12 files changed, 953 insertions, 0 deletions
diff --git a/hag/__init__.py b/hag/__init__.py
new file mode 100644
index 0000000..18496e9
--- /dev/null
+++ b/hag/__init__.py
@@ -0,0 +1,21 @@
+"""HAG: Hopfield-Augmented Generation."""
+
+from hag.config import (
+    EncoderConfig,
+    GeneratorConfig,
+    HopfieldConfig,
+    MemoryBankConfig,
+    PipelineConfig,
+)
+from hag.datatypes import HopfieldResult, PipelineResult, RetrievalResult
+
+__all__ = [
+    "HopfieldConfig",
+    "MemoryBankConfig",
+    "EncoderConfig",
+    "GeneratorConfig",
+    "PipelineConfig",
+    "HopfieldResult",
+    "RetrievalResult",
+    "PipelineResult",
+]
diff --git a/hag/config.py b/hag/config.py
new file mode 100644
index 0000000..793e3a6
--- /dev/null
+++ b/hag/config.py
@@ -0,0 +1,50 @@
+"""All hyperparameters and configuration dataclasses for HAG."""
+
+from dataclasses import dataclass, field
+
+
+@dataclass
+class HopfieldConfig:
+    """Configuration for the Hopfield retrieval module."""
+
+    beta: float = 1.0  # Inverse temperature. Higher = sharper retrieval
+    max_iter: int = 5  # Maximum Hopfield iteration steps
+    conv_threshold: float = 1e-4  # Stop if ||q_{t+1} - q_t|| < threshold
+    top_k: int = 5  # Number of passages to retrieve from final attention weights
+
+
+@dataclass
+class MemoryBankConfig:
+    """Configuration for the memory bank."""
+
+    embedding_dim: int = 768  # Must match encoder output dim
+    normalize: bool = True  # L2-normalize embeddings in memory bank
+
+
+@dataclass
+class EncoderConfig:
+    """Configuration for the query/passage encoder."""
+
+    model_name: str = "facebook/contriever-msmarco"
+    max_length: int = 512
+    batch_size: int = 64
+
+
+@dataclass
+class GeneratorConfig:
+    """Configuration for the LLM generator."""
+
+    model_name: str = "meta-llama/Llama-3.1-8B-Instruct"
+    max_new_tokens: int = 128
+    temperature: float = 0.0  # Greedy decoding for reproducibility
+
+
+@dataclass
+class PipelineConfig:
+    """Top-level pipeline configuration."""
+
+    hopfield: HopfieldConfig = field(default_factory=HopfieldConfig)
+    memory: MemoryBankConfig = field(default_factory=MemoryBankConfig)
+    encoder: EncoderConfig = field(default_factory=EncoderConfig)
+    generator: GeneratorConfig = field(default_factory=GeneratorConfig)
+    retriever_type: str = "hopfield"  # "hopfield" or "faiss"
diff --git a/hag/datatypes.py b/hag/datatypes.py
new file mode 100644
index 0000000..0f4254d
--- /dev/null
+++ b/hag/datatypes.py
@@ -0,0 +1,37 @@
+"""Data types used across HAG modules."""
+
+from dataclasses import dataclass, field
+from typing import List, Optional
+
+import torch
+
+
+@dataclass
+class HopfieldResult:
+    """Result from Hopfield iterative retrieval."""
+
+    attention_weights: torch.Tensor  # (batch, N) or (N,)
+    converged_query: torch.Tensor  # (batch, d) or (d,)
+    num_steps: int
+    trajectory: Optional[List[torch.Tensor]] = None  # list of q_t
+    energy_curve: Optional[List[torch.Tensor]] = None  # list of E(q_t)
+
+
+@dataclass
+class RetrievalResult:
+    """Result from a retriever (FAISS or Hopfield)."""
+
+    passages: List[str]
+    scores: torch.Tensor  # top-k scores
+    indices: torch.Tensor  # top-k indices
+    hopfield_result: Optional[HopfieldResult] = None
+
+
+@dataclass
+class PipelineResult:
+    """Result from the full RAG/HAG pipeline."""
+
+    question: str
+    answer: str
+    retrieved_passages: List[str]
+    retrieval_result: RetrievalResult
diff --git a/hag/encoder.py b/hag/encoder.py
new file mode 100644
index 0000000..7e103f3
--- /dev/null
+++ b/hag/encoder.py
@@ -0,0 +1,88 @@
+"""Wrapper for encoding queries and passages into embeddings."""
+
+import logging
+from typing import List, Union
+
+import torch
+
+from hag.config import EncoderConfig
+
+logger = logging.getLogger(__name__)
+
+
+class Encoder:
+    """Encodes text queries/passages into dense embeddings.
+
+    Uses a HuggingFace transformer model (e.g., Contriever).
+    For testing, use FakeEncoder instead.
+    """
+
+    def __init__(self, config: EncoderConfig) -> None:
+        self.config = config
+        self._tokenizer = None
+        self._model = None
+
+    def _load_model(self) -> None:
+        """Lazy-load the model and tokenizer."""
+        from transformers import AutoModel, AutoTokenizer
+
+        logger.info("Loading encoder model: %s", self.config.model_name)
+        self._tokenizer = AutoTokenizer.from_pretrained(self.config.model_name)
+        self._model = AutoModel.from_pretrained(self.config.model_name)
+        self._model.eval()
+
+    @torch.no_grad()
+    def encode(self, texts: Union[str, List[str]]) -> torch.Tensor:
+        """Encode text(s) into embedding(s).
