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byAK and the research community

Jan 8

LLM Interactive Optimization of Open Source Python Libraries -- Case Studies and Generalization

With the advent of large language models (LLMs) like GPT-3, a natural question is the extent to which these models can be utilized for source code optimization. This paper presents methodologically stringent case studies applied to well-known open source python libraries pillow and numpy. We find that contemporary LLM ChatGPT-4 (state September and October 2023) is surprisingly adept at optimizing energy and compute efficiency. However, this is only the case in interactive use, with a human expert in the loop. Aware of experimenter bias, we document our qualitative approach in detail, and provide transcript and source code. We start by providing a detailed description of our approach in conversing with the LLM to optimize the _getextrema function in the pillow library, and a quantitative evaluation of the performance improvement. To demonstrate qualitative replicability, we report further attempts on another locus in the pillow library, and one code locus in the numpy library, to demonstrate generalization within and beyond a library. In all attempts, the performance improvement is significant (factor up to 38). We have also not omitted reporting of failed attempts (there were none). We conclude that LLMs are a promising tool for code optimization in open source libraries, but that the human expert in the loop is essential for success. Nonetheless, we were surprised by how few iterations were required to achieve substantial performance improvements that were not obvious to the expert in the loop. We would like bring attention to the qualitative nature of this study, more robust quantitative studies would need to introduce a layer of selecting experts in a representative sample -- we invite the community to collaborate.

  • 1 authors
·
Dec 8, 2023

Downscaling Extreme Precipitation with Wasserstein Regularized Diffusion

Understanding the risks posed by extreme rainfall events requires analysis of precipitation fields with high resolution (to assess localized hazards) and extensive historical coverage (to capture sufficient examples of rare occurrences). Radar and mesonet networks provide precipitation fields at 1 km resolution but with limited historical and geographical coverage, while gauge-based records and reanalysis products cover decades of time on a global scale, but only at 30-50 km resolution. To help provide high-resolution precipitation estimates over long time scales, this study presents Wasserstein Regularized Diffusion (WassDiff), a diffusion framework to downscale (super-resolve) precipitation fields from low-resolution gauge and reanalysis products. Crucially, unlike related deep generative models, WassDiff integrates a Wasserstein distribution-matching regularizer to the denoising process to reduce empirical biases at extreme intensities. Comprehensive evaluations demonstrate that WassDiff quantitatively outperforms existing state-of-the-art generative downscaling methods at recovering extreme weather phenomena such as tropical storms and cold fronts. Case studies further qualitatively demonstrate WassDiff's ability to reproduce realistic fine-scale weather structures and accurate peak intensities. By unlocking decades of high-resolution rainfall information from globally available coarse records, WassDiff offers a practical pathway toward more accurate flood-risk assessments and climate-adaptation planning.

  • 5 authors
·
Oct 1, 2024

FinCriticalED: A Visual Benchmark for Financial Fact-Level OCR Evaluation

We introduce FinCriticalED (Financial Critical Error Detection), a visual benchmark for evaluating OCR and vision language models on financial documents at the fact level. Financial documents contain visually dense and table heavy layouts where numerical and temporal information is tightly coupled with structure. In high stakes settings, small OCR mistakes such as sign inversion or shifted dates can lead to materially different interpretations, while traditional OCR metrics like ROUGE and edit distance capture only surface level text similarity. \ficriticaled provides 500 image-HTML pairs with expert annotated financial facts covering over seven hundred numerical and temporal facts. It introduces three key contributions. First, it establishes the first fact level evaluation benchmark for financial document understanding, shifting evaluation from lexical overlap to domain critical factual correctness. Second, all annotations are created and verified by financial experts with strict quality control over signs, magnitudes, and temporal expressions. Third, we develop an LLM-as-Judge evaluation pipeline that performs structured fact extraction and contextual verification for visually complex financial documents. We benchmark OCR systems, open source vision language models, and proprietary models on FinCriticalED. Results show that although the strongest proprietary models achieve the highest factual accuracy, substantial errors remain in visually intricate numerical and temporal contexts. Through quantitative evaluation and expert case studies, FinCriticalED provides a rigorous foundation for advancing visual factual precision in financial and other precision critical domains.

  • 13 authors
·
Nov 18, 2025

Fast and Interpretable Protein Substructure Alignment via Optimal Transport

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

  • 7 authors
·
Oct 12, 2025

ParallelBench: Understanding the Trade-offs of Parallel Decoding in Diffusion LLMs

While most autoregressive LLMs are constrained to one-by-one decoding, diffusion LLMs (dLLMs) have attracted growing interest for their potential to dramatically accelerate inference through parallel decoding. Despite this promise, the conditional independence assumption in dLLMs causes parallel decoding to ignore token dependencies, inevitably degrading generation quality when these dependencies are strong. However, existing works largely overlook these inherent challenges, and evaluations on standard benchmarks (e.g., math and coding) are not sufficient to capture the quality degradation caused by parallel decoding. To address this gap, we first provide an information-theoretic analysis of parallel decoding. We then conduct case studies on analytically tractable synthetic list operations from both data distribution and decoding strategy perspectives, offering quantitative insights that highlight the fundamental limitations of parallel decoding. Building on these insights, we propose ParallelBench, the first benchmark specifically designed for dLLMs, featuring realistic tasks that are trivial for humans and autoregressive LLMs yet exceptionally challenging for dLLMs under parallel decoding. Using ParallelBench, we systematically analyze both dLLMs and autoregressive LLMs, revealing that: (i) dLLMs under parallel decoding can suffer dramatic quality degradation in real-world scenarios, and (ii) current parallel decoding strategies struggle to adapt their degree of parallelism based on task difficulty, thus failing to achieve meaningful speedup without compromising quality. Our findings underscore the pressing need for innovative decoding methods that can overcome the current speed-quality trade-off. We release our benchmark to help accelerate the development of truly efficient dLLMs.

furiosa-ai FuriosaAI
·
Oct 6, 2025 2

Masked Thought: Simply Masking Partial Reasoning Steps Can Improve Mathematical Reasoning Learning of Language Models

In reasoning tasks, even a minor error can cascade into inaccurate results, leading to suboptimal performance of large language models in such domains. Earlier fine-tuning approaches sought to mitigate this by leveraging more precise supervisory signals from human labeling, larger models, or self-sampling, although at a high cost. Conversely, we develop a method that avoids external resources, relying instead on introducing perturbations to the input. Our training approach randomly masks certain tokens within the chain of thought, a technique we found to be particularly effective for reasoning tasks. When applied to fine-tuning with GSM8K, this method achieved a 5% improvement in accuracy over standard supervised fine-tuning with a few codes modified and no additional labeling effort. Furthermore, it is complementary to existing methods. When integrated with related data augmentation methods, it leads to an average improvement of 3% improvement in GSM8K accuracy and 1% improvement in MATH accuracy across five datasets of various quality and size, as well as two base models. We further investigate the mechanisms behind this improvement through case studies and quantitative analysis, suggesting that our approach may provide superior support for the model in capturing long-distance dependencies, especially those related to questions. This enhancement could deepen understanding of premises in questions and prior steps. Our code is available at Github.

  • 9 authors
·
Mar 4, 2024