arXiv subjects

Xiaoyi Jiang

Publications and source records attributed to Xiaoyi Jiang.

34 records · Page 2Linked to original sources

arXiv2024

A Data-Centric Approach To Generate Faithful and High Quality Patient Summaries with Large Language Models

Patients often face difficulties in understanding their hospitalizations, while healthcare workers have limited resources to provide explanations. In this work, we investigate the potential of large language models to generate patient summaries based on doctors' notes and study the effect of training data on the faithfulness and quality of the generated summaries. To this end, we release (i) a rigorous labeling protocol for errors in medical texts and (ii) a publicly available dataset of annotated hallucinations in 100 doctor-written and 100 generated summaries. We show that fine-tuning on hallucination-free data effectively reduces hallucinations from 2.60 to 1.55 per summary for Llama 2, while preserving relevant information. We observe a similar effect on GPT-4 (0.70 to 0.40), when the few-shot examples are hallucination-free. We also conduct a qualitative evaluation using hallucination-free and improved training data. We find that common quantitative metrics do not correlate well with faithfulness and quality. Finally, we test GPT-4 for automatic hallucination detection, which clearly outperforms common baselines.

cs.CL↗

arXiv2024

DeepCSHAP: Utilizing Shapley Values to Explain Deep Complex-Valued Neural Networks

Deep Neural Networks are widely used in academy as well as corporate and public applications, including safety critical applications such as health care and autonomous driving. The ability to explain their output is critical for safety reasons as well as acceptance among applicants. A multitude of methods have been proposed to explain real-valued neural networks. Recently, complex-valued neural networks have emerged as a new class of neural networks dealing with complex-valued input data without the necessity of projecting them onto $\mathbb{R}^2$. This brings up the need to develop explanation algorithms for this kind of neural networks. In this paper we provide these developments. While we focus on adapting the widely used DeepSHAP algorithm to the complex domain, we also present versions of four gradient based explanation methods suitable for use in complex-valued neural networks. We evaluate the explanation quality of all presented algorithms and provide all of them as an open source library adaptable to most recent complex-valued neural network architectures.

cs.LG↗

arXiv2023

Phase-Specific Augmented Reality Guidance for Microscopic Cataract Surgery Using Long-Short Spatiotemporal Aggregation Transformer

Phacoemulsification cataract surgery (PCS) is a routine procedure conducted using a surgical microscope, heavily reliant on the skill of the ophthalmologist. While existing PCS guidance systems extract valuable information from surgical microscopic videos to enhance intraoperative proficiency, they suffer from non-phasespecific guidance, leading to redundant visual information. In this study, our major contribution is the development of a novel phase-specific augmented reality (AR) guidance system, which offers tailored AR information corresponding to the recognized surgical phase. Leveraging the inherent quasi-standardized nature of PCS procedures, we propose a two-stage surgical microscopic video recognition network. In the first stage, we implement a multi-task learning structure to segment the surgical limbus region and extract limbus region-focused spatial feature for each frame. In the second stage, we propose the long-short spatiotemporal aggregation transformer (LS-SAT) network to model local fine-grained and global temporal relationships, and combine the extracted spatial features to recognize the current surgical phase. Additionally, we collaborate closely with ophthalmologists to design AR visual cues by utilizing techniques such as limbus ellipse fitting and regional restricted normal cross-correlation rotation computation. We evaluated the network on publicly available and in-house datasets, with comparison results demonstrating its superior performance compared to related works. Ablation results further validated the effectiveness of the limbus region-focused spatial feature extractor and the combination of temporal features. Furthermore, the developed system was evaluated in a clinical setup, with results indicating remarkable accuracy and real-time performance. underscoring its potential for clinical applications.

cs.CV↗

arXiv2023

Building Blocks for a Complex-Valued Transformer Architecture

Most deep learning pipelines are built on real-valued operations to deal with real-valued inputs such as images, speech or music signals. However, a lot of applications naturally make use of complex-valued signals or images, such as MRI or remote sensing. Additionally the Fourier transform of signals is complex-valued and has numerous applications. We aim to make deep learning directly applicable to these complex-valued signals without using projections into $\mathbb{R}^2$. Thus we add to the recent developments of complex-valued neural networks by presenting building blocks to transfer the transformer architecture to the complex domain. We present multiple versions of a complex-valued Scaled Dot-Product Attention mechanism as well as a complex-valued layer normalization. We test on a classification and a sequence generation task on the MusicNet dataset and show improved robustness to overfitting while maintaining on-par performance when compared to the real-valued transformer architecture.

