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Reliable prediction of pediatric obesity can offer a valuable resource to providers, helping them engage in timely preventive interventions before the disease is established. Many efforts have been made to develop ML-based predictive models of obesity, and some studies have reported high predictive performances. However, no commonly used clinical decision support tool based on existing ML models currently exists. This study presents a novel end-to-end pipeline specifically designed for pediatric obesity prediction, which supports the entire process of data extraction, inference, and communication via an API or a user interface. While focusing only on routinely recorded data in pediatric electronic health records (EHRs), our pipeline uses a diverse expert-curated list of medical concepts to predict the 1-3 years risk of developing obesity. Furthermore, by using the Fast Healthcare Interoperability Resources (FHIR) standard in our design procedure, we specifically target facilitating low-effort integration of our pipeline with different EHR systems. In our experiments, we report the effectiveness of the predictive model as well as its alignment with the feedback from various stakeholders, including ML scientists, providers, health IT personnel, health administration representatives, and patient group representatives.

Navigating unmanned aerial vehicles in environments where GPS signals are unavailable poses a compelling and intricate challenge. This challenge is further heightened when dealing with Nano Aerial Vehicles (NAVs) due to their compact size, payload restrictions, and computational capabilities. This paper proposes an approach for localization using off-board computing, an off-board monocular camera, and modified open-source algorithms. The proposed method uses three parallel proportional-integral-derivative controllers on the off-board computer to provide velocity corrections via wireless communication, stabilizing the NAV in a custom-controlled environment. Featuring a 3.1cm localization error and a modest setup cost of 50 USD, this approach proves optimal for environments where cost considerations are paramount. It is especially well-suited for applications like teaching drone control in academic institutions, where the specified error margin is deemed acceptable. Various applications are designed to validate the proposed technique, such as landing the NAV on a moving ground vehicle, path planning in a 3D space, and localizing multi-NAVs. The created package is openly available at https://github.com/simmubhangu/eyantra_drone to foster research in this field., Comment: 26 pages. Submitted to Cyber-Physical Systems journal

Large language models (LLMs) have shown impressive potential in helping with numerous medical challenges. Deploying LLMs in high-stakes applications such as medicine, however, brings in many concerns. One major area of concern relates to biased behaviors of LLMs in medical applications, leading to unfair treatment of individuals. To pave the way for the responsible and impactful deployment of Med LLMs, rigorous evaluation is a key prerequisite. Due to the huge complexity and variability of different medical scenarios, existing work in this domain has primarily relied on using manually crafted datasets for bias evaluation. In this study, we present a new method to scale up such bias evaluations by automatically generating test cases based on rigorous medical evidence. We specifically target the challenges of a) domain-specificity of bias characterization, b) hallucinating while generating the test cases, and c) various dependencies between the health outcomes and sensitive attributes. To that end, we offer new methods to address these challenges integrated with our generative pipeline, using medical knowledge graphs, medical ontologies, and customized general LLM evaluation frameworks in our method. Through a series of extensive experiments, we show that the test cases generated by our proposed method can effectively reveal bias patterns in Med LLMs at larger and more flexible scales than human-crafted datasets. We publish a large bias evaluation dataset using our pipeline, which is dedicated to a few medical case studies. A live demo of our application for vignette generation is available at https://vignette.streamlit.app. Our code is also available at https://github.com/healthylaife/autofair.

Existing multimodal retrieval benchmarks primarily focus on evaluating whether models can retrieve and utilize external textual knowledge for question answering. However, there are scenarios where retrieving visual information is either more beneficial or easier to access than textual data. In this paper, we introduce a multimodal retrieval-augmented generation benchmark, MRAG-Bench, in which we systematically identify and categorize scenarios where visually augmented knowledge is better than textual knowledge, for instance, more images from varying viewpoints. MRAG-Bench consists of 16,130 images and 1,353 human-annotated multiple-choice questions across 9 distinct scenarios. With MRAG-Bench, we conduct an evaluation of 10 open-source and 4 proprietary large vision-language models (LVLMs). Our results show that all LVLMs exhibit greater improvements when augmented with images compared to textual knowledge, confirming that MRAG-Bench is vision-centric. Additionally, we conduct extensive analysis with MRAG-Bench, which offers valuable insights into retrieval-augmented LVLMs. Notably, the top-performing model, GPT-4o, faces challenges in effectively leveraging retrieved knowledge, achieving only a 5.82% improvement with ground-truth information, in contrast to a 33.16% improvement observed in human participants. These findings highlight the importance of MRAG-Bench in encouraging the community to enhance LVLMs' ability to utilize retrieved visual knowledge more effectively., Comment: https://mragbench.github.io

