Large annotated datasets are required for training deep learning models, but in medical imaging data sharing is often complicated due to ethics, anonymization and data protection legislation. Generative AI models, such as generative adversarial networks (GANs) and diffusion models, can today produce very realistic synthetic images, and can potentially facilitate data sharing. However, in order to share synthetic medical images it must first be demonstrated that they can be used for training different networks with acceptable performance. Here, we therefore comprehensively evaluate four GANs (progressive GAN, StyleGAN 1-3) and a diffusion model for the task of brain tumor segmentation (using two segmentation networks, U-Net and a Swin transformer). Our results show that segmentation networks trained on synthetic images reach Dice scores that are 80% - 90% of Dice scores when training with real images, but that memorization of the training images can be a problem for diffusion models if the original dataset is too small. Our conclusion is that sharing synthetic medical images is a viable option to sharing real images, but that further work is required. The trained generative models and the generated synthetic images are shared on AIDA data hub
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Modern regression applications can involve hundreds or thousands of variables which motivates the use of variable selection methods. Bayesian variable selection defines a posterior distribution on the possible subsets of the variables (which are usually termed models) to express uncertainty about which variables are strongly linked to the response. This can be used to provide Bayesian model averaged predictions or inference, and to understand the relative importance of different variables. However, there has been little work on meaningful representations of this uncertainty beyond first order summaries. We introduce Cartesian credible sets to address this gap. The elements of these sets are formed by concatenating sub-models defined on each block of a partition of the variables. Investigating these sub-models allow us to understand whether the models in the Cartesian credible set always/never/sometimes include a particular variable or group of variables and provide a useful summary of model uncertainty. We introduce methods to find these sets that emphasize ease of understanding. The potential of the method is illustrated on regression problems with both small and large numbers of variables.
The rise of the Internet and the exponential increase in data have made manual data summarization and analysis a challenging task. Instagram social network is a prominent social network widely utilized in Iran for information sharing and communication across various age groups. The inherent structure of Instagram, characterized by its text-rich content and graph-like data representation, enables the utilization of text and graph processing techniques for data analysis purposes. The degree distributions of these networks exhibit scale-free characteristics, indicating non-random growth patterns. Recently, word co-occurrence has gained attention from researchers across multiple disciplines due to its simplicity and practicality. Keyword extraction is a crucial task in natural language processing. In this study, we demonstrated that high-precision extraction of keywords from Instagram posts in the Persian language can be achieved using unsupervised word co-occurrence methods without resorting to conventional techniques such as clustering or pre-trained models. After graph visualization and community detection, it was observed that the top topics covered by news agencies are represented by these graphs. This approach is generalizable to new and diverse datasets and can provide acceptable outputs for new data. To the author's knowledge, this method has not been employed in the Persian language before on Instagram social network. The new crawled data has been publicly released on GitHub for exploration by other researchers. By employing this method, it is possible to use other graph-based algorithms, such as community detections. The results help us to identify the key role of different news agencies in information diffusion among the public, identify hidden communities, and discover latent patterns among a massive amount of data.
In the health domain, decisions are often based on different data modalities. Thus, when creating prediction models, multimodal fusion approaches that can extract and combine relevant features from different data modalities, can be highly beneficial. Furthermore, it is important to understand how each modality impacts the final prediction, especially in high-stake domains, so that these models can be used in a trustworthy and responsible manner. We propose MultiFIX: a new interpretability-focused multimodal data fusion pipeline that explicitly induces separate features from different data types that can subsequently be combined to make a final prediction. An end-to-end deep learning architecture is used to train a predictive model and extract representative features of each modality. Each part of the model is then explained using explainable artificial intelligence techniques. Attention maps are used to highlight important regions in image inputs. Inherently interpretable symbolic expressions, learned with GP-GOMEA, are used to describe the contribution of tabular inputs. The fusion of the extracted features to predict the target label is also replaced by a symbolic expression, learned with GP-GOMEA. Results on synthetic problems demonstrate the strengths and limitations of MultiFIX. Lastly, we apply MultiFIX to a publicly available dataset for the detection of malignant skin lesions.