cs.LG↗

arXiv2023

TabLLM: Few-shot Classification of Tabular Data with Large Language Models

We study the application of large language models to zero-shot and few-shot classification of tabular data. We prompt the large language model with a serialization of the tabular data to a natural-language string, together with a short description of the classification problem. In the few-shot setting, we fine-tune the large language model using some labeled examples. We evaluate several serialization methods including templates, table-to-text models, and large language models. Despite its simplicity, we find that this technique outperforms prior deep-learning-based tabular classification methods on several benchmark datasets. In most cases, even zero-shot classification obtains non-trivial performance, illustrating the method's ability to exploit prior knowledge encoded in large language models. Unlike many deep learning methods for tabular datasets, this approach is also competitive with strong traditional baselines like gradient-boosted trees, especially in the very-few-shot setting.

cs.CL↗

arXiv2022

Kernel-Based Generalized Median Computation for Consensus Learning

Computing a consensus object from a set of given objects is a core problem in machine learning and pattern recognition. One popular approach is to formulate it as an optimization problem using the generalized median. Previous methods like the Prototype and Distance-Preserving Embedding methods transform objects into a vector space, solve the generalized median problem in this space, and inversely transform back into the original space. Both of these methods have been successfully applied to a wide range of object domains, where the generalized median problem has inherent high computational complexity (typically $\mathcal{NP}$-hard) and therefore approximate solutions are required. Previously, explicit embedding methods were used in the computation, which often do not reflect the spatial relationship between objects exactly. In this work we introduce a kernel-based generalized median framework that is applicable to both positive definite and indefinite kernels. This framework computes the relationship between objects and its generalized median in kernel space, without the need of an explicit embedding. We show that the spatial relationship between objects is more accurately represented in kernel space than in an explicit vector space using easy-to-compute kernels, and demonstrate superior performance of generalized median computation on datasets of three different domains. A software toolbox resulting from our work is made publicly available to encourage other researchers to explore the generalized median computation and applications.

cs.CV↗

arXiv2022

Hierarchical Random Walker Segmentation for Large Volumetric Biomedical Images

The random walker method for image segmentation is a popular tool for semi-automatic image segmentation, especially in the biomedical field. However, its linear asymptotic run time and memory requirements make application to 3D datasets of increasing sizes impractical. We propose a hierarchical framework that, to the best of our knowledge, is the first attempt to overcome these restrictions for the random walker algorithm and achieves sublinear run time and constant memory complexity. The goal of this framework is -- rather than improving the segmentation quality compared to the baseline method -- to make interactive segmentation on out-of-core datasets possible. The method is evaluated quantitavely on synthetic data and the CT-ORG dataset where the expected improvements in algorithm run time while maintaining high segmentation quality are confirmed. The incremental (i.e., interaction update) run time is demonstrated to be in seconds on a standard PC even for volumes of hundreds of gigabytes in size. In a small case study the applicability to large real world from current biomedical research is demonstrated. An implementation of the presented method is publicly available in version 5.2 of the widely used volume rendering and processing software Voreen (https://www.uni-muenster.de/Voreen/).

cs.CV↗

arXiv2022

Voreen -- An Open-source Framework for Interactive Visualization and Processing of Large Volume Data

Technological advances for measuring or simulating volume data have led to large data sizes in many research areas such as biology, medicine, physics, and geoscience. Here, large data can refer to individual data sets with high spatial and/or temporal resolution as well as collections of data sets in the sense of cohorts or ensembles. Therefore, general-purpose and customizable volume visualization and processing systems have to provide out-of-core mechanisms that allow for handling and analyzing such data. Voreen is an open-source rapid-prototyping framework that was originally designed to quickly create custom visualization applications for volumetric imaging data using the meanwhile quite common data flow graph paradigm. In recent years, Voreen has been used in various interdisciplinary research projects with an increasing demand for large data processing capabilities without relying on cluster compute resources. In its latest release, Voreen has thus been extended by out-of-core techniques for processing and visualization of volume data with very high spatial resolution as well as collections of volume data sets including spatio-temporal multi-field simulation ensembles. In this paper we compare state-of-the-art volume processing and visualization systems and conclude that Voreen is the first system combining out-of-core processing and rendering capabilities for large volume data on consumer hardware with features important for interdisciplinary research. We describe how Voreen achieves these goals and show-case its use, performance, and capability to support interdisciplinary research by presenting typical workflows within two large volume data case studies.

