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Haruka Ozaki

Publications and source records attributed to Haruka Ozaki.

3 recordsLinked to original sources

Benchmarking locally hosted language models for journal editorial work on a compact desktop workstation

Journals are beginning to consider language models for manuscript handling, but submitted manuscripts are unpublished, and where policy forbids sending them to an external service the model must run on hardware the journal controls. The capability of locally hosted models on editorial work has not been measured. Here we constructed a benchmark of eight editorial tasks from a journal's Instructions for Authors, from manuscripts carrying defects we seeded and verified independently, and from published reviews of a preprint, and evaluated twenty open-weight models spanning a twenty-five-fold range of weight size on a compact desktop workstation of the kind a laboratory or small editorial office can adopt. The strongest model detected 36 of 40 seeded guideline violations and occupied 81 GB; a 17 GB model detected 33. Across the best configurations tested, we observed no consistent monotonic association between weight size and score: rank correlations were negligible on every task (Spearman |rho| <= 0.19), and within one model family the larger member scored below its smaller sibling. A deterministic checker of regular expressions and arithmetic, using no model, detected 31 of the same violations in a fraction of a second, and the union of its detections with those of the strongest model covered all 40. On the single peer-review case, the best model recovered 6 of 12 points from three published reviews. Prompt structure substantially altered scores within individual models. This level of performance is therefore within reach of a workstation of this class, once the deterministic checks are written.

cs.DL

Automating Care by Self-maintainability for Full Laboratory Automation

The automation of experiments in life sciences and chemistry has significantly advanced with the development of various instruments and AI technologies. However, achieving full laboratory automation, where experiments conceived by scientists are seamlessly executed in automated laboratories, remains a challenge. We identify the lack of automation in planning and operational tasks--critical human-managed processes collectively termed "care"--as a major barrier. Automating care is the key enabler for full laboratory automation. To address this, we propose the concept of self-maintainability (SeM): the ability of a laboratory system to autonomously adapt to internal and external disturbances, maintaining operational readiness akin to living cells. A SeM-enabled laboratory features autonomous recognition of its state, dynamic resource and information management, and adaptive responses to unexpected conditions. This shifts the planning and execution of experimental workflows, including scheduling and reagent allocation, from humans to the system. We present a conceptual framework for implementing SeM-enabled laboratories, comprising three modules--Requirement manager, Labware manager, and Device manager--and a Central manager. SeM not only enables scientists to execute envisioned experiments seamlessly but also provides developers with a design concept that drives the technological innovations needed for full automation.

q-bio.QM

LLMs can generate robotic scripts from goal-oriented instructions in biological laboratory automation

The use of laboratory automation by all researchers may substantially accelerate scientific activities by humans, including those in the life sciences. However, computer programs to operate robots should be written to implement laboratory automation, which requires technical knowledge and skills that may not be part of a researcher's training or expertise. In the last few years, there has been remarkable development in large language models (LLMs) such as GPT-4, which can generate computer codes based on natural language instructions. In this study, we used LLMs, including GPT-4, to generate scripts for robot operations in biological experiments based on ambiguous instructions. GPT-4 successfully generates scripts for OT-2, an automated liquid-handling robot, from simple instructions in natural language without specifying the robotic actions. Conventionally, translating the nuances of biological experiments into low-level robot actions requires researchers to understand both biology and robotics, imagine robot actions, and write robotic scripts. Our results showed that GPT-4 can connect the context of biological experiments with robot operation through simple prompts with expert-level contextual understanding and inherent knowledge. Replacing robot script programming, which is a tedious task for biological researchers, with natural-language LLM instructions that do not consider robot behavior significantly increases the number of researchers who can benefit from automating biological experiments.

q-bio.QM