In many scenarios, especially biomedical applications, the correct delineation of complex fine-scaled structures such as neurons, tissues, and vessels is critical for downstream analysis. Despite the strong predictive power of deep learning methods, they do not provide a satisfactory representation of these structures, thus creating significant barriers in scalable annotation and downstream analysis. In this dissertation, we tackle such challenges by proposing novel representations of these topological structures in a deep learning framework. We leverage the mathematical tools from topological data analysis, i.e., persistent homology and discrete Morse theory, to develop principled methods for better segmentation and uncertainty estimation, which will become powerful tools for scalable annotation.
In this paper, we present SIMAP, a novel layer integrated into deep learning models, aimed at enhancing the interpretability of the output. The SIMAP layer is an enhanced version of Simplicial-Map Neural Networks (SMNNs), an explainable neural network based on support sets and simplicial maps (functions used in topology to transform shapes while preserving their structural connectivity). The novelty of the methodology proposed in this paper is two-fold: Firstly, SIMAP layers work in combination with other deep learning architectures as an interpretable layer substituting classic dense final layers. Secondly, unlike SMNNs, the support set is based on a fixed maximal simplex, the barycentric subdivision being efficiently computed with a matrix-based multiplication algorithm.
Although an ever-growing number of applications employ deep learning based systems for prediction, decision-making, or state estimation, almost no certification processes have been established that would allow such systems to be deployed in safety-critical applications. In this work we consider real-world problems arising in aviation and other safety-critical areas, and investigate their requirements for a certified model. To this end, we investigate methodologies from the machine learning research community aimed towards verifying robustness and reliability of deep learning systems, and evaluate these methodologies with regard to their applicability to real-world problems. Then, we establish a new framework towards deep learning certification based on (i) inherently safe design, and (ii) run-time error detection. Using a concrete use case from aviation, we show how deep learning models can recover disentangled variables through the use of weakly-supervised representation learning. We argue that such a system design is inherently less prone to common model failures, and can be verified to encode underlying mechanisms governing the data. Then, we investigate four techniques related to the run-time safety of a model, namely (i) uncertainty quantification, (ii) out-of-distribution detection, (iii) feature collapse, and (iv) adversarial attacks. We evaluate each for their applicability and formulate a set of desiderata that a certified model should fulfill. Finally, we propose a novel model structure that exhibits all desired properties discussed in this work, and is able to make regression and uncertainty predictions, as well as detect out-of-distribution inputs, while requiring no regression labels to train. We conclude with a discussion of the current state and expected future progress of deep learning certification, and its industrial and social implications.
Deep neural network (DNN) inference has become an important part of many data-center workloads. This has prompted focused efforts to design ever-faster deep learning accelerators such as GPUs and TPUs. However, an end-to-end DNN-based vision application contains more than just DNN inference, including input decompression, resizing, sampling, normalization, and data transfer. In this paper, we perform a thorough evaluation of computer vision inference requests performed on a throughput-optimized serving system. We quantify the performance impact of server overheads such as data movement, preprocessing, and message brokers between two DNNs producing outputs at different rates. Our empirical analysis encompasses many computer vision tasks including image classification, segmentation, detection, depth-estimation, and more complex processing pipelines with multiple DNNs. Our results consistently demonstrate that end-to-end application performance can easily be dominated by data processing and data movement functions (up to 56% of end-to-end latency in a medium-sized image, and $\sim$ 80% impact on system throughput in a large image), even though these functions have been conventionally overlooked in deep learning system design. Our work identifies important performance bottlenecks in different application scenarios, achieves 2.25$\times$ better throughput compared to prior work, and paves the way for more holistic deep learning system design.
