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We provide the first method allowing to retrieve spaceborne SIF maps at 30 m ground resolution with a strong correlation ($r^2=0.6$) to high-quality airborne estimates of sun-induced fluorescence (SIF). SIF estimates can provide explanatory information for many tasks related to agricultural management and physiological studies. While SIF products from airborne platforms are accurate and spatially well resolved, the data acquisition of such products remains science-oriented and limited to temporally constrained campaigns. Spaceborne SIF products on the other hand are available globally with often sufficient revisit times. However, the spatial resolution of spaceborne SIF products is too small for agricultural applications. In view of ESA's upcoming FLEX mission we develop a method for SIF retrieval in the O$_2$-A band of hyperspectral DESIS imagery to provide first insights for spaceborne SIF retrieval at high spatial resolution. To this end, we train a simulation-based self-supervised network with a novel perturbation based regularizer and test performance improvements under additional supervised regularization of atmospheric variable prediction. In a validation study with corresponding HyPlant derived SIF estimates at 740 nm we find that our model reaches a mean absolute difference of 0.78 mW / nm / sr / m$^2$., Comment: submitted to ECCV CVPPA 2024, 14 pages, 8 figures

The growing volume of biomedical scholarly document abstracts presents an increasing challenge in efficiently retrieving accurate and relevant information. To address this, we introduce a novel approach that integrates an optimized topic modelling framework, OVB-LDA, with the BI-POP CMA-ES optimization technique for enhanced scholarly document abstract categorization. Complementing this, we employ the distilled MiniLM model, fine-tuned on domain-specific data, for high-precision answer extraction. Our approach is evaluated across three configurations: scholarly document abstract retrieval, gold-standard scholarly documents abstract, and gold-standard snippets, consistently outperforming established methods such as RYGH and bio-answer finder. Notably, we demonstrate that extracting answers from scholarly documents abstracts alone can yield high accuracy, underscoring the sufficiency of abstracts for many biomedical queries. Despite its compact size, MiniLM exhibits competitive performance, challenging the prevailing notion that only large, resource-intensive models can handle such complex tasks. Our results, validated across various question types and evaluation batches, highlight the robustness and adaptability of our method in real-world biomedical applications. While our approach shows promise, we identify challenges in handling complex list-type questions and inconsistencies in evaluation metrics. Future work will focus on refining the topic model with more extensive domain-specific datasets, further optimizing MiniLM and utilizing large language models (LLM) to improve both precision and efficiency in biomedical question answering.

Purpose: To present a novel generalized MR image reconstruction based on pseudoinversion of the encoding matrix (Pinv-Recon) as a simple yet powerful method, and demonstrate its computational feasibility for diverse MR imaging applications. Methods: MR image encoding constitutes a linear mapping of the unknown image to the measured k-space data mediated via an encoding matrix ($ data = Encode \times image$). Pinv-Recon addresses MR image reconstruction as a linear inverse problem ($image = Encode^{-1} \times data$), explicitly calculating the Moore-Penrose pseudoinverse of the encoding matrix using truncated singular value decomposition (tSVD). Using a discretized, algebraic notation, we demonstrate constructing a generalized encoding matrix by stacking relevant encoding mechanisms (e.g., gradient encoding, coil sensitivity encoding, chemical shift inversion) and encoding distortions (e.g., off-center positioning, B$_0$ inhomogeneity, spatiotemporal gradient imperfections, transient relaxation effects). Iterative reconstructions using the explicit generalized encoding matrix, and the computation of the spatial-response-function (SRF) and noise amplification, were demonstrated. Results: We evaluated the computation times and memory requirements (time ~ (size of the encoding matrix)$^{1.4}$). Using the Shepp-Logan phantom, we demonstrated the versatility of the method for various intertwined MR image encoding and distortion mechanisms, achieving better MSE, PSNR and SSIM metrics than conventional methods. A diversity of datasets, including the ISMRM CG-SENSE challenge, were used to validate Pinv-Recon. Conclusion: Although pseudo-inversion of large encoding matrices was once deemed computationally intractable, recent advances make Pinv-Recon feasible. It has great promise for both research and clinical applications, and for educational use., Comment: 26 pages, 8 figures, 2 tables (+ Supplementary Material). Submitted to Magnetic Resonance in Medicine

