arXiv subjects

David Barber

Publications and source records attributed to David Barber.

At least 37 records · Page 2Linked to original sources

arXiv2024

CenTime: Event-Conditional Modelling of Censoring in Survival Analysis

Survival analysis is a valuable tool for estimating the time until specific events, such as death or cancer recurrence, based on baseline observations. This is particularly useful in healthcare to prognostically predict clinically important events based on patient data. However, existing approaches often have limitations; some focus only on ranking patients by survivability, neglecting to estimate the actual event time, while others treat the problem as a classification task, ignoring the inherent time-ordered structure of the events. Furthermore, the effective utilization of censored samples - training data points where the exact event time is unknown - is essential for improving the predictive accuracy of the model. In this paper, we introduce CenTime, a novel approach to survival analysis that directly estimates the time to event. Our method features an innovative event-conditional censoring mechanism that performs robustly even when uncensored data is scarce. We demonstrate that our approach forms a consistent estimator for the event model parameters, even in the absence of uncensored data. Furthermore, CenTime is easily integrated with deep learning models with no restrictions on batch size or the number of uncensored samples. We compare our approach with standard survival analysis methods, including the Cox proportional-hazard model and DeepHit. Our results indicate that CenTime offers state-of-the-art performance in predicting time-to-death while maintaining comparable ranking performance. Our implementation is publicly available at https://github.com/ahmedhshahin/CenTime.

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arXiv2023

Generalized Multiple Intent Conditioned Slot Filling

Natural language understanding includes the tasks of intent detection (identifying a user's objectives) and slot filling (extracting the entities relevant to those objectives). Prior slot filling methods assume that each intent type cannot occur more than once within a message, however this is often not a valid assumption for real-world settings. In this work, we generalize slot filling by removing the constraint of unique intents in a message. We cast this as a JSON generation task and approach it using a language model. We create a pre-training dataset by combining DBpedia and existing slot filling datasets that we convert for JSON generation. We also generate an in-domain dataset using GPT-3. We train T5 models for this task (with and without exemplars in the prompt) and find that both training datasets improve performance, and that the model is able to generalize to intent types not seen during training.

cs.CL↗

arXiv2023

A hybrid CNN-RNN approach for survival analysis in a Lung Cancer Screening study

In this study, we present a hybrid CNN-RNN approach to investigate long-term survival of subjects in a lung cancer screening study. Subjects who died of cardiovascular and respiratory causes were identified whereby the CNN model was used to capture imaging features in the CT scans and the RNN model was used to investigate time series and thus global information. The models were trained on subjects who underwent cardiovascular and respiratory deaths and a control cohort matched to participant age, gender, and smoking history. The combined model can achieve an AUC of 0.76 which outperforms humans at cardiovascular mortality prediction. The corresponding F1 and Matthews Correlation Coefficient are 0.63 and 0.42 respectively. The generalisability of the model is further validated on an 'external' cohort. The same models were applied to survival analysis with the Cox Proportional Hazard model. It was demonstrated that incorporating the follow-up history can lead to improvement in survival prediction. The Cox neural network can achieve an IPCW C-index of 0.75 on the internal dataset and 0.69 on an external dataset. Delineating imaging features associated with long-term survival can help focus preventative interventions appropriately, particularly for under-recognised pathologies thereby potentially reducing patient morbidity.

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arXiv2023

Smoothed Q-learning

In Reinforcement Learning the Q-learning algorithm provably converges to the optimal solution. However, as others have demonstrated, Q-learning can also overestimate the values and thereby spend too long exploring unhelpful states. Double Q-learning is a provably convergent alternative that mitigates some of the overestimation issues, though sometimes at the expense of slower convergence. We introduce an alternative algorithm that replaces the max operation with an average, resulting also in a provably convergent off-policy algorithm which can mitigate overestimation yet retain similar convergence as standard Q-learning.

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arXiv2022

Spread Divergence

For distributions $\mathbb{P}$ and $\mathbb{Q}$ with different supports or undefined densities, the divergence $\textrm{D}(\mathbb{P}||\mathbb{Q})$ may not exist. We define a Spread Divergence $\tilde{\textrm{D}}(\mathbb{P}||\mathbb{Q})$ on modified $\mathbb{P}$ and $\mathbb{Q}$ and describe sufficient conditions for the existence of such a divergence. We demonstrate how to maximize the discriminatory power of a given divergence by parameterizing and learning the spread. We also give examples of using a Spread Divergence to train implicit generative models, including linear models (Independent Components Analysis) and non-linear models (Deep Generative Networks).

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arXiv2022

Generalization Gap in Amortized Inference

The ability of likelihood-based probabilistic models to generalize to unseen data is central to many machine learning applications such as lossless compression. In this work, we study the generalization of a popular class of probabilistic model - the Variational Auto-Encoder (VAE). We discuss the two generalization gaps that affect VAEs and show that overfitting is usually dominated by amortized inference. Based on this observation, we propose a new training objective that improves the generalization of amortized inference. We demonstrate how our method can improve performance in the context of image modeling and lossless compression.

