Fine-tuning large-scale pre-trained models via transfer learning is an emerging important paradigm for a wide range of downstream tasks, with performance heavily reliant on extensive data. Federated learning (FL), as a distributed framework, provides a secure solution to train models on local datasets while safeguarding raw sensitive data. However, FL networks encounter high communication costs due to the massive parameters of large-scale pre-trained models, necessitating parameter-efficient methods. Notably, parameter efficient fine tuning, such as Low-Rank Adaptation (LoRA), has shown remarkable success in fine-tuning pre-trained models. However, prior research indicates that the fixed parameter budget may be prone to the overfitting or slower convergence. To address this challenge, we propose a Simulated Annealing-based Federated Learning with LoRA tuning (SA-FedLoRA) approach by reducing trainable parameters. Specifically, SA-FedLoRA comprises two stages: initiating and annealing. (1) In the initiating stage, we implement a parameter regularization approach during the early rounds of aggregation, aiming to mitigate client drift and accelerate the convergence for the subsequent tuning. (2) In the annealing stage, we allocate higher parameter budget during the early 'heating' phase and then gradually shrink the budget until the 'cooling' phase. This strategy not only facilitates convergence to the global optimum but also reduces communication costs. Experimental results demonstrate that SA-FedLoRA is an efficient FL, achieving superior performance to FedAvg and significantly reducing communication parameters by up to 93.62%.

Heterogeneous, interconnected, systems-level, molecular data have become increasingly available and key in precision medicine. We need to utilize them to better stratify patients into risk groups, discover new biomarkers and targets, repurpose known and discover new drugs to personalize medical treatment. Existing methodologies are limited and a paradigm shift is needed to achieve quantitative and qualitative breakthroughs. In this perspective paper, we survey the literature and argue for the development of a comprehensive, general framework for embedding of multi-scale molecular network data that would enable their explainable exploitation in precision medicine in linear time. Network embedding methods map nodes to points in low-dimensional space, so that proximity in the learned space reflects the network's topology-function relationships. They have recently achieved unprecedented performance on hard problems of utilizing few omic data in various biomedical applications. However, research thus far has been limited to special variants of the problems and data, with the performance depending on the underlying topology-function network biology hypotheses, the biomedical applications and evaluation metrics. The availability of multi-omic data, modern graph embedding paradigms and compute power call for a creation and training of efficient, explainable and controllable models, having no potentially dangerous, unexpected behaviour, that make a qualitative breakthrough. We propose to develop a general, comprehensive embedding framework for multi-omic network data, from models to efficient and scalable software implementation, and to apply it to biomedical informatics. It will lead to a paradigm shift in computational and biomedical understanding of data and diseases that will open up ways to solving some of the major bottlenecks in precision medicine and other domains.

Online Continual Learning (OCL) empowers machine learning models to acquire new knowledge online across a sequence of tasks. However, OCL faces a significant challenge: catastrophic forgetting, wherein the model learned in previous tasks is substantially overwritten upon encountering new tasks, leading to a biased forgetting of prior knowledge. Moreover, the continual doman drift in sequential learning tasks may entail the gradual displacement of the decision boundaries in the learned feature space, rendering the learned knowledge susceptible to forgetting. To address the above problem, in this paper, we propose a novel rehearsal strategy, termed Drift-Reducing Rehearsal (DRR), to anchor the domain of old tasks and reduce the negative transfer effects. First, we propose to select memory for more representative samples guided by constructed centroids in a data stream. Then, to keep the model from domain chaos in drifting, a two-level angular cross-task Contrastive Margin Loss (CML) is proposed, to encourage the intra-class and intra-task compactness, and increase the inter-class and inter-task discrepancy. Finally, to further suppress the continual domain drift, we present an optional Centorid Distillation Loss (CDL) on the rehearsal memory to anchor the knowledge in feature space for each previous old task. Extensive experimental results on four benchmark datasets validate that the proposed DRR can effectively mitigate the continual domain drift and achieve the state-of-the-art (SOTA) performance in OCL.

Dimensionality reduction algorithms are often used to visualise high-dimensional data. Previously, studies have used prior information to enhance or suppress expected patterns in projections. In this paper, we adapt such techniques for domain knowledge guided interactive exploration. Inspired by Mapper and STAD, we present three types of lens functions for UMAP, a state-of-the-art dimensionality reduction algorithm. Lens functions enable analysts to adapt projections to their questions, revealing otherwise hidden patterns. They filter the modelled connectivity to explore the interaction between manually selected features and the data's structure, creating configurable perspectives each potentially revealing new insights. The effectiveness of the lens functions is demonstrated in two use cases and their computational cost is analysed in a synthetic benchmark.

Efficient and robust data clustering remains a challenging task in the field of data analysis. Recent efforts have explored the integration of granular-ball (GB) computing with clustering algorithms to address this challenge, yielding promising results. However, existing methods for generating GBs often rely on single indicators to measure GB quality and employ threshold-based or greedy strategies, potentially leading to GBs that do not accurately capture the underlying data distribution. To address these limitations, this article introduces a novel GB generation method. The originality of this method lies in leveraging the principle of justifiable granularity to measure the quality of a GB for clustering tasks. To be precise, we define the coverage and specificity of a GB and introduce a comprehensive measure for assessing GB quality. Utilizing this quality measure, the method incorporates a binary tree pruning-based strategy and an anomaly detection method to determine the best combination of sub-GBs for each GB and identify abnormal GBs, respectively. Compared to previous GB generation methods, the new method maximizes the overall quality of generated GBs while ensuring alignment with the data distribution, thereby enhancing the rationality of the generated GBs. Experimental results obtained from both synthetic and publicly available datasets underscore the effectiveness of the proposed GB generation method, showcasing improvements in clustering accuracy and normalized mutual information.

