Daily Papers

This work investigates the empirical performance of the sparse synthesis versus sparse analysis regularization for the ill-posed inverse problem of audio declipping. We develop a versatile non-convex heuristics which can be readily used with both data models. Based on this algorithm, we report that, in most cases, the two models perform almost similarly in terms of signal enhancement. However, the analysis version is shown to be amenable for real time audio processing, when certain analysis operators are considered. Both versions outperform state-of-the-art methods in the field, especially for the severely saturated signals.

Sparse Autoencoders (SAEs) have emerged as a promising approach for interpreting neural network representations by learning sparse, human-interpretable features from dense activations. We investigate whether incorporating variational methods into SAE architectures can improve feature organization and interpretability. We introduce the Variational Sparse Autoencoder (vSAE), which replaces deterministic ReLU gating with stochastic sampling from learned Gaussian posteriors and incorporates KL divergence regularization toward a standard normal prior. Our hypothesis is that this probabilistic sampling creates dispersive pressure, causing features to organize more coherently in the latent space while avoiding overlap. We evaluate a TopK vSAE against a standard TopK SAE on Pythia-70M transformer residual stream activations using comprehensive benchmarks including SAE Bench, individual feature interpretability analysis, and global latent space visualization through t-SNE. The vSAE underperforms standard SAE across core evaluation metrics, though excels at feature independence and ablation metrics. The KL divergence term creates excessive regularization pressure that substantially reduces the fraction of living features, leading to observed performance degradation. While vSAE features demonstrate improved robustness, they exhibit many more dead features than baseline. Our findings suggest that naive application of variational methods to SAEs does not improve feature organization or interpretability.

In deep learning, often the training process finds an interpolator (a solution with 0 training loss), but the test loss is still low. This phenomenon, known as benign overfitting, is a major mystery that received a lot of recent attention. One common mechanism for benign overfitting is implicit regularization, where the training process leads to additional properties for the interpolator, often characterized by minimizing certain norms. However, even for a simple sparse linear regression problem y = beta^{*top} x +xi with sparse beta^*, neither minimum ell_1 or ell_2 norm interpolator gives the optimal test loss. In this work, we give a different parametrization of the model which leads to a new implicit regularization effect that combines the benefit of ell_1 and ell_2 interpolators. We show that training our new model via gradient descent leads to an interpolator with near-optimal test loss. Our result is based on careful analysis of the training dynamics and provides another example of implicit regularization effect that goes beyond norm minimization.

Multi-channel imaging data is a prevalent data format in scientific fields such as astronomy and biology. The structured information and the high dimensionality of these 3-D tensor data makes the analysis an intriguing but challenging topic for statisticians and practitioners. The low-rank scalar-on-tensor regression model, in particular, has received widespread attention and has been re-formulated as a tensor Gaussian Process (Tensor-GP) model with multi-linear kernel in Yu et al. (2018). In this paper, we extend the Tensor-GP model by integrating a dimensionality reduction technique, called tensor contraction, with a Tensor-GP for a scalar-on-tensor regression task with multi-channel imaging data. This is motivated by the solar flare forecasting problem with high dimensional multi-channel imaging data. We first estimate a latent, reduced-size tensor for each data tensor and then apply a multi-linear Tensor-GP on the latent tensor data for prediction. We introduce an anisotropic total-variation regularization when conducting the tensor contraction to obtain a sparse and smooth latent tensor. We then propose an alternating proximal gradient descent algorithm for estimation. We validate our approach via extensive simulation studies and applying it to the solar flare forecasting problem.

Vision language models (VLMs) can flexibly address various vision tasks through text interactions. Although successful in semantic understanding, state-of-the-art VLMs including GPT-5 still struggle in understanding 3D from 2D inputs. On the other hand, expert pure vision models achieve super-human accuracy in metric depth estimation, a key 3D understanding task. However, they require task-specific architectures and losses. Such difference motivates us to ask: Can VLMs reach expert-level accuracy without architecture or loss change? We take per-pixel metric depth estimation as the representative task and show that the answer is yes! Surprisingly, comprehensive analysis shows that text-based supervised-finetuning with sparse labels is sufficient for VLMs to unlock strong 3D understanding, no dense prediction head or complex regression/regularization loss is needed. The bottleneck for VLMs lies actually in pixel reference and cross-dataset camera ambiguity, which we address through visual prompting and intrinsic-conditioned augmentation. With much smaller models, our method DepthLM surpasses the accuracy of most advanced VLMs by over 2x, making VLMs for the first time comparable with pure vision models. Interestingly, without explicit enforcement during training, VLMs trained with DepthLM naturally avoids over-smoothing, having much fewer flying points at boundary regions than pure vision models. The simplicity of DepthLM also enables a single VLM to cover various 3D tasks beyond metric depth. Our code and model will be released at the link below.

We report DynaCLR, a self-supervised method for embedding cell and organelle Dynamics via Contrastive Learning of Representations of time-lapse images. DynaCLR integrates single-cell tracking and time-aware contrastive sampling to learn robust, temporally regularized representations of cell dynamics. DynaCLR embeddings generalize effectively to in-distribution and out-of-distribution datasets, and can be used for several downstream tasks with sparse human annotations. We demonstrate efficient annotations of cell states with a human-in-the-loop using fluorescence and label-free imaging channels. DynaCLR method enables diverse downstream biological analyses: classification of cell division and infection, clustering heterogeneous cell migration patterns, cross-modal distillation of cell states from fluorescence to label-free channel, alignment of asynchronous cellular responses and broken cell tracks, and discovering organelle response due to infection. DynaCLR is a flexible method for comparative analyses of dynamic cellular responses to pharmacological, microbial, and genetic perturbations. We provide PyTorch-based implementations of the model training and inference pipeline (https://github.com/mehta-lab/viscy) and a GUI (https://github.com/czbiohub-sf/napari-iohub) for the visualization and annotation of trajectories of cells in the real space and the embedding space.