Existing multi-view clustering methods employ various strategies to address datalevel sparsity and view-level dynamic fusion. However, we identify a critical yet overlooked issue: varying sparsity across views. Cross-view sparsity variations lead to encoding discrepancies, heightening sample-level semantic heterogeneity and making view-level dynamic weighting inappropriate. To tackle these challenges, we propose Adaptive Sparse Autoencoders for Multi-View Clustering (SparseMVC), a framework with three key modules. Initially, the sparse autoencoder probes the sparsity of each view and adaptively adjusts encoding formats via an entropymatching loss term, mitigating cross-view inconsistencies. Subsequently, the correlation-informed sample reweighting module employs attention mechanisms to assign weights by capturing correlations between early-fused global and viewspecific features, reducing encoding discrepancies and balancing contributions. Furthermore, the cross-view distribution alignment module aligns feature distributions during the late fusion stage, accommodating datasets with an arbitrary number of views. Extensive experiments demonstrate that SparseMVC achieves state-of-theart clustering performance.

Neural models learn representations of high-dimensional data on low-dimensional manifolds. Multiple factors, including stochasticities in the training process, model architectures, and additional inductive biases, may induce different representations, even when learning the same task on the same data. However, it has recently been shown that when a latent structure is shared between distinct latent spaces, relative distances between representations can be preserved, up to distortions. Building on this idea, we demonstrate that exploiting the differential-geometric structure of latent spaces of neural models, it is possible to capture precisely the transformations between representational spaces trained on similar data distributions. Specifically, we assume that distinct neural models parametrize approximately the same underlying manifold, and introduce a representation based on the pullback metric that captures the intrinsic structure of the latent space, while scaling efficiently to large models.

Detecting intrusions in network traffic is a challenging task, particularly under limited supervision and constantly evolving attack patterns. While recent works have leveraged graph neural networks for network intrusion detection, they often decouple representation learning from anomaly detection, limiting the utility of the embeddings for identifying attacks. We propose GraphIDS, a self-supervised intrusion detection model that unifies these two stages by learning local graph representations of normal communication patterns through a masked autoencoder. An inductive graph neural network embeds each flow with its local topological context to capture typical network behavior, while a Transformer-based encoderdecoder reconstructs these embeddings, implicitly learning global co-occurrence patterns via self-attention without requiring explicit positional information. During inference, flows with unusually high reconstruction errors are flagged as potential intrusions. This end-to-end framework ensures that embeddings are directly optimized for the downstream task, facilitating the recognition of malicious traffic. On diverse NetFlow benchmarks, GraphIDS achieves up to 99.98% PR-AUC and 99.61% macro F1-score, outperforming baselines by 5-25 percentage points.1

The Unaligned Multi-view Clustering (UMC) aims to learn a discriminative cluster structure from unaligned multi-view data, where the features of samples are not completely aligned across multiple views. Most existing methods usually prioritize employing various alignment strategies to align sample representations across views and then conduct cross-view fusion on aligned representations for subsequent clustering. However, due to the heterogeneity of representations across different views, these alignment strategies often fail to achieve ideal view-alignment results, inevitably leading to unreliable alignment-based fusion. To address this issue, we propose an alignment-free consistency fusion framework named AF-UMC, which bypasses the traditional view-alignment operation and directly extracts consistent representations from each view to perform global cross-view consistency fusion. Specifically, we first construct a cross-view consistent basis space by a cross-view reconstruction loss and a designed Structural Clarity Regularization (SCR), where autoencoders extract consistent representations from each view through projecting view-specific data to the constructed basis space. Afterwards, these extracted representations are globally pulled together for further cross-view fusion according to a designed Instance Global Contrastive Fusion (IGCF). Compared with previous methods, AF-UMC directly extracts consistent representations from each view for global fusion instead of alignment for fusion, which significantly mitigates the degraded fusion performance caused by undesired view-alignment results while greatly reducing algorithm complexity and enhancing its efficiency. Extensive experiments on various datasets demonstrate that our AF-UMC exhibits superior performance against other state-of-the-art methods.

Extensive research has produced robust methods for unsupervised data visualization. Yet supervised visualization--where expert labels guide representations--remains underexplored, as most supervised approaches prioritize classification over visualization. Recently, RF-PHATE, a diffusion-based manifold learning method leveraging random forests and information geometry, marked significant progress in supervised visualization.

