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Roman Bauer

Publications and source records attributed to Roman Bauer.

13 recordsLinked to original sources

Parameter-Efficient Quality Estimation via Frozen Recursive Models

Tiny Recursive Models (TRM) achieve strong results on reasoning tasks through iterative refinement of a shared network. We investigate whether these recursive mechanisms transfer to Quality Estimation (QE) for low-resource languages using a three-phase methodology. Experiments on $8$ language pairs on a low-resource QE dataset reveal three findings. First, TRM's recursive mechanisms do not transfer to QE. External iteration hurts performance, and internal recursion offers only narrow benefits. Next, representation quality dominates architectural choices, and lastly, frozen pretrained embeddings match fine-tuned performance while reducing trainable parameters by 37$\times$ (7M vs 262M). TRM-QE with frozen XLM-R embeddings achieves a Spearman's correlation of 0.370, matching fine-tuned variants (0.369) and outperforming an equivalent-depth standard transformer (0.336). On Hindi and Tamil, frozen TRM-QE outperforms MonoTransQuest (560M parameters) with 80$\times$ fewer trainable parameters, suggesting that weight sharing combined with frozen embeddings enables parameter efficiency for QE. We release the code publicly for further research. Code is available at https://github.com/surrey-nlp/TRMQE.

cs.CL

Computational optimisation of slow cooling profiles for the cryopreservation of cells in suspension

The cryopreservation of biological materials is a highly complex process, as it involves numerous factors such as the cooling and thawing procedures, the administration of cryoprotective agents (CPAs), as well as the type and composition of cells. While theoretical work has yielded a better understanding of the processes occurring during cryopreservation, the design of cryopreservation protocols and their parameters is currently predominantly based on heuristic optimization. Here, we propose a mathematical method to optimise the cooling dynamics in slow-cooling, to reduce the risk of injury. We derive our method from first principles and provide computational predictions. Moreover, we assess the predictions with data obtained from the literature, as well as novel experimental results. Overall, we provide a generic computational approach to generate improved slow-cooling profiles for the cryopreservation of cells in suspension.

q-bio.OT

Evolving Excellence: Automated Optimization of LLM-based Agents

Agentic AI systems built on large language models (LLMs) offer significant potential for automating complex workflows, from software development to customer support. However, LLM agents often underperform due to suboptimal configurations; poorly tuned prompts, tool descriptions, and parameters that typically require weeks of manual refinement. Existing optimization methods either are too complex for general use or treat components in isolation, missing critical interdependencies. We present ARTEMIS, a no-code evolutionary optimization platform that jointly optimizes agent configurations through semantically-aware genetic operators. Given only a benchmark script and natural language goals, ARTEMIS automatically discovers configurable components, extracts performance signals from execution logs, and evolves configurations without requiring architectural modifications. We evaluate ARTEMIS on four representative agent systems: the \emph{ALE Agent} for competitive programming on AtCoder Heuristic Contest, achieving a \textbf{$13.6\%$ improvement} in acceptance rate; the \emph{Mini-SWE Agent} for code optimization on SWE-Perf, with a statistically significant \textbf{10.1\% performance gain}; and the \emph{CrewAI Agent} for cost and mathematical reasoning on Math Odyssey, achieving a statistically significant \textbf{$36.9\%$ reduction} in the number of tokens required for evaluation. We also evaluate the \emph{MathTales-Teacher Agent} powered by a smaller open-source model (Qwen2.5-7B) on GSM8K primary-level mathematics problems, achieving a \textbf{22\% accuracy improvement} and demonstrating that ARTEMIS can optimize agents based on both commercial and local models.

cs.SE

Self-regulated emergence of heavy-tailed weight distributions in evolving complex network architectures

