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The precise prediction of molecular properties is essential for advancements in drug development, particularly in virtual screening and compound optimization. The recent introduction of numerous deep learning-based methods has shown remarkable potential in enhancing molecular property prediction (MPP), especially improving accuracy and insights into molecular structures. Yet, two critical questions arise: does the integration of domain knowledge augment the accuracy of molecular property prediction and does employing multi-modal data fusion yield more precise results than unique data source methods? To explore these matters, we comprehensively review and quantitatively analyze recent deep learning methods based on various benchmarks. We discover that integrating molecular information will improve both MPP regression and classification tasks by upto 3.98% and 1.72%, respectively. We also discover that the utilizing 3-dimensional information with 1-dimensional and 2-dimensional information simultaneously can substantially enhance MPP upto 4.2%. The two consolidated insights offer crucial guidance for future advancements in drug discovery.

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《計算機信息》雜志發表高質量的論文,擴大了運籌學和計算的范圍,尋求有關理論、方法、實驗、系統和應用方面的原創研究論文、新穎的調查和教程論文,以及描述新的和有用的軟件工具的論文。官網鏈接: · binary · CASE · 準則 · Continuity ·
2024 年 3 月 24 日

In matched observational studies with binary treatments, the Rosenbaum bounds framework is arguably the most widely used sensitivity analysis framework for assessing sensitivity to unobserved covariates. Unlike the binary treatment case, although widely needed in practice, sensitivity analysis for matched observational studies with treatment doses (i.e., non-binary treatments such as ordinal treatments or continuous treatments) still lacks solid foundations and valid methodologies. We fill in this blank by establishing theoretical foundations and novel methodologies under a generalized Rosenbaum bounds sensitivity analysis framework. First, we present a criterion for assessing the validity of sensitivity analysis in matched observational studies with treatment doses and use that criterion to justify the necessity of incorporating the treatment dose information into sensitivity analysis through generalized Rosenbaum sensitivity bounds. We also generalize Rosenbaum's classic sensitivity parameter $\Gamma$ to the non-binary treatment case and prove its sufficiency. Second, we study the asymptotic properties of sensitivity analysis by generalizing Rosenbaum's classic design sensitivity and Bahadur efficiency for testing Fisher's sharp null to the non-binary treatment case and deriving novel formulas for them. Our theoretical results showed the importance of appropriately incorporating the treatment dose into a test, which is an intrinsic distinction with the binary treatment case. Third, for testing Neyman's weak null (i.e., null sample average treatment effect), we propose the first valid sensitivity analysis procedure for matching with treatment dose through generalizing an existing optimization-based sensitivity analysis for the binary treatment case, built on the generalized Rosenbaum sensitivity bounds and large-scale mixed integer programming.

Curating annotations for medical image segmentation is a labor-intensive and time-consuming task that requires domain expertise, resulting in "narrowly" focused deep learning (DL) models with limited translational utility. Recently, foundation models like the Segment Anything Model (SAM) have revolutionized semantic segmentation with exceptional zero-shot generalizability across various domains, including medical imaging, and hold a lot of promise for streamlining the annotation process. However, SAM has yet to be evaluated in a crowd-sourced setting to curate annotations for training 3D DL segmentation models. In this work, we explore the potential of SAM for crowd-sourcing "sparse" annotations from non-experts to generate "dense" segmentation masks for training 3D nnU-Net models, a state-of-the-art DL segmentation model. Our results indicate that while SAM-generated annotations exhibit high mean Dice scores compared to ground-truth annotations, nnU-Net models trained on SAM-generated annotations perform significantly worse than nnU-Net models trained on ground-truth annotations ($p<0.001$, all).

In clinical applications that involve ultrasound-guided intervention, the visibility of the needle can be severely impeded due to steep insertion and strong distractors such as speckle noise and anatomical occlusion. To address this challenge, we propose VibNet, a learning-based framework tailored to enhance the robustness and accuracy of needle detection in ultrasound images, even when the target becomes invisible to the naked eye. Inspired by Eulerian Video Magnification techniques, we utilize an external step motor to induce low-amplitude periodic motion on the needle. These subtle vibrations offer the potential to generate robust frequency features for detecting the motion patterns around the needle. To robustly and precisely detect the needle leveraging these vibrations, VibNet integrates learning-based Short-Time-Fourier-Transform and Hough-Transform modules to achieve successive sub-goals, including motion feature extraction in the spatiotemporal space, frequency feature aggregation, and needle detection in the Hough space. Based on the results obtained on distinct ex vivo porcine and bovine tissue samples, the proposed algorithm exhibits superior detection performance with efficient computation and generalization capability.

