js/test/bio.test.ts

import { test } from 'node:test';
import { strict as assert } from 'node:assert';
import { decodeBio, BIO_O, BIO_B, BIO_I } from '../src/bio.js';

/** Build flat (T, 3) logits from a list of class indices. Each row
 * gets a +5 bump for the chosen class so argmax is unambiguous. */
function logitsFromLabels(labels: number[]): Float32Array {
  const out = new Float32Array(labels.length * 3);
  for (let t = 0; t < labels.length; t++) {
    out[t * 3 + labels[t]] = 5;
  }
  return out;
}

test('decodeBio: B I I O → one span', () => {
  const logits = logitsFromLabels([BIO_B, BIO_I, BIO_I, BIO_O]);
  assert.deepEqual(decodeBio(logits), [[0, 2]]);
});

test('decodeBio: orphan I is dropped', () => {
  // I at the start without a preceding B should be silently skipped
  // (matches Python valid_only=True).
  const logits = logitsFromLabels([BIO_I, BIO_I, BIO_O, BIO_B, BIO_I]);
  assert.deepEqual(decodeBio(logits), [[3, 4]]);
});

test('decodeBio: attention mask zeroes positions to O', () => {
  const logits = logitsFromLabels([BIO_B, BIO_I, BIO_I, BIO_B]);
  const attn = BigInt64Array.from([1n, 1n, 0n, 0n]);
  // Positions 2,3 are masked → contribute O. So we get B I → span [0,1].
  assert.deepEqual(decodeBio(logits, attn), [[0, 1]]);
});

test('decodeBio: threshold suppresses low-confidence spans', () => {
  // Build a row where B has prob ~0.4 (below default 0.5).
  const logits = new Float32Array(3 * 3);
  // row 0: O=0.1, B=0.4 (weakest), I=0.5 (max but I-without-B is invalid)
  logits[0] = -1; logits[1] = 0.0; logits[2] = 0.4;
  // row 1: O=2, B=-1, I=-1 → O
  logits[3] = 2;  logits[4] = -1;  logits[5] = -1;
  // row 2: O=0, B=2, I=0 → B (high confidence)
  logits[6] = 0; logits[7] = 2;   logits[8] = 0;
  const spans = decodeBio(logits, undefined, 0.7);
  // The high-confidence B at position 2 should be the only B; its
  // span runs to end-of-sequence (just position 2).
  assert.deepEqual(spans, [[2, 2]]);
});

test('decodeBio: empty input', () => {
  assert.deepEqual(decodeBio(new Float32Array(0)), []);
});