Study of SK-N-AS cells' response to methamidophos using transcriptomics.
problem Understanding the transcriptional response of SK-N-AS cells to methamidophos exposure.
method Combination of statistical and machine learning methods for anomaly detection and causal network inference.
result Identification of key processes and transcripts involved in the response to methamidophos.
Model predicts HU response for sickle cell patients.
problem Predicting which sickle cell patients will respond to Hydroxyurea.
method Developed Deep Artificial Neural Network models.
result 92.6% accuracy in predicting HbF response.
ChemCPA predicts cellular responses to novel drugs using transfer learning.
problem Scaling high-throughput screens to measure cellular responses for many drugs is costly and challenging.
method ChemCPA, a new encoder-decoder architecture combined with transfer learning.
result Training on existing bulk RNA HTS datasets improves generalization performance, reducing the need for extensive single-cell screens.
Novel framework predicts cell responses to perturbations using GRNs.
problem Predicting cellular responses to perturbations for drug discovery and personalized therapeutics.
method Graph variational Bayesian causal inference framework with refined GRNs and robust estimator.
result Enhanced model performance and robust estimation of perturbation effects.
A new model for complex cells accounts for insensitivity to image shifts.
problem Complex cells' response to image shifts.
method Linear combination of Gaussian derivatives at a single position.
result Maximum response insensitive to small shifts of the image.
Model predicts anti-cancer drug responses using gene and molecular data.
problem Expensive and time-consuming cancer drug discovery and tailoring.
method Uses variational autoencoders and multi-layer perceptrons to encode gene expression and drug data.
result High average R2 of 0.83 and 0.845 in predicting drug responses for breast and pan-cancer cell lines, respectively. Collaborative filtering predicts drug responses from gene expression data.
problem Predicting drug responses from large gene expression datasets with limited samples.
method Low-rank matrix factorization and latent linear regression.
result The proposed method outperforms state-of-the-art methods in predicting drug-gene associations.
Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for integrated analyses of a large number of chemical features of drugs against the corr…
The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of anti-cancer drugs illuminated the link between genotypes and vulnerability. However,…
Bayesian model for cancer drug studies maps dose-response curves.
problem Mapping dose-response curves in cancer drug studies.
method Bayesian Tensor Filtering (BTF) with low-dimensional embeddings and structured shrinkage priors.
result BTF outperforms state-of-the-art methods in cancer drug studies.
GENOT matches cells across data modalities using neural OT solvers.
problem Scalability, privacy, and out-of-sample estimation issues in traditional OT solvers.
method Learn stochastic maps, parameterize OT maps, relax mass conservation, integrate quadratic solvers.
result Demonstrates significant potential for enhancing therapeutic strategies.
Decades of research on the neural code underlying spatial navigation have revealed a diverse set of neural response properties. The Entorhinal Cortex (EC) of the mammalian brain contains a rich set of spatial correlates, including grid cells which encode space using tessellating patterns. However, the mechanisms and fu…
Selecting the right drugs for the right patients is a primary goal of precision medicine. In this manuscript, we consider the problem of cancer drug selection in a learning-to-rank framework. We have formulated the cancer drug selection problem as to accurately predicting 1). the ranking positions of sensitive drugs an…
Deep learning model classifies drug effects based on structure and cell responses.
problem Limited ability to classify chemicals based on their modes of action.
method Integrative deep learning architecture combining molecular structures and cell responses.
result Improved classification performance, reducing error by 4.6%.
Bayesian approach for multivariate density regression of complex data.
problem Regression of multivariate density-valued responses on predictors.
method Bayesian inference using sliced Wasserstein barycenter and SW distance.
result Accurate fits and reliable predictions for complex data.
In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked …
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.
A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially va…
A new image completion method inspired by brain cells.
problem Image restoration from corrupted data.
method Biologically-inspired sub-Riemannian model with frequency and phase.
result Completion of two-dimensional images using cortical cell responses.
