OpenRaiser/Intern-Atlas huggingface dataset:
Computational complexity reduction of deep neural networks
Venue: arXiv cs.LG 2022
Year: 2022

Deep neural networks (DNN) have been widely used and play a major role in the field of computer vision and autonomous navigation. However, these DNNs are computationally complex and their deployment over resource-constrained platforms is difficult without additional optimizations and customization. In this manuscript, we describe an overview of DNN architecture and propose methods to reduce computational complexity in order to accelerate training and inference speeds to fit them on edge computing platforms with low computational resources.
"Do you follow me?": A Survey of Recent Approaches in Dialogue State Tracking
Venue: arXiv cs.CL 2022
Year: 2022

While communicating with a user, a task-oriented dialogue system has to track the user's needs at each turn according to the conversation history. This process called dialogue state tracking (DST) is crucial because it directly informs the downstream dialogue policy. DST has received a lot of interest in recent years with the text-to-text paradigm emerging as the favored approach. In this review paper, we first present the task and its associated datasets. Then, considering a large number of recent publications, we identify highlights and advances of research in 2021-2022. Although neural approaches have enabled significant progress, we argue that some critical aspects of dialogue systems such as generalizability are still underexplored. To motivate future studies, we propose several research avenues.
Phase Code Discovery for Pulse Compression Radar: A Genetic Algorithm Approach
Venue: arXiv cs.IT 2022
Year: 2022

Discovering sequences with desired properties has long been an interesting intellectual pursuit. In pulse compression radar (PCR), discovering phase codes with low aperiodic autocorrelations is essential for a good estimation performance. The design of phase code, however, is mathematically non-trivial as the aperiodic autocorrelation properties of a sequence are intractable to characterize. In this paper, we put forth a genetic algorithm (GA) approach to discover new phase codes for PCR with the mismatched filter (MMF) receiver. The developed GA, dubbed GASeq, discovers better phase codes than the state of the art. At a code length of 59, the sequence discovered by GASeq achieves a signal-to-clutter ratio (SCR) of 50.84, while the best-known sequence has an SCR of 45.16. In addition, the efficiency and scalability of GASeq enable us to search phase codes with a longer code length, which thwarts existing deep learning-based approaches. At a code length of 100, the best phase code discovered by GASeq exhibit an SCR of 63.23.
Subtype-Former: a deep learning approach for cancer subtype discovery with multi-omics data
Venue: arXiv cs.LG 2022
Year: 2022

Motivation: Cancer is heterogeneous, affecting the precise approach to personalized treatment. Accurate subtyping can lead to better survival rates for cancer patients. High-throughput technologies provide multiple omics data for cancer subtyping. However, precise cancer subtyping remains challenging due to the large amount and high dimensionality of omics data. Results: This study proposed Subtype-Former, a deep learning method based on MLP and Transformer Block, to extract the low-dimensional representation of the multi-omics data. K-means and Consensus Clustering are also used to achieve accurate subtyping results. We compared Subtype-Former with the other state-of-the-art subtyping methods across the TCGA 10 cancer types. We found that Subtype-Former can perform better on the benchmark datasets of more than 5000 tumors based on the survival analysis. In addition, Subtype-Former also achieved outstanding results in pan-cancer subtyping, which can help analyze the commonalities and differences across various cancer types at the molecular level. Finally, we applied Subtype-Former to the TCGA 10 types of cancers. We identified 50 essential biomarkers, which can be used to study targeted cancer drugs and promote the development of cancer treatments in the era of precision medicine.
Matching with AffNet based rectifications
Venue: arXiv cs.CV 2022
Year: 2022

We consider the problem of two-view matching under significant viewpoint changes with view synthesis. We propose two novel methods, minimizing the view synthesis overhead. The first one, named DenseAffNet, uses dense affine shapes estimates from AffNet, which allows it to partition the image, rectifying each partition with just a single affine map. The second one, named DepthAffNet, combines information from depth maps and affine shapes estimates to produce different sets of rectifying affine maps for different image partitions. DenseAffNet is faster than the state-of-the-art and more accurate on generic scenes. DepthAffNet is on par with the state of the art on scenes containing large planes. The evaluation is performed on 3 public datasets - EVD Dataset, Strong ViewPoint Changes Dataset and IMC Phototourism Dataset.
Renting Edge Computing Resources for Service Hosting
Venue: arXiv cs.NI 2022
Year: 2022

