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.
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…
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.
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.
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.
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.
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.
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 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.
Modeling correlated mutations in cancer for personalized treatment.
problem Identifying mutations for personalized cancer therapy in heterogeneous profiles.
method Proposed correlated zero-inflated negative binomial process with mixed beta-Bernoulli and variational inference.
result Identified biologically relevant correlations between somatic mutations.
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.
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.
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.
Universal model for soft tissue mechanics under shock waves.
problem Modeling shock wave mechanics in soft biological tissues.
method Continuum mixture theory with phase-field mechanics.
result Universal thermodynamically consistent formulation for soft porous tissues.
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.
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.
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.
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.
Robust machine learning models improve DNA regulatory sequence prediction under various shifts.
problem Real-world applications of DNA regulatory sequence prediction involve shifts not captured by standard i.i.d. assumptions.
method Introduces a robustness framework combining simulation benchmarks and real data analysis.
result Models remain accurate and calibrated under mild shifts but show higher error and miscalibration under strong shifts.
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.
A new theory explains large associative memory with biological plausibility.
problem Large associative memory in neurobiology and machine learning.
method Microscopic theory with hidden neurons and two-body interactions.
result Valid model of large associative memory with biological plausibility.
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.
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…
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.
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…
LaMBO optimizes biological sequences using autoencoders and Bayesian optimization.
problem Bayesian optimization for drug design is limited by discrete, high-dimensional decision variables.
method Jointly trains denoising autoencoder with a Gaussian process head for gradient-based optimization in latent space.
result LaMBO outperforms genetic optimizers and requires no large pretraining corpus.
`Biologically inspired' activation functions, such as the logistic sigmoid, have been instrumental in the historical advancement of machine learning. However in the field of deep learning, they have been largely displaced by rectified linear units (ReLU) or similar functions, such as its exponential linear unit (ELU) v…
New estimator corrects bias in CKA for sparsely sampled neurons.
problem Bias in CKA for sparsely sampled neurons.
method Novel estimator that corrects for input and feature sampling.
result Reliable model-to-brain alignment with sparsely sampled neurons.
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.
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…
Model captures system input variations in latent space for actionable dynamics.
problem Learning dynamical systems from data without prescribing a mathematical model.
method Structured latent ODE model with stochastic factors of variation for each input.
result Improves generation of time-series data and inference of system inputs over baselines.
The quest for biologically plausible deep learning is driven, not just by the desire to explain experimentally-observed properties of biological neural networks, but also by the hope of discovering more efficient methods for training artificial networks. In this paper, we propose a new algorithm named Variational Proba…
We propose a novel framework for combining datasets via alignment of their intrinsic geometry. This alignment can be used to fuse data originating from disparate modalities, or to correct batch effects while preserving intrinsic data structure. Importantly, we do not assume any pointwise correspondence between datasets…
QC-ST and CoCo methods correct batch effects in metabolomics data.
problem Batch effects in metabolomics data obscure biological variations.
method QC-ST for simultaneous detection of QC samples' mean vectors and covariance matrices, CoCo for covariance correction.
result QC-ST and CoCo improve batch effect correction in metabolomics datasets.
A variety of methods have been proposed for interpreting nodes in deep neural networks, which typically involve scoring nodes at lower layers with respect to their effects on the output of higher-layer nodes (where lower and higher layers are closer to the input and output layers, respectively). However, we may be inte…
Modern large-scale datasets are frequently said to be high-dimensional. However, their data point clouds frequently possess structures, significantly decreasing their intrinsic dimensionality (ID) due to the presence of clusters, points being located close to low-dimensional varieties or fine-grained lumping. We test a…
Nonnegative Boltzmann machines (NNBMs) are recurrent probabilistic neural network models that can describe multi-modal nonnegative data. NNBMs form rectified Gaussian distributions that appear in biological neural network models, positive matrix factorization, nonnegative matrix factorization, and so on. In this paper,…
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…
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.
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.
Despite its size and complexity, the human cortex exhibits striking anatomical regularities, suggesting there may simple meta-algorithms underlying cortical learning and computation. We expect such meta-algorithms to be of interest since they need to operate quickly, scalably and effectively with little-to-no specializ…
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 …
Heterosis is the improved or increased function of any biological quality in a hybrid offspring. We have studied yet the largest maize SNP dataset for traits prediction. We develop linear and non-linear models which consider relationships between different hybrids as well as other effect. Specially designed model prove…
Perceptual capabilities of artificial systems have come a long way since the advent of deep learning. These methods have proven to be effective, however they are not as efficient as their biological counterparts. Visual attention is a set of mechanisms that are employed in biological visual systems to ease computationa…
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.
Two local learning rules are investigated to avoid weight transport in neural networks.
problem Local learning rules that avoid weight transport are unstable and require tuning.
method Investigated two non-local learning rules and a more robust local rule.
result Non-local learning rules match state-of-the-art performance and operate effectively in noisy updates.
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…