Daily Papers

We introduce AInsteinBench, a large-scale benchmark for evaluating whether large language model (LLM) agents can operate as scientific computing development agents within real research software ecosystems. Unlike existing scientific reasoning benchmarks which focus on conceptual knowledge, or software engineering benchmarks that emphasize generic feature implementation and issue resolving, AInsteinBench evaluates models in end-to-end scientific development settings grounded in production-grade scientific repositories. The benchmark consists of tasks derived from maintainer-authored pull requests across six widely used scientific codebases, spanning quantum chemistry, quantum computing, molecular dynamics, numerical relativity, fluid dynamics, and cheminformatics. All benchmark tasks are carefully curated through multi-stage filtering and expert review to ensure scientific challenge, adequate test coverage, and well-calibrated difficulty. By leveraging evaluation in executable environments, scientifically meaningful failure modes, and test-driven verification, AInsteinBench measures a model's ability to move beyond surface-level code generation toward the core competencies required for computational scientific research.

Optimizing scientific software is a difficult task because codebases are often large and complex, and performance can depend upon several factors including the algorithm, its implementation, and hardware among others. Causes of poor performance can originate from disparate sources and be difficult to diagnose. Recent years have seen a multitude of work that use large language models (LLMs) to assist in software development tasks. However, these tools are trained to model the distribution of code as text, and are not specifically designed to understand performance aspects of code. In this work, we introduce a reinforcement learning based methodology to align the outputs of code LLMs with performance. This allows us to build upon the current code modeling capabilities of LLMs and extend them to generate better performing code. We demonstrate that our fine-tuned model improves the expected speedup of generated code over base models for a set of benchmark tasks from 0.9 to 1.6 for serial code and 1.9 to 4.5 for OpenMP code.

Camera-based physiological measurement is a fast growing field of computer vision. Remote photoplethysmography (rPPG) utilizes imaging devices (e.g., cameras) to measure the peripheral blood volume pulse (BVP) via photoplethysmography, and enables cardiac measurement via webcams and smartphones. However, the task is non-trivial with important pre-processing, modeling, and post-processing steps required to obtain state-of-the-art results. Replication of results and benchmarking of new models is critical for scientific progress; however, as with many other applications of deep learning, reliable codebases are not easy to find or use. We present a comprehensive toolbox, rPPG-Toolbox, that contains unsupervised and supervised rPPG models with support for public benchmark datasets, data augmentation, and systematic evaluation: https://github.com/ubicomplab/rPPG-Toolbox

Scalable oversight studies methods of training and evaluating AI systems in domains where human judgment is unreliable or expensive, such as scientific research and software engineering in complex codebases. Most work in this area has focused on methods of improving the quality of labels. Recent work by Burns et al. (2023) considers the complementary problem of training models with low-quality labels, finding that large pretrained models often have an inductive bias towards producing correct answers. In practice, however, neither label quantity nor quality is fixed: practitioners face a quantity-quality tradeoff. In this paper, we explore the microeconomics of the quantity-quality tradeoff on binary NLP classification tasks used in Burns et al. (2023). While sample-efficient learning has been studied extensively, little public research has focused on scalable elicitation: eliciting capabilities from pretrained models subject to labeling cost constraints. We find that this setting has novel dynamics caused by the tradeoff between label quantity and quality, as well as the model's existing latent capabilities. We observe three regimes of eliciting classification knowledge from pretrained models using supervised finetuning: quantity-dominant, quality-dominant, and a mixed regime involving the use of low- and high-quality data together to attain higher accuracy at a lower cost than using either alone. We explore sample-efficient elicitation methods that make use of two datasets of differing qualities, and establish a Pareto frontier of scalable elicitation methods that optimally trade off labeling cost and classifier performance. We find that the accuracy of supervised fine-tuning can be improved by up to 5 percentage points at a fixed labeling budget by adding a few-shot prompt to make use of the model's existing knowledge of the task.

Scientific user facilities, such as synchrotron beamlines, are equipped with a wide array of hardware and software tools that require a codebase for human-computer-interaction. This often necessitates developers to be involved to establish connection between users/researchers and the complex instrumentation. The advent of generative AI presents an opportunity to bridge this knowledge gap, enabling seamless communication and efficient experimental workflows. Here we present a modular architecture for the Virtual Scientific Companion (VISION) by assembling multiple AI-enabled cognitive blocks that each scaffolds large language models (LLMs) for a specialized task. With VISION, we performed LLM-based operation on the beamline workstation with low latency and demonstrated the first voice-controlled experiment at an X-ray scattering beamline. The modular and scalable architecture allows for easy adaptation to new instrument and capabilities. Development on natural language-based scientific experimentation is a building block for an impending future where a science exocortex -- a synthetic extension to the cognition of scientists -- may radically transform scientific practice and discovery.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Recent advances in large language models (LLMs) have given rise to powerful coding agents, making it possible for code assistants to evolve into code engineers. However, existing methods still face significant challenges in achieving high-fidelity document-to-codebase synthesis--such as scientific papers to code--primarily due to a fundamental conflict between information overload and the context bottlenecks of LLMs. In this work, we introduce DeepCode, a fully autonomous framework that fundamentally addresses this challenge through principled information-flow management. By treating repository synthesis as a channel optimization problem, DeepCode seamlessly orchestrates four information operations to maximize task-relevant signals under finite context budgets: source compression via blueprint distillation, structured indexing using stateful code memory, conditional knowledge injection via retrieval-augmented generation, and closed-loop error correction. Extensive evaluations on the PaperBench benchmark demonstrate that DeepCode achieves state-of-the-art performance, decisively outperforming leading commercial agents such as Cursor and Claude Code, and crucially, surpassing PhD-level human experts from top institutes on key reproduction metrics. By systematically transforming paper specifications into production-grade implementations comparable to human expert quality, this work establishes new foundations for autonomous scientific reproduction that can accelerate research evaluation and discovery.