This paper presents the design of a wireless sensor network for detecting and alerting the freezing of gait (FoG) symptoms in patients with Parkinson's disease. Three sensor nodes, each integrating a 3-axis accelerometer, can be placed on a patient at ankle, thigh, and truck. Each sensor node can independently detect FoG using an on-device deep learning (DL) model, featuring a squeeze and excitation convolutional neural network (CNN). In a validation using a public dataset, the prototype developed achieved a FoG detection sensitivity of 88.8% and an F1 score of 85.34%, using less than 20 k trainable parameters per sensor node. Once FoG is detected, an auditory signal will be generated to alert users, and the alarm signal will also be sent to mobile phones for further actions if needed. The sensor node can be easily recharged wirelessly by inductive coupling. The system is self-contained and processes all user data locally without streaming data to external devices or the cloud, thus eliminating the cybersecurity risks and power penalty associated with wireless data transmission. The developed methodology can be used in a wide range of applications.
The word alignment task, despite its prominence in the era of statistical machine translation (SMT), is niche and under-explored today. In this two-part tutorial, we argue for the continued relevance for word alignment. The first part provides a historical background to word alignment as a core component of the traditional SMT pipeline. We zero-in on GIZA++, an unsupervised, statistical word aligner with surprising longevity. Jumping forward to the era of neural machine translation (NMT), we show how insights from word alignment inspired the attention mechanism fundamental to present-day NMT. The second part shifts to a survey approach. We cover neural word aligners, showing the slow but steady progress towards surpassing GIZA++ performance. Finally, we cover the present-day applications of word alignment, from cross-lingual annotation projection, to improving translation.
Background and Purpose: Colorectal cancer is a common fatal malignancy, the fourth most common cancer in men, and the third most common cancer in women worldwide. Timely detection of cancer in its early stages is essential for treating the disease. Currently, there is a lack of datasets for histopathological image segmentation of rectal cancer, which often hampers the assessment accuracy when computer technology is used to aid in diagnosis. Methods: This present study provided a new publicly available Enteroscope Biopsy Histopathological Hematoxylin and Eosin Image Dataset for Image Segmentation Tasks (EBHI-Seg). To demonstrate the validity and extensiveness of EBHI-Seg, the experimental results for EBHI-Seg are evaluated using classical machine learning methods and deep learning methods. Results: The experimental results showed that deep learning methods had a better image segmentation performance when utilizing EBHI-Seg. The maximum accuracy of the Dice evaluation metric for the classical machine learning method is 0.948, while the Dice evaluation metric for the deep learning method is 0.965. Conclusion: This publicly available dataset contained 5,170 images of six types of tumor differentiation stages and the corresponding ground truth images. The dataset can provide researchers with new segmentation algorithms for medical diagnosis of colorectal cancer, which can be used in the clinical setting to help doctors and patients.
Jitendra Malik once said, "Supervision is the opium of the AI researcher". Most deep learning techniques heavily rely on extreme amounts of human labels to work effectively. In today's world, the rate of data creation greatly surpasses the rate of data annotation. Full reliance on human annotations is just a temporary means to solve current closed problems in AI. In reality, only a tiny fraction of data is annotated. Annotation Efficient Learning (AEL) is a study of algorithms to train models effectively with fewer annotations. To thrive in AEL environments, we need deep learning techniques that rely less on manual annotations (e.g., image, bounding-box, and per-pixel labels), but learn useful information from unlabeled data. In this thesis, we explore five different techniques for handling AEL.
Deep transfer learning (DTL) has formed a long-term quest toward enabling deep neural networks (DNNs) to reuse historical experiences as efficiently as humans. This ability is named knowledge transferability. A commonly used paradigm for DTL is firstly learning general knowledge (pre-training) and then reusing (fine-tuning) them for a specific target task. There are two consensuses of transferability of pre-trained DNNs: (1) a larger domain gap between pre-training and downstream data brings lower transferability; (2) the transferability gradually decreases from lower layers (near input) to higher layers (near output). However, these consensuses were basically drawn from the experiments based on natural images, which limits their scope of application. This work aims to study and complement them from a broader perspective by proposing a method to measure the transferability of pre-trained DNN parameters. Our experiments on twelve diverse image classification datasets get similar conclusions to the previous consensuses. More importantly, two new findings are presented, i.e., (1) in addition to the domain gap, a larger data amount and huge dataset diversity of downstream target task also prohibit the transferability; (2) although the lower layers learn basic image features, they are usually not the most transferable layers due to their domain sensitivity.
