The investigation of tumor invasion and metastasis dynamics is crucial for advancements in cancer biology and treatment. Many mathematical models have been developed to study the invasion of host tissue by tumor cells. In this paper, we develop a novel stochastic interacting particle-field (SIPF) algorithm that accurately simulates the cancer cell invasion process within the haptotaxis advection-diffusion (HAD) system. Our approach approximates solutions using empirical measures of particle interactions, combined with a smoother field variable - the extracellular matrix concentration (ECM) - computed by the spectral method. We derive a one-step time recursion for both the positions of stochastic particles and the field variable using the implicit Euler discretization, which is based on the explicit Green's function of an elliptic operator characterized by the Laplacian minus a positive constant. Our numerical experiments demonstrate the superior performance of the proposed algorithm, especially in computing cancer cell growth with thin free boundaries in three-dimensional (3D) space. Numerical results show that the SIPF algorithm is mesh-free, self-adaptive, and low-cost. Moreover, it is more accurate and efficient than traditional numerical techniques such as the finite difference method (FDM) and spectral methods.
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Optical Coherence Tomography Angiography (OCTA) is a crucial tool in the clinical screening of retinal diseases, allowing for accurate 3D imaging of blood vessels through non-invasive scanning. However, the hardware-based approach for acquiring OCTA images presents challenges due to the need for specialized sensors and expensive devices. In this paper, we introduce a novel method called TransPro, which can translate the readily available 3D Optical Coherence Tomography (OCT) images into 3D OCTA images without requiring any additional hardware modifications. Our TransPro method is primarily driven by two novel ideas that have been overlooked by prior work. The first idea is derived from a critical observation that the OCTA projection map is generated by averaging pixel values from its corresponding B-scans along the Z-axis. Hence, we introduce a hybrid architecture incorporating a 3D adversarial generative network and a novel Heuristic Contextual Guidance (HCG) module, which effectively maintains the consistency of the generated OCTA images between 3D volumes and projection maps. The second idea is to improve the vessel quality in the translated OCTA projection maps. As a result, we propose a novel Vessel Promoted Guidance (VPG) module to enhance the attention of network on retinal vessels. Experimental results on two datasets demonstrate that our TransPro outperforms state-of-the-art approaches, with relative improvements around 11.4% in MAE, 2.7% in PSNR, 2% in SSIM, 40% in VDE, and 9.1% in VDC compared to the baseline method. The code is available at: //github.com/ustlsh/TransPro.
Traumatic Brain Injury (TBI) presents a broad spectrum of clinical presentations and outcomes due to its inherent heterogeneity, leading to diverse recovery trajectories and varied therapeutic responses. While many studies have delved into TBI phenotyping for distinct patient populations, identifying TBI phenotypes that consistently generalize across various settings and populations remains a critical research gap. Our research addresses this by employing multivariate time-series clustering to unveil TBI's dynamic intricates. Utilizing a self-supervised learning-based approach to clustering multivariate time-Series data with missing values (SLAC-Time), we analyzed both the research-centric TRACK-TBI and the real-world MIMIC-IV datasets. Remarkably, the optimal hyperparameters of SLAC-Time and the ideal number of clusters remained consistent across these datasets, underscoring SLAC-Time's stability across heterogeneous datasets. Our analysis revealed three generalizable TBI phenotypes ({\alpha}, \b{eta}, and {\gamma}), each exhibiting distinct non-temporal features during emergency department visits, and temporal feature profiles throughout ICU stays. Specifically, phenotype {\alpha} represents mild TBI with a remarkably consistent clinical presentation. In contrast, phenotype \b{eta} signifies severe TBI with diverse clinical manifestations, and phenotype {\gamma} represents a moderate TBI profile in terms of severity and clinical diversity. Age is a significant determinant of TBI outcomes, with older cohorts recording higher mortality rates. Importantly, while certain features varied by age, the core characteristics of TBI manifestations tied to each phenotype remain consistent across diverse populations.
The description of gene interactions that constantly occur in the cellular environment is an extremely challenging task due to an immense number of degrees of freedom and incomplete knowledge about microscopic details. Hence, a coarse-grained and rather powerful modeling of such dynamics is provided by Boolean Networks (BNs). BNs are dynamical systems composed of Boolean agents and a record of their possible interactions over time. Stable states in these systems are called attractors which are closely related to the cellular expression of biological phenotypes. Identifying the full set of attractors is, therefore, of substantial biological interest. However, for conventional high-performance computing, this problem is plagued by an exponential growth of the dynamic state space. Here, we demonstrate a novel quantum search algorithm inspired by Grover's algorithm to be implemented on quantum computing platforms. The algorithm performs an iterative suppression of states belonging to basins of previously discovered attractors from a uniform superposition, thus increasing the amplitudes of states in basins of yet unknown attractors. This approach guarantees that a new attractor state is measured with each iteration of the algorithm, an optimization not currently achieved by any other algorithm in the literature. Tests of its resistance to noise have also shown promising performance on devices from the current Noise Intermediate Scale Quantum Computing (NISQ) era.
