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 …
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48 results for “biological data”
Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Broadly categorized in three types (i.e., sequences, images, and signals), these data are huge in amount and complex in nature. Mining such an enormous amount 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.
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 Graph Feature Auto-Encoder for the Prediction of Unobserved Node Features on Biological Networksq-bio.QM
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.
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…
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.
ODBAE detects complex phenotypes in biological data.
problem Challenges in identifying complex phenotypes from high-dimensional biological data.
method ODBAE (Outlier Detection using Balanced Autoencoders) identifies influential and high leverage points in latent relationships among multiple physiological parameters.
result ODBAE reveals novel metabolism-related genes and uncovers coordinated abnormalities across metabolic indicators.
Synthesizing Deep Neural Network Architectures using Biological Synaptic Strength Distributionscs.NE
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…
Enhances ZSL models with biologically inspired feature enhancement.
problem Limited training data leads to poor feature extraction from pre-trained models.
method Dual-channel learning framework using auxiliary data sets.
result Improves ZSL model's generalization ability and achieves state-of-the-art results.
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…
Develops DSD for analyzing multiscale biological networks.
problem Analyzing multiscale structure in biological networks.
method Data-driven diffusion process with multitemporal analysis.
result Parameter-free inference of intrinsic data structure.
Fusing heterogeneous data setsq-bio.GN
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses two types of heterogeneity. The first one is the type of data, such as metabolomic…
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.
Neural network models of early sensory processing typically reduce the dimensionality of streaming input data. Such networks learn the principal subspace, in the sense of principal component analysis (PCA), by adjusting synaptic weights according to activity-dependent learning rules. When derived from a principled cost…
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…
Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequencesq-bio.QM
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.
Sparse neural networks visualize paired transcriptomic and electrophysiological data.
problem Efficiently analyzing and visualizing paired multivariate neuroscientific data.
method Sparse deep neural networks with a two-dimensional bottleneck and group lasso penalty.
result Biologically interpretable two-dimensional visualizations of paired data.
BaGGLS models biological interactions using Bayesian shrinkage for interpretability.
problem Interpreting complex interactions in high-dimensional biological data.
method Bayesian group global-local shrinkage prior with variational approximation.
result BaGGLS outperforms other methods in interaction detection and scalability.
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.
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.
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.
TNDE quantifies dynamic gene drivers from single-cell snapshots.
problem Reconstructing time-resolved regulatory effects in biological processes.
method Time-varying Network Driver Estimation (TNDE) using shared graph attention encoder and partial optimal transport.
result TNDE identifies stage-specific driver genes in mouse erythropoiesis.
This work proposes a unified framework to leverage biological information in network propagation-based gene prioritization algorithms. Preliminary results on breast cancer data show significant improvements over state-of-the-art baselines, such as the prioritization of genes that are not identified as potential candida…
New method corrects correlation bias in feature importance.
problem Correlations between features in high-dimensional data bias statistical and machine learning models.
method Pairwise Permutation Algorithm (PPA)
result PPA corrects correlation bias, identifying biological relevant biomarkers.
Mathematical modeling with Ordinary Differential Equations (ODEs) has proven to be extremely successful in a variety of fields, including biology. However, these models are completely deterministic given a certain set of initial conditions. We convert mathematical ODE models of three benchmark biological systems to Dyn…
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.
This study benchmarks transcriptomics models for perturbation analysis, finding scVI and PCA superior.
problem Limited evaluation of transcriptomics foundation models for perturbation analysis.
method Developed a novel evaluation framework using diverse public datasets from different sequencing techniques and cell lines.
result scVI and PCA identified as superior models for understanding biological perturbations.
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we de…
The paper provides guidelines for choosing between SBI methods in complex biological models.
problem Choosing appropriate SBI methods for real-world biological data.
method Comprehensive guidelines and application to agent-based models.
result Statistical SBI methods outperform neural SBI methods with sufficient computational resources.
Unified platform for statistical and machine learning in bioinformatics.
problem Workflow inefficiencies in using multiple tools for data analysis.
method Automated hyperparameter optimization, feature importance analysis, statistical tests.
result Accelerates biological discovery workflows with methodological soundness.
Symmetry principles help in creating better AI representations.
problem Creating efficient and generalizable AI representations.
method Using symmetry transformations to guide representation learning.
result Symmetry principles improve data efficiency and generalizability in AI.
We propose a method to model multi-agent behaviors with limited observation and mechanical constraints.
problem Modeling real-world multi-agent behaviors with limited observation and mechanical constraints.
method Decentralized generative models with partial observation and mechanical constraints based on hierarchical variational recurrent neural networks.
result Our method effectively models and predicts biologically plausible behaviors with minimal constraint violations.
New method identifies key genes affecting phenotypes in biological systems.
problem Identifying genes that drive specific phenotypes in complex biological systems.
method Data-driven observability decomposition using Koopman operators.
result Koopman operator representation identifies genes that drive phenotypes.
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.
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.
engGNN: A Dual-Graph Neural Network for Omics-Based Disease Classification and Feature Selectioncs.LG
engGNN combines external and generated graphs to improve disease classification and biomarker discovery.
problem Challenges in integrating omics data due to high dimensionality and small sample sizes.
method Dual-graph framework that integrates external biological networks with data-driven generated graphs.
result engGNN outperforms state-of-the-art methods in disease classification and biomarker discovery.
scICML integrates multi-omics data from single cells using co-clustering.
problem High noise and sparsity in multi-omics data from single cells.
method Information-theoretic co-clustering-based multi-view learning.
result Improves clustering performance and provides biological insights.
New test identifies specific biological parameters for personalized CVD detection.
problem Ineffectual pathology tests fail to consider platelet activation and inter-individual variability.
method Stochastic platelet deposition model and approximate Bayesian computation with discriminative summary statistics.
result Inferred parameters help identify specific biological parameters for personalized CVD detection.
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.
Bi-GNN models drug interactions using a bi-level graph approach.
problem Predicting drug-drug interactions using machine learning.
method Bi-level graph neural networks that consider both interaction graph and representation graphs of drugs.
result Bi-GNN model improves DDI prediction accuracy compared to existing methods.
Derives a biologically plausible neural network for Slow Feature Analysis.
problem Learning latent features from time series data.
method Starting from an SFA objective, derives Bio-SFA with a biologically plausible neural network implementation.
result Validates Bio-SFA on naturalistic stimuli, reproducing interesting properties of brain cells.
Machine learning methods are used to discover complex nonlinear relationships in biological and medical data. However, sophisticated learning models are computationally unfeasible for data with millions of features. Here we introduce the first feature selection method for nonlinear learning problems that can scale up t…
Analyzing biological and artificial neural networks: challenges with opportunities for synergy?q-bio.NC
Deep neural networks (DNNs) transform stimuli across multiple processing stages to produce representations that can be used to solve complex tasks, such as object recognition in images. However, a full understanding of how they achieve this remains elusive. The complexity of biological neural networks substantially exc…
The paper introduces a new method to measure the shape relations between biological objects using r-parallel sets.
problem The influence of neighboring objects on the shape and function of biological objects.
method The authors develop a theory based on spatial point processes to measure the geometrical interaction between objects.
result The proposed measures provide detailed information about the shape of individual objects and their interactions.
Statistical learning on biological data can be challenging due to confounding variables in sample collection and processing. Confounders can cause models to generalize poorly and result in inaccurate prediction performance metrics if models are not validated thoroughly. In this paper, we propose methods to control for …