Federated Learning is a well-researched approach for collaboratively training machine learning models across decentralized data while preserving privacy. However, integrating Homomorphic Encryption to ensure data confidentiality introduces significant computational and communication overheads, particularly in heterogeneous environments where clients have varying computational capacities and security needs. In this paper, we propose HERL, a Reinforcement Learning-based approach that uses Q-Learning to dynamically optimize encryption parameters, specifically the polynomial modulus degree, $N$, and the coefficient modulus, $q$, across different client tiers. Our proposed method involves first profiling and tiering clients according to the chosen clustering approach, followed by dynamically selecting the most suitable encryption parameters using an RL-agent. Experimental results demonstrate that our approach significantly reduces the computational overhead while maintaining utility and a high level of security. Empirical results show that HERL improves utility by 17%, reduces the convergence time by up to 24%, and increases convergence efficiency by up to 30%, with minimal security loss.

Large Language Models (LLMs) have emerged as promising solutions for a variety of medical and clinical decision support applications. However, LLMs are often subject to different types of biases, which can lead to unfair treatment of individuals, worsening health disparities, and reducing trust in AI-augmented medical tools. Aiming to address this important issue, in this study, we present a new model alignment approach for aligning LLMs using a preference optimization method within a knowledge distillation framework. Prior to presenting our proposed method, we first use an evaluation framework to conduct a comprehensive (largest to our knowledge) empirical evaluation to reveal the type and nature of existing biases in LLMs used for medical applications. We then offer a bias mitigation technique to reduce the unfair patterns in LLM outputs across different subgroups identified by the protected attributes. We show that our mitigation method is effective in significantly reducing observed biased patterns. Our code is publicly available at \url{https://github.com/healthylaife/FairAlignmentLLM}., Comment: arXiv admin note: substantial text overlap with arXiv:2404.15149

Machine learning in computational pathology (CPath) often aggregates patch-level predictions from multi-gigapixel Whole Slide Images (WSIs) to generate WSI-level prediction scores for crucial tasks such as survival prediction and drug effect prediction. However, current methods do not explicitly characterize distributional differences between patch sets within WSIs. We introduce HistoKernel, a novel Maximum Mean Discrepancy (MMD) kernel that measures distributional similarity between WSIs for enhanced prediction performance on downstream prediction tasks. Our comprehensive analysis demonstrates HistoKernel's effectiveness across various machine learning tasks, including retrieval (n = 9,362), drug sensitivity regression (n = 551), point mutation classification (n = 3,419), and survival analysis (n = 2,291), outperforming existing deep learning methods. Additionally, HistoKernel seamlessly integrates multi-modal data and offers a novel perturbation-based method for patch-level explainability. This work pioneers the use of kernel-based methods for WSI-level predictive modeling, opening new avenues for research. Code is available at https://github.com/pkeller00/HistoKernel., Comment: 28 pages, 5 figures, 1 Table. Preprint for article in review at Nature Machine Intelligence

We study how well large language models (LLMs) explain their generations through rationales -- a set of tokens extracted from the input text that reflect the decision-making process of LLMs. Specifically, we systematically study rationales derived using two approaches: (1) popular prompting-based methods, where prompts are used to guide LLMs in generating rationales, and (2) technical attribution-based methods, which leverage attention or gradients to identify important tokens. Our analysis spans three classification datasets with annotated rationales, encompassing tasks with varying performance levels. While prompting-based self-explanations are widely used, our study reveals that these explanations are not always as "aligned" with the human rationale as attribution-based explanations. Even more so, fine-tuning LLMs to enhance classification task accuracy does not enhance the alignment of prompting-based rationales. Still, it does considerably improve the alignment of attribution-based methods (e.g., InputXGradient). More importantly, we show that prompting-based self-explanation is also less "faithful" than attribution-based explanations, failing to provide a reliable account of the model's decision-making process. To evaluate faithfulness, unlike prior studies that excluded misclassified examples, we evaluate all instances and also examine the impact of fine-tuning and accuracy on alignment and faithfulness. Our findings suggest that inconclusive faithfulness results reported in earlier studies may stem from low classification accuracy. These findings underscore the importance of more rigorous and comprehensive evaluations of LLM rationales.

