Search arXiv⌕ Search

arXiv · 2409.13622

pAE: An Efficient Autoencoder Architecture for Modeling the Lateral Geniculate Nucleus by Integrating Feedforward and Feedback Streams in Human Visual System

Abstract

The visual cortex is a vital part of the brain, responsible for hierarchically identifying objects. Understanding the role of the lateral geniculate nucleus (LGN) as a prior region of the visual cortex is crucial when processing visual information in both bottom-up and top-down pathways. When visual stimuli reach the retina, they are transmitted to the LGN area for initial processing before being sent to the visual cortex for further processing. In this study, we introduce a deep convolutional model that closely approximates human visual information processing. We aim to approximate the function for the LGN area using a trained shallow convolutional model which is designed based on a pruned autoencoder (pAE) architecture. The pAE model attempts to integrate feed forward and feedback streams from/to the V1 area into the problem. This modeling framework encompasses both temporal and non-temporal data feeding modes of the visual stimuli dataset containing natural images captured by a fixed camera in consecutive frames, featuring two categories: images with animals (in motion), and images without animals. Subsequently, we compare the results of our proposed deep-tuned model with wavelet filter bank methods employing Gabor and biorthogonal wavelet functions. Our experiments reveal that the proposed method based on the deep-tuned model not only achieves results with high similarity in comparison with human benchmarks but also performs significantly better than other models. The pAE model achieves the final 99.26% prediction performance and demonstrates a notable improvement of around 28% over human results in the temporal mode.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Moslem Gorji, Amin Ranjbar, Mohammad Bagher Menhaj. 2024-09-20. pAE: An Efficient Autoencoder Architecture for Modeling the Lateral Geniculate Nucleus by Integrating Feedforward and Feedback Streams in Human Visual System. https://arxiv.org/abs/2409.13622

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

Multimodal AI predicts clinical outcomes of drug combinations from preclinical data

Predicting clinical outcomes from preclinical data is essential for selecting safe and effective drug combinations and for reducing late-stage failures. AI models use molecular structure and target annotations, and do not leverage the perturbation readouts that report how a compound acts in a cellular context. Here we introduce Madrigal, a multimodal AI model that learns from structural, pathway, cell-viability, and transcriptomic data. Madrigal aligns these modalities across 21,842 compounds into a shared latent space and predicts combination outcomes even for drugs observed in only a subset of the data modalities. Trained on 158 expert-curated and 795 patient-reported combination outcomes, Madrigal outperforms single-modality and state-of-the-art multimodal methods. Ablations show that modality alignment and multimodal input each improve predictive performance. Madrigal predicts elevated risk for combinations that share membrane transporters. In head-to-head trials that compare two combination arms,the arm with the higher observed incidence of neutropenia, anemia, alopecia, or hypoglycemia receives the higher predicted risk in 25 of 28 comparisons. In MASH, Madrigal ranks resmetirom among the candidates with favorable predicted safety when paired with type 2 diabetes drugs. Madrigal also improves adverse-event prediction in a longitudinal patient cohort and an independent oncology cohort and predicts efficacy in primary acute myeloid leukemia samples and patient-derived xenografts.

q-bio.QM↗

ProteoEM: probabilistic protein abundance estimation from iterative affinity traces

Single-molecule affinity mapping enables molecular-level measurement of proteins and proteoforms, but imperfect and nonspecific probe binding makes individual affinity traces compatible with multiple molecular identities. Accurate abundance estimation therefore requires apportionment of ambiguous traces by weight rather than assignment to a single candidate. We developed ProteoEM, an expectation-maximization framework for weighted proteoform quantification, inspired by transcript abundance estimation methods for RNA sequencing and released as an open-source Python package. ProteoEM evaluates each molecule against every candidate using fixed, pre-calibrated probe-response rates held separate from the abundance estimate, while retaining the full likelihood of the observed affinity features. The framework estimates proteoform abundances, reports indistinguishable proteoforms as groups when measurements cannot separate them, and accounts for differential observation yields to distinguish the composition of observed molecules from that of the source sample. In simulations, ProteoEM accurately recovered the underlying molecular composition where approaches that reduce each trace to a hard yes/no call introduced substantial errors. ProteoEM's performance was insensitive to a moderate, uniform calibration error but was biased by informative missing data and by proteoforms absent from the reference. When observation yields were known, it also recovered source-sample composition from observed molecular counts. ProteoEM provides an open-source, reproducible framework for quantitative analysis of single-molecule affinity measurements, and these results motivate validation on experimental molecule-level data.

q-bio.QM↗

PRAXIS-VirtualCell: A Programmable and Trustworthy Framework for Agentic Virtual Cell Experiments

Virtual cells are evolving from single-task predictive models toward programmable biological simulation systems, yet heterogeneous data, models, and validation evidence still lack a unified organizational framework. Here, we present PRAXIS-VirtualCell, a modular framework that organizes biological data, predictive models, perturbations, adapters, execution environments, and validation evidence to enable reproducible and auditable virtual experiments. The system supports cross-species tasks spanning Escherichia coli, Saccharomyces cerevisiae, and human K562 cells, while using biological contracts and evidence-aware execution to distinguish supported predictions from extrapolation and abstention. By further integrating agentic orchestration, PRAXIS-VirtualCell automatically translates natural-language questions into traceable virtual experiments, providing a unified runtime foundation for trustworthy and scalable Virtual Cell systems.

q-bio.QM↗