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Histopathology plays a central role in clinical medicine and biomedical research. While artificial intelligence shows promising results on many pathological tasks, generalization and dealing with rare diseases, where training data is scarce, remains a challenge. Distilling knowledge from unlabelled data into a foundation model before learning from, potentially limited, labelled data provides a viable path to address these challenges. In this work, we extend the state of the art of foundation models for digital pathology whole slide images by semi-automated data curation and incorporating pathologist domain knowledge. Specifically, we combine computational and pathologist domain knowledge (1) to curate a diverse dataset of 133k slides corresponding to 1.2 billion image patches covering data from different fixation, staining, and scanning protocols as well as data from different indications and labs across the EU and US, (2) for grouping semantically similar slides and tissue patches, and (3) to augment the input images during training. We evaluate the resulting model on a set of public and internal benchmarks and show that although our foundation model is trained with an order of magnitude less slides, it performs on par or better than competing models. We expect that scaling our approach to more data and larger models will further increase its performance and capacity to deal with increasingly complex real world tasks in diagnostics and biomedical research.

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ACM/IEEE第23屆模型驅動工程語言和系統國際會議,是模型驅動軟件和系統工程的首要會議系列,由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來,模型涵蓋了建模的各個方面,從語言和方法到工具和應用程序。模特的參加者來自不同的背景,包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇,參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會,并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。 官網鏈接: · Automator · CASES · TOOLS · Networking ·
2024 年 4 月 23 日

Automated program repair (APR) has achieved promising results, especially using neural networks. Yet, the overwhelming majority of patches produced by APR tools are confined to one single location. When looking at the patches produced with neural repair, most of them fail to compile, while a few uncompilable ones go in the right direction. In both cases, the fundamental problem is to ignore the potential of partial patches. In this paper, we propose an iterative program repair paradigm called ITER founded on the concept of improving partial patches until they become plausible and correct. First, ITER iteratively improves partial single-location patches by fixing compilation errors and further refining the previously generated code. Second, ITER iteratively improves partial patches to construct multi-location patches, with fault localization re-execution. ITER is implemented for Java based on battle-proven deep neural networks and code representation. ITER is evaluated on 476 bugs from 10 open-source projects in Defects4J 2.0. ITER succeeds in repairing 15.5% of them, including 9 uniquely repaired multi-location bugs.

Radiance fields have demonstrated impressive performance in synthesizing lifelike 3D talking heads. However, due to the difficulty in fitting steep appearance changes, the prevailing paradigm that presents facial motions by directly modifying point appearance may lead to distortions in dynamic regions. To tackle this challenge, we introduce TalkingGaussian, a deformation-based radiance fields framework for high-fidelity talking head synthesis. Leveraging the point-based Gaussian Splatting, facial motions can be represented in our method by applying smooth and continuous deformations to persistent Gaussian primitives, without requiring to learn the difficult appearance change like previous methods. Due to this simplification, precise facial motions can be synthesized while keeping a highly intact facial feature. Under such a deformation paradigm, we further identify a face-mouth motion inconsistency that would affect the learning of detailed speaking motions. To address this conflict, we decompose the model into two branches separately for the face and inside mouth areas, therefore simplifying the learning tasks to help reconstruct more accurate motion and structure of the mouth region. Extensive experiments demonstrate that our method renders high-quality lip-synchronized talking head videos, with better facial fidelity and higher efficiency compared with previous methods.

Creating artistic 3D scenes can be time-consuming and requires specialized knowledge. To address this, recent works such as ARF, use a radiance field-based approach with style constraints to generate 3D scenes that resemble a style image provided by the user. However, these methods lack fine-grained control over the resulting scenes. In this paper, we introduce Controllable Artistic Radiance Fields (CoARF), a novel algorithm for controllable 3D scene stylization. CoARF enables style transfer for specified objects, compositional 3D style transfer and semantic-aware style transfer. We achieve controllability using segmentation masks with different label-dependent loss functions. We also propose a semantic-aware nearest neighbor matching algorithm to improve the style transfer quality. Our extensive experiments demonstrate that CoARF provides user-specified controllability of style transfer and superior style transfer quality with more precise feature matching.

Transferring human motion skills to humanoid robots remains a significant challenge. In this study, we introduce a Wasserstein adversarial imitation learning system, allowing humanoid robots to replicate natural whole-body locomotion patterns and execute seamless transitions by mimicking human motions. First, we present a unified primitive-skeleton motion retargeting to mitigate morphological differences between arbitrary human demonstrators and humanoid robots. An adversarial critic component is integrated with Reinforcement Learning (RL) to guide the control policy to produce behaviors aligned with the data distribution of mixed reference motions. Additionally, we employ a specific Integral Probabilistic Metric (IPM), namely the Wasserstein-1 distance with a novel soft boundary constraint to stabilize the training process and prevent mode collapse. Our system is evaluated on a full-sized humanoid JAXON in the simulator. The resulting control policy demonstrates a wide range of locomotion patterns, including standing, push-recovery, squat walking, human-like straight-leg walking, and dynamic running. Notably, even in the absence of transition motions in the demonstration dataset, robots showcase an emerging ability to transit naturally between distinct locomotion patterns as desired speed changes.