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arXiv2022

Parallel Neural Local Lossless Compression

The recently proposed Neural Local Lossless Compression (NeLLoC), which is based on a local autoregressive model, has achieved state-of-the-art (SOTA) out-of-distribution (OOD) generalization performance in the image compression task. In addition to the encouragement of OOD generalization, the local model also allows parallel inference in the decoding stage. In this paper, we propose two parallelization schemes for local autoregressive models. We discuss the practicalities of implementing the schemes and provide experimental evidence of significant gains in compression runtime compared to the previous, non-parallel implementation.

eess.IV↗

arXiv2022

Integrated Weak Learning

We introduce Integrated Weak Learning, a principled framework that integrates weak supervision into the training process of machine learning models. Our approach jointly trains the end-model and a label model that aggregates multiple sources of weak supervision. We introduce a label model that can learn to aggregate weak supervision sources differently for different datapoints and takes into consideration the performance of the end-model during training. We show that our approach outperforms existing weak learning techniques across a set of 6 benchmark classification datasets. When both a small amount of labeled data and weak supervision are present the increase in performance is both consistent and large, reliably getting a 2-5 point test F1 score gain over non-integrated methods.

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arXiv2022

Improving VAE-based Representation Learning

Latent variable models like the Variational Auto-Encoder (VAE) are commonly used to learn representations of images. However, for downstream tasks like semantic classification, the representations learned by VAE are less competitive than other non-latent variable models. This has led to some speculations that latent variable models may be fundamentally unsuitable for representation learning. In this work, we study what properties are required for good representations and how different VAE structure choices could affect the learned properties. We show that by using a decoder that prefers to learn local features, the remaining global features can be well captured by the latent, which significantly improves performance of a downstream classification task. We further apply the proposed model to semi-supervised learning tasks and demonstrate improvements in data efficiency.

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arXiv2022

Representation Learning for High-Dimensional Data Collection under Local Differential Privacy

The collection of individuals' data has become commonplace in many industries. Local differential privacy (LDP) offers a rigorous approach to preserving privacy whereby the individual privatises their data locally, allowing only their perturbed datum to leave their possession. LDP thus provides a provable privacy guarantee to the individual against both adversaries and database administrators. Existing LDP mechanisms have successfully been applied to low-dimensional data, but in high dimensions the privacy-inducing noise largely destroys the utility of the data. In this work, our contributions are two-fold: first, by adapting state-of-the-art techniques from representation learning, we introduce a novel approach to learning LDP mechanisms. These mechanisms add noise to powerful representations on the low-dimensional manifold underlying the data, thereby overcoming the prohibitive noise requirements of LDP in high dimensions. Second, we introduce a novel denoising approach for downstream model learning. The training of performant machine learning models using collected LDP data is a common goal for data collectors, and downstream model performance forms a proxy for the LDP data utility. Our approach significantly outperforms current state-of-the-art LDP mechanisms.

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arXiv2022

Survival Analysis for Idiopathic Pulmonary Fibrosis using CT Images and Incomplete Clinical Data

Idiopathic Pulmonary Fibrosis (IPF) is an inexorably progressive fibrotic lung disease with a variable and unpredictable rate of progression. CT scans of the lungs inform clinical assessment of IPF patients and contain pertinent information related to disease progression. In this work, we propose a multi-modal method that uses neural networks and memory banks to predict the survival of IPF patients using clinical and imaging data. The majority of clinical IPF patient records have missing data (e.g. missing lung function tests). To this end, we propose a probabilistic model that captures the dependencies between the observed clinical variables and imputes missing ones. This principled approach to missing data imputation can be naturally combined with a deep survival analysis model. We show that the proposed framework yields significantly better survival analysis results than baselines in terms of concordance index and integrated Brier score. Our work also provides insights into novel image-based biomarkers that are linked to mortality.

eess.IV↗

arXiv2021

Adaptive Optimization with Examplewise Gradients

We propose a new, more general approach to the design of stochastic gradient-based optimization methods for machine learning. In this new framework, optimizers assume access to a batch of gradient estimates per iteration, rather than a single estimate. This better reflects the information that is actually available in typical machine learning setups. To demonstrate the usefulness of this generalized approach, we develop Eve, an adaptation of the Adam optimizer which uses examplewise gradients to obtain more accurate second-moment estimates. We provide preliminary experiments, without hyperparameter tuning, which show that the new optimizer slightly outperforms Adam on a small scale benchmark and performs the same or worse on larger scale benchmarks. Further work is needed to refine the algorithm and tune hyperparameters.

