OntoLearner 1.4.7__py3-none-any.whl → 1.4.9__py3-none-any.whl

ontolearner/learner/taxonomy_discovery/sbunlp.py

@@ -0,0 +1,402 @@
+# Copyright (c) 2025 SciKnowOrg
+# License: MIT
+
+import os
+import re
+import json
+from typing import Any, Dict, List, Optional
+
+import torch
+from transformers import AutoTokenizer, AutoModelForCausalLM, BitsAndBytesConfig
+from ...base import AutoLearner
+
+
+class SBUNLPFewShotLearner(AutoLearner):
+    """
+    Few-shot taxonomy discovery via N×M batch prompting.
+
+    This learner:
+      - Caches & cleans gold parent–child pairs during `fit`.
+      - Splits (train pairs × test terms) into a grid of chunks.
+      - Builds an instruction prompt per grid cell with few-shot JSON examples.
+      - Generates and parses model outputs as JSON relations.
+      - Merges & deduplicates all predicted edges.
+    """
+
+    def __init__(
+        self,
+        model_name: str = "Qwen/Qwen2.5-0.5B-Instruct",
+        try_4bit: bool = True,
+        device: str = "cpu",
+        num_train_chunks: int = 7,
+        num_test_chunks: int = 7,
+        max_new_tokens: int = 140,
+        max_input_tokens: int = 1500,
+        temperature: float = 0.0,
+        top_p: float = 1.0,
+        limit_num_prompts: Optional[int] = None,
+        output_dir: Optional[str] = None,
+        **kwargs: Any,
+    ) -> None:
+        """
+        Initialize the learner and core generation / batching settings.
+
+        Args:
+            model_name: HF id/path of the causal LLM (e.g., Qwen Instruct).
+            try_4bit: If True and on CUDA, load with 4-bit NF4 quantization.
+            device: "cpu" or "cuda" for model execution.
+            num_train_chunks: Number of chunks for the gold (parent, child) bank.
+            num_test_chunks: Number of chunks for the test term list.
+            max_new_tokens: Max new tokens to generate per prompt call.
+            max_input_tokens: Clip the *input* prompt to this many tokens (tail kept).
+            temperature: Sampling temperature; 0.0 uses greedy decoding.
+            top_p: Nucleus sampling parameter (used when temperature > 0).
+            limit_num_prompts: Optional hard cap on prompts issued (debug/cost).
+            output_dir: Optional directory to save per-batch JSON predictions.
+            **kwargs: Forwarded to the base class.
+        """
+        super().__init__(**kwargs)
+        self.model_name = model_name
+        self.try_4bit = try_4bit
+        self.device = device
+
+        self.num_train_chunks = num_train_chunks
+        self.num_test_chunks = num_test_chunks
+        self.max_new_tokens = max_new_tokens
+        self.max_input_tokens = max_input_tokens
+        self.temperature = temperature
+        self.top_p = top_p
+        self.limit_num_prompts = limit_num_prompts
+        self.output_dir = output_dir
+
+        self.tokenizer: Optional[AutoTokenizer] = None
+        self.model: Optional[AutoModelForCausalLM] = None
+        self.train_pairs_clean: List[Dict[str, str]] = []
+
+    def _clean_pairs(self, pair_rows: List[Dict[str, str]]) -> List[Dict[str, str]]:
+        """
+        Normalize, filter, and deduplicate relation pairs.
+
+        Operations:
+          - Cast 'parent'/'child' to strings and strip whitespace.
+          - Drop rows with empty values.
+          - Drop self-relations (case-insensitive parent == child).
+          - Deduplicate by lowercase (parent, child).
+
+        Args:
+            pair_rows: Raw list of dicts with at least 'parent' and 'child'.
+
+        Returns:
+            Cleaned list of {'parent','child'} dicts.
+        """
+        cleaned, seen = [], set()
+        for rec in pair_rows or []:
+            if not isinstance(rec, dict):
+                continue
+            p = str(rec.get("parent", "")).strip()
+            c = str(rec.get("child", "")).strip()
+            if not p or not c:
+                continue
+            key = (p.lower(), c.lower())
+            if key[0] == key[1] or key in seen:
+                continue
+            seen.add(key)
+            cleaned.append({"parent": p, "child": c})
+        return cleaned
+
+    def _chunk_list(self, items: List[Any], num_chunks: int) -> List[List[Any]]:
+        """
+        Split a list into `num_chunks` near-equal contiguous parts.
+
+        Args:
+            items: Sequence to split.
+            num_chunks: Number of chunks to produce; if <= 0, returns [items].
+
+        Returns:
+            List of chunks (some may be empty if len(items) < num_chunks).
+        """
+        if num_chunks <= 0:
+            return [items]
+        n = len(items)
+        base, rem = divmod(n, num_chunks)
+        out, start = [], 0
+        for i in range(num_chunks):
+            size = base + (1 if i < rem else 0)
+            out.append(items[start : start + size])
+            start += size
+        return out
+
+    def _ensure_dir(self, path: Optional[str]) -> None:
+        """
+        Create a directory if `path` is a non-empty string.
