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  1. The genome of an individual from an admixed population consists of segments originated from different ancestral populations. Most existing ancestry inference approaches focus on calling these segments for the extant individual. In this paper, we present a general ancestry inference approach for inferring recent ancestors from an extant genome. Given the genome of an individual from a recently admixed population, our method can estimate the proportions of the genomes of the recent ancestors of this individual that originated from some ancestral populations. The key step of our method is the inference of ancestors (called founders) right after the formation of an admixed population. The inferred founders can then be used to infer the ancestry of recent ancestors of an extant individual. Our method is implemented in a computer program called PedMix2. To the best of our knowledge, there is no existing method that can practically infer ancestors beyond grandparents from an extant individual’s genome. Results on both simulated and real data show that PedMix2 performs well in ancestry inference.

     
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    Free, publicly-accessible full text available January 9, 2025
  2. We introduce the task of spotting temporally precise, fine-grained events in video (detecting the precise moment in time events occur). Precise spotting requires models to reason globally about the full-time scale of actions and locally to identify subtle frame-to-frame appearance and motion differences that identify events during these actions. Surprisingly, we find that top performing solutions to prior video understanding tasks such as action detection and segmentation do not simultaneously meet both requirements. In response, we propose E2E-Spot, a compact, end-to-end model that performs well on the precise spotting task and can be trained quickly on a single GPU. We demonstrate that E2E-Spot significantly outperforms recent baselines adapted from the video action detection, segmentation, and spotting literature to the precise spotting task. Finally, we contribute new annotations and splits to several fine-grained sports action datasets to make these datasets suitable for future work on precise spotting. 
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  3. Defect prediction aims to automatically identify potential defective code with minimal human intervention and has been widely studied in the literature. Just-in-Time (JIT) defect prediction focuses on program changes rather than whole programs, and has been widely adopted in continuous testing. CC2Vec, state-of-the-art JIT defect prediction tool, first constructs a hierarchical attention network (HAN) to learn distributed vector representations of both code additions and deletions, and then concatenates them with two other embedding vectors representing commit messages and overall code changes extracted by the existing DeepJIT approach to train a model for predicting whether a given commit is defective. Although CC2Vec has been shown to be the state of the art for JIT defect prediction, it was only evaluated on a limited dataset and not compared with all representative baselines. Therefore, to further investigate the efficacy and limitations of CC2Vec, this paper performs an extensive study of CC2Vec on a large-scale dataset with over 310,370 changes (8.3 X larger than the original CC2Vec dataset). More specifically, we also empirically compare CC2Vec against DeepJIT and representative traditional JIT defect prediction techniques. The experimental results show that CC2Vec cannot consistently outperform DeepJIT, and neither of them can consistently outperform traditional JIT defect prediction. We also investigate the impact of individual traditional defect prediction features and find that the added-line-number feature outperforms other traditional features. Inspired by this finding, we construct a simplistic JIT defect prediction approach which simply adopts the added-line- number feature with the logistic regression classifier. Surprisingly, such a simplistic approach can outperform CC2Vec and DeepJIT in defect prediction, and can be 81k X/120k X faster in training/testing. Furthermore, the paper also provides various practical guidelines for advancing JIT defect prediction in the near future. 
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  4. null (Ed.)
  5. A large body of research efforts have been dedicated to automated software debugging, including both automated fault localization and program repair. However, existing fault localization techniques have limited effectiveness on real-world software systems while even the most advanced program repair techniques can only fix a small ratio of real-world bugs. Although fault localization and program repair are inherently connected, their only existing connection in the literature is that program repair techniques usually use off-the-shelf fault localization techniques (e.g., Ochiai) to determine the potential candidate statements/elements for patching. In this work, we propose the unified debugging approach to unify the two areas in the other direction for the first time, i.e., can program repair in turn help with fault localization? In this way, we not only open a new dimension for more powerful fault localization, but also extend the application scope of program repair to all possible bugs (not only the bugs that can be directly automatically fixed). We have designed ProFL to leverage patch-execution results (from program repair) as the feedback information for fault localization. The experimental results on the widely used Defects4J benchmark show that the basic ProFL can already at least localize 37.61% more bugs within Top-1 than state-of-the-art spectrum and mutation based fault localization. Furthermore, ProFL can boost state-of-the-art fault localization via both unsupervised and supervised learning. Meanwhile, we have demonstrated ProFL's effectiveness under different settings and through a case study within Alipay, a popular online payment system with over 1 billion global users. 
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