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.
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.
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.
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
problem Efficient design of genomic perturbation experiments in drug discovery.
method Integrates Bayesian optimization with multimodal gene embeddings and enrichment analysis.
result Improves labeling efficiency by 25-40% and identifies top-performing perturbations more effectively.
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.
Proposes a new neural network architecture inspired by biology to improve learning and information flow.
problem Improving artificial neural networks to match biological neuron properties like multidirectional propagation and probabilistic modeling.
method Extends KAN approach with joint distribution neurons that can propagate values and distributions, including variance and higher-order moments.
result Proposed architecture can predict and propagate distributions, including expected values and variances.
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 …
Profiling cellular phenotypes from microscopic imaging can provide meaningful biological information resulting from various factors affecting the cells. One motivating application is drug development: morphological cell features can be captured from images, from which similarities between different drug compounds appli…
Exclusive Group Lasso improves feature selection in correlated biological data.
problem Correlated features hinder Lasso performance in biological classification problems.
method Proposes and solves the exclusive group Lasso, combining stability selection and random group allocation.
result Exclusive Group Lasso outperforms Lasso in comprehensive selection of informative features.
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.
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.
Motivation: Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample. Despite computational advances, interpreting collected measurements and determining their biological role remains a challenge. Results: To interpret measurement…
While deep learning has led to remarkable advances across diverse applications, it struggles in domains where the data distribution changes over the course of learning. In stark contrast, biological neural networks continually adapt to changing domains, possibly by leveraging complex molecular machinery to solve many t…
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.
Shannon's mathematical theory of communication defines fundamental limits on how much information can be transmitted between the different components of any man-made or biological system. This paper is an informal but rigorous introduction to the main ideas implicit in Shannon's theory. An annotated reading list is pro…
Optimal transfer learning for missing not-at-random matrix completion using source data.
problem Matrix completion in a Missing Not-at-Random setting with incomplete and noisy source data.
method Active sampling of rows and columns, feature shift in latent space, minimax lower bounds, computationally efficient estimation framework.
result Achieves minimax lower bound for active sampling setting, avoiding incoherence assumptions.
A neural network approach for feature selection using mutual information.
problem Feature ranking and selection leading to sub-optimal solutions for class separability.
method Stochastic mutual information gradient estimation for dimensionality reduction.
result The network projects features onto an output space maximizing mutual information with class labels.
This paper explores adaptive neural activation in RNNs for better learning.
problem Fixed neural activation functions limit the performance and adaptability of RNNs.
method Developed a novel parametric family of nonlinear activation functions inspired by biological neurons.
result Adaptive neural activation improves learning speed and performance in RNNs.
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…
Maximizing the speed and precision of communication while minimizing power dissipation is a fundamental engineering design goal. Also, biological systems achieve remarkable speed, precision and power efficiency using poorly understood physical design principles. Powerful theories like information theory and thermodynam…
Proposes a new phylogenetic tree space with biologically principled geometry.
problem Developing a space for statistical analysis of phylogenies with biologically informed assumptions.
method Introduces wald space, a new phylogenetic tree space, and two related geometries based on Fisher information and Gaussian processes.
result Geodesics in wald space are similar to those in the Fisher information geometry, but the two geometries are distinct.
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.
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.
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.
Spike-timing dependent plasticity (STDP) which observed in the brain has proven to be important in biological learning. On the other hand, artificial neural networks use a different way to learn, such as Back-Propagation or Contrastive Hebbian Learning. In this work, we propose a new framework called mstdp that learn a…
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
problem Improving single-cell RNA sequencing clustering by incorporating cell-cell communication.
method Integrates cell-cell communication into a variational autoencoder framework.
result Empirical results show CCCVAE outperforms standard VAEs in clustering performance.
New algorithm shows neural networks can learn without full backpropagation.
problem Stochastic gradient descent with backpropagation is non-biologically plausible.
method Random and fixed backpropagation weights in a feedback alignment algorithm.
result Error converges to zero exponentially fast in overparameterized networks.
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.
Stochastic RNNs classify biological neural network paths with robust error bounds.
problem Classifying biological neural network paths.
method Modelled as a continuous-time stochastic recurrent neural network (RNN) with identity activation function, analysed in the robust regime.
result Generalisation error bound holds with high probability, showing the empirical risk minimiser is the best-in-class hypothesis.
Physics-informed methods infer spatial dynamics from static snapshots, but limits exist.
problem Inferring spatial dynamics from static molecular patterns.
method Combining flexible representations with mechanistic constraints, analyzing structural identifiability, and adapting physics-informed schemes.
result Static spatial patterns can identify spatially varying dynamics, but limits exist due to modeling choices.
DASH simplifies neural networks for gene regulatory dynamics using domain knowledge.
problem Pruning neural networks for gene regulatory dynamics lacks biologically meaningful structure learning.
method DASH uses domain-specific structural information to guide network pruning, leading to sparser, better interpretable models.
result DASH outperforms general pruning methods in gene regulatory network inference, yielding deeper insights.
Deep neural networks (DNNs) are known for extracting useful information from large amounts of data. However, the representations learned in DNNs are typically hard to interpret, especially in dense layers. One crucial issue of the classical DNN model such as multilayer perceptron (MLP) is that neurons in the same layer…
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 …
Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a…
Understanding biological network dynamics is a fundamental issue in various scientific and engineering fields. Network theory is capable of revealing the relationship between elements and their propagation; however, for complex collective motions, the network properties often transiently and complexly change. A fundame…
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.
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.
Certain biological neurons demonstrate a remarkable capability to optimally compress the history of sensory inputs while being maximally informative about the future. In this work, we investigate if the same can be said of artificial neurons in recurrent neural networks (RNNs) trained with maximum likelihood. Empirical…
InfoSEM infers gene regulatory networks without GT labels, improving performance.
problem Inferring GRNs from gene expression data with high accuracy and avoiding biases.
method InfoSEM uses deep generative models with informative priors (textual gene embeddings).
result InfoSEM outperforms existing models by 38.5% across four datasets.
Deep neural networks correct Mie scattering in FTIR spectra of biological samples.
problem Mie scattering obscures biochemically relevant spectral information in FTIR spectra of biological samples.
method Deep neural networks to approximate the preprocessing function that removes Mie scattering.
result The model is faster and more generalizable across different tissue types.
PKB framework boosts genomic data analysis by integrating pathway knowledge.
problem Boosting discovery power and connecting new findings with biological mechanisms in genomic data.
method Pathway-based Kernel Boosting (PKB) framework integrating clinical and pathway information for prediction of various outcomes.
result PKB substantially outperforms other methods in predicting drug response and cancer survival.
Error backpropagation is a highly effective mechanism for learning high-quality hierarchical features in deep networks. Updating the features or weights in one layer, however, requires waiting for the propagation of error signals from higher layers. Learning using delayed and non-local errors makes it hard to reconcile…
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.
In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which can be of medical and biological importance. Graphs are are useful in this prob…
Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into co…
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.
Similar to humans and animals, deep artificial neural networks exhibit critical periods during which a temporary stimulus deficit can impair the development of a skill. The extent of the impairment depends on the onset and length of the deficit window, as in animal models, and on the size of the neural network. Deficit…
Paper proposes scalable method for analyzing multi-omic data.
problem Integrating high-dimensional multi-omic data for cancer subtyping.
method Mixed graphical model approach using Birth-Death MCMC algorithm.
result Our method outperforms LASSO and standard BDMCMC in computational efficiency and model selection accuracy.