This article presents a general Bayesian learning framework for multi-modal groupwise registration on medical images. The method builds on probabilistic modelling of the image generative process, where the underlying common anatomy and geometric variations of the observed images are explicitly disentangled as latent variables. Thus, groupwise registration is achieved through the solution to Bayesian inference. We propose a novel hierarchical variational auto-encoding architecture to realize the inference procedure of the latent variables, where the registration parameters can be calculated in a mathematically interpretable fashion. Remarkably, this new paradigm can learn groupwise registration in an unsupervised closed-loop self-reconstruction process, sparing the burden of designing complex intensity-based similarity measures. The computationally efficient disentangled architecture is also inherently scalable and flexible, allowing for groupwise registration on large-scale image groups with variable sizes. Furthermore, the inferred structural representations from disentanglement learning are capable of capturing the latent anatomy of the observations with visual semantics. Extensive experiments were conducted to validate the proposed framework, including four datasets from cardiac, brain and abdominal medical images. The results have demonstrated the superiority of our method over conventional similarity-based approaches in terms of accuracy, efficiency, scalability and interpretability.
We analyze recurrent neural networks trained with gradient descent in the supervised learning setting for dynamical systems, and prove that gradient descent can achieve optimality \emph{without} massive overparameterization. Our in-depth nonasymptotic analysis (i) provides sharp bounds on the network size $m$ and iteration complexity $\tau$ in terms of the sequence length $T$, sample size $n$ and ambient dimension $d$, and (ii) identifies the significant impact of long-term dependencies in the dynamical system on the convergence and network width bounds characterized by a cutoff point that depends on the Lipschitz continuity of the activation function. Remarkably, this analysis reveals that an appropriately-initialized recurrent neural network trained with $n$ samples can achieve optimality with a network size $m$ that scales only logarithmically with $n$. This sharply contrasts with the prior works that require high-order polynomial dependency of $m$ on $n$ to establish strong regularity conditions. Our results are based on an explicit characterization of the class of dynamical systems that can be approximated and learned by recurrent neural networks via norm-constrained transportation mappings, and establishing local smoothness properties of the hidden state with respect to the learnable parameters.
We analyze the behaviors of open large language models (LLMs) on the task of data-to-text (D2T) generation, i.e., generating coherent and relevant text from structured data. To avoid the issue of LLM training data contamination with standard benchmarks, we design Quintd - a tool for collecting novel structured data records from public APIs. Using a dataset collected with Quintd and leveraging reference-free evaluation, we analyze model behaviors on five D2T generation tasks. We find that recent open LLMs (Llama2, Mistral, and Zephyr) can generate fluent and coherent text from standard data formats in zero-shot settings. However, we also show that the semantic accuracy of the outputs is a major issue: both according to our GPT-4-based metric and human annotators, more than 80% of the outputs of open LLMs contain a semantic error. We publicly release the code, data, and model outputs.
Is preferred tokenization for humans also preferred for machine-learning (ML) models? This study examines the relations between preferred tokenization for humans (appropriateness and readability) and one for ML models (performance on an NLP task). The question texts of the Japanese commonsense question-answering dataset are tokenized with six different tokenizers, and the performances of human annotators and ML models were compared. Furthermore, we analyze relations among performance of answers by human and ML model, the appropriateness of tokenization for human, and response time to questions by human. This study provides a quantitative investigation result that shows that preferred tokenizations for humans and ML models are not necessarily always the same. The result also implies that existing methods using language models for tokenization could be a good compromise both for human and ML models.
