The fairness issue of clinical data modeling, especially on Electronic Health Records (EHRs), is of utmost importance due to EHR's complex latent structure and potential selection bias. It is frequently necessary to mitigate health disparity while keeping the model's overall accuracy in practice. However, traditional methods often encounter the trade-off between accuracy and fairness, as they fail to capture the underlying factors beyond observed data. To tackle this challenge, we propose a novel model called Fair Longitudinal Medical Deconfounder (FLMD) that aims to achieve both fairness and accuracy in longitudinal Electronic Health Records (EHR) modeling. Drawing inspiration from the deconfounder theory, FLMD employs a two-stage training process. In the first stage, FLMD captures unobserved confounders for each encounter, which effectively represents underlying medical factors beyond observed EHR, such as patient genotypes and lifestyle habits. This unobserved confounder is crucial for addressing the accuracy/fairness dilemma. In the second stage, FLMD combines the learned latent representation with other relevant features to make predictions. By incorporating appropriate fairness criteria, such as counterfactual fairness, FLMD ensures that it maintains high prediction accuracy while simultaneously minimizing health disparities. We conducted comprehensive experiments on two real-world EHR datasets to demonstrate the effectiveness of FLMD. Apart from the comparison of baseline methods and FLMD variants in terms of fairness and accuracy, we assessed the performance of all models on disturbed/imbalanced and synthetic datasets to showcase the superiority of FLMD across different settings and provide valuable insights into its capabilities.
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Through the Bayesian lens of data assimilation, uncertainty on model parameters is traditionally quantified through the posterior covariance matrix. However, in modern settings involving high-dimensional and computationally expensive forward models, posterior covariance knowledge must be relaxed to deterministic or stochastic approximations. In the carbon flux inversion literature, Chevallier et al. proposed a stochastic method capable of approximating posterior variances of linear functionals of the model parameters that is particularly well-suited for large-scale Earth-system data assimilation tasks. This note formalizes this algorithm and clarifies its properties. We provide a formal statement of the algorithm, demonstrate why it converges to the desired posterior variance quantity of interest, and provide additional uncertainty quantification allowing incorporation of the Monte Carlo sampling uncertainty into the method's Bayesian credible intervals. The methodology is demonstrated using toy simulations and a realistic carbon flux inversion observing system simulation experiment.
Positron emission tomography (PET) serves as an essential tool for diagnosis of encephalopathy and brain science research. However, it suffers from the limited choice of tracers. Nowadays, with the wide application of PET imaging in neuropsychiatric treatment, 6-18F-fluoro-3, 4-dihydroxy-L-phenylalanine (DOPA) has been found to be more effective than 18F-labeled fluorine-2-deoxyglucose (FDG) in the field. Nevertheless, due to the complexity of its preparation and other limitations, DOPA is far less widely used than FDG. To address this issue, a tracer conversion invertible neural network (TC-INN) for image projection is developed to map FDG images to DOPA images through deep learning. More diagnostic information is obtained by generating PET images from FDG to DOPA. Specifically, the proposed TC-INN consists of two separate phases, one for training traceable data, the other for rebuilding new data. The reference DOPA PET image is used as a learning target for the corresponding network during the training process of tracer conversion. Meanwhile, the invertible network iteratively estimates the resultant DOPA PET data and compares it to the reference DOPA PET data. Notably, the reversible model employs variable enhancement technique to achieve better power generation. Moreover, image registration needs to be performed before training due to the angular deviation of the acquired FDG and DOPA data information. Experimental results exhibited excellent generation capability in mapping between FDG and DOPA, suggesting that PET tracer conversion has great potential in the case of limited tracer applications.
We proposed a new Convolution Neural Network implementation optimized for sparse 3D data inference. This implementation uses NanoVDB as the data structure to store the sparse tensor. It leaves a relatively small memory footprint while maintaining high performance. We demonstrate that this architecture is around 20 times faster than the state-of-the-art dense CNN model on a high-resolution 3D object classification network.
