Drug-Target binding Affinity (DTA) prediction is essential for drug discovery. Despite the application of deep learning methods to DTA prediction, the achieved accuracy remain suboptimal. In this work, inspired by the recent success of retrieval methods, we propose $k$NN-DTA, a non-parametric embedding-based retrieval method adopted on a pre-trained DTA prediction model, which can extend the power of the DTA model with no or negligible cost. Different from existing methods, we introduce two neighbor aggregation ways from both embedding space and label space that are integrated into a unified framework. Specifically, we propose a \emph{label aggregation} with \emph{pair-wise retrieval} and a \emph{representation aggregation} with \emph{point-wise retrieval} of the nearest neighbors. This method executes in the inference phase and can efficiently boost the DTA prediction performance with no training cost. In addition, we propose an extension, Ada-$k$NN-DTA, an instance-wise and adaptive aggregation with lightweight learning. Results on four benchmark datasets show that $k$NN-DTA brings significant improvements, outperforming previous state-of-the-art (SOTA) results, e.g, on BindingDB IC$_{50}$ and $K_i$ testbeds, $k$NN-DTA obtains new records of RMSE $\bf{0.684}$ and $\bf{0.750}$. The extended Ada-$k$NN-DTA further improves the performance to be $\bf{0.675}$ and $\bf{0.735}$ RMSE. These results strongly prove the effectiveness of our method. Results in other settings and comprehensive studies/analyses also show the great potential of our $k$NN-DTA approach.

Graph Out-of-Distribution (OOD), requiring that models trained on biased data generalize to the unseen test data, has considerable real-world applications. One of the most mainstream methods is to extract the invariant subgraph by aligning the original and augmented data with the help of environment augmentation. However, these solutions might lead to the loss or redundancy of semantic subgraphs and result in suboptimal generalization. To address this challenge, we propose exploiting Probability of Necessity and Sufficiency (PNS) to extract sufficient and necessary invariant substructures. Beyond that, we further leverage the domain variant subgraphs related to the labels to boost the generalization performance in an ensemble manner. Specifically, we first consider the data generation process for graph data. Under mild conditions, we show that the sufficient and necessary invariant subgraph can be extracted by minimizing an upper bound, built on the theoretical advance of the probability of necessity and sufficiency. To further bridge the theory and algorithm, we devise the model called Sufficiency and Necessity Inspired Graph Learning (SNIGL), which ensembles an invariant subgraph classifier on top of latent sufficient and necessary invariant subgraphs, and a domain variant subgraph classifier specific to the test domain for generalization enhancement. Experimental results demonstrate that our SNIGL model outperforms the state-of-the-art techniques on six public benchmarks, highlighting its effectiveness in real-world scenarios.

Domain generalization involves training machine learning models to perform robustly on unseen samples from out-of-distribution datasets. Adversarial Data Augmentation (ADA) is a commonly used approach that enhances model adaptability by incorporating synthetic samples, designed to simulate potential unseen samples. While ADA effectively addresses amplitude-related distribution shifts, it falls short in managing temporal shifts, which are essential for time series data. To address this limitation, we propose the Temporal Adversarial Data Augmentation for time teries Data (TADA), which incorporates a time warping technique specifically targeting temporal shifts. Recognizing the challenge of non-differentiability in traditional time warping, we make it differentiable by leveraging phase shifts in the frequency domain. Our evaluations across diverse domains demonstrate that TADA significantly outperforms existing ADA variants, enhancing model performance across time series datasets with varied distributions.

This paper introduces a Random Survival Forest (RSF) method for functional data. The focus is specifically on defining a new functional data structure, the Censored Functional Data (CFD), for dealing with temporal observations that are censored due to study limitations or incomplete data collection. This approach allows for precise modelling of functional survival trajectories, leading to improved interpretation and prediction of survival dynamics across different groups. A medical survival study on the benchmark SOFA data set is presented. Results show good performance of the proposed approach, particularly in ranking the importance of predicting variables, as captured through dynamic changes in SOFA scores and patient mortality rates.

--Feature selection is a vital technique in machine learning, as it can reduce computational complexity, improve model performance, and mitigate the risk of overfitting. However, the increasing complexity and dimensionality of datasets pose significant challenges in the selection of features. Focusing on these challenges, this paper proposes a cascaded two-stage feature clustering and selection algorithm for fuzzy decision systems. In the first stage, we reduce the search space by clustering relevant features and addressing inter-feature redundancy. In the second stage, a clustering-based sequentially forward selection method that explores the global and local structure of data is presented. We propose a novel metric for assessing the significance of features, which considers both global separability and local consistency. Global separability measures the degree of intra-class cohesion and inter-class separation based on fuzzy membership, providing a comprehensive understanding of data separability. Meanwhile, local consistency leverages the fuzzy neighborhood rough set model to capture uncertainty and fuzziness in the data. The effectiveness of our proposed algorithm is evaluated through experiments conducted on 18 public datasets and a real-world schizophrenia dataset. The experiment results demonstrate our algorithm's superiority over benchmarking algorithms in both classification accuracy and the number of selected features. Index T erms--Feature selection, fuzzy neighborhood rough set, fuzzy decision systems, granular computing. ITH the advent of the digital era, there has been an unprecedented surge in data from various sources such as sensors, social media, financial systems, and healthcare resources. However, traditional methods struggle to handle big data due to its high dimensionality, noise, and redundant information, significantly impacting the accuracy and efficiency of both data analysis and decision-making processes.