We consider the setting where a service is hosted on a third-party edge server deployed close to the users and a cloud server at a greater distance from the users. Due to the proximity of the edge servers to the users, requests can be served at the edge with low latency. However, as the computation resources at the edge are limited, some requests must be routed to the cloud for service and incur high latency. The system's overall performance depends on the rent cost incurred to use the edge server, the latency experienced by the users, and the cost incurred to change the amount of edge computation resources rented over time. The algorithmic challenge is to determine the amount of edge computation power to rent over time. We propose a deterministic online policy and characterize its performance for adversarial and stochastic i.i.d. request arrival processes. We also characterize a fundamental bound on the performance of any deterministic online policy. Further, we compare the performance of our policy with suitably modified versions of existing policies to conclude that our policy is robust to temporal changes in the intensity of request arrivals.
Not All Dependencies are Equal: An Empirical Study on Production Dependencies in NPM
Venue: arXiv cs.SE 2022
Year: 2022

Modern software systems are often built by leveraging code written by others in the form of libraries and packages to accelerate their development. While there are many benefits to using third-party packages, software projects often become dependent on a large number of software packages. Consequently, developers are faced with the difficult challenge of maintaining their project dependencies by keeping them up-to-date and free of security vulnerabilities. However, how often are project dependencies used in production where they could pose a threat to their project's security? We conduct an empirical study on 100 JavaScript projects using the Node Package Manager (npm) to quantify how often project dependencies are released to production and analyze their characteristics and their impact on security. Our results indicate that less than 1% of the installed dependencies are released to production. Our analysis reveals that the functionality of a package is not enough to determine if it will be released to production or not. In fact, 59% of the installed dependencies configured as runtime dependencies are not used in production, and 28.2% of the dependencies configured as development dependencies are used in production, debunking two common assumptions of dependency management. Findings also indicate that most security alerts target dependencies not used in production, making them highly unlikely to be a risk for the security of the software. Our study unveils a more complex side of dependency management: not all dependencies are equal. Dependencies used in production are more sensitive to security exposure and should be prioritized. However, current tools lack the appropriate support in identifying production dependencies.
ALADIN: Distilling Fine-grained Alignment Scores for Efficient Image-Text Matching and Retrieval
Venue: arXiv cs.CV 2022
Year: 2022

Image-text matching is gaining a leading role among tasks involving the joint understanding of vision and language. In literature, this task is often used as a pre-training objective to forge architectures able to jointly deal with images and texts. Nonetheless, it has a direct downstream application: cross-modal retrieval, which consists in finding images related to a given query text or vice-versa. Solving this task is of critical importance in cross-modal search engines. Many recent methods proposed effective solutions to the image-text matching problem, mostly using recent large vision-language (VL) Transformer networks. However, these models are often computationally expensive, especially at inference time. This prevents their adoption in large-scale cross-modal retrieval scenarios, where results should be provided to the user almost instantaneously. In this paper, we propose to fill in the gap between effectiveness and efficiency by proposing an ALign And DIstill Network (ALADIN). ALADIN first produces high-effective scores by aligning at fine-grained level images and texts. Then, it learns a shared embedding space - where an efficient kNN search can be performed - by distilling the relevance scores obtained from the fine-grained alignments. We obtained remarkable results on MS-COCO, showing that our method can compete with state-of-the-art VL Transformers while being almost 90 times faster. The code for reproducing our results is available at https://github.com/mesnico/ALADIN.
SimCURL: Simple Contrastive User Representation Learning from Command Sequences
Venue: arXiv cs.AI 2022
Year: 2022

User modeling is crucial to understanding user behavior and essential for improving user experience and personalized recommendations. When users interact with software, vast amounts of command sequences are generated through logging and analytics systems. These command sequences contain clues to the users' goals and intents. However, these data modalities are highly unstructured and unlabeled, making it difficult for standard predictive systems to learn from. We propose SimCURL, a simple yet effective contrastive self-supervised deep learning framework that learns user representation from unlabeled command sequences. Our method introduces a user-session network architecture, as well as session dropout as a novel way of data augmentation. We train and evaluate our method on a real-world command sequence dataset of more than half a billion commands. Our method shows significant improvement over existing methods when the learned representation is transferred to downstream tasks such as experience and expertise classification.
Combining Evolutionary Search with Behaviour Cloning for Procedurally Generated Content
Venue: arXiv cs.AI 2022
Year: 2022

In this work, we consider the problem of procedural content generation for video game levels. Prior approaches have relied on evolutionary search (ES) methods capable of generating diverse levels, but this generation procedure is slow, which is problematic in real-time settings. Reinforcement learning (RL) has also been proposed to tackle the same problem, and while level generation is fast, training time can be prohibitively expensive. We propose a framework to tackle the procedural content generation problem that combines the best of ES and RL. In particular, our approach first uses ES to generate a sequence of levels evolved over time, and then uses behaviour cloning to distil these levels into a policy, which can then be queried to produce new levels quickly. We apply our approach to a maze game and Super Mario Bros, with our results indicating that our approach does in fact decrease the time required for level generation, especially when an increasing number of valid levels are required.
Using Multi-modal Data for Improving Generalizability and Explainability of Disease Classification in Radiology
Venue: arXiv cs.CV 2022
Year: 2022