+
+        Args:
+            path: Directory to create (recursively). Ignored if falsy.
+        """
+        if path:
+            os.makedirs(path, exist_ok=True)
+
+    def load(self, **_: Any) -> None:
+        """
+        Load tokenizer and model; optionally enable 4-bit quantization.
+
+        Assumes bitsandbytes is available if `try_4bit=True` on CUDA.
+        Sets tokenizer pad token if missing. Places model on GPU (device_map='auto')
+        when `device='cuda'`, otherwise on CPU.
+
+        Args:
+            **_: Unused kwargs for interface compatibility.
+        """
+        quant_config = None
+        if self.try_4bit and self.device == "cuda":
+            quant_config = BitsAndBytesConfig(
+                load_in_4bit=True,
+                bnb_4bit_compute_dtype=torch.float16,
+                bnb_4bit_use_double_quant=True,
+                bnb_4bit_quant_type="nf4",
+            )
+
+        self.tokenizer = AutoTokenizer.from_pretrained(self.model_name)
+        if getattr(self.tokenizer, "pad_token_id", None) is None:
+            if getattr(self.tokenizer, "eos_token", None) is not None:
+                self.tokenizer.pad_token = self.tokenizer.eos_token
+            elif getattr(self.tokenizer, "unk_token", None) is not None:
+                self.tokenizer.pad_token = self.tokenizer.unk_token
+
+        self.model = AutoModelForCausalLM.from_pretrained(
+            self.model_name,
+            device_map=("auto" if self.device == "cuda" else None),
+            torch_dtype=(torch.float16 if self.device == "cuda" else torch.float32),
+            quantization_config=quant_config,
+        )
+        if self.device == "cpu":
+            self.model.to("cpu")
+
+    def _format_chat(self, user_text: str) -> str:
+        """
+        Wrap plain text with the model's chat template, if provided.
+
+        Many instruction-tuned models expose `tokenizer.chat_template`.
+        If available, use it to construct a proper chat prompt; otherwise,
+        return the text unchanged.
+
+        Args:
+            user_text: Content of the user message.
+
+        Returns:
+            A generation-ready prompt string.
+        """
+        if hasattr(self.tokenizer, "apply_chat_template") and getattr(
+            self.tokenizer, "chat_template", None
+        ):
+            return self.tokenizer.apply_chat_template(
+                [{"role": "user", "content": user_text}],
+                tokenize=False,
+                add_generation_prompt=True,
+            )
+        return user_text
+
+    @torch.no_grad()
+    def _generate(self, prompt_text: str) -> str:
+        """
+        Generate text for a single prompt, guarding input length.
+
+        Steps:
+          1) Format prompt via chat template (if present).
+          2) Tokenize and clip the *input* to `max_input_tokens` (tail kept).
+          3) Call `model.generate` with configured decoding params.
+          4) Strip the echoed prompt from the decoded output (if present).
+
+        Args:
+            prompt_text: Textual prompt to feed the model.
+
+        Returns:
+            Model continuation string (prompt-echo stripped when applicable).
+        """
+        formatted = self._format_chat(prompt_text)
+        ids = self.tokenizer(formatted, add_special_tokens=False, return_tensors=None)[
+            "input_ids"
+        ]
+        if len(ids) > self.max_input_tokens:
+            ids = ids[-self.max_input_tokens :]
+        device = next(self.model.parameters()).device
+        input_ids = torch.tensor([ids], device=device)
+
+        out = self.model.generate(
+            input_ids=input_ids,
+            max_new_tokens=self.max_new_tokens,
+            do_sample=(self.temperature > 0.0),
+            temperature=self.temperature,
+            top_p=self.top_p,
+            pad_token_id=self.tokenizer.pad_token_id,
+            eos_token_id=getattr(self.tokenizer, "eos_token_id", None),
+            use_cache=True,
+        )
+
+        decoded_full = self.tokenizer.decode(out[0], skip_special_tokens=True)
+        decoded_prompt = self.tokenizer.decode(input_ids[0], skip_special_tokens=True)
+        return (
+            decoded_full[len(decoded_prompt) :].strip()
+            if decoded_full.startswith(decoded_prompt)
+            else decoded_full.strip()
+        )
+
+    def _build_prompt(
+        self,
+        train_pairs_chunk: List[Dict[str, str]],
+        test_terms_chunk: List[str],
+    ) -> str:
+        """
+        Construct a few-shot prompt with JSON examples and test terms.
+
+        The prompt:
+          - Shows several gold (parent, child) examples in JSON.
+          - Lists the test terms (one per line) between [PAIR] tags.
+          - Instructs to return ONLY a JSON array of {'parent','child'}.
+
+        Args:
+            train_pairs_chunk: Cleaned training relations for examples.
+            test_terms_chunk: The current chunk of test terms.
+
+        Returns:
+            The fully formatted prompt string.