Understanding human behavior fundamentally relies on accurate 3D human pose estimation. Graph Convolutional Networks (GCNs) have recently shown promising advancements, delivering state-of-the-art performance with rather lightweight architectures. In the context of graph-structured data, leveraging the eigenvectors of the graph Laplacian matrix for positional encoding is effective. Yet, the approach does not specify how to handle scenarios where edges in the input graph are missing. To this end, we propose a novel positional encoding technique, PerturbPE, that extracts consistent and regular components from the eigenbasis. Our method involves applying multiple perturbations and taking their average to extract the consistent and regular component from the eigenbasis. PerturbPE leverages the Rayleigh-Schrodinger Perturbation Theorem (RSPT) for calculating the perturbed eigenvectors. Employing this labeling technique enhances the robustness and generalizability of the model. Our results support our theoretical findings, e.g. our experimental analysis observed a performance enhancement of up to $12\%$ on the Human3.6M dataset in instances where occlusion resulted in the absence of one edge. Furthermore, our novel approach significantly enhances performance in scenarios where two edges are missing, setting a new benchmark for state-of-the-art.

Pathology reports are rich in clinical and pathological details but are often presented in free-text format. The unstructured nature of these reports presents a significant challenge limiting the accessibility of their content. In this work, we present a practical approach based on the use of large multimodal models (LMMs) for automatically extracting information from scanned images of pathology reports with the goal of generating a standardised report specifying the value of different fields along with estimated confidence about the accuracy of the extracted fields. The proposed approach overcomes limitations of existing methods which do not assign confidence scores to extracted fields limiting their practical use. The proposed framework uses two stages of prompting a Large Multimodal Model (LMM) for information extraction and validation. The framework generalises to textual reports from multiple medical centres as well as scanned images of legacy pathology reports. We show that the estimated confidence is an effective indicator of the accuracy of the extracted information that can be used to select only accurately extracted fields. We also show the prognostic significance of structured and unstructured data from pathology reports and show that the automatically extracted field values significant prognostic value for patient stratification. The framework is available for evaluation via the URL: https://labieb.dcs.warwick.ac.uk/., Comment: 19 pages, 6 figures

Large Language Models (LLMs) have emerged as powerful candidates to inform clinical decision-making processes. While these models play an increasingly prominent role in shaping the digital landscape, two growing concerns emerge in healthcare applications: 1) to what extent do LLMs exhibit social bias based on patients' protected attributes (like race), and 2) how do design choices (like architecture design and prompting strategies) influence the observed biases? To answer these questions rigorously, we evaluated eight popular LLMs across three question-answering (QA) datasets using clinical vignettes (patient descriptions) standardized for bias evaluations. We employ red-teaming strategies to analyze how demographics affect LLM outputs, comparing both general-purpose and clinically-trained models. Our extensive experiments reveal various disparities (some significant) across protected groups. We also observe several counter-intuitive patterns such as larger models not being necessarily less biased and fined-tuned models on medical data not being necessarily better than the general-purpose models. Furthermore, our study demonstrates the impact of prompt design on bias patterns and shows that specific phrasing can influence bias patterns and reflection-type approaches (like Chain of Thought) can reduce biased outcomes effectively. Consistent with prior studies, we call on additional evaluations, scrutiny, and enhancement of LLMs used in clinical decision support applications.

