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…
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48 results for “biological domain”
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…
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.
Predicting Drug Interactions and Mutagenicity with Ensemble Classifiers on Subgraphs of Moleculesstat.ML
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…
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.
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…
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.
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.
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.
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.
Part-of-speech (POS) tagging is a fundamental component for performing natural language tasks such as parsing, information extraction, and question answering. When POS taggers are trained in one domain and applied in significantly different domains, their performance can degrade dramatically. We present a methodology f…
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 …
NestedVAE isolates common factors from paired images without additional supervision.
problem Reduction of data-driven biases in machine learning models.
method Combines deep latent variable models with information bottleneck theory.
result NestedVAE significantly outperforms alternative methods in various tasks.
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…
Neural Architecture Search for Joint Optimization of Predictive Power and Biological Knowledgestat.ML
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…
COMET learns concepts for few-shot learning, improving performance.
problem Few-shot learning challenges in machine learning.
method Meta-learning with human-interpretable concept dimensions.
result Significant improvement in 1-shot learning tasks.
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.
New edge features improve GNN performance in biological datasets.
problem Inefficient use of edge features in GNNs.
method Self-supervised and unsupervised learning for new edge features, incorporating Forman-Ricci curvature.
result Improved node classification performance over baseline GNN models.
The structure of complex networks has been of interest in many scientific and engineering disciplines over the decades. A number of studies in the field have been focused on finding the common properties among different kinds of networks such as heavy-tail degree distribution, small-worldness and modular structure and …
Expanding self-supervised learning to diverse domains reveals Rotation's semantic superiority.
problem Limited self-supervised learning experiments on diverse domains.
method Experimented on various domains (satellite, textural, biological) using popular self-supervised methods.
result Rotation task is semantically most meaningful, with other tasks relying on distribution rather than semantic understanding.
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…
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.
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…
Kernel methods on discrete domains have shown great promise for many challenging data types, for instance, biological sequence data and molecular structure data. Scalable kernel methods like Support Vector Machines may offer good predictive performances but do not intrinsically provide uncertainty estimates. In contras…
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…
Invariances to translation, rotation and other spatial transformations are a hallmark of the laws of motion, and have widespread use in the natural sciences to reduce the dimensionality of systems of equations. In supervised learning, such as in image classification tasks, rotation, translation and scale invariances ar…
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.
Neural Laplace models diverse DEs in the Laplace domain for better dynamics.
problem Inadequate ODEs for long-range dependencies and discontinuities.
method Unified framework in Laplace domain, using stereographic map for smoothness.
result Superior performance in diverse DEs, including complex history dependency and abrupt changes.
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.
MIK: Modified Isolation Kernel for Biological Sequence Visualization, Classification, and Clusteringcs.LG
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.
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.
MuVI models multi-view data with structured sparsity, integrating domain knowledge.
problem Disentangling variation across multiple data views in complex systems.
method Multi-view latent variable model with structured sparsity using a modified horseshoe prior.
result MuVI outperforms state-of-the-art methods in structured sparsity modeling and integrates noisy domain expertise.
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.
The hypothesis that computational models can be reliable enough to be adopted in prognosis and patient care is revolutionizing healthcare. Deep learning, in particular, has been a game changer in building predictive models, thus leading to community-wide data curation efforts. However, due to inherent variabilities in …
The characteristics (or numerical patterns) of a feature vector in the transform domain of a perturbation model differ significantly from those of its corresponding feature vector in the input domain. These differences - caused by the perturbation techniques used for the transformation of feature patterns - degrade the…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental cycles, from day/night to seasonal. Transcriptional regulatory networks are one…
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…
Graph representations offer powerful and intuitive ways to describe data in a multitude of application domains. Here, we consider stochastic processes generating graphs and propose a methodology for detecting changes in stationarity of such processes. The methodology is general and considers a process generating attrib…
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.
Motivation: Prediction of the interaction affinity between proteins and compounds is a major challenge in the drug discovery process. WideDTA is a deep-learning based prediction model that employs chemical and biological textual sequence information to predict binding affinity. Results: WideDTA uses four text-based inf…
Archetypal analysis is a data decomposition method that describes each observation in a dataset as a convex combination of "pure types" or archetypes. These archetypes represent extrema of a data space in which there is a trade-off between features, such as in biology where different combinations of traits provide opti…
Convolutional Neural Networks (CNNs) have become the state-of-the-art method to learn from image data. However, recent research shows that they may include a texture and colour bias in their representation, contrary to the intuition that they learn the shapes of the image content and to human biological learning. Thus,…
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…
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.
Representation Learning for Integrating Multi-domain Outcomes to Optimize Individualized Treatmentscs.LG
Framework integrates mental disorder measurements for personalized treatment.
problem Optimizing treatment for mental disorders with latent mental states and heterogeneity.
method Measurement theory and multi-layer neural network for complex treatment effects.
result Learned treatment policies outperform alternatives on heterogeneous treatment effects.