Graph-based semi-supervised learning (GSSL) serves as a powerful tool to model the underlying manifold structures of samples in high-dimensional spaces. It involves two phases: constructing an affinity graph from available data and inferring labels for unlabeled nodes on this graph. While numerous algorithms have been developed for label inference, the crucial graph construction phase has received comparatively less attention, despite its significant influence on the subsequent phase. In this paper, we present an optimal asymmetric graph structure for the label inference phase with theoretical motivations. Unlike existing graph construction methods, we differentiate the distinct roles that labeled nodes and unlabeled nodes could play.

Learning binary classifiers from positive and unlabeled data (PUL) is vital in many real-world applications, especially when verifying negative examples is difficult. Despite the impressive empirical performance of recent PUL methods, challenges like accumulated errors and increased estimation bias persist due to the absence of negative labels. In this paper, we unveil an intriguing yet long-overlooked observation in PUL: resampling the positive data in each training iteration to ensure a balanced distribution between positive and unlabeled examples results in strong early-stage performance. Furthermore, predictive trends for positive and negative classes display distinctly different patterns. Specifically, the scores (output probability) of unlabeled negative examples consistently decrease, while those of unlabeled positive examples show largely chaotic trends. Instead of focusing on classification within individual time frames, we innovatively adopt a holistic approach, interpreting the scores of each example as a temporal point process (TPP).

Self-supervised learning (SSL) is a powerful tool in machine learning, but understanding the learned representations and their underlying mechanisms remains a challenge. This paper presents an in-depth empirical analysis of SSL-trained representations, encompassing diverse models, architectures, and hyperparameters. Our study reveals an intriguing aspect of the SSL training process: it inherently facilitates the clustering of samples with respect to semantic labels, which is surprisingly driven by the SSL objective's regularization term. This clustering process not only enhances downstream classification but also compresses the data information. Furthermore, we establish that SSL-trained representations align more closely with semantic classes rather than random classes. Remarkably, we show that learned representations align with semantic classes across various hierarchical levels, and this alignment increases during training and when moving deeper into the network. Our findings provide valuable insights into SSL's representation learning mechanisms and their impact on performance across different sets of classes.

Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Previous work focused on supervised learning methods for small molecules where binding affinity data is abundant, but it is hard to apply the same strategy to other ligand classes like antibodies where labelled data is limited. In this paper, we explore unsupervised approaches and reformulate binding energy prediction as a generative modeling task. Specifically, we train an energy-based model on a set of unlabelled protein-ligand complexes using SE(3) denoising score matching (DSM) and interpret its log-likelihood as binding affinity. Our key contribution is a new equivariant rotation prediction network for SE(3) DSM called Neural Euler's Rotation Equations (NERE). It predicts a rotation by modeling the force and torque between protein and ligand atoms, where the force is defined as the gradient of an energy function with respect to atom coordinates. Using two protein-ligand and antibody-antigen binding affinity prediction benchmarks, we show that NERE outperforms all unsupervised baselines (physics-based potentials and protein language models) in both cases and surpasses supervised baselines in the antibody case.

While the optimal sample complexity of binary classification in terms of the VC dimension is well-established, determining the optimal sample complexity of multiclass classification has remained open. The appropriate complexity parameter for multiclass classification is the DS dimension, and despite significant efforts, a gap of $\sqrt{\text{DS}}$ has persisted between the upper and lower bounds on sample complexity. Recent work by Hanneke et al. (2026) shows a novel algebraic characterization of multiclass hypothesis classes in terms of their DS dimension. Building up on this, we show that the maximum hypergraph density of any multiclass hypothesis class is upper-bounded by its DS dimension. This proves a longstanding conjecture of Daniely and Shalev-Shwartz (2014). As a consequence, we determine the optimal dependence of the sample complexity on the DS dimension for multiclass as well as list learning.