Problem-dependent convergence bounds for randomized linear gradient compression

In distributed optimization, the communication of model updates can be a performance bottleneck. Consequently, gradient compression has been proposed as a means of increasing optimization throughput. In general, due to information loss, compression introduces a penalty on the number of iterations needed to reach a solution. In this work, we investigate how the iteration penalty depends on the interaction between compression and problem structure, in the context of non-convex stochastic optimization. We focus on linear compression schemes, where compression and decompression can be modeled as multiplication with a random matrix. We consider several distributions of matrices, among them random orthogonal matrices and matrices with random Gaussian entries. We find that in each case, the impact of compression on convergence can be quantified in terms of the norm of the Hessian of the objective, using a norm defined by the compression scheme. The analysis reveals that in certain cases, compression performance is related to low-rank structure or other spectral properties of the problem. In these cases, our bounds predict that the penalty introduced by compression is significantly reduced compared to worst-case bounds that only consider the compression level, ignoring problem data. We verify the theoretical findings on several optimization problems, including fine-tuning an image classification model.

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge

Understanding protein interactions and pathway knowledge is crucial for unraveling the complexities of living systems and investigating the underlying mechanisms of biological functions and complex diseases. While existing databases provide curated biological data from literature and other sources, they are often incomplete and their maintenance is labor-intensive, necessitating alternative approaches. In this study, we propose to harness the capabilities of large language models to address these issues by automatically extracting such knowledge from the relevant scientific literature. Toward this goal, in this work, we investigate the effectiveness of different large language models in tasks that involve recognizing protein interactions, pathways, and gene regulatory relations. We thoroughly evaluate the performance of various models, highlight the significant findings, and discuss both the future opportunities and the remaining challenges associated with this approach. The code and data are available at: https://github.com/boxorange/BioIE-LLM