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WFO-ID-pilots / text2matrix

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desc2matrix.py: Information in species description omitted #10

Closed yjkiwilee closed 2 months ago

yjkiwilee commented 4 months ago

This issue refers to desc2matrix.py in https://github.com/WFO-ID-pilots/text2matrix/pull/7, and is split from #8. The LLM currently omits some information in the species description. Ideally the LLM should recover all the information given in the descriptions but I wonder if the model is having difficulties extracting some of the more highly condensed sentences. Please feel free to share ideas on how the prompt text / settings may be edited to resolve this issue.

For example, feeding in the following description, the model omits the information about the stipule margin.

Subshrub, ca. 3 m high, monoecious, pubescent, with both dendritic greyish trichomes, 0.1–0.4 mm long, and microscopic glandular trichomes. Stem erect, fleshy, pubescent; internodes 1–3.5 cm long. Stipules 2.5–3 × 0.7–1.5 cm, lanceolate, apex apiculate, margin entire, pubescent, carinate, appressed, caducous. Leaves: petiole 6.3–11.6 cm long, cylindrical, pubescent; blade 13–18 × 19–28 cm, transversally elliptic, deeply lobed (lobes approximately half the length of their main vein), 6 or 7 lobes, asymmetric, basifi xed; base cordate; lobes with acute apex; margin serrulate; pubescent on both surfaces, more densely so on abaxial surface, discolorous, adaxial surface green, abaxial surface green-cinereous; venation actinodromous, 6 or 7 veins at base, slightly thickened. Infl orescence: dichasial cyme 32–39 cm long, ca. 180 flowers; peduncle 23.5– 27 cm long, cinereous; fi rst order bracts 4–6 × 1.5–2.5 mm, lanceolate, apex acuminate, margin entire, caducous. Staminate fl owers: pedicel 1–1.4 cm long, pilose; tepals 4, white, the outer pair larger 6–7.2 × 3–4 mm, ovate to elliptic, apex acute to obtuse, margin entire, concave, glabrescent on abaxial surface, the inner pair 5–6.2 × 1.8–2.3 mm, oblong to oblanceolate, apex obtuse to rounded, margin entire, concave, glabrous; androecium actinomorphic, stamens 32–48, fi laments 0.2–0.9 mm long, free, anthers 1–1.3 mm long, rimose, connective prolonged. Pistillate flowers [not seen]: bracteoles 2, opposite, borne on pedicel, just below ovary, caducous [scars seen on the pedicel from capsules]; styles 3, 1.6–2 mm long, bifi d, branches spirally-arranged, stigmatic papillae covering branches, stigmatic surface papillose, yellow [obtained from capsules]; ovary 5–6.7 mm long, trilocular, placentation axile, placenta entire [observed from capsules]. Capsules 6–7.5 × 11–14.6 mm [including wings], three-winged, glabrescent, brown when mature, dehiscing at the basal portion; wings unequal, larger one 5–7 × 6–7 mm, apex obtuse to rounded, smaller ones 5.8–7 × 0.6–1.6 mm. Seeds ca. 0.3 mm long, oblong.

yjkiwilee commented 4 months ago

I'm currently experimenting with splitting the task of extracting information and turning it into JSON between two LLM runs to determine if that would improve performance.