Chemotherapeutic response of cancer cells to a given compound is one of the most fundamental information one requires to design anti-cancer drugs. Recent advances in producing large drug screens against cancer cell lines provided an opportunity to apply machine learning methods for this purpose. In addition to cytotoxi…
We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. This framework is designed to enable detection of clusters of data in the presence of structural requirements which we encode as algebraic constraints in a linear program. Our cluste…
The paper studies how grid cell patterns emerge in neural networks.
problem Understanding how grid cells in the brain form hexagonal firing patterns.
method Training recurrent neural networks with conformal normalization of velocity inputs.
result Conformal normalization is crucial for the emergence of hexagonal grid patterns in neural networks.
Model detects patterns in noisy binary data, explaining neuron activity in terms of cell assemblies.
problem Detecting structure in noisy or approximate repeats of patterns in sparse binary data.
method Probabilistic binary latent variable model based on Noisy-OR model, inferring sparse activity in latent variables.
result Model successfully extracts and explains latent structure in spiking neural data.
A central challenge in neuroscience is to understand neural computations and circuit mechanisms that underlie the encoding of ethologically relevant, natural stimuli. In multilayered neural circuits, nonlinear processes such as synaptic transmission and spiking dynamics present a significant obstacle to the creation of…
Paper introduces tCNNS model for predicting drug cell line interactions.
problem Predicting phenotypic drug responses on cancer cell lines.
method tCNNS model using SMILES format for drugs and cancer cell lines.
result Achieves 0.84 for R2 and 0.92 for Rp. Method improves microbial biomass yield estimation from noisy data.
problem Estimating microbial biomass yields from noisy cell counts and substrate measurements.
method Probabilistic macrochemical modeling to relax cell weight assumptions and improve robustness.
result Model provides accurate uncertainty estimates of key parameters.
Hexagon grid patterns emerge from conformal isometry in grid cell neural networks.
problem Understanding the algebraic, geometric, and topological properties of grid cells.
method Investigating recurrent neural network models of grid cells, focusing on Lie group and Lie algebra representations, conformal isometry, and hexagon periodic patterns.
result Conformal isometry leads to hexagon periodic patterns in grid cell responses and accurate path integration.
Accurately predicting drug responses to cancer is an important problem hindering oncologists' efforts to find the most effective drugs to treat cancer, which is a core goal in precision medicine. The scientific community has focused on improving this prediction based on genomic, epigenomic, and proteomic datasets measu…
Deep convolutional neural networks (CNNs) have demonstrated impressive performance on visual object classification tasks. In addition, it is a useful model for predication of neuronal responses recorded in visual system. However, there is still no clear understanding of what CNNs learn in terms of visual neuronal circu…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms…
A new method for analyzing shapes and forms using additive models on manifolds.
problem Analyzing shapes and forms under geometric transformations.
method Extending generalized additive regression to models for shapes/forms using squared geodesic distance and Riemannian L2-Boosting algorithm. result Automated model selection and intuitive visualization of covariate effects in shape/form space.
Enhances high-throughput imaging of microtubule networks, improving clarity and consistency.
problem Fluorescence noise obscures microtubule structures in high-throughput imaging.
method CycleGAN learning to enhance low-resolution images of microtubule networks.
result CycleGAN effectively identifies microtubules with high accuracy (0.93+ AUC-ROC).
Robust TOT regression method handles outliers in tensor data.
problem Outliers in tensor data affect standard TOT regression.
method ROTOT method using a single loss function for outliers and robust MPCA for predictor.
result ROTOT method reduces influence of both casewise and cellwise outliers.
