Protein-ligand structure prediction is an essential task in drug discovery, predicting the binding interactions between small molecules (ligands) and target proteins (receptors). Although conventional physics-based docking tools are widely utilized, their accuracy is compromised by limited conformational sampling and imprecise scoring functions. Recent advances have incorporated deep learning techniques to improve the accuracy of structure prediction. Nevertheless, the experimental validation of docking conformations remains costly, it raises concerns regarding the generalizability of these deep learning-based methods due to the limited training data. In this work, we show that by pre-training a geometry-aware SE(3)-Equivariant neural network on a large-scale docking conformation generated by traditional physics-based docking tools and then fine-tuning with a limited set of experimentally validated receptor-ligand complexes, we can achieve outstanding performance. This process involved the generation of 100 million docking conformations, consuming roughly 1 million CPU core days. The proposed model, HelixDock, aims to acquire the physical knowledge encapsulated by the physics-based docking tools during the pre-training phase. HelixDock has been benchmarked against both physics-based and deep learning-based baselines, showing that it outperforms its closest competitor by over 40% for RMSD. HelixDock also exhibits enhanced performance on a dataset that poses a greater challenge, thereby highlighting its robustness. Moreover, our investigation reveals the scaling laws governing pre-trained structure prediction models, indicating a consistent enhancement in performance with increases in model parameters and pre-training data. This study illuminates the strategic advantage of leveraging a vast and varied repository of generated data to advance the frontiers of AI-driven drug discovery.

In the realm of social media, users frequently convey personal sentiments, with some potentially indicating cognitive distortions or suicidal tendencies. Timely recognition of such signs is pivotal for effective interventions. In response, we introduce two novel annotated datasets from Chinese social media, focused on cognitive distortions and suicidal risk classification. We propose a comprehensive benchmark using both supervised learning and large language models, especially from the GPT series, to evaluate performance on these datasets. To assess the capabilities of the large language models, we employed three strategies: zero-shot, few-shot, and fine-tuning. Furthermore, we deeply explored and analyzed the performance of these large language models from a psychological perspective, shedding light on their strengths and limitations in identifying and understanding complex human emotions. Our evaluations underscore a performance difference between the two approaches, with the models often challenged by subtle category distinctions. While GPT-4 consistently delivered strong results, GPT-3.5 showed marked improvement in suicide risk classification after fine-tuning. This research is groundbreaking in its evaluation of large language models for Chinese social media tasks, accentuating the models' potential in psychological contexts. All datasets and code are made available.

Anomaly detection of time series data has wide applications in areas such as finance, health care, and manufacturing. An anomaly is usually an important sign of critical events, such as faulty operation and health deterioration, and thus capturing such signs from a data perspective is of key interest. Time series data in real life often exhibit complex patterns, which pose challenges to the methodology of anomaly detection algorithms. Particularly, high dimensionality increases the difficulty of extracting meaningful features, which is essential to algorithm performance; Highly non-linear dynamics further complicate the identification of system states. Detecting anomalies on a set of measurements over time has always been an active research area [3]. It typically consists of two phases: in the training phase, one models historical data to learn the temporal pattern of time series, and in the testing phase, one evaluates whether each observation follows a normal or abnormal pattern. Since real-world datasets usually lack labeled anomalies, and anomalies can exhibit unpredictable data behavior, the training set may only consist of data from normal operations in these scenarios.

Pre-trained vision transformers have strong representation benefits to various downstream tasks. Recently, many parameter-efficient fine-tuning (PEFT) methods have been proposed, and their experiments demonstrate that tuning only 1% of extra parameters could surpass full fine-tuning in low-data resource scenarios. However, these methods overlook the task-specific information when fine-tuning diverse downstream tasks. In this paper, we propose a simple yet effective method called "Salient Channel Tuning" (SCT) to leverage the task-specific information by forwarding the model with the task images to select partial channels in a feature map that enables us to tune only 1/8 channels leading to significantly lower parameter costs. Experiments outperform full fine-tuning on 18 out of 19 tasks in the VTAB-1K benchmark by adding only 0.11M parameters of the ViT-B, which is 780$\times$ fewer than its full fine-tuning counterpart. Furthermore, experiments on domain generalization and few-shot learning surpass other PEFT methods with lower parameter costs, demonstrating our proposed tuning technique's strong capability and effectiveness in the low-data regime.

Unsupervised contrastive learning methods have recently seen significant improvements, particularly through data augmentation strategies that aim to produce robust and generalizable representations. However, prevailing data augmentation methods, whether hand designed or based on foundation models, tend to rely heavily on prior knowledge or external data. This dependence often compromises their effectiveness and efficiency. Furthermore, the applicability of most existing data augmentation strategies is limited when transitioning to other research domains, especially science-related data. This limitation stems from the paucity of prior knowledge and labeled data available in these domains. To address these challenges, we introduce DiffAug-a novel and efficient Diffusion-based data Augmentation technique. DiffAug aims to ensure that the augmented and original data share a smoothed latent space, which is achieved through diffusion steps. Uniquely, unlike traditional methods, DiffAug first mines sufficient prior semantic knowledge about the neighborhood. This provides a constraint to guide the diffusion steps, eliminating the need for labels, external data/models, or prior knowledge. Designed as an architecture-agnostic framework, DiffAug provides consistent improvements. Specifically, it improves image classification and clustering accuracy by 1.6%~4.5%. When applied to biological data, DiffAug improves performance by up to 10.1%, with an average improvement of 5.8%. DiffAug shows good performance in both vision and biological domains.

