Search

Quality assurance (QA) tools are receiving more and more attention and are widely used by developers. Given the wide range of solutions for QA technology, it is still a question of evaluating QA tools. Most existing research is limited in the following ways: (i) They compare tools without considering scanning rules analysis. (ii) They disagree on the effectiveness of tools due to the study methodology and benchmark dataset. (iii) They do not separately analyze the role of the warnings. (iv) There is no large-scale study on the analysis of time performance. To address these problems, in the paper, we systematically select 6 free or open-source tools for a comprehensive study from a list of 148 existing Java QA tools. To carry out a comprehensive study and evaluate tools in multi-level dimensions, we first mapped the scanning rules to the CWE and analyze the coverage and granularity of the scanning rules. Then we conducted an experiment on 5 benchmarks, including 1,425 bugs, to investigate the effectiveness of these tools. Furthermore, we took substantial effort to investigate the effectiveness of warnings by comparing the real labeled bugs with the warnings and investigating their role in bug detection. Finally, we assessed these tools' time performance on 1,049 projects. The useful findings based on our comprehensive study can help developers improve their tools and provide users with suggestions for selecting QA tools., Comment: 11 pages, ISSTA-2023

We study the problem of approximate sampling from non-log-concave distributions, e.g., Gaussian mixtures, which is often challenging even in low dimensions due to their multimodality. We focus on performing this task via Markov chain Monte Carlo (MCMC) methods derived from discretizations of the overdamped Langevin diffusions, which are commonly known as Langevin Monte Carlo algorithms. Furthermore, we are also interested in two nonsmooth cases for which a large class of proximal MCMC methods have been developed: (i) a nonsmooth prior is considered with a Gaussian mixture likelihood; (ii) a Laplacian mixture distribution. Such nonsmooth and non-log-concave sampling tasks arise from a wide range of applications to Bayesian inference and imaging inverse problems such as image deconvolution. We perform numerical simulations to compare the performance of most commonly used Langevin Monte Carlo algorithms.

The strongly correlated material FeSi exhibits several unusual thermal, magnetic, and structural properties under varying pressure-temperature (P-T) conditions. It is a potential thermoelectric alloy and a materials of several geological implications as a possible constituent at the Earth's core mantle boundary (CMB). The phase transition behavior and lattice dynamics of FeSi under different P-T conditions remain elusive. A previous theoretical work predicted a pressure induced B20-B2 transition at ambient temperature, yet the transition is only observed at high P-T conditions in the experiments. Furthermore, the closing of the electronic gap due to a dramatic renormalization of the electronic structure and phonon anomalies has been reported based on density function calculations. In this study we have performed high pressure powder diffraction and Nuclear Resonant Inelastic X-ray Scattering (NRIXS) measurements up to 120 GPa to understand the phase stability and the lattice dynamics. Our study shows evidence for a nonhydrostatic stress induced B20-B2 transition in FeSi around 36 GPa for the first time. The Fe partial phonon density of states (PDOS) and thermal parameters were derived from NRIXS up to 120 GPa with the density function theoretical (DFT) calculations. These calculations further predict and are consistent with pressure-induced metallization and band gap closing around 12 GPa., Comment: 8 pages, 6 figures and supplementary information

Deep learning models have demonstrated remarkable success in multi-organ segmentation but typically require large-scale datasets with all organs of interest annotated. However, medical image datasets are often low in sample size and only partially labeled, i.e., only a subset of organs are annotated. Therefore, it is crucial to investigate how to learn a unified model on the available partially labeled datasets to leverage their synergistic potential. In this paper, we systematically investigate the partial-label segmentation problem with theoretical and empirical analyses on the prior techniques. We revisit the problem from a perspective of partial label supervision signals and identify two signals derived from ground truth and one from pseudo labels. We propose a novel two-stage framework termed COSST, which effectively and efficiently integrates comprehensive supervision signals with self-training. Concretely, we first train an initial unified model using two ground truth-based signals and then iteratively incorporate the pseudo label signal to the initial model using self-training. To mitigate performance degradation caused by unreliable pseudo labels, we assess the reliability of pseudo labels via outlier detection in latent space and exclude the most unreliable pseudo labels from each self-training iteration. Extensive experiments are conducted on one public and three private partial-label segmentation tasks over 12 CT datasets. Experimental results show that our proposed COSST achieves significant improvement over the baseline method, i.e., individual networks trained on each partially labeled dataset. Compared to the state-of-the-art partial-label segmentation methods, COSST demonstrates consistent superior performance on various segmentation tasks and with different training data sizes.

