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.
Scalable GPLVM reduces complexity in scRNA-seq data, accounting for technical and biological confounders.
Algorithm optimizes biological sequences using bootstrapped training with a score-conditioned generator.
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…
The backpropagation (BP) algorithm is often thought to be biologically implausible in the brain. One of the main reasons is that BP requires symmetric weight matrices in the feedforward and feedback pathways. To address this "weight transport problem" (Grossberg, 1987), two more biologically plausible algorithms, propo…
Develops DSD for analyzing multiscale biological networks.
AR algorithm simplifies backpropagation with improved scalability and biological plausibility.
Proposes a novel network-based neighborhood regression for biological systems.
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…
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 …
Unified platform for statistical and machine learning in bioinformatics.
Oja's rule improves neural network training without engineered tricks.
Modeling correlated mutations in cancer for personalized treatment.
Optimal transfer learning for missing not-at-random matrix completion using source data.
ODBAE detects complex phenotypes in biological data.
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
Biological data including gene expression data are generally high-dimensional and require efficient, generalizable, and scalable machine-learning methods to discover their complex nonlinear patterns. The recent advances in machine learning can be attributed to deep neural networks (DNNs), which excel in various tasks i…
scICML integrates multi-omics data from single cells using co-clustering.
New method corrects correlation bias in feature importance.
Spike-timing dependent plasticity (STDP) which observed in the brain has proven to be important in biological learning. On the other hand, artificial neural networks use a different way to learn, such as Back-Propagation or Contrastive Hebbian Learning. In this work, we propose a new framework called mstdp that learn a…
We propose a method to model multi-agent behaviors with limited observation and mechanical constraints.
We propose a novel framework for combining datasets via alignment of their intrinsic geometry. This alignment can be used to fuse data originating from disparate modalities, or to correct batch effects while preserving intrinsic data structure. Importantly, we do not assume any pointwise correspondence between datasets…
TNDE quantifies dynamic gene drivers from single-cell snapshots.
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…
Motivation: Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample. Despite computational advances, interpreting collected measurements and determining their biological role remains a challenge. Results: To interpret measurement…
Training deep neural networks with the error backpropagation algorithm is considered implausible from a biological perspective. Numerous recent publications suggest elaborate models for biologically plausible variants of deep learning, typically defining success as reaching around 98% test accuracy on the MNIST data se…
Motivation : Molecular signatures for diagnosis or prognosis estimated from large-scale gene expression data often lack robustness and stability, rendering their biological interpretation challenging. Increasing the signature's interpretability and stability across perturbations of a given dataset and, if possible, acr…
Automated digital twin discovery from biological data improves drug discovery and personalized medicine.
This study benchmarks transcriptomics models for perturbation analysis, finding scVI and PCA superior.
The backpropagation of error algorithm (BP) is impossible to implement in a real brain. The recent success of deep networks in machine learning and AI, however, has inspired proposals for understanding how the brain might learn across multiple layers, and hence how it might approximate BP. As of yet, none of these prop…
Background. Real-world data show that approximately 50% of psoriasis patients treated with a biologic agent will discontinue the drug because of loss of efficacy. History of previous therapy with another biologic, female sex and obesity were identified as predictors of drug discontinuations, but their individual predic…
Optimal algorithm selects biological models without prior info.
Error backpropagation is a highly effective mechanism for learning high-quality hierarchical features in deep networks. Updating the features or weights in one layer, however, requires waiting for the propagation of error signals from higher layers. Learning using delayed and non-local errors makes it hard to reconcile…
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…
`Biologically inspired' activation functions, such as the logistic sigmoid, have been instrumental in the historical advancement of machine learning. However in the field of deep learning, they have been largely displaced by rectified linear units (ReLU) or similar functions, such as its exponential linear unit (ELU) v…
Model captures system input variations in latent space for actionable dynamics.
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…
New edge features improve GNN performance in biological datasets.
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
Study uses NMF to reduce cancer microarray data dimensions.
Biological datasets amenable to applied machine learning are more available today than ever before, yet they lack adequate representation in the Data-for-Good community. Here we present a work in progress case study performing analysis on antimicrobial resistance (AMR) using standard ensemble machine learning technique…
New learning algorithm mimics biological neural networks.
Heterosis is the improved or increased function of any biological quality in a hybrid offspring. We have studied yet the largest maize SNP dataset for traits prediction. We develop linear and non-linear models which consider relationships between different hybrids as well as other effect. Specially designed model prove…
SENA-discrepancy-VAE interprets latent causal factors in biological pathways.
The practical success of widely used machine learning (ML) and deep learning (DL) algorithms in Artificial Intelligence (AI) community owes to availability of large datasets for training and huge computational resources. Despite the enormous practical success of AI, these algorithms are only loosely inspired from the b…
Defines metrics to compare neural network representations.
Proposes CCCVAE for better single-cell clustering with cell-cell communication.
New framework learns interaction rules from animal trajectories.
Perceptual capabilities of artificial systems have come a long way since the advent of deep learning. These methods have proven to be effective, however they are not as efficient as their biological counterparts. Visual attention is a set of mechanisms that are employed in biological visual systems to ease computationa…