Enhancing breakpoint resolution with deep segmentation model: A general refinement method for read-depth based structural variant callers

Read-depths (RDs) are frequently used in identifying structural variants (SVs) from sequencing data. For existing RD-based SV callers, it is difficult for them to determine breakpoints in single-nucleotide resolution due to the noisiness of RD data and the bin-based calculation. In this paper, we propose to use the deep segmentation model UNet to learn base-wise RD patterns surrounding breakpoints of known SVs. We integrate model predictions with an RD-based SV caller to enhance breakpoints in single-nucleotide resolution. We show that UNet can be trained with a small amount of data and can be applied both in-sample and cross-sample. An enhancement pipeline named RDBKE significantly increases the number of SVs with more precise breakpoints on simulated and real data. The source code of RDBKE is freely available at https://github.com/yaozhong/deepIntraSV.

Modeling, learning, perception, and control methods for deformable object manipulation

Perceiving and handling deformable objects is an integral part of everyday life for humans. Automating tasks such as food handling, garment sorting, or assistive dressing requires open problems of modeling, perceiving, planning, and control to be solved. Recent advances in data-driven approaches, together with classical control and planning, can provide viable solutions to these open challenges. In addition, with the development of better simulation environments, we can generate and study scenarios that allow for benchmarking of various approaches and gain better understanding of what theoretical developments need to be made and how practical systems can be implemented and evaluated to provide flexible, scalable, and robust solutions. To this end, we survey more than 100 relevant studies in this area and use it as the basis to discuss open problems. We adopt a learning perspective to unify the discussion over analytical and data-driven approaches, addressing how to use and integrate model priors and task data in perceiving and manipulating a variety of deformable objects.

Verification and testing of safety-critical airborne systems: A model-based methodology

In this paper, we address the issues of safety-critical software verification and testing that are key requirements for achieving DO-178C and DO- 331 regulatory compliance for airborne systems. Formal verification and testing are considered two different activities within airborne standards and they belong to two different levels in the avionics software development cycle. The objective is to integrate model-based verification and model-based testing within a single framework and to capture the benefits of their cross-fertilization. This is achieved by proposing a new methodology for the verification and testing of parallel communicating agents based on formal models. In this work, properties are extracted from requirements and formally verified at the design level, while the verified properties are propagated to the implementation level and checked via testing. The contributions of this paper are a methodology that integrates verification and testing, formal verification of some safety critical software properties, and a testing method for Modified Condition/Decision Coverage (MC/DC). The results of formal verification and testing can be used as evidence for avionics software certification.

A tale of two explanations: Enhancing human trust by explaining robot behavior

The ability to provide comprehensive explanations of chosen actions is a hallmark of intelligence. Lack of this ability impedes the general acceptance of AI and robot systems in critical tasks. This paper examines what forms of explanations best foster human trust in machines and proposes a framework in which explanations are generated from both functional and mechanistic perspectives. The robot system learns from human demonstrations to open medicine bottles using (i) an embodied haptic prediction model to extract knowledge from sensory feedback, (ii) a stochastic grammar model induced to capture the compositional structure of a multistep task, and (iii) an improved Earley parsing algorithm to jointly leverage both the haptic and grammar models. The robot system not only shows the ability to learn from human demonstrators but also succeeds in opening new, unseen bottles. Using different forms of explanations generated by the robot system, we conducted a psychological experiment to examine what forms of explanations best foster human trust in the robot. We found that comprehensive and real-time visualizations of the robot’s internal decisions were more effective in promoting human trust than explanations based on summary text descriptions. In addition, forms of explanation that are best suited to foster trust do not necessarily correspond to the model components contributing to the best task performance. This divergence shows a need for the robotics community to integrate model components to enhance both task execution and human trust in machines.

Properties of decision-making tasks govern the tradeoff between model-based and model-free learning

When decisions must be made between uncertain options, optimal behavior depends on accurate estimations of the likelihoods of different outcomes. The contextual factors that govern whether these estimations depend on model-free learning (tracking outcomes) vs. model-based learning (learning generative stimulus distributions) are poorly understood. We studied model-free and model-based learning using serial decision-making tasks in which subjects selected a rule and then used it to flexibly act on visual stimuli. A factorial approach defined a family of behavioral models that could integrate model-free and model-based strategies to predict rule selection trial-by-trial. Bayesian model selection demonstrated that the subjects strategies varied depending on lower-level task characteristics such as the identities of the rule options. In certain conditions, subjects integrated learned stimulus distributions and tracked reward rates to guide their behavior. The results thus identify tradeoffs between model-based and model-free decision strategies, and in some cases parallel utilization, depending on task context.

Model Pembelajaran Terpadu Mata Pelajaran IPS Kelas IV Madrasah Ibtidaiyah Tema Indahnya Kebersamaan

Model pembelajaran adalah sebuah kerangka konseptual yang melukiskan prosedur secara sistematis agar dapat mencapai tujuan pembelajaran. Model pembelajaran juga menjadi sebuah pedoman bagi guru dalam merancang dan melaksanakan proses pembelajaran maka sangatlah perlu melakukan pembaruan tentang sebuah model pembelajaran pada kurikulum terpadu (tematik) yang sangat mudah di pahami oleh peserta didik terutama dalam mata pelajaran Ilmu Pengetahuan Sosial (IPS), tentang keragaman sosial, ekonomi, budaya, etnis, dan agama di provinsi setempat sebagai identitas bangsa Indonesia. Model-model pembelajaran terpadu, meliputi: Model dalam satu desain ilmu meliputi model keterhubungan, yaitu model connected dan model nested. Model antar mata pelajaran yaitu keterurutan antar mata pelajaran, meliputi: sequenced, shared, webbed, threaded, integrate. Model lintas siswa yaitu: Immersed dan networked. Dan model pembelajaran terpadu Ilmu Pengetahuan Sosial (IPS), meliputi: Model integrasi berdasarkan tema, Model integrasi berdasarkan potensi utama dan Model integrasi berdasarkan masalah. Penulis menggunakan model integrasi berbasis tema agar siswa lebih mudah memahami, terutama kelas IV tema indahnya kebersamaan di madrasah ibtidaiyah.

Deep CNN Denoiser and Multi-layer Neighbor Component Embedding for Face Hallucination

Most of the current face hallucination methods, whether they are shallow learning-based or deep learning-based, all try to learn a relationship model between Low-Resolution (LR) and High-Resolution (HR) spaces with the help of a training set. They mainly focus on modeling image prior through either model-based optimization or discriminative inference learning. However, when the input LR face is tiny, the learned prior knowledge is no longer effective and their performance will drop sharply. To solve this problem, in this paper we propose a general face hallucination method that can integrate model-based optimization and discriminative inference. In particular, to exploit the model based prior, the Deep Convolutional Neural Networks (CNN) denoiser prior is plugged into the super-resolution optimization model with the aid of image-adaptive Laplacian regularization. Additionally, we further develop a high-frequency details compensation method by dividing the face image to facial components and performing face hallucination in a multi-layer neighbor embedding manner. Experiments demonstrate that the proposed method can achieve promising super-resolution results for tiny input LR faces.