Deep learning, despite its remarkable achievements, is still a young field. Like the early stages of many scientific disciplines, it is marked by the discovery of new phenomena, ad-hoc design decisions, and the lack of a uniform and compositional mathematical foundation. From the intricacies of the implementation of backpropagation, through a growing zoo of neural network architectures, to the new and poorly understood phenomena such as double descent, scaling laws or in-context learning, there are few unifying principles in deep learning. This thesis develops a novel mathematical foundation for deep learning based on the language of category theory. We develop a new framework that is a) end-to-end, b) unform, and c) not merely descriptive, but prescriptive, meaning it is amenable to direct implementation in programming languages with sufficient features. We also systematise many existing approaches, placing many existing constructions and concepts from the literature under the same umbrella. In Part I we identify and model two main properties of deep learning systems parametricity and bidirectionality by we expand on the previously defined construction of actegories and Para to study the former, and define weighted optics to study the latter. Combining them yields parametric weighted optics, a categorical model of artificial neural networks, and more. Part II justifies the abstractions from Part I, applying them to model backpropagation, architectures, and supervised learning. We provide a lens-theoretic axiomatisation of differentiation, covering not just smooth spaces, but discrete settings of boolean circuits as well. We survey existing, and develop new categorical models of neural network architectures. We formalise the notion of optimisers and lastly, combine all the existing concepts together, providing a uniform and compositional framework for supervised learning.
Machine Translation Quality Estimation (MTQE) is the task of estimating the quality of machine-translated text in real time without the need for reference translations, which is of great importance for the development of MT. After two decades of evolution, QE has yielded a wealth of results. This article provides a comprehensive overview of QE datasets, annotation methods, shared tasks, methodologies, challenges, and future research directions. It begins with an introduction to the background and significance of QE, followed by an explanation of the concepts and evaluation metrics for word-level QE, sentence-level QE, document-level QE, and explainable QE. The paper categorizes the methods developed throughout the history of QE into those based on handcrafted features, deep learning, and Large Language Models (LLMs), with a further division of deep learning-based methods into classic deep learning and those incorporating pre-trained language models (LMs). Additionally, the article details the advantages and limitations of each method and offers a straightforward comparison of different approaches. Finally, the paper discusses the current challenges in QE research and provides an outlook on future research directions.
Predictions of opaque black-box systems are frequently deployed in high-stakes applications such as healthcare. For such applications, it is crucial to assess how models handle samples beyond the domain of training data. While several metrics and tests exist to detect out-of-distribution (OoD) data from in-distribution (InD) data to a deep neural network (DNN), their performance varies significantly across datasets, models, and tasks, which limits their practical use. In this paper, we propose a hypothesis-driven approach to quantify whether a new sample is InD or OoD. Given a trained DNN and some input, we first feed the input through the DNN and compute an ensemble of OoD metrics, which we term latent responses. We then formulate the OoD detection problem as a hypothesis test between latent responses of different groups, and use permutation-based resampling to infer the significance of the observed latent responses under a null hypothesis. We adapt our method to detect an unseen sample of bacteria to a trained deep learning model, and show that it reveals interpretable differences between InD and OoD latent responses. Our work has implications for systematic novelty detection and informed decision-making from classifiers trained on a subset of labels.
The integration of deep learning techniques with biophotonic setups has opened new horizons in bioimaging. A compelling trend in this field involves deliberately compromising certain measurement metrics to engineer better bioimaging tools in terms of cost, speed, and form-factor, followed by compensating for the resulting defects through the utilization of deep learning models trained on a large amount of ideal, superior or alternative data. This strategic approach has found increasing popularity due to its potential to enhance various aspects of biophotonic imaging. One of the primary motivations for employing this strategy is the pursuit of higher temporal resolution or increased imaging speed, critical for capturing fine dynamic biological processes. This approach also offers the prospect of simplifying hardware requirements/complexities, thereby making advanced imaging standards more accessible in terms of cost and/or size. This article provides an in-depth review of the diverse measurement aspects that researchers intentionally impair in their biophotonic setups, including the point spread function, signal-to-noise ratio, sampling density, and pixel resolution. By deliberately compromising these metrics, researchers aim to not only recuperate them through the application of deep learning networks, but also bolster in return other crucial parameters, such as the field-of-view, depth-of-field, and space-bandwidth product. Here, we discuss various biophotonic methods that have successfully employed this strategic approach. These techniques span broad applications and showcase the versatility and effectiveness of deep learning in the context of compromised biophotonic data. Finally, by offering our perspectives on the future possibilities of this rapidly evolving concept, we hope to motivate our readers to explore novel ways of balancing hardware compromises with compensation via AI.