Automatic labelling of anatomical structures, such as coronary arteries, is critical for diagnosis, yet existing (non-deep learning) methods are limited by a reliance on prior topological knowledge of the expected tree-like structures. As the structure such vascular systems is often difficult to conceptualize, graph-based representations have become popular due to their ability to capture the geometric and topological properties of the morphology in an orientation-independent and abstract manner. However, graph-based learning for automated labeling of tree-like anatomical structures has received limited attention in the literature. The majority of prior studies have limitations in the entity graph construction, are dependent on topological structures, and have limited accuracy due to the anatomical variability between subjects. In this paper, we propose an intuitive graph representation method, well suited to use with 3D coordinate data obtained from angiography scans. We subsequently seek to analyze subject-specific graphs using geometric deep learning. The proposed models leverage expert annotated labels from 141 patients to learn representations of each coronary segment, while capturing the effects of anatomical variability within the training data. We investigate different variants of so-called message passing neural networks. Through extensive evaluations, our pipeline achieves a promising weighted F1-score of 0.805 for labeling coronary artery (13 classes) for a five-fold cross-validation. Considering the ability of graph models in dealing with irregular data, and their scalability for data segmentation, this work highlights the potential of such methods to provide quantitative evidence to support the decisions of medical experts.
Deep learning, especially convolutional neural networks, has triggered accelerated advancements in computer vision, bringing changes into our daily practice. Furthermore, the standardized deep learning modules (also known as backbone networks), i.e., ResNet and EfficientNet, have enabled efficient and rapid development of new computer vision solutions. Yet, deep learning methods still suffer from several drawbacks. One of the most concerning problems is the high memory and computational cost, such that dedicated computing units, typically GPUs, have to be used for training and development. Therefore, in this paper, we propose a quantifiable evaluation method, the convolutional kernel redundancy measure, which is based on perceived image differences, for guiding the network structure simplification. When applying our method to the chest X-ray image classification problem with ResNet, our method can maintain the performance of the network and reduce the number of parameters from over $23$ million to approximately $128$ thousand (reducing $99.46\%$ of the parameters).
Many challenges from natural world can be formulated as a graph matching problem. Previous deep learning-based methods mainly consider a full two-graph matching setting. In this work, we study the more general partial matching problem with multi-graph cycle consistency guarantees. Building on a recent progress in deep learning on graphs, we propose a novel data-driven method (URL) for partial multi-graph matching, which uses an object-to-universe formulation and learns latent representations of abstract universe points. The proposed approach advances the state of the art in semantic keypoint matching problem, evaluated on Pascal VOC, CUB, and Willow datasets. Moreover, the set of controlled experiments on a synthetic graph matching dataset demonstrates the scalability of our method to graphs with large number of nodes and its robustness to high partiality.
Deep learning models, though having achieved great success in many different fields over the past years, are usually data hungry, fail to perform well on unseen samples, and lack of interpretability. Various prior knowledge often exists in the target domain and their use can alleviate the deficiencies with deep learning. To better mimic the behavior of human brains, different advanced methods have been proposed to identify domain knowledge and integrate it into deep models for data-efficient, generalizable, and interpretable deep learning, which we refer to as knowledge-augmented deep learning (KADL). In this survey, we define the concept of KADL, and introduce its three major tasks, i.e., knowledge identification, knowledge representation, and knowledge integration. Different from existing surveys that are focused on a specific type of knowledge, we provide a broad and complete taxonomy of domain knowledge and its representations. Based on our taxonomy, we provide a systematic review of existing techniques, different from existing works that survey integration approaches agnostic to taxonomy of knowledge. This survey subsumes existing works and offers a bird's-eye view of research in the general area of knowledge-augmented deep learning. The thorough and critical reviews of numerous papers help not only understand current progresses but also identify future directions for the research on knowledge-augmented deep learning.
Embedded and IoT devices, largely powered by microcontroller units (MCUs), could be made more intelligent by leveraging on-device deep learning. One of the main challenges of neural network inference on an MCU is the extremely limited amount of read-write on-chip memory (SRAM, < 512 kB). SRAM is consumed by the neural network layer (operator) input and output buffers, which, traditionally, must be in memory (materialised) for an operator to execute. We discuss a novel execution paradigm for microcontroller deep learning, which modifies the execution of neural networks to avoid materialising full buffers in memory, drastically reducing SRAM usage with no computation overhead. This is achieved by exploiting the properties of operators, which can consume/produce a fraction of their input/output at a time. We describe a partial execution compiler, Pex, which produces memory-efficient execution schedules automatically by identifying subgraphs of operators whose execution can be split along the feature ("channel") dimension. Memory usage is reduced further by targeting memory bottlenecks with structured pruning, leading to the co-design of the network architecture and its execution schedule. Our evaluation of image and audio classification models: (a) establishes state-of-the-art performance in low SRAM usage regimes for considered tasks with up to +2.9% accuracy increase; (b) finds that a 4x memory reduction is possible by applying partial execution alone, or up to 10.5x when using the compiler-pruning co-design, while maintaining the classification accuracy compared to prior work; (c) uses the recovered SRAM to process higher resolution inputs instead, increasing accuracy by up to +3.9% on Visual Wake Words.
