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Register a new userMIA-Prognosis: A Deep Learning Framework to Predict Therapy Response
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Jiancheng Yang
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Predicting clinical outcome is remarkably important but challenging. Research efforts have been paid on seeking significant biomarkers associated with the therapy response or/and patient survival. However, these biomarkers are generally costly and invasive, and possibly dissatifactory for novel therapy. On the other hand, multi-modal, heterogeneous, unaligned temporal data is continuously generated in clinical practice. This paper aims at a unified deep learning approach to predict patient prognosis and therapy response, with easily accessible data, e.g., radiographics, laboratory and clinical information. Prior arts focus on modeling single data modality, or ignore the temporal changes. Importantly, the clinical time series is asynchronous in practice, i.e., recorded with irregular intervals. In this study, we formalize the prognosis modeling as a multi-modal asynchronous time series classification task, and propose a MIA-Prognosis framework with Measurement, Intervention and Assessment (MIA) information to predict therapy response, where a Simple Temporal Attention (SimTA) module is developed to process the asynchronous time series. Experiments on synthetic dataset validate the superiory of SimTA over standard RNN-based approaches. Furthermore, we experiment the proposed method on an in-house, retrospective dataset of real-world non-small cell lung cancer patients under anti-PD-1 immunotherapy. The proposed method achieves promising performance on predicting the immunotherapy response. Notably, our predictive model could further stratify low-risk and high-risk patients in terms of long-term survival.
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The major challenge in designing a discriminative learning algorithm for predicting structured data is to address the computational issues arising from the exponential size of the output space. Existing algorithms make different assumptions to ensure efficient, polynomial time estimation of model parameters. For several combinatorial structures, including cycles, partially ordered sets, permutations and other graph classes, these assumptions do not hold. In this thesis, we address the problem of designing learning algorithms for predicting combinatorial structures by introducing two new assumptions: (i) The first assumption is that a particular counting problem can be solved efficiently. The consequence is a generalisation of the classical ridge regression for structured prediction. (ii) The second assumption is that a particular sampling problem can be solved efficiently. The consequence is a new technique for designing and analysing probabilistic structured prediction models. These results can be applied to solve several complex learning problems including but not limited to multi-label classification, multi-category hierarchical classification, and label ranking.
Understanding the role of (stochastic) gradient descent (SGD) in the training and generalisation of deep neural networks (DNNs) with ReLU activation has been the object study in the recent past. In this paper, we make use of deep gated networks (DGNs) as a framework to obtain insights about DNNs with ReLU activation. In DGNs, a single neuronal unit has two components namely the pre-activation input (equal to the inner product the weights of the layer and the previous layer outputs), and a gating value which belongs to $[0,1]$ and the output of the neuronal unit is equal to the multiplication of pre-activation input and the gating value. The standard DNN with ReLU activation, is a special case of the DGNs, wherein the gating value is $1/0$ based on whether or not the pre-activation input is positive or negative. We theoretically analyse and experiment with several variants of DGNs, each variant suited to understand a particular aspect of either training or generalisation in DNNs with ReLU activation. Our theory throws light on two questions namely i) why increasing depth till a point helps in training and ii) why increasing depth beyond a point hurts training? We also present experimental evidence to show that gate adaptation, i.e., the change of gating value through the course of training is key for generalisation.
Blood Pressure (BP) is one of the four primary vital signs indicating the status of the bodys vital (life-sustaining) functions. BP is difficult to continuously monitor using a sphygmomanometer (i.e. a blood pressure cuff), especially in everyday-setting. However, other health signals which can be easily and continuously acquired, such as photoplethysmography (PPG), show some similarities with the Aortic Pressure waveform. Based on these similarities, in recent years several methods were proposed to predict BP from the PPG signal. Building on these results, we propose an advanced personalized data-driven approach that uses a three-layer deep neural network to estimate BP based on PPG signals. Different from previous work, the proposed model analyzes the PPG signal in time-domain and automatically extracts the most critical features for this specific application, then uses a variation of recurrent neural networks called Long-Short-Term-Memory (LSTM) to map the extracted features to the BP value associated with that time window. Experimental results on two separate standard hospital datasets, yielded absolute errors mean and absolute error standard deviation for systolic and diastolic BP values outperforming prior works.
Based on the notion of information bottleneck (IB), we formulate a quantization problem called IB quantization. We show that IB quantization is equivalent to learning based on the IB principle. Under this equivalence, the standard neural network models can be viewed as scalar (single sample) IB quantizers. It is known, from conventional rate-distortion theory, that scalar quantizers are inferior to vector (multi-sample) quantizers. Such a deficiency then inspires us to develop a novel learning framework, AgrLearn, that corresponds to vector IB quantizers for learning with neural networks. Unlike standard networks, AgrLearn simultaneously optimizes against multiple data samples. We experimentally verify that AgrLearn can result in significant improvements when applied to several current deep learning architectures for image recognition and text classification. We also empirically show that AgrLearn can reduce up to 80% of the training samples needed for ResNet training.
We present a novel multimodal deep learning framework for cardiac resynchronisation therapy (CRT) response prediction from 2D echocardiography and cardiac magnetic resonance (CMR) data. The proposed method first uses the `nnU-Net segmentation model to extract segmentations of the heart over the full cardiac cycle from the two modalities. Next, a multimodal deep learning classifier is used for CRT response prediction, which combines the latent spaces of the segmentation models of the two modalities. At inference time, this framework can be used with 2D echocardiography data only, whilst taking advantage of the implicit relationship between CMR and echocardiography features learnt from the model. We evaluate our pipeline on a cohort of 50 CRT patients for whom paired echocardiography/CMR data were available, and results show that the proposed multimodal classifier results in a statistically significant improvement in accuracy compared to the baseline approach that uses only 2D echocardiography data. The combination of multimodal data enables CRT response to be predicted with 77.38% accuracy (83.33% sensitivity and 71.43% specificity), which is comparable with the current state-of-the-art in machine learning-based CRT response prediction. Our work represents the first multimodal deep learning approach for CRT response prediction.
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