In response to the growing complexity and volume of scientific literature, this paper introduces the LLMs4Synthesis framework, designed to enhance the capabilities of Large Language Models (LLMs) in generating high-quality scientific syntheses. This framework addresses the need for rapid, coherent, and contextually rich integration of scientific insights, leveraging both open-source and proprietary LLMs. It also examines the effectiveness of LLMs in evaluating the integrity and reliability of these syntheses, alleviating inadequacies in current quantitative metrics. Our study contributes to this field by developing a novel methodology for processing scientific papers, defining new synthesis types, and establishing nine detailed quality criteria for evaluating syntheses. The integration of LLMs with reinforcement learning and AI feedback is proposed to optimize synthesis quality, ensuring alignment with established criteria. The LLMs4Synthesis framework and its components are made available, promising to enhance both the generation and evaluation processes in scientific research synthesis., Comment: 12 pages, 3 figures, Accepted to JCDL 2024 Research Track

This paper outlines the LLMs4OL 2024, the first edition of the Large Language Models for Ontology Learning Challenge. LLMs4OL is a community development initiative collocated with the 23rd International Semantic Web Conference (ISWC) to explore the potential of Large Language Models (LLMs) in Ontology Learning (OL), a vital process for enhancing the web with structured knowledge to improve interoperability. By leveraging LLMs, the challenge aims to advance understanding and innovation in OL, aligning with the goals of the Semantic Web to create a more intelligent and user-friendly web. In this paper, we give an overview of the 2024 edition of the LLMs4OL challenge and summarize the contributions., Comment: 15 pages, 1 figure, Will appear in "The 1st LLMs4OL Challenge @ ISWC 2024" proceedings

The increasing amount of published scholarly articles, exceeding 2.5 million yearly, raises the challenge for researchers in following scientific progress. Integrating the contributions from scholarly articles into a novel type of cognitive knowledge graph (CKG) will be a crucial element for accessing and organizing scholarly knowledge, surpassing the insights provided by titles and abstracts. This research focuses on effectively conveying structured scholarly knowledge by utilizing large language models (LLMs) to categorize scholarly articles and describe their contributions in a structured and comparable manner. While previous studies explored language models within specific research domains, the extensive domain-independent knowledge captured by LLMs offers a substantial opportunity for generating structured contribution descriptions as CKGs. Additionally, LLMs offer customizable pathways through prompt engineering or fine-tuning, thus facilitating to leveraging of smaller LLMs known for their efficiency, cost-effectiveness, and environmental considerations. Our methodology involves harnessing LLM knowledge, and complementing it with domain expert-verified scholarly data sourced from a CKG. This strategic fusion significantly enhances LLM performance, especially in tasks like scholarly article categorization and predicate recommendation. Our method involves fine-tuning LLMs with CKG knowledge and additionally injecting knowledge from a CKG with a novel prompting technique significantly increasing the accuracy of scholarly knowledge extraction. We integrated our approach in the Open Research Knowledge Graph (ORKG), thus enabling precise access to organized scholarly knowledge, crucially benefiting domain-independent scholarly knowledge exchange and dissemination among policymakers, industrial practitioners, and the general public.

While the power of quantum computers is commonly acknowledged to rise exponentially, it is often overlooked that the complexity of quantum noise mechanisms generally grows much faster. In particular, quantifying whether the instructions on a quantum processor are close to being unitary has important consequences concerning error rates, e.g., for the confidence in their estimation, the ability to mitigate them efficiently, or their relation to fault-tolerance thresholds in error correction. However, the complexity of estimating the coherence, or unitarity, of noise generally scales exponentially in system size. Here, we obtain an upper bound on the average unitarity of Pauli noise and develop a protocol allowing us to estimate the average unitarity of operations in a digital quantum device efficiently and feasibly for mid-size quantum systems. We demonstrate our results through both experimental execution on IQM Spark (TM), a 5-qubit superconducting quantum computer, and in simulation with up to 10 qubits, discussing the prospects for extending our technique to arbitrary scales., Comment: 11+21 pages, 10 figures

