Graph property prediction tasks are important and numerous. While each task offers a small size of labeled examples, unlabeled graphs have been collected from various sources and at a large scale. A conventional approach is training a model with the unlabeled graphs on self-supervised tasks and then fine-tuning the model on the prediction tasks. However, the self-supervised task knowledge could not be aligned or sometimes conflicted with what the predictions needed. In this paper, we propose to extract the knowledge underlying the large set of unlabeled graphs as a specific set of useful data points to augment each property prediction model. We use a diffusion model to fully utilize the unlabeled graphs and design two new objectives to guide the model's denoising process with each task's labeled data to generate task-specific graph examples and their labels. Experiments demonstrate that our data-centric approach performs significantly better than fifteen existing various methods on fifteen tasks. The performance improvement brought by unlabeled data is visible as the generated labeled examples unlike the self-supervised learning.

Knowledge graphs (KGs) are structured representations of diversified knowledge. They are widely used in various intelligent applications. In this article, we provide a comprehensive survey on the evolution of various types of knowledge graphs (i.e., static KGs, dynamic KGs, temporal KGs, and event KGs) and techniques for knowledge extraction and reasoning. Furthermore, we introduce the practical applications of different types of KGs, including a case study in financial analysis. Finally, we propose our perspective on the future directions of knowledge engineering, including the potential of combining the power of knowledge graphs and large language models (LLMs), and the evolution of knowledge extraction, reasoning, and representation.

Despite the massive success of fine-tuning large Pre-trained Language Models (PLMs) on a wide range of Natural Language Processing (NLP) tasks, they remain susceptible to out-of-distribution (OOD) and adversarial inputs. Data map (DM) is a simple yet effective dual-model approach that enhances the robustness of fine-tuned PLMs, which involves fine-tuning a model on the original training set (i.e. However, it suffers from the drawback of requiring fine-tuning the same model twice, which is computationally expensive for large models. In this paper, we first show that 1) training dynamics are highly transferable across different model sizes and different pre-training methods, and that 2) main models fine-tuned using DM learn faster than when using conventional Empirical Risk Minimization (ERM). Building on these observations, we propose a novel fine-tuning approach based on the DM method: Fine-Tuning by transFerring Training dynamics (FTFT). Compared with DM, FTFT uses more efficient reference models and then fine-tunes more capable main models for fewer steps. Our experiments show that FTFT achieves better generalization robustness than ERM while spending less than half of the training cost. Current state-of-the-art performance in Natural Language Processing (NLP) is dominated by large, pretrained language models (PLMs), which are typically fine-tuned for downstream tasks. Scaling laws (Kaplan et al., 2020; Hoffmann et al., 2022) suggest that better downstream performance is achieved with larger pretrained language models.

Virtual screening, which identifies potential drugs from vast compound databases to bind with a particular protein pocket, is a critical step in AI-assisted drug discovery. Traditional docking methods are highly time-consuming, and can only work with a restricted search library in real-life applications. Recent supervised learning approaches using scoring functions for binding-affinity prediction, although promising, have not yet surpassed docking methods due to their strong dependency on limited data with reliable binding-affinity labels. In this paper, we propose a novel contrastive learning framework, DrugCLIP, by reformulating virtual screening as a dense retrieval task and employing contrastive learning to align representations of binding protein pockets and molecules from a large quantity of pairwise data without explicit binding-affinity scores. We also introduce a biological-knowledge inspired data augmentation strategy to learn better protein-molecule representations. Extensive experiments show that DrugCLIP significantly outperforms traditional docking and supervised learning methods on diverse virtual screening benchmarks with highly reduced computation time, especially in zero-shot setting.

Contrastive learning, along with its variations, has been a highly effective self-supervised learning method across diverse domains. Contrastive learning measures the distance between representations using cosine similarity and uses cross-entropy for representation learning. Within the same framework of cosine-similarity-based representation learning, margins have played a significant role in enhancing face and speaker recognition tasks. Interestingly, despite the shared reliance on the same similarity metrics and objective functions, contrastive learning has not actively adopted margins. Furthermore, decision-boundary-based explanations are the only ones that have been used to explain the effect of margins in contrastive learning. In this work, we propose a new perspective to understand the role of margins based on gradient analysis. Based on the new perspective, we analyze how margins affect gradients of contrastive learning and separate the effect into more elemental levels. We separately analyze each and provide possible directions for improving contrastive learning. Our experimental results demonstrate that emphasizing positive samples and scaling gradients depending on positive sample angles and logits are the keys to improving the generalization performance of contrastive learning in both seen and unseen datasets, and other factors can only marginally improve performance.