The discharge summary is a one of critical documents in the patient journey, encompassing all events experienced during hospitalization, including multiple visits, medications, tests, surgery/procedures, and admissions/discharge. Providing a summary of the patient's progress is crucial, as it significantly influences future care and planning. Consequently, clinicians face the laborious and resource-intensive task of manually collecting, organizing, and combining all the necessary data for a discharge summary. Therefore, we propose "NOTE", which stands for "Notable generation Of patient Text summaries through an Efficient approach based on direct preference optimization". NOTE is based on Medical Information Mart for Intensive Care- III dataset and summarizes a single hospitalization of a patient. Patient events are sequentially combined and used to generate a discharge summary for each hospitalization. In the present circumstances, large language models' application programming interfaces (LLMs' APIs) are widely available, but importing and exporting medical data presents significant challenges due to privacy protection policies in healthcare institutions. Moreover, to ensure optimal performance, it is essential to implement a lightweight model for internal server or program within the hospital. Therefore, we utilized DPO and parameter efficient fine tuning (PEFT) techniques to apply a fine-tuning method that guarantees superior performance. To demonstrate the practical application of the developed NOTE, we provide a webpage-based demonstration software. In the future, we will aim to deploy the software available for actual use by clinicians in hospital. NOTE can be utilized to generate various summaries not only discharge summaries but also throughout a patient's journey, thereby alleviating the labor-intensive workload of clinicians and aiming for increased efficiency.
We present a minimal phase oscillator model for learning quadrupedal locomotion. Each of the four oscillators is coupled only to itself and its corresponding leg through local feedback of the ground reaction force, which can be interpreted as an observer feedback gain. We interpret the oscillator itself as a latent contact state-estimator. Through a systematic ablation study, we show that the combination of phase observations, simple phase-based rewards, and the local feedback dynamics induces policies that exhibit emergent gait preferences, while using a reduced set of simple rewards, and without prescribing a specific gait. The code is open-source, and a video synopsis available at //youtu.be/1NKQ0rSV3jU.
The increasing availability of hydrological and physiographic spatiotemporal data has boosted machine learning's role in rapid flood mapping. Yet, data scarcity, especially high-resolution DEMs, challenges regions with limited access. This paper examines how DEM type and resolution affect flood prediction accuracy, utilizing a cutting-edge deep learning (DL) method called 1D convolutional neural network (CNN). It utilizes synthetic hydrographs as training input and water depth data obtained from LISFLOOD-FP, a 2D hydrodynamic model, as target data. This study investigates digital surface models (DSMs) and digital terrain models (DTMs) derived from a 1 m LIDAR-based DTM, with resolutions from 15 to 30 m. The methodology is applied and assessed in an established benchmark, the city of Carlisle, UK. The models' performance is then evaluated and compared against an observed flood event using RMSE, Bias, and Fit indices. Leveraging the insights gained from this region, the paper discusses the applicability of the methodology to address the challenges encountered in a data-scarce flood-prone region, exemplified by Pakistan. Results indicated that utilizing a 30 m DTM outperformed a 30 m DSM in terms of flood depth prediction accuracy by about 21% during the flood peak stage, highlighting the superior performance of DTM at lower resolutions. Increasing the resolution of DTM to 15 m resulted in a minimum 50% increase in RMSE and a 20% increase in fit index across all flood stages. The findings emphasize that while a coarser resolution DEM may impact the accuracy of machine learning models, it remains a viable option for rapid flood prediction. However, even a slight improvement in data resolution in data-scarce regions would provide significant added value, ultimately enhancing flood risk management.
