Daily Papers

Single-cell RNA sequencing (scRNA-seq) data are often confounded by technical or biological batch effects. Existing deep learning models mitigate these effects but often discard batch-specific information, potentially losing valuable biological insights. We propose a Mixed Effects Deep Learning (MEDL) autoencoder framework that separately models batch-invariant (fixed effects) and batch-specific (random effects) components. By decoupling batch-invariant biological states from batch variations, our framework integrates both into predictive models. Our approach also generates 2D visualizations of how the same cell appears across batches, enhancing interpretability. Retaining both fixed and random effect latent spaces improves classification accuracy. We applied our framework to three datasets spanning the cardiovascular system (Healthy Heart), Autism Spectrum Disorder (ASD), and Acute Myeloid Leukemia (AML). With 147 batches in the Healthy Heart dataset, far exceeding typical numbers, we tested our framework's ability to handle many batches. In the ASD dataset, our approach captured donor heterogeneity between autistic and healthy individuals. In the AML dataset, it distinguished donor heterogeneity despite missing cell types and diseased donors exhibiting both healthy and malignant cells. These results highlight our framework's ability to characterize fixed and random effects, enhance batch effect visualization, and improve prediction accuracy across diverse datasets.

Accelerating large language model (LLM) inference is critical for real-world deployments requiring high throughput and low latency. Contextual sparsity, where each token dynamically activates only a small subset of the model parameters, shows promise but does not scale to large batch sizes due to union of active neurons quickly approaching dense computation. We introduce Polar Sparsity, highlighting a key shift in sparsity importance from MLP to Attention layers as we scale batch size and sequence length. While MLP layers become more compute-efficient under batching, their sparsity vanishes. In contrast, attention becomes increasingly more expensive at scale, while their head sparsity remains stable and batch-invariant. We develop hardware-efficient, sparsity-aware GPU kernels for selective MLP and Attention computations, delivering up to \(2.2\times\) end-to-end speedups for models like OPT, LLaMA-2 \& 3, across various batch sizes and sequence lengths without compromising accuracy. To our knowledge, this is the first work to demonstrate that contextual sparsity can scale effectively to large batch sizes, delivering substantial inference acceleration with minimal changes, making Polar Sparsity practical for large-scale, high-throughput LLM deployment systems. Our code is available at: https://github.com/susavlsh10/Polar-Sparsity.

We say an algorithm is batch size-invariant if changes to the batch size can largely be compensated for by changes to other hyperparameters. Stochastic gradient descent is well-known to have this property at small batch sizes, via the learning rate. However, some policy optimization algorithms (such as PPO) do not have this property, because of how they control the size of policy updates. In this work we show how to make these algorithms batch size-invariant. Our key insight is to decouple the proximal policy (used for controlling policy updates) from the behavior policy (used for off-policy corrections). Our experiments help explain why these algorithms work, and additionally show how they can make more efficient use of stale data.

In Self-Supervised Learning (SSL), models are typically pretrained, fine-tuned, and evaluated on the same domains. However, they tend to perform poorly when evaluated on unseen domains, a challenge that Unsupervised Domain Generalization (UDG) seeks to address. Current UDG methods rely on domain labels, which are often challenging to collect, and domain-specific architectures that lack scalability when confronted with numerous domains, making the current methodology impractical and rigid. Inspired by contrastive-based UDG methods that mitigate spurious correlations by restricting comparisons to examples from the same domain, we hypothesize that eliminating style variability within a batch could provide a more convenient and flexible way to reduce spurious correlations without requiring domain labels. To verify this hypothesis, we introduce Batch Styles Standardization (BSS), a relatively simple yet powerful Fourier-based method to standardize the style of images in a batch specifically designed for integration with SSL methods to tackle UDG. Combining BSS with existing SSL methods offers serious advantages over prior UDG methods: (1) It eliminates the need for domain labels or domain-specific network components to enhance domain-invariance in SSL representations, and (2) offers flexibility as BSS can be seamlessly integrated with diverse contrastive-based but also non-contrastive-based SSL methods. Experiments on several UDG datasets demonstrate that it significantly improves downstream task performances on unseen domains, often outperforming or rivaling with UDG methods. Finally, this work clarifies the underlying mechanisms contributing to BSS's effectiveness in improving domain-invariance in SSL representations and performances on unseen domain.

Supervised contrastive loss (SCL) is a competitive and often superior alternative to the cross-entropy loss for classification. While prior studies have demonstrated that both losses yield symmetric training representations under balanced data, this symmetry breaks under class imbalances. This paper presents an intriguing discovery: the introduction of a ReLU activation at the final layer effectively restores the symmetry in SCL-learned representations. We arrive at this finding analytically, by establishing that the global minimizers of an unconstrained features model with SCL loss and entry-wise non-negativity constraints form an orthogonal frame. Extensive experiments conducted across various datasets, architectures, and imbalance scenarios corroborate our finding. Importantly, our experiments reveal that the inclusion of the ReLU activation restores symmetry without compromising test accuracy. This constitutes the first geometry characterization of SCL under imbalances. Additionally, our analysis and experiments underscore the pivotal role of batch selection strategies in representation geometry. By proving necessary and sufficient conditions for mini-batch choices that ensure invariant symmetric representations, we introduce batch-binding as an efficient strategy that guarantees these conditions hold.