The celebrated Birkhoff Ergodic Theorem asserts that, for an ergodic map, orbits of almost every point equidistributes when sampled at integer times. This result was generalized by Bourgain to many natural sparse subsets of the integers. On the other hand, the behaviour of orbits of \textbf{all} points in a dynamical system is much less understood, especially for sparse subsets of the integers. We generalize a method introduced by A. Venkatesh to tackle this problem in two directions, general $\mathbb{R}^d$ actions instead of flows, and weak mixing, rather than mixing, actions. Along the way, we also establish some basic properties of weak mixing and show weak mixing for the time 1-map of a weak mixing flow. The main examples are equidistribution along $\{(n^{1+\epsilon_i})_{i=1}^d\}$, which is a direct generalisation of Venkatesh's example, and equidistribution along random subsets of $\mathbb{Z}^d$ for horosperical action., Comment: 45 pages, no figures, comments are welcome!

This technical report introduces Docling, an easy to use, self-contained, MIT-licensed open-source package for PDF document conversion. It is powered by state-of-the-art specialized AI models for layout analysis (DocLayNet) and table structure recognition (TableFormer), and runs efficiently on commodity hardware in a small resource budget. The code interface allows for easy extensibility and addition of new features and models.

After some normalization, the logarithms of the ordered singular values of Brownian motions on $GL(N,\mathbb F)$ with $\mathbb F=\mathbb R, \mathbb C$ form Weyl-group invariant Heckman-Opdam processes on $\mathbb R^N$ of type $A_{N-1}$. We use classical elementary formulas for the spherical functions of $GL(N,\mathbb C)/SU(N)$ and the associated Euclidean spaces $H(N,\mathbb C)$ of Hermitian matrices, and show that in the $GL(N,\mathbb C)$-case, these processes can be also interpreted as ordered eigenvalues of Brownian motions on $H(N,\mathbb C)$ with particular drifts. This leads to an explicit description for the free limits for the associated empirical processes for $N\to\infty$ where these limits are independent from the parameter $k$ of the Heckman-Opdam processes. In particular we get new formulas for the distributions of the free multiplicative Browniam motion of Biane. We also show how this approach works for the root systems $B_N, C_N, D_N$.

Authoring survey or review articles still requires significant tedious manual effort, despite many advancements in research knowledge management having the potential to improve efficiency, reproducibility, and reuse. However, these advancements bring forth an increasing number of approaches, tools, and systems, which often cover only specific stages and lack a comprehensive workflow utilizing their task-specific strengths. We propose the Streamlined Workflow Automation for Machine-actionable Systematic Literature Reviews (SWARM-SLR) to crowdsource the improvement of SLR efficiency while maintaining scientific integrity in a state-of-the-art knowledge discovery and distribution process. The workflow aims to domain-independently support researchers in collaboratively and sustainably managing the rising scholarly knowledge corpus. By synthesizing guidelines from the literature, we have composed a set of 65 requirements, spanning from planning to reporting a review. Existing tools were assessed against these requirements and synthesized into the SWARM-SLR workflow prototype, a ready-for-operation software support tool. The SWARM-SLR was evaluated via two online surveys, which largely confirmed the validity of the 65 requirements and situated 11 tools to the different life-cycle stages. The SWARM-SLR workflow was similarly evaluated and found to be supporting almost the entire span of an SLR, excelling specifically in search and retrieval, information extraction, knowledge synthesis, and distribution. Our SWARM-SLR requirements and workflow support tool streamlines the SLR support for researchers, allowing sustainable collaboration by linking individual efficiency improvements to crowdsourced knowledge management. If these efforts are continued, we expect the increasing number of tools to be manageable and usable inside fully structured, (semi-)automated literature review workflows., Comment: This preprint has not undergone peer review (when applicable) or any post-submission improvements or corrections

