Agentic Publications: An LLM-Driven Framework for Interactive Scientific Publishing, Supplementing Traditional Papers with AI-Powered Knowledge Systems

The exponential growth of scientific literature presents significant challenges for researchers navigating the complex knowledge landscape. We propose "Agentic Publications", a novel LLM-driven framework complementing traditional publishing by transforming papers into interactive knowledge systems. Our architecture integrates structured data with unstructured content through retrieval-augmented generation and multi-agent verification. The framework offers interfaces for both humans and machines, combining narrative explanations with machine-readable outputs while addressing ethical considerations through automated validation and transparent governance. Key features include continuous knowledge updates, automatic integration of new findings, and customizable detail levels. Our proof-of-concept demonstrates multilingual interaction, API accessibility, and structured knowledge representation through vector databases, knowledge graphs, and verification agents. This approach enhances scientific communication across disciplines, improving efficiency and collaboration while preserving traditional publishing pathways, particularly valuable for interdisciplinary fields where knowledge integration remains challenging.

Three-dimensional coherent diffraction snapshot imaging using extreme ultraviolet radiation from a free electron laser

The possibility to obtain a three-dimensional representation of a single object with sub-$\mu$m resolution is crucial in many fields, from material science to clinical diagnostics. This is typically achieved through tomography, which combines multiple two-dimensional images of the same object captured at different orientations. However, this serial imaging method prevents single-shot acquisition in imaging experiments at free electron lasers. In the present experiment, we report on a new approach to 3D imaging using extreme-ultraviolet radiation. In this method, two EUV pulses hit simultaneously an isolated 3D object from different sides, generating independent coherent diffraction patterns, resulting in two distinct bidimensional views obtained via phase retrieval. These views are then used to obtain a 3D reconstruction using a ray tracing algorithm. This EUV stereoscopic imaging approach, similar to the natural process of binocular vision, provides sub-$\mu$m spatial resolution and single shot capability. Moreover, ultrafast time resolution and spectroscopy can be readily implemented, a further extension to X-ray wavelengths can be envisioned as well.

A modular software framework for the design and implementation of ptychography algorithms

Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware programming constructs to speed up the reconstruction. In this paper, we present SciComPty, a new ptychography software framework aiming at simulating ptychography datasets and testing state-of-the-art and new reconstruction algorithms. Despite its simplicity, the software leverages GPU accelerated processing through the PyTorch CUDA interface. This is essential to design new methods that can readily be employed. As an example, we present an improved position refinement method based on Adam and a new version of the rPIE algorithm, adapted for partial coherence setups. Results are shown on both synthetic and real datasets. The software is released as open-source.

A parameter refinement method for Ptychography based on Deep Learning concepts

X-ray Ptychography is an advanced computational microscopy technique which is delivering exceptionally detailed quantitative imaging of biological and nanotechnology specimens. However coarse parametrisation in propagation distance, position errors and partial coherence frequently menaces the experiment viability. In this work we formally introduced these actors, solving the whole reconstruction as an optimisation problem. A modern Deep Learning framework is used to correct autonomously the setup incoherences, thus improving the quality of a ptychography reconstruction. Automatic procedures are indeed crucial to reduce the time for a reliable analysis, which has a significant impact on all the fields that use this kind of microscopy. We implemented our algorithm in our software framework, SciComPty, releasing it as open-source. We tested our system on both synthetic datasets and also on real data acquired at the TwinMic beamline of the Elettra synchrotron facility.