Model predicts cannabis use disorder risk for adolescents and young adults.
problem Predicting cannabis use disorder progression in adolescents and young adults.
method Bayesian machine learning model trained on longitudinal data.
result Model provides personalized risk assessment with AUC of 0.68-0.75 and E/O ratio of 0.95-1.
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.
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.
A new CVaR test reduces group performance disparity detection complexity.
problem Detecting performance disparities across multiple sensitive groups in ML models.
method Conditional Value-at-Risk (CVaR) testing to reduce sample complexity.
result Sample complexity reduced exponentially to be at most the square root of the number of groups.
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.
Bias in training data affects diagnostic algorithms' performance.
problem Bias in training data leads to biased predictions in diagnostic algorithms.
method Survey of MICCAI 2018 proceedings, analysis of a skin lesions dataset, adversarial training setup.
result Classifier performance varies significantly between subgroups based on age and sex.
Machine learning algorithms can unintentionally discriminate; tools detect and fix this.
problem Unintentional discrimination in machine learning algorithms.
method Statistical tools to detect and eliminate biases.
result Tools can identify and mitigate algorithmic discrimination.
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.
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.
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.
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex multi-level systems. We go one step further and advocate for the consideration of …
Scalable GPLVM reduces complexity in scRNA-seq data, accounting for technical and biological confounders.
problem Complexity and confounders in scRNA-seq data hamper interpretation.
method Extended Gaussian process latent variable model (GPLVM) to handle large datasets.
result Framework reconstructs latent signatures and captures disease-specific gene expression.
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
problem Predicting biological effects of chemical structures for drug discovery.
method Siamese Graph Convolutional Neural Networks for structure-biological effect mapping.
result Highly accurate predictions of biological effects for structurally dissimilar compounds.
New methods improve uncertainty quantification in dynamic biological systems.
problem Uncertainty in dynamic biological models due to nonlinearity and parameter sensitivity.
method Conformal inference methods for non-asymptotic guarantees.
result Enhanced robustness and scalability for diverse biological data structures.
Proposes a novel network-based neighborhood regression for biological systems.
problem Lack of comprehensive analysis on biological modules using both global and local network data.
method Develops a community-wise least square optimization approach to analyze gene modules and their regulatory strength.
result Achieves exact minimax optimality and linear consistency in identifying gene module associations.
AR algorithm simplifies backpropagation with improved scalability and biological plausibility.
problem Improving backpropagation algorithms for complex neural networks and biological plausibility.
method Introducing learnable backwards weights and avoiding nonlinear derivative computations; relaxing frozen feedforward pass assumption.
result Simplified AR algorithm maintains performance on complex CNN architectures and challenging datasets.
We solve a lifecycle model in which the consumer's chronological age does not move in lockstep with calendar time. Instead, biological age increases at a stochastic non-linear rate in time like a broken clock that might occasionally move backwards. In other words, biological age could actually decline. Our paper is ins…
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
problem Optimizing biological sequences for a black-box score function.
method Bootstrapped training of score-conditioned generator (BootGen) algorithm.
result Our method outperforms competitive baselines on biological sequential design tasks.
Fault-tolerant neural networks inspired by biological error correction codes.
problem Achieving reliable computation with unreliable neurons.
method Using biological error correction codes from grid cells in the mammalian cortex to develop a fault-tolerant neural network.
result Noisy biological neurons operate below a fault-tolerance threshold, suggesting a mechanism for reliable computation in the brain.
Probabilistic graphical models (PGMs) have become a popular tool for computational analysis of biological data in a variety of domains. But, what exactly are they and how do they work? How can we use PGMs to discover patterns that are biologically relevant? And to what extent can PGMs help us formulate new hypotheses t…
New risk control method for non-monotonic losses in complex parameters.
problem Controlling risk for non-monotonic losses with multidimensional parameters.
method Stability-based guarantees for generic algorithms applied to non-monotonic losses.
result Guarantees depend on algorithm stability, with looser guarantees for unstable algorithms.
New learning rules for wide neural networks without backpropagation.
problem Training wide neural networks efficiently and without backpropagation.
method Input-weight alignment driven by gradient descent in the NTK regime.
result Biologically-motivated learning rules equivalent to backpropagation in wide networks.
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 …
We introduce bio-inspired artificial neural networks consisting of neurons that are additionally characterized by spatial positions. To simulate properties of biological systems we add the costs penalizing long connections and the proximity of neurons in a two-dimensional space. Our experiments show that in the case wh…
Oja's rule improves neural network training without engineered tricks.
problem Training deep neural networks with biological constraints.
method Incorporating Oja's plasticity rule into error-driven training.
result Stable, efficient learning in feedforward and recurrent architectures.
DCNs mimic neuronal networks for improved neural classification.
problem Lack of topological similarity between DNNs and biological neural networks.
method Developed DCNs with topologies inspired by real-world neuronal networks.
result High classification accuracy achieved by DCNs.
Graph auto-encoder predicts unobserved node features from biological networks and omics data.
problem Integrating biological networks and continuous node features for better prediction.
method Graph neural networks and feature auto-encoders trained on feature reconstruction.
result Graph feature auto-encoder outperforms auto-encoders trained on graph reconstruction for predicting unobserved node features.
Unified framework improves gene prioritization in disease studies.
problem Identifying genes involved in diseases using heterogeneous biological data.
method Network propagation-based gene prioritization with integrated biological information.
result Significant improvements in prioritizing genes not identified by traditional methods.
Was it fair that Harry was hired but not Barry? Was it fair that Pam was fired instead of Sam? How can one ensure fairness when an intelligent algorithm takes these decisions instead of a human? How can one ensure that the decisions were taken based on merit and not on protected attributes like race or sex? These are t…
Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Seco…
In this work, we perform an exploratory study on synthesizing deep neural networks using biological synaptic strength distributions, and the potential influence of different distributions on modelling performance particularly for the scenario associated with small data sets. Surprisingly, a CNN with convolutional layer…
Biological neural network mimics CCA for multi-channel data.
problem Implementing CCA in a biologically plausible neural network.
method Derive an online CCA algorithm with local synaptic updates for multi-compartmental neurons.
result The derived neural network architecture and synaptic updates resemble cortical pyramidal neuron behavior.
High-dimensional data acquired from biological experiments such as next generation sequencing are subject to a number of confounding effects. These effects include both technical effects, such as variation across batches from instrument noise or sample processing, or institution-specific differences in sample acquisiti…