Distribution estimation has been demonstrated as one of the most effective approaches in dealing with few-shot image classification, as the low-level patterns and underlying representations can be easily transferred across different tasks in computer vision domain. However, directly applying this approach to few-shot text classification is challenging, since leveraging the statistics of known classes with sufficient samples to calibrate the distributions of novel classes may cause negative effects due to serious category difference in text domain. To alleviate this issue, we propose two simple yet effective strategies to estimate the distributions of the novel classes by utilizing unlabeled query samples, thus avoiding the potential negative transfer issue. Specifically, we first assume a class or sample follows the Gaussian distribution, and use the original support set and the nearest few query samples to estimate the corresponding mean and covariance. Then, we augment the labeled samples by sampling from the estimated distribution, which can provide sufficient supervision for training the classification model. Extensive experiments on eight few-shot text classification datasets show that the proposed method outperforms state-of-the-art baselines significantly., Comment: Accepted to AAAI 2023

Automated segmentation of multiple sclerosis (MS) lesions from MRI scans is important to quantify disease progression. In recent years, convolutional neural networks (CNNs) have shown top performance for this task when a large amount of labeled data is available. However, the accuracy of CNNs suffers when dealing with few and/or sparsely labeled datasets. A potential solution is to leverage the information available in large public datasets in conjunction with a target dataset which only has limited labeled data. In this paper, we propose a training framework, SSL2 (self-supervised-semi-supervised), for multi-modality MS lesion segmentation with limited supervision. We adopt self-supervised learning to leverage the knowledge from large public 3T datasets to tackle the limitations of a small 7T target dataset. To leverage the information from unlabeled 7T data, we also evaluate state-of-the-art semi-supervised methods for other limited annotation settings, such as small labeled training size and sparse annotations. We use the shifted-window (Swin) transformer1 as our backbone network. The effectiveness of self-supervised and semi-supervised training strategies is evaluated in our in-house 7T MRI dataset. The results indicate that each strategy improves lesion segmentation for both limited training data size and for sparse labeling scenarios. The combined overall framework further improves the performance substantially compared to either of its components alone. Our proposed framework thus provides a promising solution for future data/label-hungry 7T MS studies., Comment: Accepted at the International Society for Optics and Photonics - Medical Imaging (SPIE-MI) 2023

Algorithmic case-based decision support provides examples to help human make sense of predicted labels and aid human in decision-making tasks. Despite the promising performance of supervised learning, representations learned by supervised models may not align well with human intuitions: what models consider as similar examples can be perceived as distinct by humans. As a result, they have limited effectiveness in case-based decision support. In this work, we incorporate ideas from metric learning with supervised learning to examine the importance of alignment for effective decision support. In addition to instance-level labels, we use human-provided triplet judgments to learn human-compatible decision-focused representations. Using both synthetic data and human subject experiments in multiple classification tasks, we demonstrate that such representation is better aligned with human perception than representation solely optimized for classification. Human-compatible representations identify nearest neighbors that are perceived as more similar by humans and allow humans to make more accurate predictions, leading to substantial improvements in human decision accuracies (17.8% in butterfly vs. moth classification and 13.2% in pneumonia classification)., Comment: Accepted at ICLR 2023