cs.GR↗

arXiv2022

A Bhattacharyya Coefficient-Based Framework for Noise Model-Aware Random Walker Image Segmentation

One well established method of interactive image segmentation is the random walker algorithm. Considerable research on this family of segmentation methods has been continuously conducted in recent years with numerous applications. These methods are common in using a simple Gaussian weight function which depends on a parameter that strongly influences the segmentation performance. In this work we propose a general framework of deriving weight functions based on probabilistic modeling. This framework can be concretized to cope with virtually any well-defined noise model. It eliminates the critical parameter and thus avoids time-consuming parameter search. We derive the specific weight functions for common noise types and show their superior performance on synthetic data as well as different biomedical image data (MRI images from the NYU fastMRI dataset, larvae images acquired with the FIM technique). Our framework can also be used in multiple other applications, e.g., the graph cut algorithm and its extensions.

cs.CV↗

arXiv2022

A Streaming Volumetric Image Generation Framework for Development and Evaluation of Out-of-Core Methods

Advances in 3D imaging technology in recent years have allowed for increasingly high resolution volumetric images of large specimen. The resulting datasets of hundreds of Gigabytes in size call for new scalable and memory efficient approaches in the field of image processing, where some progress has been made already. At the same time, quantitative evaluation of these new methods is difficult both in terms of the availability of specific data sizes and in the generation of associated ground truth data. In this paper we present an algorithmic framework that can be used to efficiently generate test (and ground truth) volume data, optionally even in a streaming fashion. As the proposed nested sweeps algorithm is fast, it can be used to generate test data on demand. We analyze the asymptotic run time of the presented algorithm and compare it experimentally to alternative approaches as well as a hypothetical best-case baseline method. In a case study, the framework is applied to the popular VascuSynth software for vascular image generation, making it capable of efficiently producing larger-than-main memory volumes which is demonstrated by generating a trillion voxel (1TB) image. Implementations of the presented framework are available online in the form of the modified version of Vascusynth and the code used for the experimental evaluation. In addition, the test data generation procedure has been integrated into the popular volume rendering and processing framework Voreen.

cs.CV↗

arXiv2021

PHOTONAI -- A Python API for Rapid Machine Learning Model Development

PHOTONAI is a high-level Python API designed to simplify and accelerate machine learning model development. It functions as a unifying framework allowing the user to easily access and combine algorithms from different toolboxes into custom algorithm sequences. It is especially designed to support the iterative model development process and automates the repetitive training, hyperparameter optimization and evaluation tasks. Importantly, the workflow ensures unbiased performance estimates while still allowing the user to fully customize the machine learning analysis. PHOTONAI extends existing solutions with a novel pipeline implementation supporting more complex data streams, feature combinations, and algorithm selection. Metrics and results can be conveniently visualized using the PHOTONAI Explorer and predictive models are shareable in a standardized format for further external validation or application. A growing add-on ecosystem allows researchers to offer data modality specific algorithms to the community and enhance machine learning in the areas of the life sciences. Its practical utility is demonstrated on an exemplary medical machine learning problem, achieving a state-of-the-art solution in few lines of code. Source code is publicly available on Github, while examples and documentation can be found at www.photon-ai.com.

cs.LG↗

arXiv2021

Systematic Misestimation of Machine Learning Performance in Neuroimaging Studies of Depression

We currently observe a disconcerting phenomenon in machine learning studies in psychiatry: While we would expect larger samples to yield better results due to the availability of more data, larger machine learning studies consistently show much weaker performance than the numerous small-scale studies. Here, we systematically investigated this effect focusing on one of the most heavily studied questions in the field, namely the classification of patients suffering from major depressive disorder (MDD) and healthy control (HC) based on neuroimaging data. Drawing upon structural magnetic resonance imaging (MRI) data from a balanced sample of $N = 1,868$ MDD patients and HC from our recent international Predictive Analytics Competition (PAC), we first trained and tested a classification model on the full dataset which yielded an accuracy of $61\,\%$. Next, we mimicked the process by which researchers would draw samples of various sizes ($N = 4$ to $N = 150$) from the population and showed a strong risk of misestimation. Specifically, for small sample sizes ($N = 20$), we observe accuracies of up to $95\,\%$. For medium sample sizes ($N = 100$) accuracies up to $75\,\%$ were found. Importantly, further investigation showed that sufficiently large test sets effectively protect against performance misestimation whereas larger datasets per se do not. While these results question the validity of a substantial part of the current literature, we outline the relatively low-cost remedy of larger test sets, which is readily available in most cases.

