arXiv subjects

Samuel G Rodriques

Publications and source records attributed to Samuel G Rodriques.

5 recordsLinked to original sources

arXiv2026

MarkushGlyph and OCSRGlyph: Improved Chemical Structure Recognition

Chemical structures appear in patents and the scientific literature as images. For programmatic usage, such as indexing in databases or constructing machine learning model training sets, they must be transformed into line notations. The two common forms of this task are translating an image of a single molecule (optical chemical structure recognition - OCSR) and translating a Markush structure that represents a family of molecules. While prior work in the former case is quite mature, Markush structure parsing remains a challenging task. In this work, we treat both tasks as an image-to-text translation problem. We then propose OCSRGlyph, a state-of-the-art OCSR model, improving performance over prior methods by carefully considering stereochemistry. For the Markush task, we introduce MarkushGlyph, a vision-language model that reads the entire Markush structure as an image. This contrasts with prior systems, which often use multiple stages to separately process visual and text input content. Finally, we introduce a new metric for determining the accuracy of Markush structure translations, handling failure modes present in prior metrics.

cs.CV↗

arXiv2026

LABBench2: An Improved Benchmark for AI Systems Performing Biology Research

Optimism for accelerating scientific discovery with AI continues to grow. Current applications of AI in scientific research range from training dedicated foundation models on scientific data to agentic autonomous hypothesis generation systems to AI-driven autonomous labs. The need to measure progress of AI systems in scientific domains correspondingly must not only accelerate, but increasingly shift focus to more real-world capabilities. Beyond rote knowledge and even just reasoning to actually measuring the ability to perform meaningful work. Prior work introduced the Language Agent Biology Benchmark LAB-Bench as an initial attempt at measuring these abilities. Here we introduce an evolution of that benchmark, LABBench2, for measuring real-world capabilities of AI systems performing useful scientific tasks. LABBench2 comprises nearly 1,900 tasks and is, for the most part, a continuation of LAB-Bench, measuring similar capabilities but in more realistic contexts. We evaluate performance of current frontier models, and show that while abilities measured by LAB-Bench and LABBench2 have improved substantially, LABBench2 provides a meaningful jump in difficulty (model-specific accuracy differences range from -26% to -46% across subtasks) and underscores continued room for performance improvement. LABBench2 continues the legacy of LAB-Bench as a de facto benchmark for AI scientific research capabilities and we hope that it continues to help advance development of AI tools for these core research functions. To facilitate community use and development, we provide the task dataset at https://huggingface.co/datasets/futurehouse/labbench2 and a public eval harness at https://github.com/EdisonScientific/labbench2.

cs.AI↗

arXiv2025

BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge tasks, towards more practical work such as literature review and experimental planning. Bioinformatics is a domain where fully autonomous AI-driven discovery may be near, but no extensive benchmarks for measuring progress have been introduced to date. We therefore present the Bioinformatics Benchmark (BixBench), a dataset comprising over 50 real-world scenarios of practical biological data analysis with nearly 300 associated open-answer questions designed to measure the ability of LLM-based agents to explore biological datasets, perform long, multi-step analytical trajectories, and interpret the nuanced results of those analyses. We evaluate the performance of two frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent framework we open source. We find that even the latest frontier models only achieve 17% accuracy in the open-answer regime, and no better than random in a multiple-choice setting. By exposing the current limitations of frontier models, we hope BixBench can spur the development of agents capable of conducting rigorous bioinformatic analysis and accelerate scientific discovery.

q-bio.QM↗

arXiv2023

BioPlanner: Automatic Evaluation of LLMs on Protocol Planning in Biology

The ability to automatically generate accurate protocols for scientific experiments would represent a major step towards the automation of science. Large Language Models (LLMs) have impressive capabilities on a wide range of tasks, such as question answering and the generation of coherent text and code. However, LLMs can struggle with multi-step problems and long-term planning, which are crucial for designing scientific experiments. Moreover, evaluation of the accuracy of scientific protocols is challenging, because experiments can be described correctly in many different ways, require expert knowledge to evaluate, and cannot usually be executed automatically. Here we present an automatic evaluation framework for the task of planning experimental protocols, and we introduce BioProt: a dataset of biology protocols with corresponding pseudocode representations. To measure performance on generating scientific protocols, we use an LLM to convert a natural language protocol into pseudocode, and then evaluate an LLM's ability to reconstruct the pseudocode from a high-level description and a list of admissible pseudocode functions. We evaluate GPT-3 and GPT-4 on this task and explore their robustness. We externally validate the utility of pseudocode representations of text by generating accurate novel protocols using retrieved pseudocode, and we run a generated protocol successfully in our biological laboratory. Our framework is extensible to the evaluation and improvement of language model planning abilities in other areas of science or other areas that lack automatic evaluation.

cs.CL↗

arXiv2015

Multiplexed Neural Recording Down a Single Optical Fiber via Optical Reflectometry with Capacitive Signal Enhancement

We introduce a fiber-optic architecture for neural recording without contrast agents, and study its properties theoretically. Our sensor design is inspired by electrooptic modulators, which modulate the refractive index of a waveguide by applying an electric field across an electrooptic core material, and allows recording of the activities of individual neurons located at points along a 10 cm length of optical fiber with 20 um axial resolution, sensitivity down to 100 uV and a dynamic range of up to 1V using commercially available optical reflectometers as readout devices. A key concept of the design is the ability to create an "intensified" electric field inside an optical waveguide by applying the extracellular voltage from a neural spike over a nanoscopic distance. Implementing this concept requires the use of ultrathin high-dielectric capacitor layers. If suitable materials can be found -- possessing favorable properties with respect to toxicity, ohmic junctions, and surface capacitance -- then such sensing fibers could, in principle, be scaled down to few-micron cross-sections for minimally invasive neural interfacing. Custom-designed multi-material optical fibers, probed using a reflectometric readout, may therefore provide a powerful platform for neural sensing.

q-bio.NC↗