bioRxiv

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Steering Vector Fields for Property-Controlled Molecular Generation with Chemical Language Models

bioRxiv Jan 1, 2025
Chemical language models have recently become a powerful tool for the de novo generation of drug-like molecules represented as SMILES strings. A central challenge is steering generation toward compounds with favorable properties such as solubility an...
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Mesoscopic analysis of GABAergic marker expression in acetylcholine neurons in the whole mouse brain

bioRxiv Jan 1, 2025
In the central nervous system, acetylcholine (ACh) neurons coordinate neural network activity required for higher brain functions, such as attention, learning, and memory, as well as locomotion. Disturbances in cholinergic signaling have been describ...
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The Human Omnibus of Targetable Pockets

bioRxiv Jan 1, 2025
Hundreds of computational methods for predicting ligand binding pockets exist, but the problem of finding druggable pockets throughout the human proteome persists. Different strategies for pocket-finding excel in different use cases. Ensemble models ...
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Augmented prediction of multi-species protein–RNA interactions using evolutionary conservation of RNA-binding proteins

bioRxiv Jan 1, 2025
RNA-binding proteins (RBPs) play critical roles in gene expression regulation. Recent studies have begun to detail the RNA recognition mechanisms of diverse RBPs. However, given the array of RBPs studied so far, it is implausible to experimentally pr...
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Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding

bioRxiv Jan 1, 2025
Forming an episodic memory requires binding together disparate elements that co-occur in a single experience. One model of this process is that neurons representing different components of a memory bind to an “index” — a subset of neurons unique to t...
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Multi-omics integration at cell type resolution uncovers gene-metabolite mechanisms underlying osteoarthritis heterogeneity

bioRxiv Jan 1, 2025
Metabolic dysregulation is an important factor for osteoarthritis pathogenesis, but comprehensive studies of underlying mechanisms and pathways are rare. We analyzed newly generated metabolomics data on bone marrow from 119 osteoarthritis patients, a...
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A GWAS–machine learning framework reveals protein-synthesis pathway signals for yield in Theobroma cacao after population-structure correction

bioRxiv Jan 1, 2025
Improving cacao yield, a key objective in post-domestication crop improvement, remains a primary goal for breeders, but progress is often hindered by the confounding effects of population structure. To overcome this, we analyzed 346 diverse cacao acc...
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The Rational Irrational: Better Learners Show Stronger Frequency Heuristics

bioRxiv Jan 1, 2025
Does favoring less valuable options that deliver more frequent rewards reflect flawed decision-making or an adaptive strategy under complex environments? Frequency effects, defined as a bias toward more frequently rewarded but less valuable options, ...
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A Reinforcement Learning and Sequential Sampling Model Constrained by Gaze Data

bioRxiv Jan 1, 2025
Reinforcement learning models can be combined with sequential sampling models to fit choice-RT data. The combined models, known as RL-SSMs, explain a wide range of choice-RT patterns in repeated decision tasks. The present study shows how constrainin...
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SpaceExpress enables differential spatial transcriptomics with natural coordinate systems

bioRxiv Jan 1, 2025
Spatial transcriptomics (ST) technologies have enabled new explorations into the spatial organization of tissues and their functional implications. However, one of the most fundamental analyses – comparative analysis of spatial gene expression across...
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