David Blaauw

Yichen Gu, David Blaauw, Joshua Welch

A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at the same point in real time may be at different stages of the transition process. This can be viewed as a problem of learning the behavior of a dynamical system from observations whose times are unknown. Additionally, a single progenitor cell type often bifurcates into multiple child cell types, further complicating the problem of modeling the dynamics. To address this problem, we developed an approach called variational mixtures of ordinary differential equations. By using a simple family of ODEs informed by the biochemistry of gene expression to constrain the likelihood of a deep generative model, we can simultaneously infer the latent time and latent state of each cell and predict its future gene expression state. The model can be interpreted as a mixture of ODEs whose parameters vary continuously across a latent space of cell states. Our approach dramatically improves data fit, latent time inference, and future cell state estimation of single-cell gene expression data compared to previous approaches.

Pierre Abillama, Changwoo Lee, Juechu Dong et al.

Recent advances in transformer-based foundation models have made them the default choice for many tasks, but their rapidly growing size makes fitting a full model on a single GPU increasingly difficult and their computational cost prohibitive. Block low-rank (BLR) compression techniques address this challenge by learning compact representations of weight matrices. While traditional low-rank (LR) methods often incur sharp accuracy drops, BLR approaches such as Monarch and BLAST can better capture the underlying structure, thus preserving accuracy while reducing computations and memory footprints. In this work, we use roofline analysis to show that, although BLR methods achieve theoretical savings and practical speedups for single-token inference, multi-token inference often becomes memory-bound in practice, increasing latency despite compiler-level optimizations in PyTorch. To address this, we introduce custom Triton kernels with partial fusion and memory layout optimizations for both Monarch and BLAST. On memory-constrained NVIDIA GPUs such as Jetson Orin Nano and A40, our kernels deliver up to $3.76\times$ speedups and $3\times$ model size compression over PyTorch dense baselines using CUDA backend and compiler-level optimizations, while supporting various models including Llama-7/1B, GPT2-S, DiT-XL/2, and ViT-B. Our code is available at https://github.com/pabillam/mem-efficient-blr.

Mingyu Yang, Roger Hsiao, Gordy Carichner et al.

Details of Monarch butterfly migration from the U.S. to Mexico remain a mystery due to lack of a proper localization technology to accurately localize and track butterfly migration. In this paper, we propose a deep learning based butterfly localization algorithm that can estimate a butterfly's daily location by analyzing a light and temperature sensor data log continuously obtained from an ultra-low power, mm-scale sensor attached to the butterfly. To train and test the proposed neural network based multi-sensor fusion localization algorithm, we collected over 1500 days of real world sensor measurement data with 82 volunteers all over the U.S. The proposed algorithm exhibits a mean absolute error of <1.5 degree in latitude and <0.5 degree in longitude Earth coordinate, satisfying our target goal for the Monarch butterfly migration study.

Charles Eckert, Xiaowei Wang, Jingcheng Wang et al.

This paper presents the Neural Cache architecture, which re-purposes cache structures to transform them into massively parallel compute units capable of running inferences for Deep Neural Networks. Techniques to do in-situ arithmetic in SRAM arrays, create efficient data mapping and reducing data movement are proposed. The Neural Cache architecture is capable of fully executing convolutional, fully connected, and pooling layers in-cache. The proposed architecture also supports quantization in-cache. Our experimental results show that the proposed architecture can improve inference latency by 18.3x over state-of-art multi-core CPU (Xeon E5), 7.7x over server class GPU (Titan Xp), for Inception v3 model. Neural Cache improves inference throughput by 12.4x over CPU (2.2x over GPU), while reducing power consumption by 50% over CPU (53% over GPU).