Neural Information Processing Systems http://nips.cc/

This paper introduces the novel concept of few-shot weakly supervised learning for pathology Whole Slide Image (WSI) classification, denoted as FSWC. A solution is proposed based on prompt learning and the utilization of a large language model, GPT-4. Since a WSI is too large and needs to be divided into patches for processing, WSI classification is commonly approached as a Multiple Instance Learning (MIL) problem. In this context, each WSI is considered a bag, and the obtained patches are treated as instances. The objective of FSWC is to classify both bags and instances with only a limited number of labeled bags. Unlike conventional few-shot learning problems, FSWC poses additional challenges due to its weak bag labels within the MIL framework.

Sparse Optimal Scoring (SOS) reformulates linear discriminant analysis to enable feature selection through elastic net regularization, making it well-suited for high-dimensional settings where the number of features exceeds observations. Most existing SOS methods use deflation-based strategies that compute discriminant vectors sequentially, which can propagate errors and produce suboptimal solutions. We propose a novel approach that estimates all discriminant vectors simultaneously under an explicit global orthogonality constraint, which we call Deflation-Free Sparse Optimal Scoring (DFSOS). DFSOS combines Bregman iteration with orthogonality-constrained optimization, decomposing the problem into tractable subproblems for scoring vectors, discriminant vectors, and orthogonality enforcement. We establish convergence to stationary points of the augmented Lagrangian under mild conditions. Extensive experiments using synthetic data and real-world time series data demonstrate that DFSOS achieves classification accuracy comparable to or better than existing deflation-based methods. These results indicate that deflation-free approaches offer a robust and effective framework for sparse discriminant analysis in high-dimensional problems.

Graph Neural Networks (GNNs) have achieved great success on a node classification task. Despite the broad interest in developing and evaluating GNNs, they have been assessed with limited benchmark datasets. As a result, the existing evaluation of GNNs lacks fine-grained analysis from various characteristics of graphs. Motivated by this, we conduct extensive experiments with a synthetic graph generator that can generate graphs having controlled characteristics for fine-grained analysis. Our empirical studies clarify the strengths and weaknesses of GNNs from four major characteristics of real-world graphs with class labels of nodes, i.e., 1) class size distributions (balanced vs. imbalanced), 2) edge connection proportions between classes (homophilic vs. heterophilic), 3) attribute values (biased vs. random), and 4) graph sizes (small vs. large). In addition, to foster future research on GNNs, we publicly release our codebase that allows users to evaluate various GNNs with various graphs. We hope this work offers interesting insights for future research.

Blue arrows indicate node feature vectors hv of the latent space, and the orange area/point indicate possible range of graph feature vector hG obtained by applying READOUT to hv. We elaborate our motivation behind orthogonal regularization (15) proposed in Section 4.2.3. The biggest motivation behind orthognoal regularization lies in understanding (8) and (12) that the node features H becomes full rank matrix with good condition number. Figure 5 visually demonstrates the geometric effect of attention-based READOUT and orthogonal regularization with two example node features h1 and h2. Only one graph feature vector hG is possible from the combination of two node features with conventional READOUT, while vectors within the range of the orange rhombus can represent the whole graph feature with attention-based READOUT. With orthogonal regularization, area of the range that the graph feature vector hG can represent become even larger, with lower possibility of null subspace within H. Accordingly, the subspace that H can span can be rich enough.

Here we compute the mean and standard deviation across seeds. Model Robustness score Baseline 100% MTL with real responses 109% MTL with predicted responses (MTL-Monkey) 118% MTL with shuffled predicted responses (MTL-Shuffled) 98% Table 3: Comparing our MTL model co-trained on predicted neural responses -MTL-Monkey in the paper-to the MTL model co-trained directly on real monkey V1 responses. We computed the robustness score of each model after averaging the accuracies of 3 seeds per model for each corruption type in TIN-TC and normalizing against the baseline test accuracies, i.e. the baseline score is 100%. We find that we can obtain a general increase in robustness when using real neural data. However, co-training on predicted neural responses improves the robustness of the models even more.

Single-cell RNA-seq data analysis typically requires representations that capture heterogeneous local structure across multiple scales while remaining stable and interpretable. In this work, we propose a hierarchical sheaf spectral embedding (HSSE) framework that constructs informative cell-level features based on persistent sheaf Laplacian analysis. Starting from scale-dependent low-dimensional embeddings, we define cell-centered local neighborhoods at multiple resolutions. For each local neighborhood, we construct a data-driven cellular sheaf that encodes local relationships among cells. We then compute persistent sheaf Laplacians over sampled filtration intervals and extract spectral statistics that summarize the evolution of local relational structure across scales. These spectral descriptors are aggregated into a unified feature vector for each cell and can be directly used in downstream learning tasks without additional model training. We evaluate HSSE on twelve benchmark single-cell RNA-seq datasets covering diverse biological systems and data scales. Under a consistent classification protocol, HSSE achieves competitive or improved performance compared with existing multiscale and classical embedding-based methods across multiple evaluation metrics. The results demonstrate that sheaf spectral representations provide a robust and interpretable approach for single-cell RNA-seq data representation learning.

Data collection is often difficult in critical fields such as medicine, physics, and chemistry, yielding typically only small tabular datasets. However, classification methods tend to struggle with these small datasets, leading to poor predictive performance. Increasing the training set with additional synthetic data, similar to data augmentation in images, is commonly believed to improve downstream tabular classification performance. However, current tabular generative methods that learn either the joint distribution $ p(\mathbf{x}, y) $ or the class-conditional distribution $ p(\mathbf{x} \mid y) $ often overfit on small datasets, resulting in poor-quality synthetic data, usually worsening classification performance compared to using real data alone. To solve these challenges, we introduce TabEBM, a novel class-conditional generative method using Energy-Based Models (EBMs). Unlike existing tabular methods that use a shared model to approximate all class-conditional densities, our key innovation is to create distinct EBM generative models for each class, each modelling its class-specific data distribution individually. This approach creates robust energy landscapes, even in ambiguous class distributions. Our experiments show that TabEBM generates synthetic data with higher quality and better statistical fidelity than existing methods. When used for data augmentation, our synthetic data consistently leads to improved classification performance across diverse datasets of various sizes, especially small ones.

Imbalanced datasets pose a difficulty in fraud detection, as classifiers are often biased toward the majority class and perform poorly on rare fraudulent transactions. Synthetic data generation is therefore commonly used to mitigate this problem. In this work, we propose the Clustered Embedding Diffusion-Transformer (EmDT), a diffusion model designed to generate fraudulent samples. Our key innovation is to leverage UMAP clustering to identify distinct fraudulent patterns, and train a Transformer denoising network with sinusoidal positional embeddings to capture feature relationships throughout the diffusion process. Once the synthetic data has been generated, we employ a standard decision-tree-based classifier (e.g., XGBoost) for classification, as this type of model remains better suited to tabular datasets. Experiments on a credit card fraud detection dataset demonstrate that EmDT significantly improves downstream classification performance compared to existing oversampling and generative methods, while maintaining comparable privacy protection and preserving feature correlations present in the original data.