Our study explores how well the state-of-the-art Large Language Models (LLMs), like GPT-4 and Mistral, can assess the quality of scientific summaries or, more fittingly, scientific syntheses, comparing their evaluations to those of human annotators. We used a dataset of 100 research questions and their syntheses made by GPT-4 from abstracts of five related papers, checked against human quality ratings. The study evaluates both the closed-source GPT-4 and the open-source Mistral model's ability to rate these summaries and provide reasons for their judgments. Preliminary results show that LLMs can offer logical explanations that somewhat match the quality ratings, yet a deeper statistical analysis shows a weak correlation between LLM and human ratings, suggesting the potential and current limitations of LLMs in scientific synthesis evaluation., Comment: 4 pages, forthcoming as part of the KONVENS 2024 proceedings https://konvens-2024.univie.ac.at/

This paper introduces a scholarly Question Answering (QA) system on top of the NFDI4DataScience Gateway, employing a Retrieval Augmented Generation-based (RAG) approach. The NFDI4DS Gateway, as a foundational framework, offers a unified and intuitive interface for querying various scientific databases using federated search. The RAG-based scholarly QA, powered by a Large Language Model (LLM), facilitates dynamic interaction with search results, enhancing filtering capabilities and fostering a conversational engagement with the Gateway search. The effectiveness of both the Gateway and the scholarly QA system is demonstrated through experimental analysis., Comment: 13 pages main content, 16 pages overall, 3 Figures, accepted for publication at NSLP 2024 workshop at ESWC 2024

This paper explores the impact of context selection on the efficiency of Large Language Models (LLMs) in generating Artificial Intelligence (AI) research leaderboards, a task defined as the extraction of (Task, Dataset, Metric, Score) quadruples from scholarly articles. By framing this challenge as a text generation objective and employing instruction finetuning with the FLAN-T5 collection, we introduce a novel method that surpasses traditional Natural Language Inference (NLI) approaches in adapting to new developments without a predefined taxonomy. Through experimentation with three distinct context types of varying selectivity and length, our study demonstrates the importance of effective context selection in enhancing LLM accuracy and reducing hallucinations, providing a new pathway for the reliable and efficient generation of AI leaderboards. This contribution not only advances the state of the art in leaderboard generation but also sheds light on strategies to mitigate common challenges in LLM-based information extraction., Comment: arXiv admin note: substantial text overlap with arXiv:2406.04383

The rapid advancements in Large Language Models (LLMs) have opened new avenues for automating complex tasks in AI research. This paper investigates the efficacy of different LLMs-Mistral 7B, Llama-2, GPT-4-Turbo and GPT-4.o in extracting leaderboard information from empirical AI research articles. We explore three types of contextual inputs to the models: DocTAET (Document Title, Abstract, Experimental Setup, and Tabular Information), DocREC (Results, Experiments, and Conclusions), and DocFULL (entire document). Our comprehensive study evaluates the performance of these models in generating (Task, Dataset, Metric, Score) quadruples from research papers. The findings reveal significant insights into the strengths and limitations of each model and context type, providing valuable guidance for future AI research automation efforts.

Access control is the enforcement of the authorization policy, which defines subjects, resources, and access rights. Graph-structured data requires advanced, flexible, and fine-grained access control due to its complex structure as sequences of alternating vertices and edges. Several research works focus on protecting property graph-structured data, enforcing fine-grained access control, and proving the feasibility and applicability of their concept. However, they differ conceptually and technically. We select works from our systematic literature review on authorization and access control for different database models in addition to recent ones. Based on defined criteria, we exclude research works with different objectives, such as no protection of graph-structured data, graph models other than the property graph, coarse-grained access control approaches, or no application in a graph datastore (i.e., no proof-of-concept implementation). The latest version of the remaining works are discussed in detail in terms of their access control approach as well as authorization policy definition and enforcement. Finally, we analyze the strengths and limitations of the selected works and provide a comparison with respect to different aspects, including the base access control model, open/closed policy, negative permission support, and datastore-independent enforcement., Comment: Extended version of an accepted paper at the 21st International Conference on Security and Cryptography (SECRYPT), 2024