Traditional datasets for the radiological diagnosis tend to only provide the radiology image alongside the radiology report. However, radiology reading as performed by radiologists is a complex process, and information such as the radiologist's eye-fixations over the course of the reading has the potential to be an invaluable data source to learn from. Nonetheless, the collection of such data is expensive and time-consuming. This leads to the question of whether such data is worth the investment to collect. This paper utilizes the recently published Eye-Gaze dataset to perform an exhaustive study on the impact on performance and explainability of deep learning (DL) classification in the face of varying levels of input features, namely: radiology images, radiology report text, and radiologist eye-gaze data. We find that the best classification performance of X-ray images is achieved with a combination of radiology report free-text and radiology image, with the eye-gaze data providing no performance boost. Nonetheless, eye-gaze data serving as secondary ground truth alongside the class label results in highly explainable models that generate better attention maps compared to models trained to do classification and attention map generation without eye-gaze data.
FastGeodis: Fast Generalised Geodesic Distance Transform
Venue: arXiv cs.CV 2022
Year: 2022

The FastGeodis package provides an efficient implementation for computing Geodesic and Euclidean distance transforms (or a mixture of both), targeting efficient utilisation of CPU and GPU hardware. In particular, it implements the paralellisable raster scan method from Criminisi et al. (2009), where elements in a row (2D) or plane (3D) can be computed with parallel threads. This package is able to handle 2D as well as 3D data, where it achieves up to a 20x speedup on a CPU and up to a 74x speedup on a GPU as compared to an existing open-source library (Wang, 2020) that uses a non-parallelisable single-thread CPU implementation. The performance speedups reported here were evaluated using 3D volume data on an Nvidia GeForce Titan X (12 GB) with a 6-Core Intel Xeon E5-1650 CPU. Further in-depth comparison of performance improvements are discussed in the FastGeodis documentation: https://fastgeodis.readthedocs.io
What to share, when, and where: balancing the objectives and complexities of open source software contributions
Venue: arXiv cs.SE 2022
Year: 2022

Context: Software-intensive organizations' rationale for sharing Open Source Software (OSS) may be driven by both idealistic, strategic and commercial objectives, and include both monetary as well as non-monetary benefits. To gain the potential benefits, an organization may need to consider what they share and how, while taking into account risks, costs and other complexities. Objective: This study aims to empirically investigate objectives and complexities organizations need to consider and balance between when deciding on what software to share as OSS, when to share it, and whether to create a new or contribute to an existing community. Method: A multiple-case study of three case organizations was conducted in two research cycles, with data gathered from interviews with 20 practitioners from these organizations. The data was analyzed qualitatively in an inductive and iterative coding process. Results: 12 contribution objectives and 15 contribution complexities were found. Objectives include opportunities for improving reputation, managing suppliers, managing partners and competitors, and exploiting externally available knowledge and resources. Complexities include risk of loosing control, risk of giving away competitive advantage, risk of creating negative exposure, costs of contributing, and the possibility and need to contribute to an existing or new community. Conclusions: Cross-case analysis and interview validation show that the identified objectives and complexities offer organizations a possibility to reflect on and adapt their contribution strategies based on their specific contexts and business goals.
Improved Policy Optimization for Online Imitation Learning
Venue: arXiv cs.LG 2022
Year: 2022

We consider online imitation learning (OIL), where the task is to find a policy that imitates the behavior of an expert via active interaction with the environment. We aim to bridge the gap between the theory and practice of policy optimization algorithms for OIL by analyzing one of the most popular OIL algorithms, DAGGER. Specifically, if the class of policies is sufficiently expressive to contain the expert policy, we prove that DAGGER achieves constant regret. Unlike previous bounds that require the losses to be strongly-convex, our result only requires the weaker assumption that the losses be strongly-convex with respect to the policy's sufficient statistics (not its parameterization). In order to ensure convergence for a wider class of policies and losses, we augment DAGGER with an additional regularization term. In particular, we propose a variant of Follow-the-Regularized-Leader (FTRL) and its adaptive variant for OIL and develop a memory-efficient implementation, which matches the memory requirements of FTL. Assuming that the loss functions are smooth and convex with respect to the parameters of the policy, we also prove that FTRL achieves constant regret for any sufficiently expressive policy class, while retaining $O(\sqrt{T})$ regret in the worst-case. We demonstrate the effectiveness of these algorithms with experiments on synthetic and high-dimensional control tasks.
Weakly Supervised Deep Instance Nuclei Detection using Points Annotation in 3D Cardiovascular Immunofluorescent Images
Venue: arXiv cs.CV 2022
Year: 2022

