Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one by one. However, in real-world molecular systems, the interactions among atoms in an entire molecule are global, leading to the energy function pair-coupled among atoms. With such energy-based consideration, the modeling of probability should be based on joint distributions, rather than sequentially conditional ones. Thus, the unnatural sequentially auto-regressive modeling of molecule generation is likely to violate the physical rules, thus resulting in poor properties of the generated molecules. In this work, a generative diffusion model for molecular 3D structures based on target proteins as contextual constraints is established, at a full-atom level in a non-autoregressive way. Given a designated 3D protein binding site, our model learns the generative process that denoises both element types and 3D coordinates of an entire molecule, with an equivariant network. Experimentally, the proposed method shows competitive performance compared with prevailing works in terms of high affinity with proteins and appropriate molecule sizes as well as other drug properties such as drug-likeness of the generated molecules.

伪LIDAR表示的建议显着缩小了基于视觉的基于视觉激光痛的3D对象检测之间的差距。但是，当前的研究仅专注于通过利用复杂且耗时的神经网络来推动伪LIDAR的准确性提高。很少探索伪LIDAR代表的深刻特征来获得促进机会。在本文中，我们深入研究伪激光雷达表示，并认为3D对象检测的性能并不完全取决于高精度立体声深度估计。我们证明，即使对于不可靠的深度估计，通过适当的数据处理和精炼，它也可以达到可比的3D对象检测准确性。有了这一发现，我们进一步表明了使用伪大部分系统中快速但不准确的立体声匹配算法来实现低潜伏期响应的可能性。在实验中，我们开发了一个具有功能较低的立体声匹配预测指标的系统，并采用了提出的改进方案来提高准确性。对KITTI基准测试的评估表明，所提出的系统仅使用23毫秒的计算来实现最先进方法的竞争精度，这表明它是部署到真实CAR-HOLD应用程序的合适候选者。

Despite significant progress in object categorization, in recent years, a number of important challenges remain; mainly, the ability to learn from limited labeled data and to recognize object classes within large, potentially open, set of labels. Zero-shot learning is one way of addressing these challenges, but it has only been shown to work with limited sized class vocabularies and typically requires separation between supervised and unsupervised classes, allowing former to inform the latter but not vice versa. We propose the notion of vocabulary-informed learning to alleviate the above mentioned challenges and address problems of supervised, zero-shot, generalized zero-shot and open set recognition using a unified framework. Specifically, we propose a weighted maximum margin framework for semantic manifold-based recognition that incorporates distance constraints from (both supervised and unsupervised) vocabulary atoms. Distance constraints ensure that labeled samples are projected closer to their correct prototypes, in the embedding space, than to others. We illustrate that resulting model shows improvements in supervised, zero-shot, generalized zero-shot, and large open set recognition, with up to 310K class vocabulary on Animal with Attributes and ImageNet datasets.

Deploying reliable deep learning techniques in interdisciplinary applications needs learned models to output accurate and ({even more importantly}) explainable predictions. Existing approaches typically explicate network outputs in a post-hoc fashion, under an implicit assumption that faithful explanations come from accurate predictions/classifications. We have an opposite claim that explanations boost (or even determine) classification. That is, end-to-end learning of explanation factors to augment discriminative representation extraction could be a more intuitive strategy to inversely assure fine-grained explainability, e.g., in those neuroimaging and neuroscience studies with high-dimensional data containing noisy, redundant, and task-irrelevant information. In this paper, we propose such an explainable geometric deep network dubbed as NeuroExplainer, with applications to uncover altered infant cortical development patterns associated with preterm birth. Given fundamental cortical attributes as network input, our NeuroExplainer adopts a hierarchical attention-decoding framework to learn fine-grained attentions and respective discriminative representations to accurately recognize preterm infants from term-born infants at term-equivalent age. NeuroExplainer learns the hierarchical attention-decoding modules under subject-level weak supervision coupled with targeted regularizers deduced from domain knowledge regarding brain development. These prior-guided constraints implicitly maximizes the explainability metrics (i.e., fidelity, sparsity, and stability) in network training, driving the learned network to output detailed explanations and accurate classifications. Experimental results on the public dHCP benchmark suggest that NeuroExplainer led to quantitatively reliable explanation results that are qualitatively consistent with representative neuroimaging studies.

Medical image segmentation (MIS) is essential for supporting disease diagnosis and treatment effect assessment. Despite considerable advances in artificial intelligence (AI) for MIS, clinicians remain skeptical of its utility, maintaining low confidence in such black box systems, with this problem being exacerbated by low generalization for out-of-distribution (OOD) data. To move towards effective clinical utilization, we propose a foundation model named EvidenceCap, which makes the box transparent in a quantifiable way by uncertainty estimation. EvidenceCap not only makes AI visible in regions of uncertainty and OOD data, but also enhances the reliability, robustness, and computational efficiency of MIS. Uncertainty is modeled explicitly through subjective logic theory to gather strong evidence from features. We show the effectiveness of EvidenceCap in three segmentation datasets and apply it to the clinic. Our work sheds light on clinical safe applications and explainable AI, and can contribute towards trustworthiness in the medical domain.

Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of sequence-structure data. With the development of Artificial Intelligence (AI) techniques, Protein Representation Learning (PRL) has recently emerged as a promising research topic for extracting informative knowledge from massive protein sequences or structures. To pave the way for AI researchers with little bioinformatics background, we present a timely and comprehensive review of PRL formulations and existing PRL methods from the perspective of model architectures, pretext tasks, and downstream applications. We first briefly introduce the motivations for protein representation learning and formulate it in a general and unified framework. Next, we divide existing PRL methods into three main categories: sequence-based, structure-based, and sequence-structure co-modeling. Finally, we discuss some technical challenges and potential directions for improving protein representation learning. The latest advances in PRL methods are summarized in a GitHub repository https://github.com/LirongWu/awesome-protein-representation-learning.

While inferring common actor states (such as position or velocity) is an important and well-explored task of the perception system aboard a self-driving vehicle (SDV), it may not always provide sufficient information to the SDV. This is especially true in the case of active emergency vehicles (EVs), where light-based signals also need to be captured to provide a full context. We consider this problem and propose a sequential methodology for the detection of active EVs, using an off-the-shelf CNN model operating at a frame level and a downstream smoother that accounts for the temporal aspect of flashing EV lights. We also explore model improvements through data augmentation and training with additional hard samples.

Seismic data often undergoes severe noise due to environmental factors, which seriously affects subsequent applications. Traditional hand-crafted denoisers such as filters and regularizations utilize interpretable domain knowledge to design generalizable denoising techniques, while their representation capacities may be inferior to deep learning denoisers, which can learn complex and representative denoising mappings from abundant training pairs. However, due to the scarcity of high-quality training pairs, deep learning denoisers may sustain some generalization issues over various scenarios. In this work, we propose a self-supervised method that combines the capacities of deep denoiser and the generalization abilities of hand-crafted regularization for seismic data random noise attenuation. Specifically, we leverage the Self2Self (S2S) learning framework with a trace-wise masking strategy for seismic data denoising by solely using the observed noisy data. Parallelly, we suggest the weighted total variation (WTV) to further capture the horizontal local smooth structure of seismic data. Our method, dubbed as S2S-WTV, enjoys both high representation abilities brought from the self-supervised deep network and good generalization abilities of the hand-crafted WTV regularizer and the self-supervised nature. Therefore, our method can more effectively and stably remove the random noise and preserve the details and edges of the clean signal. To tackle the S2S-WTV optimization model, we introduce an alternating direction multiplier method (ADMM)-based algorithm. Extensive experiments on synthetic and field noisy seismic data demonstrate the effectiveness of our method as compared with state-of-the-art traditional and deep learning-based seismic data denoising methods.

With the development of natural language processing techniques(NLP), automatic diagnosis of eye diseases using ophthalmology electronic medical records (OEMR) has become possible. It aims to evaluate the condition of both eyes of a patient respectively, and we formulate it as a particular multi-label classification task in this paper. Although there are a few related studies in other diseases, automatic diagnosis of eye diseases exhibits unique characteristics. First, descriptions of both eyes are mixed up in OEMR documents, with both free text and templated asymptomatic descriptions, resulting in sparsity and clutter of information. Second, OEMR documents contain multiple parts of descriptions and have long document lengths. Third, it is critical to provide explainability to the disease diagnosis model. To overcome those challenges, we present an effective automatic eye disease diagnosis framework, NEEDED. In this framework, a preprocessing module is integrated to improve the density and quality of information. Then, we design a hierarchical transformer structure for learning the contextualized representations of each sentence in the OEMR document. For the diagnosis part, we propose an attention-based predictor that enables traceable diagnosis by obtaining disease-specific information. Experiments on the real dataset and comparison with several baseline models show the advantage and explainability of our framework.

Feature transformation for AI is an essential task to boost the effectiveness and interpretability of machine learning (ML). Feature transformation aims to transform original data to identify an optimal feature space that enhances the performances of a downstream ML model. Existing studies either combines preprocessing, feature selection, and generation skills to empirically transform data, or automate feature transformation by machine intelligence, such as reinforcement learning. However, existing studies suffer from: 1) high-dimensional non-discriminative feature space; 2) inability to represent complex situational states; 3) inefficiency in integrating local and global feature information. To fill the research gap, we formulate the feature transformation task as an iterative, nested process of feature generation and selection, where feature generation is to generate and add new features based on original features, and feature selection is to remove redundant features to control the size of feature space. Finally, we present extensive experiments and case studies to illustrate 24.7\% improvements in F1 scores compared with SOTAs and robustness in high-dimensional data.