arXiv subjects

Daniel Adams

Publications and source records attributed to Daniel Adams.

8 recordsLinked to original sources

arXiv2025

Leveraging large language models for structured information extraction from pathology reports

Background: Structured information extraction from unstructured histopathology reports facilitates data accessibility for clinical research. Manual extraction by experts is time-consuming and expensive, limiting scalability. Large language models (LLMs) offer efficient automated extraction through zero-shot prompting, requiring only natural language instructions without labeled data or training. We evaluate LLMs' accuracy in extracting structured information from breast cancer histopathology reports, compared to manual extraction by a trained human annotator. Methods: We developed the Medical Report Information Extractor, a web application leveraging LLMs for automated extraction. We developed a gold standard extraction dataset to evaluate the human annotator alongside five LLMs including GPT-4o, a leading proprietary model, and the Llama 3 model family, which allows self-hosting for data privacy. Our assessment involved 111 histopathology reports from the Breast Cancer Now (BCN) Generations Study, extracting 51 pathology features specified in the study's data dictionary. Results: Evaluation against the gold standard dataset showed that both Llama 3.1 405B (94.7% accuracy) and GPT-4o (96.1%) achieved extraction accuracy comparable to the human annotator (95.4%; p = 0.146 and p = 0.106, respectively). While Llama 3.1 70B (91.6%) performed below human accuracy (p <0.001), its reduced computational requirements make it a viable option for self-hosting. Conclusion: We developed an open-source tool for structured information extraction that can be customized by non-programmers using natural language. Its modular design enables reuse for various extraction tasks, producing standardized, structured data from unstructured text reports to facilitate analytics through improved accessibility and interoperability.

cs.CL↗

arXiv2025

Self-interfering high harmonic beam arrays driven by Hermite-Gaussian beams

The use of structured light to drive highly nonlinear processes in matter not only enables imprinting spatially-resolved properties onto short-wavelength radiation, but also opens alternative avenues for exploring the dynamics of nonlinear laser-matter interactions. In this work, we experimentally and theoretically explore the unique properties of driving high-order harmonic generation (HHG) with Hermite-Gaussian beams. HHG driven by Laguerre-Gauss modes results in harmonics that inherit the azimuthal Laguerre-Gauss modal structure, with their topological charge scaling according to orbital angular momentum conservation. In contrast, when HHG is driven by Hermite-Gauss beams, the harmonic modes do not show a direct correspondence to the driving modal profile. Our experimental measurements using HG$_{0,1}$ and HG$_{1,1}$ modes, which are in excellent agreement with our numerical simulations, show that the lobes of the Hermite-Gauss driving beams effectively produce a set of separate phase-locked harmonic beamlets which can interfere downstream. This self-interference, which can be adjusted through the relative position between the gas target and the driving beam focus, can be exploited for precision extreme-ultraviolet interferometry. We demonstrate a simple application to calibrate the dispersion of an extreme-ultraviolet diffraction grating. In addition, we show through simulations that the array of harmonic beamlets can be used as an illumination source for single-shot extreme-ultraviolet ptychography.

physics.optics↗

arXiv2024

Attosecond vortex pulse trains

The landscape of ultrafast structured light pulses has recently evolved driven by the capability of high-order harmonic generation (HHG) to up-convert orbital angular momentum (OAM) from the infrared to the extreme-ultraviolet (EUV) spectral regime. Accordingly, HHG has been proven to produce EUV vortex pulses at the femtosecond timescale. Here we demonstrate the generation of attosecond vortex pulse trains, i.e. a succession of attosecond pulses with a helical wavefront, resulting from the synthesis of a comb of EUV high-order harmonics with the same OAM. By driving HHG with a polarization tilt-angle fork grating, two spatially separated circularly polarized high-order harmonic beams with order-independent OAM are created. Our work opens the route towards attosecond-resolved OAM light-matter interactions.