q-bio.NC↗

arXiv2021

Scalable Robust Graph and Feature Extraction for Arbitrary Vessel Networks in Large Volumetric Datasets

Recent advances in 3D imaging technologies provide novel insights to researchers and reveal finer and more detail of examined specimen, especially in the biomedical domain, but also impose huge challenges regarding scalability for automated analysis algorithms due to rapidly increasing dataset sizes. In particular, existing research towards automated vessel network analysis does not consider memory requirements of proposed algorithms and often generates a large number of spurious branches for structures consisting of many voxels. Additionally, very often these algorithms have further restrictions such as the limitation to tree topologies or relying on the properties of specific image modalities. We present a scalable pipeline (in terms of computational cost, required main memory and robustness) that extracts an annotated abstract graph representation from the foreground segmentation of vessel networks of arbitrary topology and vessel shape. Only a single, dimensionless, a-priori determinable parameter is required. By careful engineering of individual pipeline stages and a novel iterative refinement scheme we are, for the first time, able to analyze the topology of volumes of roughly 1TB on commodity hardware. An implementation of the presented pipeline is publicly available in version 5.1 of the volume rendering and processing engine Voreen (https://www.uni-muenster.de/Voreen/).

cs.CV↗

arXiv2020

Biological sex classification with structural MRI data shows increased misclassification in transgender women

Transgender individuals (TIs) show brain structural alterations that differ from their biological sex as well as their perceived gender. To substantiate evidence that the brain structure of TIs differs from male and female, we use a combined multivariate and univariate approach. Gray matter segments resulting from voxel-based morphometry preprocessing of $N = 1753$ cisgender (CG) healthy participants were used to train ($N=1402$) and validate (20 % hold-out; $N = 351$) a support-vector machine classifying the biological sex. As a second validation, we classified $N = 1104$ patients with depression. A third validation was performed using the matched CG sample of the transgender women (TWs) application-sample. Subsequently, the classifier was applied to $N = 26$ TWs. Finally, we compared brain volumes of CG-men, women and TW-pre/post treatment (cross-sex hormone treatment) in a univariate analysis controlling for sexual orientation, age and total brain volume. The application of our biological sex classifier to the transgender sample resulted in a significantly lower true positive rate (TPR) (TPR-male = 56.0 %). The TPR did not differ between CG-individuals with (TPR-male = 86.9 %) and without depression (TPR-male = 88.5 %). The univariate analysis of the transgender application-sample revealed that TW-pre/post treatment show brain structural differences from CG-women and CG-men in the putamen and insula, as well as the whole-brain analysis. Our results support the hypothesis that brain structure in TW differs from brain structure of their biological sex (male) as well as their perceived gender (female). This finding substantiates evidence that TIs show specific brain structural alterations leading to a different pattern of brain structure than CG-individuals.

q-bio.NC↗

arXiv2020

The PHOTON Wizard -- Towards Educational Machine Learning Code Generators

Despite the tremendous efforts to democratize machine learning, especially in applied-science, the application is still often hampered by the lack of coding skills. As we consider programmatic understanding key to building effective and efficient machine learning solutions, we argue for a novel educational approach that builds upon the accessibility and acceptance of graphical user interfaces to convey programming skills to an applied-science target group. We outline a proof-of-concept, open-source web application, the PHOTON Wizard, which dynamically translates GUI interactions into valid source code for the Python machine learning framework PHOTON. Thereby, users possessing theoretical machine learning knowledge gain key insights into the model development workflow as well as an intuitive understanding of custom implementations. Specifically, the PHOTON Wizard integrates the concept of Educational Machine Learning Code Generators to teach users how to write code for designing, training, optimizing and evaluating custom machine learning pipelines.

cs.SE↗

arXiv2018

Barista - a Graphical Tool for Designing and Training Deep Neural Networks

In recent years, the importance of deep learning has significantly increased in pattern recognition, computer vision, and artificial intelligence research, as well as in industry. However, despite the existence of multiple deep learning frameworks, there is a lack of comprehensible and easy-to-use high-level tools for the design, training, and testing of deep neural networks (DNNs). In this paper, we introduce Barista, an open-source graphical high-level interface for the Caffe deep learning framework. While Caffe is one of the most popular frameworks for training DNNs, editing prototext files in order to specify the net architecture and hyper parameters can become a cumbersome and error-prone task. Instead, Barista offers a fully graphical user interface with a graph-based net topology editor and provides an end-to-end training facility for DNNs, which allows researchers to focus on solving their problems without having to write code, edit text files, or manually parse logged data.

cs.LG↗