The data consistency for the physical forward model is crucial in inverse problems, especially in MR imaging reconstruction. The standard way is to unroll an iterative algorithm into a neural network with a forward model embedded. The forward model always changes in clinical practice, so the learning component's entanglement with the forward model makes the reconstruction hard to generalize. The deep learning-based proximal gradient descent was proposed and use a network as regularization term that is independent of the forward model, which makes it more generalizable for different MR acquisition settings. This one-time pre-trained regularization is applied to different MR acquisition settings and was compared to conventional L1 regularization showing ~3 dB improvement in the peak signal-to-noise ratio. We also demonstrated the flexibility of the proposed method in choosing different undersampling patterns.
This is a theoretical paper, as a companion paper of the plenary talk for the same conference ISAIC 2022. In contrast to the author's plenary talk in the same conference, conscious learning (Weng, 2022b; Weng, 2022c) which develops a single network for a life (many tasks), "Deep Learning" trains multiple networks for each task. Although "Deep Learning" may use different learning modes, including supervised, reinforcement and adversarial modes, almost all "Deep Learning" projects apparently suffer from the same misconduct, called "data deletion" and "test on training data". This paper establishes a theorem that a simple method called Pure-Guess Nearest Neighbor (PGNN) reaches any required errors on validation data set and test data set, including zero-error requirements, through the same misconduct, as long as the test data set is in the possession of the authors and both the amount of storage space and the time of training are finite but unbounded. The misconduct violates well-known protocols called transparency and cross-validation. The nature of the misconduct is fatal, because in the absence of any disjoint test, "Deep Learning" is clearly not generalizable.
Deep learning (DL) relies heavily on data, and the quality of data influences its performance significantly. However, obtaining high-quality, well-annotated datasets can be challenging or even impossible in many real-world applications, such as structural risk estimation and medical diagnosis. This presents a significant barrier to the practical implementation of DL in these fields. Physics-guided deep learning (PGDL) is a novel type of DL that can integrate physics laws to train neural networks. This can be applied to any systems that are controlled or governed by physics laws, such as mechanics, finance and medical applications. It has been demonstrated that, with the additional information provided by physics laws, PGDL achieves great accuracy and generalisation in the presence of data scarcity. This review provides a detailed examination of PGDL and offers a structured overview of its use in addressing data scarcity across various fields, including physics, engineering and medical applications. Moreover, the review identifies the current limitations and opportunities for PGDL in relation to data scarcity and offers a thorough discussion on the future prospects of PGDL.
We conduct a systematic study of backdoor vulnerabilities in normally trained Deep Learning models. They are as dangerous as backdoors injected by data poisoning because both can be equally exploited. We leverage 20 different types of injected backdoor attacks in the literature as the guidance and study their correspondences in normally trained models, which we call natural backdoor vulnerabilities. We find that natural backdoors are widely existing, with most injected backdoor attacks having natural correspondences. We categorize these natural backdoors and propose a general detection framework. It finds 315 natural backdoors in the 56 normally trained models downloaded from the Internet, covering all the different categories, while existing scanners designed for injected backdoors can at most detect 65 backdoors. We also study the root causes and defense of natural backdoors.
Oxidation states are the charges of atoms after their ionic approximation of their bonds, which have been widely used in charge-neutrality verification, crystal structure determination, and reaction estimation. Currently only heuristic rules exist for guessing the oxidation states of a given compound with many exceptions. Recent work has developed machine learning models based on heuristic structural features for predicting the oxidation states of metal ions. However, composition based oxidation state prediction still remains elusive so far, which is more important in new material discovery for which the structures are not even available. This work proposes a novel deep learning based BERT transformer language model BERTOS for predicting the oxidation states of all elements of inorganic compounds given only their chemical composition. Our model achieves 96.82\% accuracy for all-element oxidation states prediction benchmarked on the cleaned ICSD dataset and achieves 97.61\% accuracy for oxide materials. We also demonstrate how it can be used to conduct large-scale screening of hypothetical material compositions for materials discovery.