Remote sensing through unmanned aerial systems (UAS) has been increasing in forestry in recent years, along with using machine learning for data processing. Deep learning architectures, extensively applied in natural language and image processing, have recently been extended to the point cloud domain. However, the availability of point cloud datasets for training and testing remains limited. Creating forested environment point cloud datasets is expensive, requires high-precision sensors, and is time-consuming as manual point classification is required. Moreover, forest areas could be inaccessible or dangerous for humans, further complicating data collection. Then, a question arises whether it is possible to use synthetic data to train deep learning networks without the need to rely on large volumes of real forest data. To answer this question, we developed a realistic simulator that procedurally generates synthetic forest scenes. Thanks to this, we have conducted a comparative study of different state-of-the-art point-based deep learning networks for forest segmentation. Using created datasets, we determined the feasibility of using synthetic data to train deep learning networks to classify point clouds from real forest datasets. Both the simulator and the datasets are released as part of this work.
Trajectory computing is a pivotal domain encompassing trajectory data management and mining, garnering widespread attention due to its crucial role in various practical applications such as location services, urban traffic, and public safety. Traditional methods, focusing on simplistic spatio-temporal features, face challenges of complex calculations, limited scalability, and inadequate adaptability to real-world complexities. In this paper, we present a comprehensive review of the development and recent advances in deep learning for trajectory computing (DL4Traj). We first define trajectory data and provide a brief overview of widely-used deep learning models. Systematically, we explore deep learning applications in trajectory management (pre-processing, storage, analysis, and visualization) and mining (trajectory-related forecasting, trajectory-related recommendation, trajectory classification, travel time estimation, anomaly detection, and mobility generation). Notably, we encapsulate recent advancements in Large Language Models (LLMs) that hold the potential to augment trajectory computing. Additionally, we summarize application scenarios, public datasets, and toolkits. Finally, we outline current challenges in DL4Traj research and propose future directions. Relevant papers and open-source resources have been collated and are continuously updated at: \href{https://github.com/yoshall/Awesome-Trajectory-Computing}{DL4Traj Repo}.
Machine-learning techniques, especially deep convolutional neural networks, are pivotal for image-based identification of biological species in many Citizen Science platforms. In this paper, we describe the construction of a dataset for the Portuguese native flora based on publicly available research-grade datasets, and the derivation of a high-accuracy model from it using off-the-shelf deep convolutional neural networks. We anchored the dataset in high-quality data provided by Sociedade Portuguesa de Bot\^anica and added further sampled data from research-grade datasets available from GBIF. We find that with a careful dataset design, off-the-shelf machine-learning cloud services such as Google's AutoML Vision produce accurate models, with results comparable to those of Pl@ntNet, a state-of-the-art citizen science platform. The best model we derived, dubbed Floralens, has been integrated into the public website of Project Biolens, where we gather models for other taxa as well. The dataset used to train the model is also publicly available on Zenodo.
Coronary artery disease (CAD) is the dominant cause of death and hospitalization across the globe. Atherosclerosis, an inflammatory condition that gradually narrows arteries and has potentially fatal effects, is the most frequent cause of CAD. Nonetheless, the circulation regularly adapts in the presence of atherosclerosis, through the formation of collateral arteries, resulting in significant long-term health benefits. Therefore, timely detection of coronary collateral circulation (CCC) is crucial for CAD personalized medicine. We propose a novel deep learning based method to detect CCC in angiographic images. Our method relies on a convolutional backbone to extract spatial features from each frame of an angiography sequence. The features are then concatenated, and subsequently processed by another convolutional layer that processes embeddings temporally. Due to scarcity of data, we also experiment with pretraining the backbone on coronary artery segmentation, which improves the results consistently. Moreover, we experiment with few-shot learning to further improve performance, given our low data regime. We present our results together with subgroup analyses based on Rentrop grading, collateral flow, and collateral grading, which provide valuable insights into model performance. Overall, the proposed method shows promising results in detecting CCC, and can be further extended to perform landmark based CCC detection and CCC quantification.