Optical quantum sensing promises measurement precision beyond classical sensors termed the Heisenberg limit (HL). However, conventional methodologies often rely on prior knowledge of the target system to achieve HL, presenting challenges in practical applications. Addressing this limitation, we introduce an innovative Deep Learning-based Quantum Sensing scheme (DQS), enabling optical quantum sensors to attain HL in agnostic environments. DQS incorporates two essential components: a Graph Neural Network (GNN) predictor and a trigonometric interpolation algorithm. Operating within a data-driven paradigm, DQS utilizes the GNN predictor, trained on offline data, to unveil the intrinsic relationships between the optical setups employed in preparing the probe state and the resulting quantum Fisher information (QFI) after interaction with the agnostic environment. This distilled knowledge facilitates the identification of optimal optical setups associated with maximal QFI. Subsequently, DQS employs a trigonometric interpolation algorithm to recover the unknown parameter estimates for the identified optical setups. Extensive experiments are conducted to investigate the performance of DQS under different settings up to eight photons. Our findings not only offer a new lens through which to accelerate optical quantum sensing tasks but also catalyze future research integrating deep learning and quantum mechanics.
Infertility is a global health problem, and an increasing number of couples are seeking medical assistance to achieve reproduction, at least half of which are caused by men. The success rate of assisted reproductive technologies depends on sperm assessment, in which experts determine whether sperm can be used for reproduction based on morphology and motility of sperm. Previous sperm assessment studies with deep learning have used datasets comprising images that include only sperm heads, which cannot consider motility and other morphologies of sperm. Furthermore, the labels of the dataset are one-hot, which provides insufficient support for experts, because assessment results are inconsistent between experts, and they have no absolute answer. Therefore, we constructed the video dataset for sperm assessment whose videos include sperm head as well as neck and tail, and its labels were annotated with soft-label. Furthermore, we proposed the sperm assessment framework and the neural network, RoSTFine, for sperm video recognition. Experimental results showed that RoSTFine could improve the sperm assessment performances compared to existing video recognition models and focus strongly on important sperm parts (i.e., head and neck).
Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges:(1) word ambiguity, (2) word synonymity, and (3) dynamic contextual dependency. To address these challenges, we propose a novel GNN-based sparse structure learning model for inductive document classification. Specifically, a document-level graph is initially generated by a disjoint union of sentence-level word co-occurrence graphs. Our model collects a set of trainable edges connecting disjoint words between sentences and employs structure learning to sparsely select edges with dynamic contextual dependencies. Graphs with sparse structures can jointly exploit local and global contextual information in documents through GNNs. For inductive learning, the refined document graph is further fed into a general readout function for graph-level classification and optimization in an end-to-end manner. Extensive experiments on several real-world datasets demonstrate that the proposed model outperforms most state-of-the-art results, and reveal the necessity to learn sparse structures for each document.
Recent contrastive representation learning methods rely on estimating mutual information (MI) between multiple views of an underlying context. E.g., we can derive multiple views of a given image by applying data augmentation, or we can split a sequence into views comprising the past and future of some step in the sequence. Contrastive lower bounds on MI are easy to optimize, but have a strong underestimation bias when estimating large amounts of MI. We propose decomposing the full MI estimation problem into a sum of smaller estimation problems by splitting one of the views into progressively more informed subviews and by applying the chain rule on MI between the decomposed views. This expression contains a sum of unconditional and conditional MI terms, each measuring modest chunks of the total MI, which facilitates approximation via contrastive bounds. To maximize the sum, we formulate a contrastive lower bound on the conditional MI which can be approximated efficiently. We refer to our general approach as Decomposed Estimation of Mutual Information (DEMI). We show that DEMI can capture a larger amount of MI than standard non-decomposed contrastive bounds in a synthetic setting, and learns better representations in a vision domain and for dialogue generation.
When learning tasks over time, artificial neural networks suffer from a problem known as Catastrophic Forgetting (CF). This happens when the weights of a network are overwritten during the training of a new task causing forgetting of old information. To address this issue, we propose MetA Reusable Knowledge or MARK, a new method that fosters weight reusability instead of overwriting when learning a new task. Specifically, MARK keeps a set of shared weights among tasks. We envision these shared weights as a common Knowledge Base (KB) that is not only used to learn new tasks, but also enriched with new knowledge as the model learns new tasks. Key components behind MARK are two-fold. On the one hand, a metalearning approach provides the key mechanism to incrementally enrich the KB with new knowledge and to foster weight reusability among tasks. On the other hand, a set of trainable masks provides the key mechanism to selectively choose from the KB relevant weights to solve each task. By using MARK, we achieve state of the art results in several popular benchmarks, surpassing the best performing methods in terms of average accuracy by over 10% on the 20-Split-MiniImageNet dataset, while achieving almost zero forgetfulness using 55% of the number of parameters. Furthermore, an ablation study provides evidence that, indeed, MARK is learning reusable knowledge that is selectively used by each task.
Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.
Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.
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