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arXiv2021

Sample Efficient Model Evaluation

Labelling data is a major practical bottleneck in training and testing classifiers. Given a collection of unlabelled data points, we address how to select which subset to label to best estimate test metrics such as accuracy, $F_1$ score or micro/macro $F_1$. We consider two sampling based approaches, namely the well-known Importance Sampling and we introduce a novel application of Poisson Sampling. For both approaches we derive the minimal error sampling distributions and how to approximate and use them to form estimators and confidence intervals. We show that Poisson Sampling outperforms Importance Sampling both theoretically and experimentally.

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arXiv2021

Addressing Catastrophic Forgetting in Few-Shot Problems

Neural networks are known to suffer from catastrophic forgetting when trained on sequential datasets. While there have been numerous attempts to solve this problem in large-scale supervised classification, little has been done to overcome catastrophic forgetting in few-shot classification problems. We demonstrate that the popular gradient-based model-agnostic meta-learning algorithm (MAML) indeed suffers from catastrophic forgetting and introduce a Bayesian online meta-learning framework that tackles this problem. Our framework utilises Bayesian online learning and meta-learning along with Laplace approximation and variational inference to overcome catastrophic forgetting in few-shot classification problems. The experimental evaluations demonstrate that our framework can effectively achieve this goal in comparison with various baselines. As an additional utility, we also demonstrate empirically that our framework is capable of meta-learning on sequentially arriving few-shot tasks from a stationary task distribution.

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arXiv2021

Reducing the Computational Cost of Deep Generative Models with Binary Neural Networks

Deep generative models provide a powerful set of tools to understand real-world data. But as these models improve, they increase in size and complexity, so their computational cost in memory and execution time grows. Using binary weights in neural networks is one method which has shown promise in reducing this cost. However, whether binary neural networks can be used in generative models is an open problem. In this work we show, for the first time, that we can successfully train generative models which utilize binary neural networks. This reduces the computational cost of the models massively. We develop a new class of binary weight normalization, and provide insights for architecture designs of these binarized generative models. We demonstrate that two state-of-the-art deep generative models, the ResNet VAE and Flow++ models, can be binarized effectively using these techniques. We train binary models that achieve loss values close to those of the regular models but are 90%-94% smaller in size, and also allow significant speed-ups in execution time.

cs.LG↗

arXiv2021

Locally-Contextual Nonlinear CRFs for Sequence Labeling

Linear chain conditional random fields (CRFs) combined with contextual word embeddings have achieved state of the art performance on sequence labeling tasks. In many of these tasks, the identity of the neighboring words is often the most useful contextual information when predicting the label of a given word. However, contextual embeddings are usually trained in a task-agnostic manner. This means that although they may encode information about the neighboring words, it is not guaranteed. It can therefore be beneficial to design the sequence labeling architecture to directly extract this information from the embeddings. We propose locally-contextual nonlinear CRFs for sequence labeling. Our approach directly incorporates information from the neighboring embeddings when predicting the label for a given word, and parametrizes the potential functions using deep neural networks. Our model serves as a drop-in replacement for the linear chain CRF, consistently outperforming it in our ablation study. On a variety of tasks, our results are competitive with those of the best published methods. In particular, we outperform the previous state of the art on chunking on CoNLL 2000 and named entity recognition on OntoNotes 5.0 English.

cs.CL↗

arXiv2020

Learning disentangled representations with the Wasserstein Autoencoder

Disentangled representation learning has undoubtedly benefited from objective function surgery. However, a delicate balancing act of tuning is still required in order to trade off reconstruction fidelity versus disentanglement. Building on previous successes of penalizing the total correlation in the latent variables, we propose TCWAE (Total Correlation Wasserstein Autoencoder). Working in the WAE paradigm naturally enables the separation of the total-correlation term, thus providing disentanglement control over the learned representation, while offering more flexibility in the choice of reconstruction cost. We propose two variants using different KL estimators and perform extensive quantitative comparisons on data sets with known generative factors, showing competitive results relative to state-of-the-art techniques. We further study the trade off between disentanglement and reconstruction on more-difficult data sets with unknown generative factors, where the flexibility of the WAE paradigm in the reconstruction term improves reconstructions.

stat.ML↗

arXiv2020

Learning Deep-Latent Hierarchies by Stacking Wasserstein Autoencoders

Probabilistic models with hierarchical-latent-variable structures provide state-of-the-art results amongst non-autoregressive, unsupervised density-based models. However, the most common approach to training such models based on Variational Autoencoders (VAEs) often fails to leverage deep-latent hierarchies; successful approaches require complex inference and optimisation schemes. Optimal Transport is an alternative, non-likelihood-based framework for training generative models with appealing theoretical properties, in principle allowing easier training convergence between distributions. In this work we propose a novel approach to training models with deep-latent hierarchies based on Optimal Transport, without the need for highly bespoke models and inference networks. We show that our method enables the generative model to fully leverage its deep-latent hierarchy, avoiding the well known "latent variable collapse" issue of VAEs; therefore, providing qualitatively better sample generations as well as more interpretable latent representation than the original Wasserstein Autoencoder with Maximum Mean Discrepancy divergence.

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