The nervous system continuously adjusts connection strengths and reorganizes its structure to form and maintain complex connectivity patterns with heavy-tailed weight distributions. We propose a parsimonious model in which structural and synaptic plasticity are driven by common diffusion dynamics. Synaptic plasticity alone generates heavy-tailed weight distributions, but only when activity spreading remains predominantly local. However, when combined with structural plasticity through adaptive rewiring, the model also generates these distributions with more extensive activity flow. Furthermore, adaptive rewiring produces complex network structures with convergent-divergent circuits. These circuits contain motifs that are pervasive in nervous systems and are responsible for context-sensitive signal propagation and enhanced signal to noise ratios. Our model robustly reproduces these results across diverse dynamical regimes while capturing key connectivity features of both C. elegans and mouse brain networks. These findings suggest that the underlying principles are shared across species of varying complexity.

q-bio.NC

Applied Antifragility in Natural Systems: Evolutionary Antifragility

This chapter introduces evolutionary antifragility as the time-scale interaction characteristics of a natural dynamic system. It describes the benefit derived from input distribution unevenness, based on the emergent system dynamics and its uncertain and volatile interactions with the operating environment described by unknown disturbances. We consider methods for the detection, analysis, and modelling of cancer, environmental, microbiota, and social systems antifragility. This is a preprint of the following work Cristian Axenie, Roman Bauer, Oliver Lopez Corona, Jeffrey West, Applied Antifragility in Natural Systems From Principles to Applications, Springer Nature reproduced with the permissions of Springer Nature. The final authenticated version is available online at https://link.springer.com/book/9783031903908

q-bio.PE

Calibration of stochastic, agent-based neuron growth models with Approximate Bayesian Computation

Understanding how genetically encoded rules drive and guide complex neuronal growth processes is essential to comprehending the brain's architecture, and agent-based models (ABMs) offer a powerful simulation approach to further develop this understanding. However, accurately calibrating these models remains a challenge. Here, we present a novel application of Approximate Bayesian Computation (ABC) to address this issue. ABMs are based on parametrized stochastic rules that describe the time evolution of small components -- the so-called agents -- discretizing the system, leading to stochastic simulations that require appropriate treatment. Mathematically, the calibration defines a stochastic inverse problem. We propose to address it in a Bayesian setting using ABC. We facilitate the repeated comparison between data and simulations by quantifying the morphological information of single neurons with so-called morphometrics and resort to statistical distances to measure discrepancies between populations thereof. We conduct experiments on synthetic as well as experimental data. We find that ABC utilizing Sequential Monte Carlo sampling and the Wasserstein distance finds accurate posterior parameter distributions for representative ABMs. We further demonstrate that these ABMs capture specific features of pyramidal cells of the hippocampus (CA1). Overall, this work establishes a robust framework for calibrating agent-based neuronal growth models and opens the door for future investigations using Bayesian techniques for model building, verification, and adequacy assessment.

cs.CE

Recipes for calibration and validation of agent-based models in cancer biomedicine

Computational models and simulations are not just appealing because of their intrinsic characteristics across spatiotemporal scales, scalability, and predictive power, but also because the set of problems in cancer biomedicine that can be addressed computationally exceeds the set of those amenable to analytical solutions. Agent-based models and simulations are especially interesting candidates among computational modelling strategies in cancer research due to their capabilities to replicate realistic local and global interaction dynamics at a convenient and relevant scale. Yet, the absence of methods to validate the consistency of the results across scales can hinder adoption by turning fine-tuned models into black boxes. This review compiles relevant literature to explore strategies to leverage high-fidelity simulations of multi-scale, or multi-level, cancer models with a focus on validation approached as simulation calibration. We argue that simulation calibration goes beyond parameter optimization by embedding informative priors to generate plausible parameter configurations across multiple dimensions.

