arXiv subjects

Benjamin Davis

Publications and source records attributed to Benjamin Davis.

6 recordsLinked to original sources

arXiv2026

Statistical methods for reference-free single-molecule localisation microscopy

MINFLUX (Minimal Photon Flux) is a single-molecule imaging technique capable of resolving fluorophores at a precision of <5 nm. Interpretation of the point patterns generated by this technique presents challenges due to variable emitter density, incomplete bio-labelling of target molecules and their detection, error prone measurement processes, and the presence of spurious (non-structure associated) fluorescent detections. Together, these challenges ensure structural inferences from single-molecule imaging datasets are non-trivial in the absence of strong a priori information, for all but the smallest of point patterns. In addition, current methods often require subjective parameter tuning and presuppose known structural templates, limiting reference-free discovery. We present a statistically grounded, end-to-end analysis framework. Focusing on MINFLUX derived datasets and leveraging Bayesian and spatial statistical methods, a pipeline is presented that demonstrates 1) uncertainty aware clustering of measurements into emitter groups that performs better than current gold standards, 2) rapid identification of molecular structure supergroups, and 3) reconstruction of repeating structures within the dataset without substantial prior knowledge. This pipeline is demonstrated using simulated and real MINFLUX datasets, where emitter clustering and centre detection maintain high performance (emitter subset assignment accuracy > 0.75) across all conditions evaluated, while structural inference achieves reliable discrimination (F1 approx. 0.9) at high labelling efficiency. Template-free reconstruction of Nup96 and DNA-Origami 3x3 grids are achieved.

stat.AP↗

arXiv2026

An extension to reversible jump Markov chain Monte Carlo for change point problems with heterogeneous temporal dynamics

Detecting brief changes in time-series data remains a major challenge in fields where short-lived states carry meaning. In single-molecule localisation microscopy, this problem is particularly acute as fluorescent molecules used to tag protein oligomers display heterogenous photophysical behaviour that can complicate photobleach step analysis; a key step in resolving nanoscale protein organisation. Existing methods often require extensive filtering or prior calibration, and can fail to accurately account for blinking or reversible dark states that may contaminate downstream analysis. In this paper, an extension to RJMCMC is proposed for change point detection with heterogeneous temporal dynamics. This approach is applied to the problem of estimating per-frame active fluorophore counts from one-dimensional integrated intensity traces derived from Fluorescence Localisation Imaging with Photobleaching (FLImP), where compound change point pair moves are introduced to better account for short-lived events known as blinking and dark states. The approach is validated using simulated and experimental data, demonstrating improved accuracy and robustness when compared with current photobleach step analysis methods and with the existing analysis approach for FLImP data. This Compound RJMCMC (CRJMCMC) algorithm performs reliably across a wide range of fluorophore counts and signal-to-noise conditions, with signal-to-noise ratio (SNR) down to 0.001 and counts as high as nineteen fluorophores, while also effectively estimating low counts observed when studying EGFR oligomerisation. Beyond single molecule imaging, this work has applications for a variety of time series change point detection problems with heterogeneous state persistence. For example, electrocorticography brain-state segmentation, fault detection in industrial process monitoring and realised volatility in financial time series.

stat.ME↗

arXiv2025

Characterizing the Resilience and Sensitivity of Polyurethane Vision-Based Tactile Sensors

Vision-based tactile sensors (VBTSs) are a promising technology for robots, providing them with dense signals that can be translated into a multi-faceted understanding of contact. However, existing VBTS tactile surfaces make use of silicone gels, which provide high sensitivity but easily deteriorate from loading and surface wear. We propose that polyurethane rubber, a typically harder material used for high-load applications like shoe soles, rubber wheels, and industrial gaskets, may provide improved physical gel resilience, potentially at the cost of sensitivity. To compare the resilience and sensitivity of two polyurethane gel formulations against a common silicone baseline, we propose a series of repeatable characterization protocols. Our resilience tests assess sensor durability across normal loading, shear loading, and abrasion. For sensitivity, we introduce learning-free assessments of force and spatial sensitivity to directly measure the physical capabilities of each gel without effects introduced from data and model quality. We also include a bottle cap loosening and tightening demonstration to validate the results of our controlled tests with a real-world example. Our results show that polyurethane yields a more robust sensor. While it sacrifices sensitivity at low forces, the effective force range is largely increased, revealing the utility of polyurethane VBTSs over silicone versions in more rugged, high-load applications.

