Age-related macular degeneration (AMD) is a major cause of blindness in older adults, severely affecting vision and quality of life. Despite advances in understanding AMD, the molecular factors driving the severity of subretinal scarring (fibrosis) remain elusive, hampering the development of effective therapies. This study introduces a machine learning-based framework to predict key genes that are strongly correlated with lesion severity and to identify potential therapeutic targets to prevent subretinal fibrosis in AMD. Using an original RNA sequencing (RNA-seq) dataset from the diseased retinas of JR5558 mice, we developed a novel and specific feature engineering technique, including pathway-based dimensionality reduction and gene-based feature expansion, to enhance prediction accuracy. Two iterative experiments were conducted by leveraging Ridge and ElasticNet regression models to assess biological relevance and gene impact. The results highlight the biological significance of several key genes and demonstrate the framework's effectiveness in identifying novel therapeutic targets. The key findings provide valuable insights for advancing drug discovery efforts and improving treatment strategies for AMD, with the potential to enhance patient outcomes by targeting the underlying genetic mechanisms of subretinal lesion development.

We address the problem of person re-identification (reID), that is, retrieving person images from a large dataset, given a query image of the person of interest. A key challenge is to learn person representations robust to intra-class variations, as different persons could have the same attribute, and persons' appearances look different, e.g., with viewpoint changes. Recent reID methods focus on learning person features discriminative only for a particular factor of variations (e.g., human pose), which also requires corresponding supervisory signals (e.g., pose annotations). To tackle this problem, we propose to factorize person images into identity-related and unrelated features. Identity-related features contain information useful for specifying a particular person (e.g., clothing), while identity-unrelated ones hold other factors (e.g., human pose). To this end, we propose a new generative adversarial network, dubbed identity shuffle GAN (IS-GAN). It disentangles identity-related and unrelated features from person images through an identity-shuffling technique that exploits identification labels alone without any auxiliary supervisory signals. We restrict the distribution of identity-unrelated features or encourage the identity-related and unrelated features to be uncorrelated, facilitating the disentanglement process. Experimental results validate the effectiveness of IS-GAN, showing state-of-the-art performance on standard reID benchmarks, including Market-1501, CUHK03, and DukeMTMC-reID. We further demonstrate the advantages of disentangling person representations on a long-term reID task, setting a new state of the art on a Celeb-reID dataset.

We propose a flexible and theoretically supported framework for scalable nonnegative matrix factorization. The goal is to find nonnegative low-rank components directly from compressed measurements, accessing the original data only once or twice. We consider compression through randomized sketching methods that can be adapted to the data, or can be oblivious. We formulate optimization problems that only depend on the compressed data, but which can recover a nonnegative factorization which closely approximates the original matrix. The defined problems can be approached with a variety of algorithms, and in particular, we discuss variations of the popular multiplicative updates method for these compressed problems. We demonstrate the success of our approaches empirically and validate their performance in real-world applications.

Probability estimation of tree topologies is one of the fundamental tasks in phylogenetic inference. The recently proposed subsplit Bayesian networks (SBNs) provide a powerful probabilistic graphical model for tree topology probability estimation by properly leveraging the hierarchical structure of phylogenetic trees. However, the expectation maximization (EM) method currently used for learning SBN parameters does not scale up to large data sets. In this paper, we introduce several computationally efficient methods for training SBNs and show that variance reduction could be the key for better performance. Furthermore, we also introduce the variance reduction technique to improve the optimization of SBN parameters for variational Bayesian phylogenetic inference (VBPI). Extensive synthetic and real data experiments demonstrate that our methods outperform previous baseline methods on the tasks of tree topology probability estimation as well as Bayesian phylogenetic inference using SBNs.

Large Vision-Language Models (LVLMs) have demonstrated their powerful multimodal capabilities. However, they also face serious safety problems, as adversaries can induce robustness issues in LVLMs through the use of well-designed adversarial examples. Therefore, LVLMs are in urgent need of detection tools for adversarial examples to prevent incorrect responses. In this work, we first discover that LVLMs exhibit regular attention patterns for clean images when presented with probe questions. We propose an unconventional method named PIP, which utilizes the attention patterns of one randomly selected irrelevant probe question (e.g., "Is there a clock?") to distinguish adversarial examples from clean examples. Regardless of the image to be tested and its corresponding question, PIP only needs to perform one additional inference of the image to be tested and the probe question, and then achieves successful detection of adversarial examples. Even under black-box attacks and open dataset scenarios, our PIP, coupled with a simple SVM, still achieves more than 98% recall and a precision of over 90%. Our PIP is the first attempt to detect adversarial attacks on LVLMs via simple irrelevant probe questions, shedding light on deeper understanding and introspection within LVLMs. The code is available at https://github.com/btzyd/pip.