Deformable image registration (alignment) is highly sought after in numerous clinical applications, such as computer aided diagnosis and disease progression analysis. Deep Convolutional Neural Network (DCNN)-based image registration methods have demonstrated advantages in terms of registration accuracy and computational speed. However, while most methods excel at global alignment, they often perform worse in aligning local regions. To address this challenge, this paper proposes a mask-guided encoder-decoder DCNN-based image registration method, named as MrRegNet. This approach employs a multi-resolution encoder for feature extraction and subsequently estimates multi-resolution displacement fields in the decoder to handle the substantial deformation of images. Furthermore, segmentation masks are employed to direct the model's attention toward aligning local regions. The results show that the proposed method outperforms traditional methods like Demons and a well-known deep learning method, VoxelMorph, on a public 3D brain MRI dataset (OASIS) and a local 2D brain MRI dataset with large deformations. Importantly, the image alignment accuracies are significantly improved at local regions guided by segmentation masks. Github link:https://github.com/ruizhe-l/MrRegNet., Comment: Accepted for publication at IEEE International Symposium on Biomedical Imaging (ISBI) 2024

In the 1990s, the constant error carousel and gating were introduced as the central ideas of the Long Short-Term Memory (LSTM). Since then, LSTMs have stood the test of time and contributed to numerous deep learning success stories, in particular they constituted the first Large Language Models (LLMs). However, the advent of the Transformer technology with parallelizable self-attention at its core marked the dawn of a new era, outpacing LSTMs at scale. We now raise a simple question: How far do we get in language modeling when scaling LSTMs to billions of parameters, leveraging the latest techniques from modern LLMs, but mitigating known limitations of LSTMs? Firstly, we introduce exponential gating with appropriate normalization and stabilization techniques. Secondly, we modify the LSTM memory structure, obtaining: (i) sLSTM with a scalar memory, a scalar update, and new memory mixing, (ii) mLSTM that is fully parallelizable with a matrix memory and a covariance update rule. Integrating these LSTM extensions into residual block backbones yields xLSTM blocks that are then residually stacked into xLSTM architectures. Exponential gating and modified memory structures boost xLSTM capabilities to perform favorably when compared to state-of-the-art Transformers and State Space Models, both in performance and scaling.

In recent years, the challenge of extracting information from business documents has emerged as a critical task, finding applications across numerous domains. This effort has attracted substantial interest from both industry and academy, highlighting its significance in the current technological landscape. Most datasets in this area are primarily focused on Key Information Extraction (KIE), where the extraction process revolves around extracting information using a specific, predefined set of keys. Unlike most existing datasets and benchmarks, our focus is on discovering key-value pairs (KVPs) without relying on predefined keys, navigating through an array of diverse templates and complex layouts. This task presents unique challenges, primarily due to the absence of comprehensive datasets and benchmarks tailored for non-predetermined KVP extraction. To address this gap, we introduce KVP10k , a new dataset and benchmark specifically designed for KVP extraction. The dataset contains 10707 richly annotated images. In our benchmark, we also introduce a new challenging task that combines elements of KIE as well as KVP in a single task. KVP10k sets itself apart with its extensive diversity in data and richly detailed annotations, paving the way for advancements in the field of information extraction from complex business documents., Comment: accepted ICDAR2024

Ontology Matching (OM), is a critical task in knowledge integration, where aligning heterogeneous ontologies facilitates data interoperability and knowledge sharing. Traditional OM systems often rely on expert knowledge or predictive models, with limited exploration of the potential of Large Language Models (LLMs). We present the LLMs4OM framework, a novel approach to evaluate the effectiveness of LLMs in OM tasks. This framework utilizes two modules for retrieval and matching, respectively, enhanced by zero-shot prompting across three ontology representations: concept, concept-parent, and concept-children. Through comprehensive evaluations using 20 OM datasets from various domains, we demonstrate that LLMs, under the LLMs4OM framework, can match and even surpass the performance of traditional OM systems, particularly in complex matching scenarios. Our results highlight the potential of LLMs to significantly contribute to the field of OM., Comment: 8 pages, 1 figure, accepted to ESWC 2024 Special Track on LLMs for Knowledge Engineering (https://2024.eswc-conferences.org/call-for-papers-llms/)

