A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
Develops DSD for analyzing multiscale biological networks.
PGEL learns embeddings to diversify protein motifs while maintaining biological function.
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
Graph auto-encoder predicts unobserved node features from biological networks and omics data.
Bi-GNN models drug interactions using a bi-level graph approach.
Researchers create exact minimal surfaces with helical motifs in biological structures.
Proposes a novel network-based neighborhood regression for biological systems.
New methods improve uncertainty quantification in dynamic biological systems.
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we de…
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…
While neural networks are powerful approximators used to classify or embed data into lower dimensional spaces, they are often regarded as black boxes with uninterpretable features. Here we propose Graph Spectral Regularization for making hidden layers more interpretable without significantly impacting performance on th…
New learning rules from information bottleneck improve deep learning without precise labels.
By and large, Backpropagation (BP) is regarded as one of the most important neural computation algorithms at the basis of the progress in machine learning, including the recent advances in deep learning. However, its computational structure has been the source of many debates on its arguable biological plausibility. In…
A new model for sequential memory using temporal predictive coding.
Optimal algorithm selects biological models without prior info.
MIK improves t-SNE's local structure preservation in biological sequence data.
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…
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…
BaGGLS models biological interactions using Bayesian shrinkage for interpretability.
Symmetry principles help in creating better AI representations.
TNDE quantifies dynamic gene drivers from single-cell snapshots.
Exclusive Group Lasso improves feature selection in correlated biological data.
In this paper, we propose a novel application of Generative Adversarial Networks (GAN) to the synthesis of cells imaged by fluorescence microscopy. Compared to natural images, cells tend to have a simpler and more geometric global structure that facilitates image generation. However, the correlation between the spatial…
In this publication, we combine two Bayesian non-parametric models: the Gaussian Process (GP) and the Dirichlet Process (DP). Our innovation in the GP model is to introduce a variation on the GP prior which enables us to model structured time-series data, i.e. data containing groups where we wish to model inter- and in…
New learning algorithm mimics biological neural networks.
DASH simplifies neural networks for gene regulatory dynamics using domain knowledge.
Modeling correlated mutations in cancer for personalized treatment.
SENA-discrepancy-VAE interprets latent causal factors in biological pathways.
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture methods such as HiC have recently been employed. However, computational methods…
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…
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 …
Deep learning applied to biological data mining.
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.
Efficiently models tree-like data with coupled branches using HMMs.
We develop a latent variable model and an efficient spectral algorithm motivated by the recent emergence of very large data sets of chromatin marks from multiple human cell types. A natural model for chromatin data in one cell type is a Hidden Markov Model (HMM); we model the relationship between multiple cell types by…
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…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled markers, offer an alternative approach. As these technologies mature towards becom…
Model captures system input variations in latent space for actionable dynamics.
AR algorithm simplifies backpropagation with improved scalability and biological plausibility.
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…
Bayesian Cox model identifies biomarkers from multi-omics data.
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…
scICML integrates multi-omics data from single cells using co-clustering.
Maximizing the speed and precision of communication while minimizing power dissipation is a fundamental engineering design goal. Also, biological systems achieve remarkable speed, precision and power efficiency using poorly understood physical design principles. Powerful theories like information theory and thermodynam…
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
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…