3D simulated environments play a critical role in Embodied AI, but their creation requires expertise and extensive manual effort, restricting their diversity and scope. To mitigate this limitation, we present Holodeck, a system that generates 3D environments to match a user-supplied prompt fully automatedly. Holodeck can generate diverse scenes, e.g., arcades, spas, and museums, adjust the designs for styles, and can capture the semantics of complex queries such as "apartment for a researcher with a cat" and "office of a professor who is a fan of Star Wars". Holodeck leverages a large language model (i.e., GPT-4) for common sense knowledge about what the scene might look like and uses a large collection of 3D assets from Objaverse to populate the scene with diverse objects. To address the challenge of positioning objects correctly, we prompt GPT-4 to generate spatial relational constraints between objects and then optimize the layout to satisfy those constraints. Our large-scale human evaluation shows that annotators prefer Holodeck over manually designed procedural baselines in residential scenes and that Holodeck can produce high-quality outputs for diverse scene types. We also demonstrate an exciting application of Holodeck in Embodied AI, training agents to navigate in novel scenes like music rooms and daycares without human-constructed data, which is a significant step forward in developing general-purpose embodied agents.

Deep time-series forecasting plays an integral role in numerous practical applications. However, existing research fall short by focusing narrowly on either neural architecture designs for long-term point forecasts or probabilistic models for short-term scenarios. By proposing a comprehensive framework, facilitated by a novel tool, ProbTS, that integrates diverse data scenarios, evaluation metrics, and methodological focuses, we aim to transcend the limitations of current forecasting practices. Rigorous experimentation uncovers pivotal insights, including the supreme importance of aligning forecasting methodologies with the unique characteristics of the data; the necessity of a broad spectrum of metrics for accurately assessing both point and distributional forecasts; and the challenges inherent in adapting existing forecasting methods to a wider range of scenarios. These findings not only challenge conventional approaches but also illuminate promising avenues for future research, suggesting a more nuanced and effective strategy for advancing the field of deep time-series forecasting.

Large language models primarily rely on inductive reasoning for decision making. This results in unreliable decisions when applied to real-world tasks that often present incomplete contexts and conditions. Thus, accurate probability estimation and appropriate interpretations are required to enhance decision-making reliability. In this paper, we propose a Bayesian inference framework called BIRD for large language models. BIRD provides controllable and interpretable probability estimation for model decisions, based on abductive factors, LLM entailment, as well as learnable deductive Bayesian modeling. Experiments show that BIRD produces probability estimations that align with human judgments over 65% of the time using open-sourced Llama models, outperforming the state-of-the-art GPT-4 by 35%. We also show that BIRD can be directly used for trustworthy decision making on many real-world applications.

Neural radiance fields (NeRFs) have gained popularity in the autonomous driving (AD) community. Recent methods show NeRFs' potential for closed-loop simulation, enabling testing of AD systems, and as an advanced training data augmentation technique. However, existing methods often require long training times, dense semantic supervision, or lack generalizability. This, in turn, hinders the application of NeRFs for AD at scale. In this paper, we propose NeuRAD, a robust novel view synthesis method tailored to dynamic AD data. Our method features simple network design, extensive sensor modeling for both camera and lidar -- including rolling shutter, beam divergence and ray dropping -- and is applicable to multiple datasets out of the box. We verify its performance on five popular AD datasets, achieving state-of-the-art performance across the board. To encourage further development, we will openly release the NeuRAD source code. See //github.com/georghess/NeuRAD .

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce \ours, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol), outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at //github.com/AlgoMole/MolCRAFT.

The past few years have seen rapid progress in combining reinforcement learning (RL) with deep learning. Various breakthroughs ranging from games to robotics have spurred the interest in designing sophisticated RL algorithms and systems. However, the prevailing workflow in RL is to learn tabula rasa, which may incur computational inefficiency. This precludes continuous deployment of RL algorithms and potentially excludes researchers without large-scale computing resources. In many other areas of machine learning, the pretraining paradigm has shown to be effective in acquiring transferable knowledge, which can be utilized for a variety of downstream tasks. Recently, we saw a surge of interest in Pretraining for Deep RL with promising results. However, much of the research has been based on different experimental settings. Due to the nature of RL, pretraining in this field is faced with unique challenges and hence requires new design principles. In this survey, we seek to systematically review existing works in pretraining for deep reinforcement learning, provide a taxonomy of these methods, discuss each sub-field, and bring attention to open problems and future directions.

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