q-bio.TO

BioDynaMo: a general platform for scalable agent-based simulation

Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results: We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a general-purpose and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology, and epidemiology. For each use case we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baseline. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research. Availability: BioDynaMo is an open-source project under the Apache 2.0 license and is available at www.biodynamo.org. Instructions to reproduce the results are available in supplementary information. Contact: lukas.breitwieser@inf.ethz.ch, a.s.hesam@tudelft.nl, omutlu@ethz.ch, r.bauer@surrey.ac.uk Supplementary information: Available at https://doi.org/10.5281/zenodo.4501515

cs.CE

Quantitative disentanglement of coherent and incoherent laser-induced surface deformations by time-resolved x-ray reflectivity

We present time-resolved x-ray reflectivity measurements on laser excited coherent and incoherent surface deformations of thin metallic films. Based on a kinematical diffraction model, we derive the surface amplitude from the diffracted x-ray intensity and resolve transient surface excursions with sub-Angstrom spatial precision and 70 ps temporal resolution. The novel analysis allows for decomposition of the surface amplitude into multiple coherent acoustic modes and a substantial contribution from incoherent phonons which constitute the sample heating.

cond-mat.mtrl-sci

The KdV, the Burgers, and the Whitham limit for a spatially periodic Boussinesq model

We are interested in the Korteweg-de Vries (KdV), the Burgers, and the Whitham limit for a spatially periodic Boussinesq model with non-small contrast. We prove estimates between the KdV, the Burgers, and the Whitham approximation and true solutions of the original system which guarantee that these amplitude equations make correct predictions about the dynamics of the spatially periodic Boussinesq model over the natural time scales of the amplitude equations. The proof is based on Bloch wave analysis and energy estimates. The result is the first justification result of the KdV, the Burgers, and the Whitham approximation for a dispersive PDE posed in a spatially periodic medium of non-small contrast.

math.AP

The BioDynaMo Project: Creating a Platform for Large-Scale Reproducible Biological Simulations

Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be executable on hybrid cloud computing systems. This paper describes challenges and lessons learnt during the early stages of the software development process, in the context of implementation issues and the international nature of the collaboration.

cs.DC

The BioDynaMo Project

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems (such as the human brain) comprise an extremely complex organization and heterogeneous interactions across different spatial and temporal scales. In order to facilitate research on such problems, the BioDynaMo project (\url{https://biodynamo.web.cern.ch/}) aims at a general platform for computer simulations for biological research. Since the scientific investigations require extensive computer resources, this platform should be executable on hybrid cloud computing systems, allowing for the efficient use of state-of-the-art computing technology. This paper describes challenges during the early stages of the software development process. In particular, we describe issues regarding the implementation and the highly interdisciplinary as well as international nature of the collaboration. Moreover, we explain the methodologies, the approach, and the lessons learnt by the team during these first stages.

cs.NE

A Computational Model Incorporating Neural Stem Cell Dynamics Reproduces Glioma Incidence across the Lifespan in the Human Population

Glioma is the most common form of primary brain tumor. Demographically, the risk of occurrence increases until old age. Here we present a novel computational model to reproduce the probability of glioma incidence across the lifespan. Previous mathematical models explaining glioma incidence are framed in a rather abstract way, and do not directly relate to empirical findings. To decrease this gap between theory and experimental observations, we incorporate recent data on cellular and molecular factors underlying gliomagenesis. Since evidence implicates the adult neural stem cell as the likely cell-of-origin of glioma, we have incorporated empirically-determined estimates of neural stem cell number, cell division rate, mutation rate and oncogenic potential into our model. We demonstrate that our model yields results which match actual demographic data in the human population. In particular, this model accounts for the observed peak incidence of glioma at approximately 80 years of age, without the need to assert differential susceptibility throughout the population. Overall, our model supports the hypothesis that glioma is caused by randomly-occurring oncogenic mutations within the neural stem cell population. Based on this model, we assess the influence of the (experimentally indicated) decrease in the number of neural stem cells and increase of cell division rate during aging. Our model provides multiple testable predictions, and suggests that different temporal sequences of oncogenic mutations can lead to tumorigenesis. Finally, we conclude that four or five oncogenic mutations are sufficient for the formation of glioma.

q-bio.CB