This paper focuses on the integration of generative techniques into spatial-temporal data mining, considering the significant growth and diverse nature of spatial-temporal data. With the advancements in RNNs, CNNs, and other non-generative techniques, researchers have explored their application in capturing temporal and spatial dependencies within spatial-temporal data. However, the emergence of generative techniques such as LLMs, SSL, Seq2Seq and diffusion models has opened up new possibilities for enhancing spatial-temporal data mining further. The paper provides a comprehensive analysis of generative technique-based spatial-temporal methods and introduces a standardized framework specifically designed for the spatial-temporal data mining pipeline. By offering a detailed review and a novel taxonomy of spatial-temporal methodology utilizing generative techniques, the paper enables a deeper understanding of the various techniques employed in this field. Furthermore, the paper highlights promising future research directions, urging researchers to delve deeper into spatial-temporal data mining. It emphasizes the need to explore untapped opportunities and push the boundaries of knowledge to unlock new insights and improve the effectiveness and efficiency of spatial-temporal data mining. By integrating generative techniques and providing a standardized framework, the paper contributes to advancing the field and encourages researchers to explore the vast potential of generative techniques in spatial-temporal data mining.

Recent advances in experimental methods have enabled researchers to collect data on thousands of analytes simultaneously. This has led to correlational studies that associated molecular measurements with diseases such as Alzheimer's, Liver, and Gastric Cancer. However, the use of thousands of biomarkers selected from the analytes is not practical for real-world medical diagnosis and is likely undesirable due to potentially formed spurious correlations. In this study, we evaluate 4 different methods for biomarker selection and 4 different machine learning (ML) classifiers for identifying correlations - evaluating 16 approaches in all. We found that contemporary methods outperform previously reported logistic regression in cases where 3 and 10 biomarkers are permitted. When specificity is fixed at 0.9, ML approaches produced a sensitivity of 0.240 (3 biomarkers) and 0.520 (10 biomarkers), while standard logistic regression provided a sensitivity of 0.000 (3 biomarkers) and 0.040 (10 biomarkers). We also noted that causal-based methods for biomarker selection proved to be the most performant when fewer biomarkers were permitted, while univariate feature selection was the most performant when a greater number of biomarkers were permitted.

Recent years have experienced increasing utilization of complex machine learning models across multiple sources of data to inform more generalizable decision-making. However, distribution shifts across data sources and privacy concerns related to sharing individual-level data, coupled with a lack of uncertainty quantification from machine learning predictions, make it challenging to achieve valid inferences in multi-source environments. In this paper, we consider the problem of obtaining distribution-free prediction intervals for a target population, leveraging multiple potentially biased data sources. We derive the efficient influence functions for the quantiles of unobserved outcomes in the target and source populations, and show that one can incorporate machine learning prediction algorithms in the estimation of nuisance functions while still achieving parametric rates of convergence to nominal coverage probabilities. Moreover, when conditional outcome invariance is violated, we propose a data-adaptive strategy to upweight informative data sources for efficiency gain and downweight non-informative data sources for bias reduction. We highlight the robustness and efficiency of our proposals for a variety of conformal scores and data-generating mechanisms via extensive synthetic experiments. Hospital length of stay prediction intervals for pediatric patients undergoing a high-risk cardiac surgical procedure between 2016-2022 in the U.S. illustrate the utility of our methodology.

Classical results in asymptotic statistics show that the Fisher information matrix controls the difficulty of estimating a statistical model from observed data. In this work, we introduce a companion measure of robustness of an estimation problem: the radius of statistical efficiency (RSE) is the size of the smallest perturbation to the problem data that renders the Fisher information matrix singular. We compute RSE up to numerical constants for a variety of test bed problems, including principal component analysis, generalized linear models, phase retrieval, bilinear sensing, and matrix completion. In all cases, the RSE quantifies the compatibility between the covariance of the population data and the latent model parameter. Interestingly, we observe a precise reciprocal relationship between RSE and the intrinsic complexity/sensitivity of the problem instance, paralleling the classical Eckart-Young theorem in numerical analysis.

Autonomous systems often encounter environments and scenarios beyond the scope of their training data, which underscores a critical challenge: the need to generalize and adapt to unseen scenarios in real time. This challenge necessitates new mathematical and algorithmic tools that enable adaptation and zero-shot transfer. To this end, we leverage the theory of function encoders, which enables zero-shot transfer by combining the flexibility of neural networks with the mathematical principles of Hilbert spaces. Using this theory, we first present a method for learning a space of dynamics spanned by a set of neural ODE basis functions. After training, the proposed approach can rapidly identify dynamics in the learned space using an efficient inner product calculation. Critically, this calculation requires no gradient calculations or retraining during the online phase. This method enables zero-shot transfer for autonomous systems at runtime and opens the door for a new class of adaptable control algorithms. We demonstrate state-of-the-art system modeling accuracy for two MuJoCo robot environments and show that the learned models can be used for more efficient MPC control of a quadrotor.