cs.RO↗

arXiv2024

AI-AI Bias: large language models favor communications generated by large language models

Are large language models (LLMs) biased in favor of communications produced by LLMs, leading to possible antihuman discrimination? Using a classical experimental design inspired by employment discrimination studies, we tested widely used LLMs, including GPT-3.5, GPT-4 and a selection of recent open-weight models in binary choice scenarios. These involved LLM-based assistants selecting between goods (the goods we study include consumer products, academic papers, and film-viewings) described either by humans or LLMs. Our results show a consistent tendency for LLM-based AIs to prefer LLM-presented options. This suggests the possibility of future AI systems implicitly discriminating against humans as a class, giving AI agents and AI-assisted humans an unfair advantage.

cs.CL↗

arXiv2024

Macaw: A Machine Code Toolbox for the Busy Binary Analyst

When attempting to understand the behavior of an executable, a binary analyst can make use of many different techniques. These include program slicing, dynamic instrumentation, binary-level rewriting, symbolic execution, and formal verification, all of which can uncover insights into how a piece of machine code behaves. As a result, there is no one-size-fits-all binary analysis tool, so a binary analysis researcher will often combine several different tools. Sometimes, a researcher will even need to design new tools to study problems that existing frameworks are not well equipped to handle. Designing such tools from complete scratch is rarely time- or cost-effective, however, given the scale and complexity of modern ISAs. We present Macaw, a modular framework that makes it possible to rapidly build reliable binary analysis tools across a range of use cases. Statically typed functional programming techniques are used pervasively throughout Macaw -- these range from using functional optimization passes to encoding tricky architectural invariants at the type level to statically check correctness properties. The level of assurance that functional programming ideas afford us allow us to iterate rapidly on Macaw while still having confidence that the underlying semantics are correct. Over a decade of development, we have used Macaw to support an industrial research team in building tools for machine code-related tasks. As such, the name 'Macaw' refers not just to the framework, but also a suite of tools that are built on top of it. We describe Macaw in depth and describe the different static and dynamic analyses that it performs, many powered by an SMT-based symbolic execution engine. We put a particular focus on interoperability between machine code and higher-level languages, including binary lifting from x86 to LLVM, as well verifying the correctness of mixed C and assembly code.

cs.PL↗

arXiv2020

Cm2 Scale Synthesis of MoTe2 Thin Films with Large Grains and Layer Control David

Owing to the small energy differences between its polymorphs, MoTe2 can access a full spectrum of electronic states, from the 2H semiconducting state to the 1T semimetallic state, and from the Td Weyl semimetallic state to the superconducting state in the 1T and Td phase at low temperature. Thus, it is a model system for phase transformation studies as well as quantum phenomena such as the quantum spin Hall effect and topological superconductivity. Careful studies of MoTe2 and its potential applications require large area MoTe2 thin films with high crystallinity and thickness control. Here, we present cm2 scale synthesis of 2H MoTe2 thin films with layer control and large grains that span several microns. Layer control is achieved by controlling the initial thickness of the precursor MoOx thin films, which are deposited on sapphire substrates by atomic layer deposition and subsequently tellurized. Despite the van der Waals epitaxy, the precursor-substrate interface is found to critically determine the uniformity in thickness and grain size of the resulting MoTe2 films: MoTe2 grown on sapphire show uniform films while MoTe2 grown on amorphous SiO2 substrates form islands. This synthesis strategy decouples the layer control from the variabilities of growth conditions for robust growth results, and is applicable to grow other transition metal dichalcogenides with layer control.

cond-mat.mtrl-sci↗