Graph Neural Networks (GNNs) have emerged as powerful representation learning tools for capturing complex dependencies within diverse graph-structured data. Despite their success in a wide range of graph mining tasks, GNNs have raised serious concerns regarding their trustworthiness, including susceptibility to distribution shift, biases towards certain populations, and lack of explainability. Recently, integrating causal learning techniques into GNNs has sparked numerous ground-breaking studies since most of the trustworthiness issues can be alleviated by capturing the underlying data causality rather than superficial correlations. In this survey, we provide a comprehensive review of recent research efforts on causality-inspired GNNs. Specifically, we first present the key trustworthy risks of existing GNN models through the lens of causality. Moreover, we introduce a taxonomy of Causality-Inspired GNNs (CIGNNs) based on the type of causal learning capability they are equipped with, i.e., causal reasoning and causal representation learning. Besides, we systematically discuss typical methods within each category and demonstrate how they mitigate trustworthiness risks. Finally, we summarize useful resources and discuss several future directions, hoping to shed light on new research opportunities in this emerging field. The representative papers, along with open-source data and codes, are available in //github.com/usail-hkust/Causality-Inspired-GNNs.
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Introduction This study explores the use of the latest You Only Look Once (YOLO V7) object detection method to enhance kidney detection in medical imaging by training and testing a modified YOLO V7 on medical image formats. Methods Study includes 878 patients with various subtypes of renal cell carcinoma (RCC) and 206 patients with normal kidneys. A total of 5657 MRI scans for 1084 patients were retrieved. 326 patients with 1034 tumors recruited from a retrospective maintained database, and bounding boxes were drawn around their tumors. A primary model was trained on 80% of annotated cases, with 20% saved for testing (primary test set). The best primary model was then used to identify tumors in the remaining 861 patients and bounding box coordinates were generated on their scans using the model. Ten benchmark training sets were created with generated coordinates on not-segmented patients. The final model used to predict the kidney in the primary test set. We reported the positive predictive value (PPV), sensitivity, and mean average precision (mAP). Results The primary training set showed an average PPV of 0.94 +/- 0.01, sensitivity of 0.87 +/- 0.04, and mAP of 0.91 +/- 0.02. The best primary model yielded a PPV of 0.97, sensitivity of 0.92, and mAP of 0.95. The final model demonstrated an average PPV of 0.95 +/- 0.03, sensitivity of 0.98 +/- 0.004, and mAP of 0.95 +/- 0.01. Conclusion Using a semi-supervised approach with a medical image library, we developed a high-performing model for kidney detection. Further external validation is required to assess the model's generalizability.
Existing Large Language Models (LLMs) usually remain static after deployment, which might make it hard to inject new knowledge into the model. We aim to build models containing a considerable portion of self-updatable parameters, enabling the model to integrate new knowledge effectively and efficiently. To this end, we introduce MEMORYLLM, a model that comprises a transformer and a fixed-size memory pool within the latent space of the transformer. MEMORYLLM can self-update with text knowledge and memorize the knowledge injected earlier. Our evaluations demonstrate the ability of MEMORYLLM to effectively incorporate new knowledge, as evidenced by its performance on model editing benchmarks. Meanwhile, the model exhibits long-term information retention capacity, which is validated through our custom-designed evaluations and long-context benchmarks. MEMORYLLM also shows operational integrity without any sign of performance degradation even after nearly a million memory updates.
The Convolutional Neural Network (CNN) has emerged as a powerful and versatile tool for artificial intelligence (AI) applications. Conventional computing architectures face challenges in meeting the demanding processing requirements of compute-intensive CNN applications, as they suffer from limited throughput and low utilization. To this end, specialized accelerators have been developed to speed up CNN computations. However, as we demonstrate in this paper via extensive design space exploration, different neural network models have different characteristics, which calls for different accelerator architectures and configurations to match their computing demand. We show that a one-size-fits-all fixed architecture does not guarantee optimal power/energy/performance trade-off. To overcome this challenge, this paper proposes ARMAN, a novel reconfigurable systolic-array-based accelerator architecture based on Monolithic 3D (M3D) technology for CNN inference. The proposed accelerator offers the flexibility to reconfigure among different scale-up or scale-out arrangements depending on the neural network structure, providing the optimal trade-off across power, energy, and performance for various neural network models. We demonstrate the effectiveness of our approach through evaluations of multiple benchmarks. The results demonstrate that the proposed accelerator exhibits up to 2x, 2.24x, 1.48x, and 2x improvements in terms of execution cycles, power, energy, and EDP respectively, over the non-configurable architecture.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.