Prognosis prediction is crucial for determining optimal treatment plans for lung cancer patients. Traditionally, such predictions relied on models developed from retrospective patient data. Recently, large language models (LLMs) have gained attention for their ability to process and generate text based on extensive learned knowledge. In this study, we evaluate the potential of GPT-4o mini and GPT-3.5 in predicting the prognosis of lung cancer patients. We collected two prognosis datasets, i.e., survival and post-operative complication datasets, and designed multiple tasks to assess the models' performance comprehensively. Logistic regression models were also developed as baselines for comparison. The experimental results demonstrate that LLMs can achieve competitive, and in some tasks superior, performance in lung cancer prognosis prediction compared to data-driven logistic regression models despite not using additional patient data. These findings suggest that LLMs can be effective tools for prognosis prediction in lung cancer, particularly when patient data is limited or unavailable.
Large Language Models (LLMs) offer significant potential for clinical symptom extraction, but their deployment in healthcare settings is constrained by privacy concerns, computational limitations, and operational costs. This study investigates the optimization of compact LLMs for cancer toxicity symptom extraction using a novel iterative refinement approach. We employ a student-teacher architecture, utilizing Zephyr-7b-beta and Phi3-mini-128 as student models and GPT-4o as the teacher, to dynamically select between prompt refinement, Retrieval-Augmented Generation (RAG), and fine-tuning strategies. Our experiments on 294 clinical notes covering 12 post-radiotherapy toxicity symptoms demonstrate the effectiveness of this approach. The RAG method proved most efficient, improving average accuracy scores from 0.32 to 0.73 for Zephyr-7b-beta and from 0.40 to 0.87 for Phi3-mini-128 during refinement. In the test set, both models showed an approximate 0.20 increase in accuracy across symptoms. Notably, this improvement was achieved at a cost 45 times lower than GPT-4o for Zephyr and 79 times lower for Phi-3. These results highlight the potential of iterative refinement techniques in enhancing the capabilities of compact LLMs for clinical applications, offering a balance between performance, cost-effectiveness, and privacy preservation in healthcare settings.
Machine-based brain tumor segmentation can help doctors make better diagnoses. However, the complex structure of brain tumors and expensive pixel-level annotations present challenges for automatic tumor segmentation. In this paper, we propose a counterfactual generation framework that not only achieves exceptional brain tumor segmentation performance without the need for pixel-level annotations, but also provides explainability. Our framework effectively separates class-related features from class-unrelated features of the samples, and generate new samples that preserve identity features while altering class attributes by embedding different class-related features. We perform topological data analysis on the extracted class-related features and obtain a globally explainable manifold, and for each abnormal sample to be segmented, a meaningful normal sample could be effectively generated with the guidance of the rule-based paths designed within the manifold for comparison for identifying the tumor regions. We evaluate our proposed method on two datasets, which demonstrates superior performance of brain tumor segmentation. The code is available at //github.com/xrt11/tumor-segmentation.
We study the problem of multi-agent control of a dynamical system with known dynamics and adversarial disturbances. Our study focuses on optimal control without centralized precomputed policies, but rather with adaptive control policies for the different agents that are only equipped with a stabilizing controller. We give a reduction from any (standard) regret minimizing control method to a distributed algorithm. The reduction guarantees that the resulting distributed algorithm has low regret relative to the optimal precomputed joint policy. Our methodology involves generalizing online convex optimization to a multi-agent setting and applying recent tools from nonstochastic control derived for a single agent. We empirically evaluate our method on a model of an overactuated aircraft. We show that the distributed method is robust to failure and to adversarial perturbations in the dynamics.
Human doctors with well-structured medical knowledge can diagnose a disease merely via a few conversations with patients about symptoms. In contrast, existing knowledge-grounded dialogue systems often require a large number of dialogue instances to learn as they fail to capture the correlations between different diseases and neglect the diagnostic experience shared among them. To address this issue, we propose a more natural and practical paradigm, i.e., low-resource medical dialogue generation, which can transfer the diagnostic experience from source diseases to target ones with a handful of data for adaptation. It is capitalized on a commonsense knowledge graph to characterize the prior disease-symptom relations. Besides, we develop a Graph-Evolving Meta-Learning (GEML) framework that learns to evolve the commonsense graph for reasoning disease-symptom correlations in a new disease, which effectively alleviates the needs of a large number of dialogues. More importantly, by dynamically evolving disease-symptom graphs, GEML also well addresses the real-world challenges that the disease-symptom correlations of each disease may vary or evolve along with more diagnostic cases. Extensive experiment results on the CMDD dataset and our newly-collected Chunyu dataset testify the superiority of our approach over state-of-the-art approaches. Besides, our GEML can generate an enriched dialogue-sensitive knowledge graph in an online manner, which could benefit other tasks grounded on knowledge graph.
The potential of graph convolutional neural networks for the task of zero-shot learning has been demonstrated recently. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, knowledge from distant nodes can get diluted when propagating through intermediate nodes, because current approaches to zero-shot learning use graph propagation schemes that perform Laplacian smoothing at each layer. We show that extensive smoothing does not help the task of regressing classifier weights in zero-shot learning. In order to still incorporate information from distant nodes and utilize the graph structure, we propose an Attentive Dense Graph Propagation Module (ADGPM). ADGPM allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants and an attention scheme is further used to weigh their contribution depending on the distance to the node. Finally, we illustrate that finetuning of the feature representation after training the ADGPM leads to considerable improvements. Our method achieves competitive results, outperforming previous zero-shot learning approaches.
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
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