physics.optics↗

arXiv2023

Second Class Particle Behaviour in Blocking ASEP

We consider any fixed $d\in\mathbb{Z}_{>0}$ number of second class particles in the asymmetric simple exclusion process (ASEP), constructed via a basic coupling of two ASEPs. We give the joint distribution of the positions of the second class particles and also the probability of there being a second class particle at a given site, under the natural blocking measure for ASEP. In order to find these distributions we use results about the number of particles in half-infinite and finite site ranges of ASEP. Our investigations also lead to probabilistic proofs of well-known combinatorial identities; the Durfee rectangles identity, Euler's identity, and the $q$-Binomial Theorem.

math.PR↗

arXiv2021

Operator-splitting schemes for degenerate, non-local, conservative-dissipative systems

In this paper, we develop a natural operator-splitting variational scheme for a general class of non-local, degenerate conservative-dissipative evolutionary equations. The splitting-scheme consists of two phases: a conservative (transport) phase and a dissipative (diffusion) phase. The first phase is solved exactly using the method of characteristic and DiPerna-Lions theory while the second phase is solved approximately using a JKO-type variational scheme that minimizes an energy functional with respect to a certain Kantorovich optimal transport cost functional. In addition, we also introduce an entropic-regularisation of the scheme. We prove the convergence of both schemes to a weak solution of the evolutionary equation. We illustrate the generality of our work by providing a number of examples, including the kinetic Fokker-Planck equation and the (regularized) Vlasov-Poisson-Fokker-Planck equation.

math.AP↗

arXiv2021

Entropic regularisation of non-gradient systems

The theory of Wasserstein gradient flows in the space of probability measures has made an enormous progress over the last twenty years. It constitutes a unified and powerful framework in the study of dissipative partial differential equations (PDEs) providing the means to prove well-posedness, regularity, stability and quantitative convergence to the equilibrium. The recently developed entropic regularisation technique paves the way for fast and efficient numerical methods for solving these gradient flows. However, many PDEs of interest do not have a gradient flow structure and, a priori, the theory is not applicable. In this paper, we develop a time-discrete entropy regularised variational scheme for a general class of such non-gradient PDEs. We prove the convergence of the scheme and illustrate the breadth of the proposed framework with concrete examples including the non-linear kinetic Fokker-Planck (Kramers) equation and a non-linear degenerate diffusion of Kolmogorov type. Numerical simulations are also provided.

math.AP↗

arXiv2020

Wavelength-multiplexed single-shot ptychography

Diagnostics capable of interrogating dynamics in harsh environments such as plasma have remained essentially unchanged in recent decades. Developments in advanced microscopy techniques will improve our understanding of the physics involved in these events. Recently developed single-shot ptychography (SSP) provides a pathway towards sophisticated plasma metrologies. Here we introduce wavelength-multiplexed single-shot ptychography (WM-SSP), which allows for hyperspectral, spatially and temporally resolved phase and amplitude contrast imaging. Furthermore, we introduce a novel probe constraint common to all wavelength multiplexed modalities in the single-shot geometry and present modifications to SSP that improve reconstruction fidelity and robustness. WM-SSP was experimentally realized and simulations show the technique's ability to deconvolve the electron and neutral densities within the plasma. WM-SSP will pave the way to a new generation of quantitative plasma imaging techniques.

physics.optics↗

arXiv2020

Large Deviations and Exit-times for reflected McKean-Vlasov equations with self-stabilizing terms and superlinear drifts

We study a class of reflected McKean-Vlasov diffusions over a convex domain with self-stabilizing coefficients. This includes coefficients that do not satisfy the classical Wasserstein Lipschitz condition. Further, the process is constrained to a (not necessarily bounded) convex domain by a local time on the boundary. These equations include the subclass of reflected self-stabilizing diffusions that drift towards their mean via a convolution of the solution law with a stabilizing potential. Firstly, we establish existence and uniqueness results for this class and address the propagation of chaos. We work with a broad class of coefficients, including drift terms that are locally Lipschitz in spatial and measure variables. However, we do not rely on the boundedness of the domain or the coefficients to account for these non-linearities and instead use the self-stabilizing properties. We prove a Freidlin-Wentzell type Large Deviations Principle and an Eyring-Kramer's law for the exit-time from subdomains contained in the interior of the reflecting domain.

math.PR↗