arXiv subjects

Herbert Sauro

Publications and source records attributed to Herbert Sauro.

3 recordsLinked to original sources

arXiv2026

BioModelsRAG: A Biological Modeling Assistant Using RAG (Retrieval Augmented Generation)

The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the machine-readable format, SBML. Although SBML can be translated into the human readable Antimony format, analyzing the models can still be time consuming. In order to bridge this gap, a LLM (large language model) assistant was created to analyze the BioModels and allow interaction between the user and the model using natural language. By doing so, a user can easily and rapidly extract the salient points in a given model. Our analysis workflow involved 'chunking' BioModels and converting them to plain text using llama3, and then embedding them in a ChromaDB database. The user-provided query was also embedded, and a similarity search was performed between the query and the BioModels in ChromaDB to extract the most relevant BioModels. The BioModels were then used as context to create the most accurate output in the chat between the user and the LLM. This approach greatly minimized the chance of hallucination and kept the LLM focused on the problem at hand.

q-bio.MN↗

arXiv2021

Computing Sensitivities in Reaction Networks using Finite Difference Methods

In this article, we investigate various numerical methods for computing scaled or logarithmic sensitivities of the form $\partial \ln y/\partial \ln x$. The methods tested include One Point, Two Point, Five Point, and the Richardson Extrapolation. The different methods were applied to a variety of mathematical functions as well as a reaction network model. The algorithms were validated by comparing results with known analytical solutions for functions and using the Reder method for computing the sensitivities in reaction networks via the Tellurium package. For evaluation, two aspects were looked at, accuracy and time taken to compute the sensitivities. Of the four methods, Richardson's extrapolation was by far the most accurate but also the slowest in terms of performance. For fast, reasonably accurate estimates, we recommend the two-point method. For most other cases where the derivatives are changing rapidly, the five-point method is a good choice, although it is three times slower than the two-point method. For ultimate accuracy which would apply particularly to very fast changing derivatives the Richardson method is without doubt the best, but it is seven-times slower than the two point method. We do not recommend the one-point method in any circumstance. The Python software that was used in the study with documentation is available at: \url{https://github.com/evanyfyip/SensitivityAnalysis}.

q-bio.QM↗

arXiv2009

Fundamental Dynamic Units: Feedforward Networks and Adjustable Gates

The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and between different TFs specify the dynamic responses of the gene under different physiological conditions. By choosing specific regulatory interactions with up to three transcription factors, we designed several functional motifs, each of which is shown to perform a certain function and can be integrated into larger networks. We analyzed three kinds of networks: (i) Motifs derived from incoherent feedforward motifs, which behave as `amplitude filters', or `concentration detectors'. These motifs respond maximally to input transcription factors with concentrations within a certain range. From these motifs homeostatic and pulse generating networks are derived. (ii) Tunable network motifs, which can behave as oscillators or switches for low and high concentrations of an input transcription factor, respectively. (iii) Transcription factor controlled adjustable gates, which switch between AND/OR gate characteristics, depending on the concentration of the input transcription factor. This study has demonstrated the utility of feedforward networks and the flexibility of specific transcriptional binding kinetics in generating new novel behaviors. The flexibility of feedforward networks as dynamic units may explain the apparent frequency that such motifs are found in real biological networks.

q-bio.MN↗