Like fingerprints, cortical folding patterns are unique to each brain even though they follow a general species-specific organization. Some folding patterns have been linked with neurodevelopmental disorders. However, due to the high inter-individual variability, the identification of rare folding patterns that could become biomarkers remains a very complex task. This paper proposes a novel unsupervised deep learning approach to identify rare folding patterns and assess the degree of deviations that can be detected. To this end, we preprocess the brain MR images to focus the learning on the folding morphology and train a beta-VAE to model the inter-individual variability of the folding. We compare the detection power of the latent space and of the reconstruction errors, using synthetic benchmarks and one actual rare configuration related to the central sulcus. Finally, we assess the generalization of our method on a developmental anomaly located in another region. Our results suggest that this method enables encoding relevant folding characteristics that can be enlightened and better interpreted based on the generative power of the beta-VAE. The latent space and the reconstruction errors bring complementary information and enable the identification of rare patterns of different nature. This method generalizes well to a different region on another dataset. Code is available at https://github.com/neurospin-projects/2022_lguillon_rare_folding_detection.
We propose a PiggyBack, a Visual Question Answering platform that allows users to apply the state-of-the-art visual-language pretrained models easily. The PiggyBack supports the full stack of visual question answering tasks, specifically data processing, model fine-tuning, and result visualisation. We integrate visual-language models, pretrained by HuggingFace, an open-source API platform of deep learning technologies; however, it cannot be runnable without programming skills or deep learning understanding. Hence, our PiggyBack supports an easy-to-use browser-based user interface with several deep learning visual language pretrained models for general users and domain experts. The PiggyBack includes the following benefits: Free availability under the MIT License, Portability due to web-based and thus runs on almost any platform, A comprehensive data creation and processing technique, and ease of use on deep learning-based visual language pretrained models. The demo video is available on YouTube and can be found at https://youtu.be/iz44RZ1lF4s.
Deep learning methods have gained increased attention in various applications due to their outstanding performance. For exploring how this high performance relates to the proper use of data artifacts and the accurate problem formulation of a given task, interpretation models have become a crucial component in developing deep learning-based systems. Interpretation models enable the understanding of the inner workings of deep learning models and offer a sense of security in detecting the misuse of artifacts in the input data. Similar to prediction models, interpretation models are also susceptible to adversarial inputs. This work introduces two attacks, AdvEdge and AdvEdge$^{+}$, that deceive both the target deep learning model and the coupled interpretation model. We assess the effectiveness of proposed attacks against two deep learning model architectures coupled with four interpretation models that represent different categories of interpretation models. Our experiments include the attack implementation using various attack frameworks. We also explore the potential countermeasures against such attacks. Our analysis shows the effectiveness of our attacks in terms of deceiving the deep learning models and their interpreters, and highlights insights to improve and circumvent the attacks.
Recent advances in deep learning (dl) have led to the release of several dl software libraries such as pytorch, Caffe, and TensorFlow, in order to assist machine learning (ml) practitioners in developing and deploying state-of-the-art deep neural networks (DNN), but they are not able to properly cope with limitations in the dl libraries such as testing or data processing. In this paper, we present a qualitative and quantitative analysis of the most frequent dl libraries combination, the distribution of dl library dependencies across the ml workflow, and formulate a set of recommendations to (i) hardware builders for more optimized accelerators and (ii) library builder for more refined future releases. Our study is based on 1,484 open-source dl projects with 46,110 contributors selected based on their reputation. First, we found an increasing trend in the usage of deep learning libraries. Second, we highlight several usage patterns of deep learning libraries. In addition, we identify dependencies between dl libraries and the most frequent combination where we discover that pytorch and Scikit-learn and, Keras and TensorFlow are the most frequent combination in 18% and 14% of the projects. The developer uses two or three dl libraries in the same projects and tends to use different multiple dl libraries in both the same function and the same files. The developer shows patterns in using various deep-learning libraries and prefers simple functions with fewer arguments and straightforward goals. Finally, we present the implications of our findings for researchers, library maintainers, and hardware vendors.
In this paper, deep-learning-based approaches namely fine-tuning of pretrained convolutional neural networks (VGG16 and VGG19), and end-to-end training of a developed CNN model, have been used in order to classify X-Ray images into four different classes that include COVID-19, normal, opacity and pneumonia cases. A dataset containing more than 20,000 X-ray scans was retrieved from Kaggle and used in this experiment. A two-stage classification approach was implemented to be compared to the one-shot classification approach. Our hypothesis was that a two-stage model will be able to achieve better performance than a one-shot model. Our results show otherwise as VGG16 achieved 95% accuracy using one-shot approach over 5-fold of training. Future work will focus on a more robust implementation of the two-stage classification model Covid-TSC. The main improvement will be allowing data to flow from the output of stage-1 to the input of stage-2, where stage-1 and stage-2 models are VGG16 models fine-tuned on the Covid-19 dataset.