Energy based models (EBMs) are appealing for their generality and simplicity in data likelihood modeling, but have conventionally been difficult to train due to the unstable and time-consuming implicit MCMC sampling during contrastive divergence training. In this paper, we present a novel energy-based generative framework, Variational Potential Flow (VAPO), that entirely dispenses with implicit MCMC sampling and does not rely on complementary latent models or cooperative training. The VAPO framework aims to learn a potential energy function whose gradient (flow) guides the prior samples, so that their density evolution closely follows an approximate data likelihood homotopy. An energy loss function is then formulated to minimize the Kullback-Leibler divergence between density evolution of the flow-driven prior and the data likelihood homotopy. Images can be generated after training the potential energy, by initializing the samples from Gaussian prior and solving the ODE governing the potential flow on a fixed time interval using generic ODE solvers. Experiment results show that the proposed VAPO framework is capable of generating realistic images on various image datasets. In particular, our proposed framework achieves competitive FID scores for unconditional image generation on the CIFAR-10 and CelebA datasets.

Instruction tuning [Wei et al., 2022a, Ouyang et al., 2022] is the most important strategy for customizing Large Language Models (LLMs) for downstream tasks, which allows them to precisely understand human intentions and accurately generate responses in natural languages. Recently, many existing works Wang et al. [2023a] expand the amount and diversity of instructions for instruction tuning to further enhance the LLM's capability. However, the increased quantity of the dataset also leads to significantly higher computational costs for instruction tuning. Meanwhile, Zhou et al. [2023] revealed that only 1,000 high-quality, human-created data samples could substantially improve the ability of LLMs to follow instructions, which suggest that there exists severe redundancy in current instruction datasets, and only a high-quality subset may suffice for achieving promising performance. To address the above issue, selecting a small, highly informative subset (i.e., coreset) of training samples from the original dataset is a promising solution. This approach ensures that training on the coreset achieves performance comparable to the full dataset while significantly reducing costs. However, coreset selection is challenging as it must not only consider the quality of individual samples, but also their importance within the entire subset. For example, if two high-quality samples are very similar, selecting only one may be sufficient. This global perspective on sample importance is crucial for the quality of the selected subset.

This paper demonstrates how to use generative models trained for image synthesis as tools for visual data mining. Our insight is that since contemporary generative models learn an accurate representation of their training data, we can use them to summarize the data by mining for visual patterns. Concretely, we show that after finetuning conditional diffusion models to synthesize images from a specific dataset, we can use these models to define a typicality measure on that dataset. This measure assesses how typical visual elements are for different data labels, such as geographic location, time stamps, semantic labels, or even the presence of a disease. This analysis-by-synthesis approach to data mining has two key advantages. First, it scales much better than traditional correspondence-based approaches since it does not require explicitly comparing all pairs of visual elements. Second, while most previous works on visual data mining focus on a single dataset, our approach works on diverse datasets in terms of content and scale, including a historical car dataset, a historical face dataset, a large worldwide street-view dataset, and an even larger scene dataset. Furthermore, our approach allows for translating visual elements across class labels and analyzing consistent changes.

In recent years, healthcare professionals are increasingly emphasizing on personalized and evidence-based patient care through the exploration of prognostic pathways. To study this, structured clinical variables from Electronic Health Records (EHRs) data have traditionally been employed by many researchers. Presently, Natural Language Processing models have received great attention in clinical research which expanded the possibilities of using clinical narratives. In this paper, we propose a systematic methodology for developing sepsis prognostic pathways derived from clinical notes, focusing on diverse patient subgroups identified by exploring comorbidities associated with sepsis and generating explanations of these subgroups using SHAP. The extracted prognostic pathways of these subgroups provide valuable insights into the dynamic trajectories of sepsis severity over time. Visualizing these pathways sheds light on the likelihood and direction of disease progression across various contexts and reveals patterns and pivotal factors or biomarkers influencing the transition between sepsis stages, whether toward deterioration or improvement. This empowers healthcare providers to implement more personalized and effective healthcare strategies for individual patients.

The diversity in disease profiles and therapeutic approaches between hospitals and health professionals underscores the need for patient-centric personalized strategies in healthcare. Alongside this, similarities in disease progression across patients can be utilized to improve prediction models in survival analysis. The need for patient privacy and the utility of prediction models can be simultaneously addressed in the framework of Federated Learning (FL). This paper outlines an approach in the domain of federated survival analysis, specifically the Cox Proportional Hazards (CoxPH) model, with a specific focus on mitigating data heterogeneity and elevating model performance. We present an FL approach that employs feature-based clustering to enhance model accuracy across synthetic datasets and real-world applications, including the Surveillance, Epidemiology, and End Results (SEER) database. Furthermore, we consider an event-based reporting strategy that provides a dynamic approach to model adaptation by responding to local data changes. Our experiments show the efficacy of our approach and discuss future directions for a practical application of FL in healthcare.