Multimodality Representation Learning, as a technique of learning to embed information from different modalities and their correlations, has achieved remarkable success on a variety of applications, such as Visual Question Answering (VQA), Natural Language for Visual Reasoning (NLVR), and Vision Language Retrieval (VLR). Among these applications, cross-modal interaction and complementary information from different modalities are crucial for advanced models to perform any multimodal task, e.g., understand, recognize, retrieve, or generate optimally. Researchers have proposed diverse methods to address these tasks. The different variants of transformer-based architectures performed extraordinarily on multiple modalities. This survey presents the comprehensive literature on the evolution and enhancement of deep learning multimodal architectures to deal with textual, visual and audio features for diverse cross-modal and modern multimodal tasks. This study summarizes the (i) recent task-specific deep learning methodologies, (ii) the pretraining types and multimodal pretraining objectives, (iii) from state-of-the-art pretrained multimodal approaches to unifying architectures, and (iv) multimodal task categories and possible future improvements that can be devised for better multimodal learning. Moreover, we prepare a dataset section for new researchers that covers most of the benchmarks for pretraining and finetuning. Finally, major challenges, gaps, and potential research topics are explored. A constantly-updated paperlist related to our survey is maintained at //github.com/marslanm/multimodality-representation-learning.
We present VeriX, a first step towards verified explainability of machine learning models in safety-critical applications. Specifically, our sound and optimal explanations can guarantee prediction invariance against bounded perturbations. We utilise constraint solving techniques together with feature sensitivity ranking to efficiently compute these explanations. We evaluate our approach on image recognition benchmarks and a real-world scenario of autonomous aircraft taxiing.
Graph neural networks (GNNs) have emerged as a series of competent graph learning methods for diverse real-world scenarios, ranging from daily applications like recommendation systems and question answering to cutting-edge technologies such as drug discovery in life sciences and n-body simulation in astrophysics. However, task performance is not the only requirement for GNNs. Performance-oriented GNNs have exhibited potential adverse effects like vulnerability to adversarial attacks, unexplainable discrimination against disadvantaged groups, or excessive resource consumption in edge computing environments. To avoid these unintentional harms, it is necessary to build competent GNNs characterised by trustworthiness. To this end, we propose a comprehensive roadmap to build trustworthy GNNs from the view of the various computing technologies involved. In this survey, we introduce basic concepts and comprehensively summarise existing efforts for trustworthy GNNs from six aspects, including robustness, explainability, privacy, fairness, accountability, and environmental well-being. Additionally, we highlight the intricate cross-aspect relations between the above six aspects of trustworthy GNNs. Finally, we present a thorough overview of trending directions for facilitating the research and industrialisation of trustworthy GNNs.
Graph neural networks generalize conventional neural networks to graph-structured data and have received widespread attention due to their impressive representation ability. In spite of the remarkable achievements, the performance of Euclidean models in graph-related learning is still bounded and limited by the representation ability of Euclidean geometry, especially for datasets with highly non-Euclidean latent anatomy. Recently, hyperbolic space has gained increasing popularity in processing graph data with tree-like structure and power-law distribution, owing to its exponential growth property. In this survey, we comprehensively revisit the technical details of the current hyperbolic graph neural networks, unifying them into a general framework and summarizing the variants of each component. More importantly, we present various HGNN-related applications. Last, we also identify several challenges, which potentially serve as guidelines for further flourishing the achievements of graph learning in hyperbolic spaces.
Since deep neural networks were developed, they have made huge contributions to everyday lives. Machine learning provides more rational advice than humans are capable of in almost every aspect of daily life. However, despite this achievement, the design and training of neural networks are still challenging and unpredictable procedures. To lower the technical thresholds for common users, automated hyper-parameter optimization (HPO) has become a popular topic in both academic and industrial areas. This paper provides a review of the most essential topics on HPO. The first section introduces the key hyper-parameters related to model training and structure, and discusses their importance and methods to define the value range. Then, the research focuses on major optimization algorithms and their applicability, covering their efficiency and accuracy especially for deep learning networks. This study next reviews major services and toolkits for HPO, comparing their support for state-of-the-art searching algorithms, feasibility with major deep learning frameworks, and extensibility for new modules designed by users. The paper concludes with problems that exist when HPO is applied to deep learning, a comparison between optimization algorithms, and prominent approaches for model evaluation with limited computational resources.
Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require that a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with an arbitrary depth. Although the primitive graph neural networks have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on graph convolutional network (GCN) and gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research.
We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.