Moire patterns appear frequently when taking photos of digital screens, drastically degrading the image quality. Despite the advance of CNNs in image demoireing, existing networks are with heavy design, causing redundant computation burden for mobile devices. In this paper, we launch the first study on accelerating demoireing networks and propose a dynamic demoireing acceleration method (DDA) towards a real-time deployment on mobile devices. Our stimulus stems from a simple-yet-universal fact that moire patterns often unbalancedly distribute across an image. Consequently, excessive computation is wasted upon non-moire areas. Therefore, we reallocate computation costs in proportion to the complexity of image patches. In order to achieve this aim, we measure the complexity of an image patch by designing a novel moire prior that considers both colorfulness and frequency information of moire patterns. Then, we restore image patches with higher-complexity using larger networks and the ones with lower-complexity are assigned with smaller networks to relieve the computation burden. At last, we train all networks in a parameter-shared supernet paradigm to avoid additional parameter burden. Extensive experiments on several benchmarks demonstrate the efficacy of our proposed DDA. In addition, the acceleration evaluated on the VIVO X80 Pro smartphone equipped with a chip of Snapdragon 8 Gen 1 shows that our method can drastically reduce the inference time, leading to a real-time image demoireing on mobile devices. Source codes and models are released at https://github.com/zyxxmu/DDA, Comment: To appear in the eleventh International Conference on Learning Representations (ICLR 2023)

An efficient solution to the large-scale recommender system is to represent users and items as binary hash codes in the Hamming space. Towards this end, existing methods tend to code users by modeling their Hamming similarities with the items they historically interact with, which are termed as the first-order similarities in this work. Despite their efficiency, these methods suffer from the suboptimal representative capacity, since they forgo the correlation established by connecting multiple first-order similarities, i.e., the relation among the indirect instances, which could be defined as the high-order similarity. To tackle this drawback, we propose to model both the first- and the high-order similarities in the Hamming space through the user-item bipartite graph. Therefore, we develop a novel learning to hash framework, namely Hamming Spatial Graph Convolutional Networks (HS-GCN), which explicitly models the Hamming similarity and embeds it into the codes of users and items. Extensive experiments on three public benchmark datasets demonstrate that our proposed model significantly outperforms several state-of-the-art hashing models, and obtains performance comparable with the real-valued recommendation models.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

The material science literature contains up-to-date and comprehensive scientific knowledge of materials. However, their content is unstructured and diverse, resulting in a significant gap in providing sufficient information for material design and synthesis. To this end, we used natural language processing (NLP) and computer vision (CV) techniques based on convolutional neural networks (CNN) to discover valuable experimental-based information about nanomaterials and synthesis methods in energy-material-related publications. Our first system, TextMaster, extracts opinions from texts and classifies them into challenges and opportunities, achieving 94% and 92% accuracy, respectively. Our second system, GraphMaster, realizes data extraction of tables and figures from publications with 98.3\% classification accuracy and 4.3% data extraction mean square error. Our results show that these systems could assess the suitability of materials for a certain application by evaluation of synthesis insights and case analysis with detailed references. This work offers a fresh perspective on mining knowledge from scientific literature, providing a wide swatch to accelerate nanomaterial research through CNN., Comment: Paper at NeurIPS 2022 AI for Science: Progress and Promises

Background: Computational drug repurposing is a cost- and time-efficient approach that aims to identify new therapeutic targets or diseases (indications) of existing drugs/compounds. It is especially critical for emerging and/or orphan diseases due to its cheaper investment and shorter research cycle compared with traditional wet-lab drug discovery approaches. However, the underlying mechanisms of action (MOAs) between repurposed drugs and their target diseases remain largely unknown, which is still a main obstacle for computational drug repurposing methods to be widely adopted in clinical settings. Results: In this work, we propose KGML-xDTD: a Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases. It is a two-module framework that not only predicts the treatment probabilities between drugs/compounds and diseases but also biologically explains them via knowledge graph (KG) path-based, testable mechanisms of action (MOAs). We leverage knowledge-and-publication based information to extract biologically meaningful "demonstration paths" as the intermediate guidance in the Graph-based Reinforcement Learning (GRL) path-finding process. Comprehensive experiments and case study analyses show that the proposed framework can achieve state-of-the-art performance in both predictions of drug repurposing and recapitulation of human-curated drug MOA paths. Conclusions: KGML-xDTD is the first model framework that can offer KG-path explanations for drug repurposing predictions by leveraging the combination of prediction outcomes and existing biological knowledge and publications. We believe it can effectively reduce "black-box" concerns and increase prediction confidence for drug repurposing based on predicted path-based explanations, and further accelerate the process of drug discovery for emerging diseases.