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.
Deep learning has become the dominant approach in coping with various tasks in Natural LanguageProcessing (NLP). Although text inputs are typically represented as a sequence of tokens, there isa rich variety of NLP problems that can be best expressed with a graph structure. As a result, thereis a surge of interests in developing new deep learning techniques on graphs for a large numberof NLP tasks. In this survey, we present a comprehensive overview onGraph Neural Networks(GNNs) for Natural Language Processing. We propose a new taxonomy of GNNs for NLP, whichsystematically organizes existing research of GNNs for NLP along three axes: graph construction,graph representation learning, and graph based encoder-decoder models. We further introducea large number of NLP applications that are exploiting the power of GNNs and summarize thecorresponding benchmark datasets, evaluation metrics, and open-source codes. Finally, we discussvarious outstanding challenges for making the full use of GNNs for NLP as well as future researchdirections. To the best of our knowledge, this is the first comprehensive overview of Graph NeuralNetworks for Natural Language Processing.
Knowledge base question answering (KBQA) aims to answer a question over a knowledge base (KB). Recently, a large number of studies focus on semantically or syntactically complicated questions. In this paper, we elaborately summarize the typical challenges and solutions for complex KBQA. We begin with introducing the background about the KBQA task. Next, we present the two mainstream categories of methods for complex KBQA, namely semantic parsing-based (SP-based) methods and information retrieval-based (IR-based) methods. We then review the advanced methods comprehensively from the perspective of the two categories. Specifically, we explicate their solutions to the typical challenges. Finally, we conclude and discuss some promising directions for future research.
Deep learning methods are achieving ever-increasing performance on many artificial intelligence tasks. A major limitation of deep models is that they are not amenable to interpretability. This limitation can be circumvented by developing post hoc techniques to explain the predictions, giving rise to the area of explainability. Recently, explainability of deep models on images and texts has achieved significant progress. In the area of graph data, graph neural networks (GNNs) and their explainability are experiencing rapid developments. However, there is neither a unified treatment of GNN explainability methods, nor a standard benchmark and testbed for evaluations. In this survey, we provide a unified and taxonomic view of current GNN explainability methods. Our unified and taxonomic treatments of this subject shed lights on the commonalities and differences of existing methods and set the stage for further methodological developments. To facilitate evaluations, we generate a set of benchmark graph datasets specifically for GNN explainability. We summarize current datasets and metrics for evaluating GNN explainability. Altogether, this work provides a unified methodological treatment of GNN explainability and a standardized testbed for evaluations.
Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at \url{//github.com/IBM/EvolveGCN}.
Convolutional Neural Networks (CNNs) have gained significant traction in the field of machine learning, particularly due to their high accuracy in visual recognition. Recent works have pushed the performance of GPU implementations of CNNs to significantly improve their classification and training times. With these improvements, many frameworks have become available for implementing CNNs on both CPUs and GPUs, with no support for FPGA implementations. In this work we present a modified version of the popular CNN framework Caffe, with FPGA support. This allows for classification using CNN models and specialized FPGA implementations with the flexibility of reprogramming the device when necessary, seamless memory transactions between host and device, simple-to-use test benches, and the ability to create pipelined layer implementations. To validate the framework, we use the Xilinx SDAccel environment to implement an FPGA-based Winograd convolution engine and show that the FPGA layer can be used alongside other layers running on a host processor to run several popular CNNs (AlexNet, GoogleNet, VGG A, Overfeat). The results show that our framework achieves 50 GFLOPS across 3x3 convolutions in the benchmarks. This is achieved within a practical framework, which will aid in future development of FPGA-based CNNs.
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