Spacecraft operations are highly critical, demanding impeccable reliability and safety. Ensuring the optimal performance of a spacecraft requires the early detection and mitigation of anomalies, which could otherwise result in unit or mission failures. With the advent of deep learning, a surge of interest has been seen in leveraging these sophisticated algorithms for anomaly detection in space operations. This study aims to compare the efficacy of various deep learning architectures in detecting anomalies in spacecraft data. The deep learning models under investigation include Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Long Short-Term Memory (LSTM) networks, and Transformer-based architectures. Each of these models was trained and validated using a comprehensive dataset sourced from multiple spacecraft missions, encompassing diverse operational scenarios and anomaly types. Initial results indicate that while CNNs excel in identifying spatial patterns and may be effective for some classes of spacecraft data, LSTMs and RNNs show a marked proficiency in capturing temporal anomalies seen in time-series spacecraft telemetry. The Transformer-based architectures, given their ability to focus on both local and global contexts, have showcased promising results, especially in scenarios where anomalies are subtle and span over longer durations. Additionally, considerations such as computational efficiency, ease of deployment, and real-time processing capabilities were evaluated. While CNNs and LSTMs demonstrated a balance between accuracy and computational demands, Transformer architectures, though highly accurate, require significant computational resources. In conclusion, the choice of deep learning architecture for spacecraft anomaly detection is highly contingent on the nature of the data, the type of anomalies, and operational constraints.
Delicate cloth simulations have long been desired in computer graphics. Various methods were proposed to improve engaged force interactions, collision handling, and numerical integrations. Deep learning has the potential to achieve fast and real-time simulation, but common neural network structures often demand many parameters to capture cloth dynamics. This paper proposes a physics-embedded learning framework that directly encodes physical features of cloth simulation. The convolutional neural network is used to represent spatial correlations of the mass-spring system, after which three branches are designed to learn linear, nonlinear, and time derivate features of cloth physics. The framework can also integrate with other external forces and collision handling through either traditional simulators or sub neural networks. The model is tested across different cloth animation cases, without training with new data. Agreement with baselines and predictive realism successfully validate its generalization ability. Inference efficiency of the proposed model also defeats traditional physics simulation. This framework is also designed to easily integrate with other visual refinement techniques like wrinkle carving, which leaves significant chances to incorporate prevailing macing learning techniques in 3D cloth amination.
We propose a learning-based method for adaptively generating low probability of detection (LPD) radar waveforms that blend into their operating environment. Our waveforms are designed to follow a distribution that is indistinguishable from the ambient radio frequency (RF) background -- while still being effective at ranging and sensing. To do so, we use an unsupervised, adversarial learning framework; our generator network produces waveforms designed to confuse a critic network, which is optimized to differentiate generated waveforms from the background. To ensure our generated waveforms are still effective for sensing, we introduce and minimize an ambiguity function-based loss on the generated waveforms. We evaluate the performance of our method by comparing the single-pulse detectability of our generated waveforms with traditional LPD waveforms using a separately trained detection neural network. We find that our method can generate LPD waveforms that reduce detectability by up to 90% while simultaneously offering improved ambiguity function (sensing) characteristics. Our framework also provides a mechanism to trade-off detectability and sensing performance.
In recent years, we have witnessed the emergence of scientific machine learning as a data-driven tool for the analysis, by means of deep-learning techniques, of data produced by computational science and engineering applications. At the core of these methods is the supervised training algorithm to learn the neural network realization, a highly non-convex optimization problem that is usually solved using stochastic gradient methods. However, distinct from deep-learning practice, scientific machine-learning training problems feature a much larger volume of smooth data and better characterizations of the empirical risk functions, which make them suited for conventional solvers for unconstrained optimization. We introduce a lightweight software framework built on top of the Portable and Extensible Toolkit for Scientific computation to bridge the gap between deep-learning software and conventional solvers for unconstrained minimization. We empirically demonstrate the superior efficacy of a trust region method based on the Gauss-Newton approximation of the Hessian in improving the generalization errors arising from regression tasks when learning surrogate models for a wide range of scientific machine-learning techniques and test cases. All the conventional second-order solvers tested, including L-BFGS and inexact Newton with line-search, compare favorably, either in terms of cost or accuracy, with the adaptive first-order methods used to validate the surrogate models.