This paper proposes grid cells encode position via a conformal isometric embedding of 2D physical space.
problem Hexagonal grid firing patterns in grid cells.
method Learning a distance-preserving position embedding in neural space using a recurrent neural network.
result The conformal isometric embedding of 2D physical space into neural space explains hexagonal grid firing patterns.
sEM uses optimal transport to improve EM algorithm for better convergence and avoiding local optima.
problem Improving the EM algorithm for better convergence and avoiding local optima.
method sEM uses entropic optimal transport to compute responsibilities in the expectation step, leading to better global convergence guarantees and avoiding local optima.
result sEM learns cell labels significantly better than other approaches, improving convergence and avoiding local optima.
The paper develops methods for causal inference from single-cell RNA sequencing data with multiple outcomes.
problem Causal inference from single-cell RNA sequencing data with multiple heterogeneous outcomes.
method Generic semiparametric inference framework for doubly robust estimation with multiple derived outcomes.
result Demonstrates the use of semiparametric inferential results for estimating causal effects in genomics.
Feature selection predicts immune state changes in RA mouse model.
problem Predicting the immune state change after RA immunotherapy.
method Feature selection algorithms applied to mouse CIA model data.
result Selected features predict both T cell markers and treatment efficacy.
The vast majority of current machine learning algorithms are designed to predict single responses or a vector of responses, yet many types of response are more naturally organized as matrices or higher-order tensor objects where characteristics are shared across modes. We present a new machine learning algorithm BaTFLE…
Autoencoder identifies cancer cells from normal ones using gene expression data.
problem Distinguishing between normal and cancer cells using gene expression profiles.
method Autoencoder trained on large tumor dataset to capture latent representations, using HPC toolkit for efficiency.
result Autoencoder node saliency identifies key differentiating features between normal and cancer cells.
We introduce principal differences analysis (PDA) for analyzing differences between high-dimensional distributions. The method operates by finding the projection that maximizes the Wasserstein divergence between the resulting univariate populations. Relying on the Cramer-Wold device, it requires no assumptions about th…
ROD reconstructs conditional mean surfaces from observational data, invariant to term order.
problem Regression estimates from observational data can be biased by multicollinearity and term order.
method Retrospective Orthogonal Design (ROD) reconstructs surfaces on a probability-balanced lattice, preserving observed and completing unsupported cells.
result ROD outperformed polynomial regression across various data-generating processes, achieving high out-of-sample R2. MFM integrates multiple evolving populations using Wasserstein manifold flows.
problem Learning dynamics of multiple interacting populations evolving over time.
method Meta Flow Matching (MFM) integrates vector fields on Wasserstein manifold using amortized flow models and GNN embeddings.
result MFM improves prediction of individual treatment responses on multi-patient single-cell drug screen data.
A new method improves data representation for diverse tasks.
problem Learning meaningful representations for tasks like batch correction and counterfactual inference.
method Contrastive Mixture of Posteriors (CoMP) method using misalignment penalties.
result CoMP achieves state-of-the-art performance on challenging tasks.
LOT framework embeds high-dimensional cell data into interpretable Euclidean space.
problem Lack of interpretable methods for high-dimensional cell data.
method Adapts Linear Optimal Transport (LOT) to irregular point clouds.
result Accurate and interpretable classification and synthetic data generation.
Model predicts phytoplankton subpopulations based on environmental factors.
problem Predicting phytoplankton dynamics under changing environmental conditions.
method Sparse mixture of multivariate regressions model.
result Identifies environmental covariates influencing phytoplankton subpopulations.
In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While c…
CAST models time-varying treatment effects in cancer patients.
problem Estimating treatment effects at fixed time points limits understanding of dynamic changes over time.
method CAST combines parametric and non-parametric methods to model continuous time-varying treatment effects.
result CAST reveals how treatment effects rise, peak, and decline over the follow-up period.
Model explains optical illusions using geometric sub-Riemannian geodesics.
problem Understanding and explaining geometrical optical illusions.
method Neuro-mathematical model based on sub-Riemannian geodesics in the Roto-Translation Group.
result Illusory contours are described as geodesics in a new metric.