Accurate segmentation of punctate white matter lesions (PWMLs) are fundamental for the timely diagnosis and treatment of related developmental disorders. Automated PWMLs segmentation from infant brain MR images is challenging, considering that the lesions are typically small and low-contrast, and the number of lesions may dramatically change across subjects. Existing learning-based methods directly apply general network architectures to this challenging task, which may fail to capture detailed positional information of PWMLs, potentially leading to severe under-segmentations. In this paper, we propose to leverage the idea of counterfactual reasoning coupled with the auxiliary task of brain tissue segmentation to learn fine-grained positional and morphological representations of PWMLs for accurate localization and segmentation. A simple and easy-to-implement deep-learning framework (i.e., DeepPWML) is accordingly designed. It combines the lesion counterfactual map with the tissue probability map to train a lightweight PWML segmentation network, demonstrating state-of-the-art performance on a real-clinical dataset of infant T1w MR images.

Forensic pathology is critical in analyzing death manner and time from the microscopic aspect to assist in the establishment of reliable factual bases for criminal investigation. In practice, even the manual differentiation between different postmortem organ tissues is challenging and relies on expertise, considering that changes like putrefaction and autolysis could significantly change typical histopathological appearance. Developing AI-based computational pathology techniques to assist forensic pathologists is practically meaningful, which requires reliable discriminative representation learning to capture tissues' fine-grained postmortem patterns. To this end, we propose a framework called FPath, in which a dedicated self-supervised contrastive learning strategy and a context-aware multiple-instance learning (MIL) block are designed to learn discriminative representations from postmortem histopathological images acquired at varying magnification scales. Our self-supervised learning step leverages multiple complementary contrastive losses and regularization terms to train a double-tier backbone for fine-grained and informative patch/instance embedding. Thereafter, the context-aware MIL adaptively distills from the local instances a holistic bag/image-level representation for the recognition task. On a large-scale database of $19,607$ experimental rat postmortem images and $3,378$ real-world human decedent images, our FPath led to state-of-the-art accuracy and promising cross-domain generalization in recognizing seven different postmortem tissues. The source code will be released on \href{https://github.com/ladderlab-xjtu/forensic_pathology}{https://github.com/ladderlab-xjtu/forensic\_pathology}.

Brain tissue segmentation is essential for neuroscience and clinical studies. However, segmentation on longitudinal data is challenging due to dynamic brain changes across the lifespan. Previous researches mainly focus on self-supervision with regularizations and will lose longitudinal generalization when fine-tuning on a specific age group. In this paper, we propose a dual meta-learning paradigm to learn longitudinally consistent representations and persist when fine-tuning. Specifically, we learn a plug-and-play feature extractor to extract longitudinal-consistent anatomical representations by meta-feature learning and a well-initialized task head for fine-tuning by meta-initialization learning. Besides, two class-aware regularizations are proposed to encourage longitudinal consistency. Experimental results on the iSeg2019 and ADNI datasets demonstrate the effectiveness of our method. Our code is available at https://github.com/ladderlab-xjtu/DuMeta.

Since the advent of Neural Radiance Fields, novel view synthesis has received tremendous attention. The existing approach for the generalization of radiance field reconstruction primarily constructs an encoding volume from nearby source images as additional inputs. However, these approaches cannot efficiently encode the geometric information of real scenes with various scale objects/structures. In this work, we propose constructing multi-scale encoding volumes and providing multi-scale geometry information to NeRF models. To make the constructed volumes as close as possible to the surfaces of objects in the scene and the rendered depth more accurate, we propose to perform depth prediction and radiance field reconstruction simultaneously. The predicted depth map will be used to supervise the rendered depth, narrow the depth range, and guide points sampling. Finally, the geometric information contained in point volume features may be inaccurate due to occlusion, lighting, etc. To this end, we propose enhancing the point volume feature from depth-guided neighbor feature fusion. Experiments demonstrate the superior performance of our method in both novel view synthesis and dense geometry modeling without per-scene optimization.

Quadruped robots have the potential to guide blind and low vision (BLV) people due to their highly flexible locomotion and emotional value provided by their bionic forms. However, the development of quadruped guide robots rarely involves BLV users' participatory designs and evaluations. In this paper, we conducted two empirical experiments both in indoor controlled and outdoor field scenarios, exploring the benefits and drawbacks of quadruped guide robots. The results show that the nowadays commercial quadruped robots exposed significant disadvantages in usability and trust compared with wheeled robots. It is concluded that the moving gait and walking noise of quadruped robots would limit the guiding effectiveness to a certain extent, and the empathetic effect of its bionic form for BLV users could not be fully reflected. Based on the findings of wheeled robots and quadruped robots' advantages, we discuss the design implications for the future guide robot design for BLV users. This paper reports the first empirical experiment about quadruped guide robots with BLV users and preliminary explores their potential improvement space in substituting guide dogs, which can inspire the further specialized design of quadruped guide robots.