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 experiments”
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.
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…
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.
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.
Paper uses transfer learning and Bayesian optimization to reduce DNA sequence design experiments.
problem Designing many similar DNA sequences for specific applications is expensive and time-consuming.
method Combines transfer learning with Bayesian optimization to reduce experiment count.
result Total number of experiments can be significantly reduced by sharing information between tasks.
Digital Twin Calibration for Biological System-of-Systems: Cell Culture Manufacturing Processq-bio.QM
Optimizes biomanufacturing processes with a new digital twin calibration method.
problem Lack of interpretability and sample efficiency in traditional DoE methods.
method Developed a computational approach to calibrate Bio-SoS digital twin model.
result Guides sample-efficient and interpretable DoEs by quantifying sub-model parameter estimation errors.
P3BO optimizes biological sequence design by combining multiple methods.
problem Variability in performance of black-box optimization methods for biological sequence design.
method Population-Based Black-Box Optimization (P3BO) that samples sequences from an ensemble of methods, weighting by past performance.
result P3BO outperforms individual methods, proposing higher quality and more diverse sequences.
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…
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.
GAIT-prop derives a biologically plausible learning rule from backpropagation.
problem Biological implausibility in traditional backpropagation for neural networks.
method GAIT-prop uses a top-down model to convert output error into plausible targets for weight updates.
result GAIT-prop and backpropagation give identical weight updates under certain conditions.
Our research is focused on understanding and applying biological memory transfers to new AI systems that can fundamentally improve their performance, throughout their fielded lifetime experience. We leverage current understanding of biological memory transfer to arrive at AI algorithms for memory consolidation and repl…
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.
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…
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.
Recent years have witnessed a trend that advanced mathematical tools, such as algebraic topology, differential geometry, graph theory, and partial differential equations, have been developed for describing biological macromolecules. These tools have considerably strengthened our ability to understand the molecular mech…
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.
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…
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.
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.
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…
Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various measurements. Two main supervised frameworks have been proposed: the local appro…
Learning may need only a few bits of synaptic precisioncond-mat.dis-nn
Learning in neural networks poses peculiar challenges when using discretized rather then continuous synaptic states. The choice of discrete synapses is motivated by biological reasoning and experiments, and possibly by hardware implementation considerations as well. In this paper we extend a previous large deviations a…
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.
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…
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.
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.
A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques f…
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.
We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize t…
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.
With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical investigations. In the study, we will be using the dataset collected by the authors of Sys…
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.
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…
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.
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that molecules interact with each other, both in terms of steric complementarity, as well …
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.
In biological research machine learning algorithms are part of nearly every analytical process. They are used to identify new insights into biological phenomena, interpret data, provide molecular diagnosis for diseases and develop personalized medicine that will enable future treatments of diseases. In this paper we (1…
New algorithm uses random projections for robust, sparse data classification.
problem Improving robustness and sparsity in data classification.
method Randomly projects data into a high-dimensional space, truncates small entries, and applies a cap operation.
result The method enhances classification accuracy with minimal loss, especially in noisy conditions.
GeneDisco benchmarks experimental design for drug discovery.
problem Vast experimental design space in drug discovery.
method Machine learning for optimal experimental design.
result Standardised benchmark suite for active learning.
Investigating the Scalability and Biological Plausibility of the Activation Relaxation Algorithmcs.AI
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…
The paper examines how timing of observations affects causal discovery methods.
problem The sensitivity of causal discovery methods to mismatched observation timing.
method Empirical and theoretical analysis of classical and recent causal discovery methods.
result Causal discovery methods are sensitive to sampling rate and window length.
Biological evolution has distilled the experiences of many learners into the general learning algorithms of humans. Our novel meta reinforcement learning algorithm MetaGenRL is inspired by this process. MetaGenRL distills the experiences of many complex agents to meta-learn a low-complexity neural objective function th…
Learning Causality: Synthesis of Large-Scale Causal Networks from High-Dimensional Time Series Datacs.LG
There is an abundance of complex dynamic systems that are critical to our daily lives and our society but that are hardly understood, and even with today's possibilities to sense and collect large amounts of experimental data, they are so complex and continuously evolving that it is unlikely that their dynamics will ev…
Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation tec…
Backpropagation is the workhorse of deep learning, however, several other biologically-motivated learning rules have been introduced, such as random feedback alignment and difference target propagation. None of these methods have produced a competitive performance against backpropagation. In this paper, we show that bi…