Detecting abrupt changes in real-time data streams from scientific simulations presents a challenging task, demanding the deployment of accurate and efficient algorithms. Identifying change points in live data stream involves continuous scrutiny of incoming observations for deviations in their statistical characteristics, particularly in high-volume data scenarios. Maintaining a balance between sudden change detection and minimizing false alarms is vital. Many existing algorithms for this purpose rely on known probability distributions, limiting their feasibility. In this study, we introduce the Kernel-based Cumulative Sum (KCUSUM) algorithm, a non-parametric extension of the traditional Cumulative Sum (CUSUM) method, which has gained prominence for its efficacy in online change point detection under less restrictive conditions. KCUSUM splits itself by comparing incoming samples directly with reference samples and computes a statistic grounded in the Maximum Mean Discrepancy (MMD) non-parametric framework. This approach extends KCUSUM's pertinence to scenarios where only reference samples are available, such as atomic trajectories of proteins in vacuum, facilitating the detection of deviations from the reference sample without prior knowledge of the data's underlying distribution. Furthermore, by harnessing MMD's inherent random-walk structure, we can theoretically analyze KCUSUM's performance across various use cases, including metrics like expected delay and mean runtime to false alarms. Finally, we discuss real-world use cases from scientific simulations such as NWChem CODAR and protein folding data, demonstrating KCUSUM's practical effectiveness in online change point detection.
Recently, graph neural networks have been gaining a lot of attention to simulate dynamical systems due to their inductive nature leading to zero-shot generalizability. Similarly, physics-informed inductive biases in deep-learning frameworks have been shown to give superior performance in learning the dynamics of physical systems. There is a growing volume of literature that attempts to combine these two approaches. Here, we evaluate the performance of thirteen different graph neural networks, namely, Hamiltonian and Lagrangian graph neural networks, graph neural ODE, and their variants with explicit constraints and different architectures. We briefly explain the theoretical formulation highlighting the similarities and differences in the inductive biases and graph architecture of these systems. We evaluate these models on spring, pendulum, gravitational, and 3D deformable solid systems to compare the performance in terms of rollout error, conserved quantities such as energy and momentum, and generalizability to unseen system sizes. Our study demonstrates that GNNs with additional inductive biases, such as explicit constraints and decoupling of kinetic and potential energies, exhibit significantly enhanced performance. Further, all the physics-informed GNNs exhibit zero-shot generalizability to system sizes an order of magnitude larger than the training system, thus providing a promising route to simulate large-scale realistic systems.
Deep learning-based semi-supervised learning (SSL) algorithms have led to promising results in medical images segmentation and can alleviate doctors' expensive annotations by leveraging unlabeled data. However, most of the existing SSL algorithms in literature tend to regularize the model training by perturbing networks and/or data. Observing that multi/dual-task learning attends to various levels of information which have inherent prediction perturbation, we ask the question in this work: can we explicitly build task-level regularization rather than implicitly constructing networks- and/or data-level perturbation-and-transformation for SSL? To answer this question, we propose a novel dual-task-consistency semi-supervised framework for the first time. Concretely, we use a dual-task deep network that jointly predicts a pixel-wise segmentation map and a geometry-aware level set representation of the target. The level set representation is converted to an approximated segmentation map through a differentiable task transform layer. Simultaneously, we introduce a dual-task consistency regularization between the level set-derived segmentation maps and directly predicted segmentation maps for both labeled and unlabeled data. Extensive experiments on two public datasets show that our method can largely improve the performance by incorporating the unlabeled data. Meanwhile, our framework outperforms the state-of-the-art semi-supervised medical image segmentation methods. Code is available at: //github.com/Luoxd1996/DTC
Although measuring held-out accuracy has been the primary approach to evaluate generalization, it often overestimates the performance of NLP models, while alternative approaches for evaluating models either focus on individual tasks or on specific behaviors. Inspired by principles of behavioral testing in software engineering, we introduce CheckList, a task-agnostic methodology for testing NLP models. CheckList includes a matrix of general linguistic capabilities and test types that facilitate comprehensive test ideation, as well as a software tool to generate a large and diverse number of test cases quickly. We illustrate the utility of CheckList with tests for three tasks, identifying critical failures in both commercial and state-of-art models. In a user study, a team responsible for a commercial sentiment analysis model found new and actionable bugs in an extensively tested model. In another user study, NLP practitioners with CheckList created twice as many tests, and found almost three times as many bugs as users without it.
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