Deep neural networks often underperform on tabular data due to sensitivity to irrelevant features and a spectral bias toward smooth, low-frequency functions, limiting their ability to capture sharp, high-frequency signals in low-label regimes. While self-supervised learning (SSL) holds promise in such settings, it remains challenging in tabular domains due to the limited availability of effective data augmentations. We introduce TANDEM (Tree-And-Neural Dual Encoder Model), a hybrid autoencoder that trains a neural encoder alongside an oblivious soft decision tree (OSDT) encoder, both guided by dedicated stochastic gating networks for sample-specific feature selection. The encoders share a decoder and are coupled via alignment losses, encouraging complementary yet consistent representations. The training-only use of the tree operates as model-based augmentation, nudging representations toward tabular-relevant features while preserving a lean inference path (only the neural encoder is deployed). Spectral analysis highlights distinct yet complementary inductive biases across encoders, and experiments on classification and regression benchmarks in low-label settings show consistent gains over strong deep, tree-based, and SSL baselines.

Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a novel graph autoencoder that encodes and decodes graphs of varying sizes into a shared embedding space. GRALE is trained using an Optimal Transport-inspired loss that compares the original and reconstructed graphs and leverages a differentiable node matching module, which is trained jointly with the encoder and decoder. The proposed attention-based architecture relies on Evoformer, the core component of AlphaFold, which we extend to support both graph encoding and decoding. We show, in numerical experiments on simulated and molecular data, that GRALE enables a highly general form of pre-training, applicable to a wide range of downstream tasks, from classification and regression to more complex tasks such as graph interpolation, editing, matching, and prediction.1

However, the interpretability of the alignment component remains uninvestigated due to the difficulty in mapping the semantics of multi-modal representations into a unified concept set. To address this problem, we propose VL-SAE, a sparse autoencoder that encodes vision-language representations into its hidden activations. Each neuron in its hidden layer correlates to a concept represented by semantically similar images and texts, thereby interpreting these representations with a unified concept set. To establish the neuron-concept correlation, we encourage semantically similar representations to exhibit consistent neuron activations during self-supervised training. First, to measure the semantic similarity of multi-modal representations, we perform their alignment in an explicit form based on cosine similarity. Second, we construct the VL-SAE with a distance-based encoder and two modality-specific decoders to ensure the activation consistency of semantically similar representations. Experiments across multiple VLMs (e.g., CLIP, LLaVA) demonstrate the superior capability of VL-SAE in interpreting and enhancing the vision-language alignment. For interpretation, the alignment between vision and language representations can be understood by comparing their semantics with concepts. For enhancement, the alignment can be strengthened by aligning vision-language representations at the concept level, contributing to performance improvements in downstream tasks, including zero-shot image classification and hallucination elimination.

Semantic segmentation of electron microscopy (EM) images of biological samples remains a challenge in the life sciences. EM data captures details of biological structures, sometimes with such complexity that even human observers can find it overwhelming. We introduce ϵ-Seg, a method based on hierarchical variational autoencoders (HVAES), employing center-region masking, sparse label contrastive learning (CL), a Gaussian mixture model (GMM) prior, and clustering-free label prediction. Center-region masking and the inpainting loss encourage the model to learn robust and representative embeddings to distinguish the desired classes, even if training labels are sparse (0.05% of the total image data or less). For optimal performance, we employ CL and a GMM prior to shape the latent space of the HVAE such that encoded input patches tend to cluster w.r.t. the semantic classes we wish to distinguish. Finally, instead of clustering latent embeddings for semantic segmentation, we propose a MLP semantic segmentation head to directly predict class labels from latent embeddings. We show empirical results of ϵ-Seg and baseline methods on 2dense EM datasets of biological tissues and demonstrate the applicability of our method also on fluorescence microscopy data. Our results show that ϵ-Seg is capable of achieving competitive sparsely-supervised segmentation results on complex biological image data, even if only limited amounts of training labels are available.

Autoregressive language models dominate modern text generation, yet their sequential nature introduces fundamental limitations: decoding is slow, and maintaining global coherence remains challenging. Diffusion models offer a promising alternative by enabling parallel generation and flexible control; however, their application to text generation is hindered by the high dimensionality of token-level representations. We introduce COSMOS, a novel approach to text generation that operates entirely in a compressed, smooth latent space tailored specifically for diffusion. This space is learned using an autoencoder trained simultaneously for token-level reconstruction and alignment with frozen activations from a pretrained language encoder, providing robust semantic grounding and enabling effective perturbation-based augmentations. Empirically, we demonstrate that text representations can be compressed up to 8 while maintaining generation quality comparable to token-level diffusion models. Furthermore, increasing the latent sequence length allows COSMOS to surpass both diffusion-based and autoregressive baselines. We evaluate COSMOS on four diverse generative tasks including story generation, question generation, summarization, and detoxification and compare it with various generative paradigms. COSMOS achieves comparable or superior generation quality while offering more than 2 faster inference. Code is released at GitHub.