Adaptive optimizers have emerged as powerful tools in deep learning, dynamically adjusting the learning rate based on iterative gradients. These adaptive methods have significantly succeeded in various deep learning tasks, outperforming stochastic gradient descent (SGD). However, although AdaGrad is a cornerstone adaptive optimizer, its theoretical analysis is inadequate in addressing asymptotic convergence and non-asymptotic convergence rates on non-convex optimization. This study aims to provide a comprehensive analysis and complete picture of AdaGrad. We first introduce a novel stopping time technique from probabilistic theory to establish stability for the norm version of AdaGrad under milder conditions. We further derive two forms of asymptotic convergence: almost sure and mean-square. Furthermore, we demonstrate the near-optimal non-asymptotic convergence rate measured by the average-squared gradients in expectation, which is rarely explored and stronger than the existing high-probability results, under the mild assumptions. The techniques developed in this work are potentially independent of interest for future research on other adaptive stochastic algorithms.

Communication efficiency is a widely recognised research problem in Federated Learning (FL), with recent work focused on developing techniques for efficient compression, distribution and aggregation of model parameters between clients and the server. Particularly within distributed systems, it is important to balance the need for computational cost and communication efficiency. However, existing methods are often constrained to specific applications and are less generalisable. In this paper, we introduce FedFT (federated frequency-space transformation), a simple yet effective methodology for communicating model parameters in a FL setting. FedFT uses Discrete Cosine Transform (DCT) to represent model parameters in frequency space, enabling efficient compression and reducing communication overhead. FedFT is compatible with various existing FL methodologies and neural architectures, and its linear property eliminates the need for multiple transformations during federated aggregation. This methodology is vital for distributed solutions, tackling essential challenges like data privacy, interoperability, and energy efficiency inherent to these environments. We demonstrate the generalisability of the FedFT methodology on four datasets using comparative studies with three state-of-the-art FL baselines (FedAvg, FedProx, FedSim). Our results demonstrate that using FedFT to represent the differences in model parameters between communication rounds in frequency space results in a more compact representation compared to representing the entire model in frequency space. This leads to a reduction in communication overhead, while keeping accuracy levels comparable and in some cases even improving it. Our results suggest that this reduction can range from 5% to 30% per client, depending on dataset.

Due to their data-driven nature, Machine Learning (ML) models are susceptible to bias inherited from data, especially in classification problems where class and group imbalances are prevalent. Class imbalance (in the classification target) and group imbalance (in protected attributes like sex or race) can undermine both ML utility and fairness. Although class and group imbalances commonly coincide in real-world tabular datasets, limited methods address this scenario. While most methods use oversampling techniques, like interpolation, to mitigate imbalances, recent advancements in synthetic tabular data generation offer promise but have not been adequately explored for this purpose. To this end, this paper conducts a comparative analysis to address class and group imbalances using state-of-the-art models for synthetic tabular data generation and various sampling strategies. Experimental results on four datasets, demonstrate the effectiveness of generative models for bias mitigation, creating opportunities for further exploration in this direction.

We study the identification of quantum phases of matter, at zero temperature, when only part of the phase diagram is known in advance. Following a supervised learning approach, we show how to use our previous knowledge to construct an observable capable of classifying the phase even in the unknown region. By using a combination of classical and quantum techniques, such as tensor networks, kernel methods, generalization bounds, quantum algorithms, and shadow estimators, we show that, in some cases, the certification of new ground states can be obtained with a polynomial number of measurements. An important application of our findings is the classification of the phases of matter obtained in quantum simulators, e.g., cold atom experiments, capable of efficiently preparing ground states of complex many-particle systems and applying simple measurements, e.g., single qubit measurements, but unable to perform a universal set of gates.

Weakly supervised learning aims to reduce the cost of labeling data by using expert-designed labeling rules. However, existing methods require experts to design effective rules in a single shot, which is difficult in the absence of proper guidance and tooling. Therefore, it is still an open question whether experts should spend their limited time writing rules or instead providing instance labels via active learning. In this paper, we investigate how to exploit an expert's limited time to create effective supervision. First, to develop practical guidelines for rule creation, we conduct an exploratory analysis of diverse collections of existing expert-designed rules and find that rule precision is more important than coverage across datasets. Second, we compare rule creation to individual instance labeling via active learning and demonstrate the importance of both across 6 datasets. Third, we propose an interactive learning framework, INTERVAL, that achieves efficiency by automatically extracting candidate rules based on rich patterns (e.g., by prompting a language model), and effectiveness by soliciting expert feedback on both candidate rules and individual instances. Across 6 datasets, INTERVAL outperforms state-of-the-art weakly supervised approaches by 7% in F1. Furthermore, it requires as few as 10 queries for expert feedback to reach F1 values that existing active learning methods cannot match even with 100 queries.