+        """
+        examples_json = json.dumps(train_pairs_chunk, ensure_ascii=False, indent=2)
+        test_block = "\n".join(test_terms_chunk)
+        prompt = (
+            "From this file, extract all parent–child relations like in the examples.\n"
+            "Return ONLY a JSON array of objects with keys 'parent' and 'child'.\n"
+            "Output format:\n"
+            "[\n"
+            '  {"parent": "parent1", "child": "child1"},\n'
+            '  {"parent": "parent2", "child": "child2"}\n'
+            "]\n\n"
+            "EXAMPLES (JSON):\n"
+            f"{examples_json}\n\n"
+            "TEST TYPES (between [PAIR] tags):\n"
+            "[PAIR]\n"
+            f"{test_block}\n"
+            "[PAIR]\n"
+            "Return only JSON."
+        )
+        return prompt
+
+    def _parse_pairs(self, text: str) -> List[Dict[str, str]]:
+        """
+        Parse a generation string into a list of relation dicts.
+
+        Parsing strategy:
+          1) Try to parse the entire string as JSON; expect a list.
+          2) Else, regex-extract the outermost JSON-like array and parse that.
+          3) On failure, return an empty list.
+
+        Args:
+            text: Raw model output.
+
+        Returns:
+            Cleaned list of {'parent','child'} dicts (possibly empty).
+        """
+        text = text.strip()
+        try:
+            obj = json.loads(text)
+            if isinstance(obj, list):
+                return self._clean_pairs(obj)
+        except Exception:
+            pass
+        m = re.search(r"\[\s*(?:\{[\s\S]*?\}\s*,?\s*)*\]", text)
+        if m:
+            try:
+                obj = json.loads(m.group(0))
+                if isinstance(obj, list):
+                    return self._clean_pairs(obj)
+            except Exception:
+                pass
+        return []
+
+    def fit(self, train_data: Any, task: str, ontologizer: bool = True):
+        """
+        Cache and clean gold relations for few-shot prompting.
+
+        For `task == "taxonomy-discovery"`:
+          - If `ontologizer=True`, convert ontology-like input into
+            a list of {'parent','child'} via the base helper.
+          - Otherwise, accept a user-provided list directly.
+          - Store a cleaned, deduplicated bank in `self.train_pairs_clean`.
+
+        Args:
+            train_data: Ontology-like object or list of relation dicts.
+            task: Task selector (expects "taxonomy-discovery").
+            ontologizer: Whether to transform ontology inputs.
+
+        Returns:
+            None. (State is stored on the instance.)
+        """
+        if task != "taxonomy-discovery":
+            return super().fit(train_data, task, ontologizer)
+        if ontologizer:
+            gold = self.tasks_ground_truth_former(train_data, task="taxonomy-discovery")
+            self.train_pairs_clean = self._clean_pairs(gold)
+        else:
+            self.train_pairs_clean = self._clean_pairs(train_data)
+
+    def _taxonomy_discovery(
+        self, data: Any, test: bool = False
+    ) -> Optional[List[Dict[str, str]]]:
+        """
+        Run few-shot inference (test=True) or no-op during training.
+
+        Inference steps:
+          - Ensure tokenizer/model are loaded.
+          - Normalize `data` to a list of test terms (via base helper if needed).
+          - Create the N×M grid across (train_pairs_chunk × test_terms_chunk).
+          - For each cell: build prompt → generate → parse → (optionally) save.
+          - Merge and deduplicate all predicted pairs before returning.
+
+        Args:
+            data: Test input (ontology-like, list of strings, or mixed).
+            test: If True, perform prediction; otherwise return None.
+
+        Returns:
+            On `test=True`: deduplicated list of {'parent','child'}.
+            On `test=False`: None.
+        """
+        if not test:
+            return None
+        if self.model is None or self.tokenizer is None:
+            self.load()
+
+        if isinstance(data, list) and (len(data) == 0 or isinstance(data[0], str)):
+            test_terms: List[str] = data
+        else:
+            test_terms = super().tasks_data_former(
+                data=data, task="taxonomy-discovery", test=True
+            )
+
+        train_chunks = self._chunk_list(self.train_pairs_clean, self.num_train_chunks)
+        test_chunks = self._chunk_list(test_terms, self.num_test_chunks)
+
+        self._ensure_dir(self.output_dir)
+
+        merged: List[Dict[str, str]] = []
+        issued = 0
+
+        for ti, tr in enumerate(train_chunks, 1):
+            for si, ts in enumerate(test_chunks, 1):
+                issued += 1
+                if self.limit_num_prompts and issued > self.limit_num_prompts:
+                    break
+                prompt = self._build_prompt(tr, ts)
+                resp = self._generate(prompt)
+                pairs = self._parse_pairs(resp)
+
+                if self.output_dir:
+                    path = os.path.join(self.output_dir, f"pairs_T{ti}_S{si}.json")
+                    with open(path, "w", encoding="utf-8") as f:
+                        json.dump(pairs, f, ensure_ascii=False, indent=2)
+
+                merged.extend(pairs)
+
+            if self.limit_num_prompts and issued >= (self.limit_num_prompts or 0):
+                break
+
+        return self._clean_pairs(merged)