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.

Face recognition technology has advanced significantly in recent years due largely to the availability of large and increasingly complex training datasets for use in deep learning models. These datasets, however, typically comprise images scraped from news sites or social media platforms and, therefore, have limited utility in more advanced security, forensics, and military applications. These applications require lower resolution, longer ranges, and elevated viewpoints. To meet these critical needs, we collected and curated the first and second subsets of a large multi-modal biometric dataset designed for use in the research and development (R&D) of biometric recognition technologies under extremely challenging conditions. Thus far, the dataset includes more than 350,000 still images and over 1,300 hours of video footage of approximately 1,000 subjects. To collect this data, we used Nikon DSLR cameras, a variety of commercial surveillance cameras, specialized long-rage R&D cameras, and Group 1 and Group 2 UAV platforms. The goal is to support the development of algorithms capable of accurately recognizing people at ranges up to 1,000 m and from high angles of elevation. These advances will include improvements to the state of the art in face recognition and will support new research in the area of whole-body recognition using methods based on gait and anthropometry. This paper describes methods used to collect and curate the dataset, and the dataset's characteristics at the current stage.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.

In contrast to batch learning where all training data is available at once, continual learning represents a family of methods that accumulate knowledge and learn continuously with data available in sequential order. Similar to the human learning process with the ability of learning, fusing, and accumulating new knowledge coming at different time steps, continual learning is considered to have high practical significance. Hence, continual learning has been studied in various artificial intelligence tasks. In this paper, we present a comprehensive review of the recent progress of continual learning in computer vision. In particular, the works are grouped by their representative techniques, including regularization, knowledge distillation, memory, generative replay, parameter isolation, and a combination of the above techniques. For each category of these techniques, both its characteristics and applications in computer vision are presented. At the end of this overview, several subareas, where continuous knowledge accumulation is potentially helpful while continual learning has not been well studied, are discussed.

Small data challenges have emerged in many learning problems, since the success of deep neural networks often relies on the availability of a huge amount of labeled data that is expensive to collect. To address it, many efforts have been made on training complex models with small data in an unsupervised and semi-supervised fashion. In this paper, we will review the recent progresses on these two major categories of methods. A wide spectrum of small data models will be categorized in a big picture, where we will show how they interplay with each other to motivate explorations of new ideas. We will review the criteria of learning the transformation equivariant, disentangled, self-supervised and semi-supervised representations, which underpin the foundations of recent developments. Many instantiations of unsupervised and semi-supervised generative models have been developed on the basis of these criteria, greatly expanding the territory of existing autoencoders, generative adversarial nets (GANs) and other deep networks by exploring the distribution of unlabeled data for more powerful representations. While we focus on the unsupervised and semi-supervised methods, we will also provide a broader review of other emerging topics, from unsupervised and semi-supervised domain adaptation to the fundamental roles of transformation equivariance and invariance in training a wide spectrum of deep networks. It is impossible for us to write an exclusive encyclopedia to include all related works. Instead, we aim at exploring the main ideas, principles and methods in this area to reveal where we are heading on the journey towards addressing the small data challenges in this big data era.

Dialogue systems have attracted more and more attention. Recent advances on dialogue systems are overwhelmingly contributed by deep learning techniques, which have been employed to enhance a wide range of big data applications such as computer vision, natural language processing, and recommender systems. For dialogue systems, deep learning can leverage a massive amount of data to learn meaningful feature representations and response generation strategies, while requiring a minimum amount of hand-crafting. In this article, we give an overview to these recent advances on dialogue systems from various perspectives and discuss some possible research directions. In particular, we generally divide existing dialogue systems into task-oriented and non-task-oriented models, then detail how deep learning techniques help them with representative algorithms and finally discuss some appealing research directions that can bring the dialogue system research into a new frontier.

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