Two major causes of death in the United States and worldwide are stroke and myocardial infarction. The underlying cause of both is thrombi released from ruptured or eroded unstable atherosclerotic plaques that occlude vessels in the heart (myocardial infarction) or the brain (stroke). Clinical studies show that plaque composition plays a more important role than lesion size in plaque rupture or erosion events. To determine the plaque composition, various cell types in 3D cardiovascular immunofluorescent images of plaque lesions are counted. However, counting these cells manually is expensive, time-consuming, and prone to human error. These challenges of manual counting motivate the need for an automated approach to localize and count the cells in images. The purpose of this study is to develop an automatic approach to accurately detect and count cells in 3D immunofluorescent images with minimal annotation effort. In this study, we used a weakly supervised learning approach to train the HoVer-Net segmentation model using point annotations to detect nuclei in fluorescent images. The advantage of using point annotations is that they require less effort as opposed to pixel-wise annotation. To train the HoVer-Net model using point annotations, we adopted a popularly used cluster labeling approach to transform point annotations into accurate binary masks of cell nuclei. Traditionally, these approaches have generated binary masks from point annotations, leaving a region around the object unlabeled (which is typically ignored during model training). However, these areas may contain important information that helps determine the boundary between cells. Therefore, we used the entropy minimization loss function in these areas to encourage the model to output more confident predictions on the unlabeled areas. Our comparison studies indicate that the HoVer-Net model trained using our weakly ...
Adding Context to Source Code Representations for Deep Learning
Venue: arXiv cs.SE 2022
Year: 2022

Deep learning models have been successfully applied to a variety of software engineering tasks, such as code classification, summarisation, and bug and vulnerability detection. In order to apply deep learning to these tasks, source code needs to be represented in a format that is suitable for input into the deep learning model. Most approaches to representing source code, such as tokens, abstract syntax trees (ASTs), data flow graphs (DFGs), and control flow graphs (CFGs) only focus on the code itself and do not take into account additional context that could be useful for deep learning models. In this paper, we argue that it is beneficial for deep learning models to have access to additional contextual information about the code being analysed. We present preliminary evidence that encoding context from the call hierarchy along with information from the code itself can improve the performance of a state-of-the-art deep learning model for two software engineering tasks. We outline our research agenda for adding further contextual information to source code representations for deep learning.
Tackling Neural Architecture Search With Quality Diversity Optimization
Venue: arXiv cs.LG 2022
Year: 2022

Neural architecture search (NAS) has been studied extensively and has grown to become a research field with substantial impact. While classical single-objective NAS searches for the architecture with the best performance, multi-objective NAS considers multiple objectives that should be optimized simultaneously, e.g., minimizing resource usage along the validation error. Although considerable progress has been made in the field of multi-objective NAS, we argue that there is some discrepancy between the actual optimization problem of practical interest and the optimization problem that multi-objective NAS tries to solve. We resolve this discrepancy by formulating the multi-objective NAS problem as a quality diversity optimization (QDO) problem and introduce three quality diversity NAS optimizers (two of them belonging to the group of multifidelity optimizers), which search for high-performing yet diverse architectures that are optimal for application-specific niches, e.g., hardware constraints. By comparing these optimizers to their multi-objective counterparts, we demonstrate that quality diversity NAS in general outperforms multi-objective NAS with respect to quality of solutions and efficiency. We further show how applications and future NAS research can thrive on QDO.
Joint Precoding and Phase Shift Design in Reconfigurable Intelligent Surfaces-Assisted Secret Key Generation
Venue: arXiv cs.IT 2022
Year: 2022

Key generation is a promising technique to establish symmetric keys between resource-constrained legitimate users. However, key generation suffers from low secret key rate (SKR) in harsh environments where channel randomness is limited. To address the problem, reconfigurable intelligent surfaces (RISs) are introduced to reshape the channels by controlling massive reflecting elements, which can provide more channel diversity. In this paper, we design a channel probing protocol to fully extract the randomness from the cascaded channel, i.e., the channel through reflecting elements. We derive the analytical expressions of SKR and design a water-filling algorithm based on the Karush-Kuhn-Tucker (KKT) conditions to find the upper bound. To find the optimal precoding and phase shift matrices, we propose an algorithm based on the Grassmann manifold optimization methods. The system is evaluated in terms of SKR, bit disagreement rate (BDR) and randomness. Simulation results show that our protocols significantly improve the SKR as compared to existing protocol.