Recently, learning with soft labels has been shown to achieve better performance than learning with hard labels in terms of model generalization, calibration, and robustness. However, collecting pointwise labeling confidence for all training examples can be challenging and time-consuming in real-world scenarios. This paper delves into a novel weakly supervised binary classification problem called confidence-difference (ConfDiff) classification. Instead of pointwise labeling confidence, we are given only unlabeled data pairs with confidence difference that specifies the difference in the probabilities of being positive. We propose a risk-consistent approach to tackle this problem and show that the estimation error bound achieves the optimal convergence rate. We also introduce a risk correction approach to mitigate overfitting problems, whose consistency and convergence rate are also proven. Extensive experiments on benchmark data sets and a real-world recommender system data set validate the effectiveness of our proposed approaches in exploiting the supervision information of the confidence difference.

In the wheat nutrient deficiencies classification challenge, we present the DividE and EnseMble (DEEM) method for progressive test data predictions. We find that (1) test images are provided in the challenge; (2) samples are equipped with their collection dates; (3) the samples of different dates show notable discrepancies. Based on the findings, we partition the dataset into discrete groups by the dates and train models on each divided group. We then adopt the pseudo-labeling approach to label the test data and incorporate those with high confidence into the training set. In pseudo-labeling, we leverage models ensemble with different architectures to enhance the reliability of predictions. The pseudo-labeling and ensembled model training are iteratively conducted until all test samples are labeled. Finally, the separated models for each group are unified to obtain the model for the whole dataset. Our method achieves an average of 93.6\% Top-1 test accuracy~(94.0\% on WW2020 and 93.2\% on WR2021) and wins the 1$st$ place in the Deep Nutrient Deficiency Challenge~\footnote{https://cvppa2023.github.io/challenges/}.

Sickle Cell Disease (SCD) is a chronic genetic disorder characterized by recurrent acute painful episodes. Opioids are often used to manage these painful episodes; the extent of their use in managing pain in this disorder is an issue of debate. The risk of addiction and side effects of these opioid treatments can often lead to more pain episodes in the future. Hence, it is crucial to forecast future patient pain trajectories to help patients manage their SCD to improve their quality of life without compromising their treatment. It is challenging to obtain many pain records to design forecasting models since it is mainly recorded by patients' self-report. Therefore, it is expensive and painful (due to the need for patient compliance) to solve pain forecasting problems in a purely supervised manner. In light of this challenge, we propose to solve the pain forecasting problem using self-supervised learning methods. Also, clustering such time-series data is crucial for patient phenotyping, anticipating patients' prognoses by identifying "similar" patients, and designing treatment guidelines tailored to homogeneous patient subgroups. Hence, we propose a self-supervised learning approach for clustering time-series data, where each cluster comprises patients who share similar future pain profiles. Experiments on five years of real-world datasets show that our models achieve superior performance over state-of-the-art benchmarks and identify meaningful clusters that can be translated into actionable information for clinical decision-making.

Histopathology image analysis plays a crucial role in cancer diagnosis. However, training a clinically applicable segmentation algorithm requires pathologists to engage in labour-intensive labelling. In contrast, weakly supervised learning methods, which only require coarse-grained labels at the image level, can significantly reduce the labeling efforts. Unfortunately, while these methods perform reasonably well in slide-level prediction, their ability to locate cancerous regions, which is essential for many clinical applications, remains unsatisfactory. Previously, we proposed CAMEL, which achieves comparable results to those of fully supervised baselines in pixel-level segmentation. However, CAMEL requires 1,280x1,280 image-level binary annotations for positive WSIs. Here, we present CAMEL2, by introducing a threshold of the cancerous ratio for positive bags, it allows us to better utilize the information, consequently enabling us to scale up the image-level setting from 1,280x1,280 to 5,120x5,120 while maintaining the accuracy. Our results with various datasets, demonstrate that CAMEL2, with the help of 5,120x5,120 image-level binary annotations, which are easy to annotate, achieves comparable performance to that of a fully supervised baseline in both instance- and slide-level classifications.

Recent trends in AIGC effectively boosted the application of visual inspection. However, most of the available systems work in a human-in-the-loop manner and can not provide long-term support to the online application. To make a step forward, this paper outlines an automatic annotation system called SsaA, working in a self-supervised learning manner, for continuously making the online visual inspection in the manufacturing automation scenarios. Benefit from the self-supervised learning, SsaA is effective to establish a visual inspection application for the whole life-cycle of manufacturing. In the early stage, with only the anomaly-free data, the unsupervised algorithms are adopted to process the pretext task and generate coarse labels for the following data. Then supervised algorithms are trained for the downstream task. With user-friendly web-based interfaces, SsaA is very convenient to integrate and deploy both of the unsupervised and supervised algorithms. So far, the SsaA system has been adopted for some real-life industrial applications.