In numerous studies, deep learning algorithms have proven their potential for the analysis of histopathology images, for example, for revealing the subtypes of tumors or the primary origin of metastases. These models require large datasets for training, which must be anonymized to prevent possible patient identity leaks. This study demonstrates that even relatively simple deep learning algorithms can re-identify patients in large histopathology datasets with substantial accuracy. We evaluated our algorithms on two TCIA datasets including lung squamous cell carcinoma (LSCC) and lung adenocarcinoma (LUAD). We also demonstrate the algorithm's performance on an in-house dataset of meningioma tissue. We predicted the source patient of a slide with F1 scores of 50.16 % and 52.30 % on the LSCC and LUAD datasets, respectively, and with 62.31 % on our meningioma dataset. Based on our findings, we formulated a risk assessment scheme to estimate the risk to the patient's privacy prior to publication.
The recent advances in deep learning (DL) have been accelerated by access to large-scale data and compute. These large-scale resources have been used to train progressively larger models which are resource intensive in terms of compute, data, energy, and carbon emissions. These costs are becoming a new type of entry barrier to researchers and practitioners with limited access to resources at such scale, particularly in the Global South. In this work, we take a comprehensive look at the landscape of existing DL models for medical image analysis tasks and demonstrate their usefulness in settings where resources are limited. To account for the resource consumption of DL models, we introduce a novel measure to estimate the performance per resource unit, which we call the PePR score. Using a diverse family of 131 unique DL architectures (spanning 1M to 130M trainable parameters) and three medical image datasets, we capture trends about the performance-resource trade-offs. In applications like medical image analysis, we argue that small-scale, specialized models are better than striving for large-scale models. Furthermore, we show that using existing pretrained models that are fine-tuned on new data can significantly reduce the computational resources and data required compared to training models from scratch. We hope this work will encourage the community to focus on improving AI equity by developing methods and models with smaller resource footprints.
Stereophotogrammetry is an emerging technique of scene understanding. Its origins go back to at least the 1800s when people first started to investigate using photographs to measure the physical properties of the world. Since then, thousands of approaches have been explored. The classic geometric techniques of Shape from Stereo is built on using geometry to define constraints on scene and camera geometry and then solving the non-linear systems of equations. More recent work has taken an entirely different approach, using end-to-end deep learning without any attempt to explicitly model the geometry. In this survey, we explore the overlap for geometric-based and deep learning-based frameworks. We compare and contrast geometry enforcing constraints integrated into a deep learning framework for depth estimation or other closely related problems. We present a new taxonomy for prevalent geometry enforcing constraints used in modern deep learning frameworks. We also present insightful observations and potential future research directions.
Despite the development of various deep learning methods for Wi-Fi sensing, package loss often results in noncontinuous estimation of the Channel State Information (CSI), which negatively impacts the performance of the learning models. To overcome this challenge, we propose a deep learning model based on Bidirectional Encoder Representations from Transformers (BERT) for CSI recovery, named CSI-BERT. CSI-BERT can be trained in an self-supervised manner on the target dataset without the need for additional data. Furthermore, unlike traditional interpolation methods that focus on one subcarrier at a time, CSI-BERT captures the sequential relationships across different subcarriers. Experimental results demonstrate that CSI-BERT achieves lower error rates and faster speed compared to traditional interpolation methods, even when facing with high loss rates. Moreover, by harnessing the recovered CSI obtained from CSI-BERT, other deep learning models like Residual Network and Recurrent Neural Network can achieve an average increase in accuracy of approximately 15\% in Wi-Fi sensing tasks. The collected dataset WiGesture and code for our model are publicly available at https://github.com/RS2002/CSI-BERT.