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 developments in machine-learning algorithms have led to impressive performance increases in many traditional application scenarios of artificial intelligence research. In the area of deep reinforcement learning, deep learning functional architectures are combined with incremental learning schemes for sequential …
Significant advances have been made in artificial systems by using biological systems as a guide. However, there is often little interaction between computational models for emergent communication and biological models of the emergence of language. Many researchers in language origins and emergent communication take co…
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.
AI enhances microbiology and microbiome research through machine learning.
problem Understanding microbial life and its impact on health and the environment.
method AI-driven approaches including machine learning and deep learning.
result Transformative role in enhancing microbial life understanding.
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.
The interplay between inter-neuronal network topology and cognition has been studied deeply by connectomics researchers and network scientists, which is crucial towards understanding the remarkable efficacy of biological neural networks. Curiously, the deep learning revolution that revived neural networks has not paid …
Finding biologically plausible alternatives to back-propagation of errors is a fundamentally important challenge in artificial neural network research. In this paper, we propose a learning algorithm called error-driven Local Representation Alignment (LRA-E), which has strong connections to predictive coding, a theory t…
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…
MIK improves t-SNE's local structure preservation in biological sequence data.
problem Efficiently preserving local structure in high-dimensional biological sequence data.
method Modified Isolation Kernel (MIK) using adaptive density estimation.
result MIK preserves local and global structure better than Gaussian and isolation kernels.
One conjecture in both deep learning and classical connectionist viewpoint is that the biological brain implements certain kinds of deep networks as its back-end. However, to our knowledge, a detailed correspondence has not yet been set up, which is important if we want to bridge between neuroscience and machine learni…
A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the …
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.
Automated digital twin discovery from biological data improves drug discovery and personalized medicine.
problem Developing reliable digital twins from noisy, incomplete biological data.
method Symbolic and sparse regression, Bayesian frameworks, deep learning, and large language models.
result Sparse regression generally outperforms symbolic regression, especially with Bayesian frameworks.
Rapid advances of hardware-based technologies during the past decades have opened up new possibilities for Life scientists to gather multimodal data in various application domains (e.g., Omics, Bioimaging, Medical Imaging, and [Brain/Body]-Machine Interfaces), thus generating novel opportunities for development of dedi…
Paper semantifies bioassay text using neural networks.
problem Semantifying unstructured bioassay text descriptions.
method Neural-network-based approach to automatically semantify bioassay text.
result Neural-based semantification significantly outperforms a frequency-based baseline (72% F1 vs 47% F1).
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.
In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for classifying biologically produced fuel compounds with regard to Research Octane Number. T…
We report a neural architecture search framework, BioNAS, that is tailored for biomedical researchers to easily build, evaluate, and uncover novel knowledge from interpretable deep learning models. The introduction of knowledge dissimilarity functions in BioNAS enables the joint optimization of predictive power and bio…
Study adapts AI research methods to analyze image augmentation impacts on neural network operations.
problem Understanding how image augmentation affects neural network performance and sensitivity.
method Adapted treatment-control paradigm, uses variance decomposition, Sobol indices, and Shapley values for sensitivity analysis.
result Visualizes and quantifies sensitivity to different image augmentation parameters.
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.
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.
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.
Researchers create exact minimal surfaces with helical motifs in biological structures.
problem Analyzing helical motifs in minimal surfaces of biological structures.
method Developed a method to construct exact minimal surfaces with arbitrary helical motifs.
result Exact minimal surfaces with helical motifs can be created and analyzed.
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.
In the past few years, deep learning has transformed artificial intelligence research and led to impressive performance in various difficult tasks. However, it is still unclear how the brain can perform credit assignment across many areas as efficiently as backpropagation does in deep neural networks. In this paper, we…
Defines metrics to compare neural network representations.
problem Comparing neural network representations across different architectures and tasks.
method Developed a family of metric spaces and modified existing measures to quantify representational dissimilarity.
result Identified relationships between neural representations and anatomical features.
Study evaluates consistency of feature attribution in deep learning for multi-omics data.
problem Challenges in interpretability of deep learning models in biological research.
method Investigation of Shapley Additive Explanations (SHAP) on multi-view deep learning models applied to multi-omics data.
result SHAP rankings are sensitive to architecture and random initialization, suggesting caution.
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…
Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to analyze. Typical challenges include a large number of possibly correlated featur…
New algorithm for online training of Spiking Neural Networks (SNNs).
problem Training Spiking Neural Networks (SNNs) online with BPTT-equivalent gradients.
method Clear separation of spatial and temporal gradient components, derived from biological insights.
result Online training of SNNs with BPTT-equivalent gradients and low time complexity.
DCMIX learns channel importance for high content imaging.
problem Lack of channel importance information in deep learning-based image analysis.
method Image blending concepts with alpha compositing for arbitrary channels.
result DCMIX learns biologically relevant channel importance without sacrificing prediction performance.
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.
We used machine learning methods to predict NaV1.7 inhibitors and found the model RF-CDK that performed best on the imbalanced dataset. Using the RF-CDK model for screening drugs, we got effective compounds K1. We use the cell patch clamp method to verify K1. However, because the model evaluation method in this article…
Enhanced BCPNN learns hidden representations without labels.
problem Unsupervised learning of hierarchical representations in neural networks.
method Extended BCPNN architecture with local Hebbian learning mechanisms.
result Demonstrated capability for unsupervised learning of salient hidden representations.
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…
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.
Machine learning predicts plant phenotypes from soil microbiome data.
problem Predicting plant phenotypes from soil microbiome data.
method Two models (random forest and Bayesian neural network) were used to predict plant phenotypes from soil properties and microbial population density.
result Human decisions and normalization strategies significantly impact model performance.
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.
HTMRL uses HTM for RL, adapting faster to changing environments.
problem Adapting to non-stationary environments in RL.
method Strictly HTM-based RL algorithm.
result HTMRL adapts faster to changing environments in a 10-armed bandit.
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.
Bayesian Cox model identifies biomarkers from multi-omics data.
problem Produce interpretable survival prognosis from multi-omics data.
method Penalized semiparametric Bayesian Cox model with graph-structured selection priors.
result Model identifies new biomarkers and improves survival prediction.
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.
Inspired by the human visual perception system, hexagonal image processing in the context of machine learning deals with the development of image processing systems that combine the advantages of evolutionary motivated structures based on biological models. While conventional state-of-the-art image processing systems o…
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.