Creating plasmonic nanoparticles on a tapered optical fiber tip enables a remote SERS sensing probe, ideal for challenging sampling scenarios like biological tissue, specific cells, on-site environmental monitoring, and deep brain structures. However, nanoparticle patterns fabricated from current bottom-up methods are mostly random, making geometry control difficult. Uneven statistical distribution, clustering, and multilayer deposition introduce uncertainty in correlating device performance with morphology. Here, we employ a tunable solid-state dewetting method to create densely packed monolayer Au nanoislands (NIs) with varied geometric parameters, directly contacting the silica TF surface. These patterns exhibit analyzable nanoparticle sizes, densities, and uniform distribution across the entire taper surface, enabling a systematic investigation of particle size, density, and analyte effects on the SERS performance of the through-fiber detection system. The study is focused on the SERS response of a widely employed benchmark Rhodamine 6G molecule and Serotonin, a neurotransmitter with high relevance for the neuroscience field. The numerical simulations and limit of detection (LOD) experiments on R6G show that the increase of the total near-field enhancement volume promotes the SERS sensitivity of the probe. However, for serotonin we observed a different behavior linked to its interaction with the nanoparticle's surface. The obtained LOD is as low as 10-7 M, a value not achieved so far in a through-fiber detection scheme. Therefore, we believe our work offers a strategy to design nanoparticle-based remote SERS sensing probes and provide new clues to discover and understand the intricate plasmonic-driven chemical reactions.

While current large language models (LLMs) perform well on many knowledge-related tasks, they are limited by relying on their parameters as an implicit storage mechanism. As a result, they struggle with memorizing rare events and with updating their memory as facts change over time. In addition, the uninterpretable nature of parametric memory makes it challenging to prevent hallucination. Model editing and augmenting LLMs with parameters specialized for memory are only partial solutions. In this paper, we introduce MemLLM, a novel method of enhancing LLMs by integrating a structured and explicit read-and-write memory module. MemLLM tackles the aforementioned challenges by enabling dynamic interaction with the memory and improving the LLM's capabilities in using stored knowledge. Our experiments indicate that MemLLM enhances the LLM's performance and interpretability, in language modeling in general and knowledge-intensive tasks in particular. We see MemLLM as an important step towards making LLMs more grounded and factual through memory augmentation.

Polysomnography (PSG) is a type of sleep study that records multimodal physiological signals and is widely used for purposes such as sleep staging and respiratory event detection. Conventional machine learning methods assume that each sleep study is associated with a fixed set of observed modalities and that all modalities are available for each sample. However, noisy and missing modalities are a common issue in real-world clinical settings. In this study, we propose a comprehensive pipeline aiming to compensate for the missing or noisy modalities when performing sleep apnea detection. Unlike other existing studies, our proposed model works with any combination of available modalities. Our experiments show that the proposed model outperforms other state-of-the-art approaches in sleep apnea detection using various subsets of available data and different levels of noise, and maintains its high performance (AUROC>0.9) even in the presence of high levels of noise or missingness. This is especially relevant in settings where the level of noise and missingness is high (such as pediatric or outside-of-clinic scenarios).

Digital pathology has gained significant traction in modern healthcare systems. This shift from optical microscopes to digital imagery brings with it the potential for improved diagnosis, efficiency, and the integration of AI tools into the pathologists workflow. A critical aspect of this is visualization. Throughout the development of a machine learning (ML) model in digital pathology, it is crucial to have flexible, openly available tools to visualize models, from their outputs and predictions to the underlying annotations and images used to train or test a model. We introduce TIAViz, a Python-based visualization tool built into TIAToolbox which allows flexible, interactive, fully zoomable overlay of a wide variety of information onto whole slide images, including graphs, heatmaps, segmentations, annotations and other WSIs. The UI is browser-based, allowing use either locally, on a remote machine, or on a server to provide publicly available demos. This tool is open source and is made available at: https://github.com/TissueImageAnalytics/tiatoolbox and via pip installation (pip install tiatoolbox) and conda as part of TIAToolbox., Comment: Application note to be submitted to bioinformatics

Quantum machine learning with quantum kernels for classification problems is a growing area of research. Recently, quantum kernel alignment techniques that parameterise the kernel have been developed, allowing the kernel to be trained and therefore aligned with a specific dataset. While quantum kernel alignment is a promising technique, it has been hampered by considerable training costs because the full kernel matrix must be constructed at every training iteration. Addressing this challenge, we introduce a novel method that seeks to balance efficiency and performance. We present a sub-sampling training approach that uses a subset of the kernel matrix at each training step, thereby reducing the overall computational cost of the training. In this work, we apply the sub-sampling method to synthetic datasets and a real-world breast cancer dataset and demonstrate considerable reductions in the number of circuits required to train the quantum kernel while maintaining classification accuracy., Comment: Paper as accepted on Quantum on 2024-09-18. The method showcased in this work is also available as a Jupyter notebook at https://github.com/qiskit-community/qiskit-machine-learning/tree/IEEE2024