Search engines these days can serve datasets as search results. Datasets get picked up by search technologies based on structured descriptions on their official web pages, informed by metadata ontologies such as the Dataset content type of schema.org. Despite this promotion of the content type dataset as a first-class citizen of search results, a vast proportion of datasets, particularly research datasets, still need to be made discoverable and, therefore, largely remain unused. This is due to the sheer volume of datasets released every day and the inability of metadata to reflect a dataset's content and context accurately. This work seeks to improve this situation for a specific class of datasets, namely research datasets, which are the result of research endeavors and are accompanied by a scholarly publication. We propose the ORKG-Dataset content type, a specialized branch of the Open Research Knowledge Graoh (ORKG) platform, which provides descriptive information and a semantic model for research datasets, integrating them with their accompanying scholarly publications. This work aims to establish a standardized framework for recording and reporting research datasets within the ORKG-Dataset content type. This, in turn, increases research dataset transparency on the web for their improved discoverability and applied use. In this paper, we present a proposal -- the minimum FAIR, comparable, semantic description of research datasets in terms of salient properties of their supporting publication. We design a specific application of the ORKG-Dataset semantic model based on 40 diverse research datasets on scientific information extraction., Comment: 8 pages, 1 figure, published in the Joint Proceedings of the Onto4FAIR 2023 Workshops

Engineering sciences, such as energy system research, play an important role in developing solutions to technical, environmental, economic, and social challenges of our modern society. In this context, the transformation of energy systems into climate-neutral systems is one of the key strategies for mitigating climate change. For the transformation of energy systems, engineers model, simulate and analyze scenarios and transformation pathways to initiate debates about possible transformation strategies. For these debates and research in general, all steps of the research process must be traceable to guarantee the trustworthiness of published results, avoid redundancies, and ensure their social acceptance. However, the analysis of energy systems is an interdisciplinary field as the investigations of large, complex energy systems often require the use of different software applications and large amounts of heterogeneous data. Engineers must therefore communicate, understand, and (re)use heterogeneous scientific knowledge and data. Although the importance of FAIR scientific knowledge and data in the engineering sciences and energy system research is increasing, little research has been conducted on this topic. When it comes to publishing scientific knowledge and data from publications, software, and datasets (such as models, scenarios, and simulations) openly available and transparent, energy system research lags behind other research domains. According to Schmitt et al. and Nie{\ss}e et al., engineers need technical support in the form of infrastructures, services, and terminologies to improve communication, understanding, and (re)use of scientific knowledge and data., Comment: 1. NFDI4Energy Conference

A pristine suspended carbon nanotube is a near ideal environment to host long-lived quantum states. For this reason, they have been used as the core element of qubits and to explore numerous condensed matter physics phenomena. One of the most advanced technique to realize complex carbon nanotube based quantum circuits relies on a mechanical integration of the nanotube into the circuit. Despite the high-quality and complexity of the fabricated circuits, the range of possible experiments was limited to the closed quantum dot regime. Here, by engineering a transparent metal-nanotube interface, we developed a technique that overcomes this limitation. We reliably reach the open quantum dot regime as demonstrated by measurements of Fabry-Perot interferences and Kondo physics in multiple devices. A circuit-nanotube alignment precision of +/-200nm is demonstrated. Our technique allows to envision experiments requiring the combination of complex circuits and strongly coupled carbon nanotubes such as the realization of carbon nanotube superconducting qubits or flux-mediated optomechanics experiments.

We establish abstract local limit theorems for hitting times and return-times of suitable sequences (A_{l}) of asymptotically rare events in ergodic probability preserving dynamical systems, including versions for tuples of consecutive times and positions of the hits. These results are shown to apply in the setup of Gibbs-Markov systems.

The value of structured scholarly knowledge for research and society at large is well understood, but producing scholarly knowledge (i.e., knowledge traditionally published in articles) in structured form remains a challenge. We propose an approach for automatically extracting scholarly knowledge from published software packages by static analysis of their metadata and contents (scripts and data) and populating a scholarly knowledge graph with the extracted knowledge. Our approach is based on mining scientific software packages linked to article publications by extracting metadata and analyzing the Abstract Syntax Tree (AST) of the source code to obtain information about the used and produced data as well as operations performed on data. The resulting knowledge graph includes articles, software packages metadata, and computational techniques applied to input data utilized as materials in research work. The knowledge graph also includes the results reported as scholarly knowledge in articles., Comment: 10 pages, 5 figures. arXiv admin note: text overlap with arXiv:2212.07921