+
+        Args:
+            texts: single string or list of strings
+
+        Returns:
+            (1, d) tensor for single input, (N, d) for list input.
+        """
+        if self._model is None:
+            self._load_model()
+
+        if isinstance(texts, str):
+            texts = [texts]
+
+        inputs = self._tokenizer(
+            texts,
+            max_length=self.config.max_length,
+            padding=True,
+            truncation=True,
+            return_tensors="pt",
+        )
+        outputs = self._model(**inputs)
+        # Mean pooling over token embeddings
+        embeddings = outputs.last_hidden_state.mean(dim=1)  # (N, d)
+        return embeddings
+
+
+class FakeEncoder:
+    """Deterministic hash-based encoder for testing. No model download needed."""
+
+    def __init__(self, dim: int = 64) -> None:
+        self.dim = dim
+
+    def encode(self, texts: Union[str, List[str]]) -> torch.Tensor:
+        """Produce deterministic embeddings based on text hash.
+
+        Args:
+            texts: single string or list of strings
+
+        Returns:
+            (1, d) or (N, d) normalized tensor.
+        """
+        if isinstance(texts, str):
+            texts = [texts]
+
+        embeddings = []
+        for text in texts:
+            torch.manual_seed(hash(text) % 2**32)
+            emb = torch.randn(1, self.dim)
+            embeddings.append(emb)
+
+        result = torch.cat(embeddings, dim=0)  # (N, d)
+        return torch.nn.functional.normalize(result, dim=-1)
diff --git a/hag/energy.py b/hag/energy.py
new file mode 100644
index 0000000..62a39e9
--- /dev/null
+++ b/hag/energy.py
@@ -0,0 +1,83 @@
+"""Energy computation and analysis utilities for Hopfield retrieval."""
+
+import logging
+from typing import List
+
+import torch
+
+from hag.datatypes import HopfieldResult
+
+logger = logging.getLogger(__name__)
+
+
+def compute_energy_curve(hopfield_result: HopfieldResult) -> List[float]:
+    """Extract energy values at each iteration step.
+
+    Args:
+        hopfield_result: result from HopfieldRetrieval.retrieve() with return_energy=True
+
+    Returns:
+        List of energy values (floats) at each step.
+    """
+    if hopfield_result.energy_curve is None:
+        return []
+    return [e.item() if e.dim() == 0 else e.mean().item() for e in hopfield_result.energy_curve]
+
+
+def compute_energy_gap(energy_curve: List[float]) -> float:
+    """Compute the energy gap: Delta_E = E(q_0) - E(q_T).
+
+    Larger gap means more refinement happened during iteration.
+
+    Args:
+        energy_curve: list of energy values at each step
+
+    Returns:
+        Energy gap (float). Positive if energy decreased.
+    """
+    if len(energy_curve) < 2:
+        return 0.0
+    return energy_curve[0] - energy_curve[-1]
+
+
+def verify_monotonic_decrease(energy_curve: List[float], tol: float = 1e-6) -> bool:
+    """Check that E(q_{t+1}) <= E(q_t) for all t.
+
+    This should always be True for the Modern Hopfield Network.
+
+    Args:
+        energy_curve: list of energy values at each step
+        tol: numerical tolerance for comparison
+
+    Returns:
+        True if energy decreases monotonically (within tolerance).
+    """
+    for i in range(len(energy_curve) - 1):
+        if energy_curve[i + 1] > energy_curve[i] + tol:
+            return False
+    return True
+
+
+def compute_attention_entropy(attention_weights: torch.Tensor) -> float:
+    """Compute the entropy of attention weights.
+
+    H(alpha) = -sum_i alpha_i * log(alpha_i)
+
+    Low entropy = sharp retrieval (confident).
+    High entropy = diffuse retrieval (uncertain).
+
+    Args:
+        attention_weights: (N,) or (batch, N) — attention distribution
+
+    Returns:
+        Entropy value (float). Averaged over batch if batched.
+    """
+    if attention_weights.dim() == 1:
+        attention_weights = attention_weights.unsqueeze(0)  # (1, N)
+
+    # Clamp to avoid log(0)
+    eps = 1e-12
+    alpha = attention_weights.clamp(min=eps)
+    entropy = -(alpha * alpha.log()).sum(dim=-1)  # (batch,)
+
+    return entropy.mean().item()
diff --git a/hag/generator.py b/hag/generator.py
new file mode 100644
index 0000000..2142e0c
--- /dev/null
+++ b/hag/generator.py
@@ -0,0 +1,87 @@
+"""LLM generation wrapper for producing answers from retrieved context."""
+
+import logging
+from typing import List
+
+from hag.config import GeneratorConfig
+
+logger = logging.getLogger(__name__)
+
+PROMPT_TEMPLATE = """Answer the following question based on the provided context passages.
+
+Context:
+{context}
+
+Question: {question}
+
+Answer:"""
+
+
+class Generator:
+    """LLM-based answer generator.
+
+    Uses a HuggingFace causal LM (e.g., Llama-3.1-8B-Instruct).
+    For testing, use FakeGenerator instead.
+    """
+
+    def __init__(self, config: GeneratorConfig) -> None:
+        self.config = config
+        self._tokenizer = None
+        self._model = None
+
+    def _load_model(self) -> None:
+        """Lazy-load the model and tokenizer."""
+        from transformers import AutoModelForCausalLM, AutoTokenizer
+
+        logger.info("Loading generator model: %s", self.config.model_name)
+        self._tokenizer = AutoTokenizer.from_pretrained(self.config.model_name)
+        self._model = AutoModelForCausalLM.from_pretrained(
+            self.config.model_name,
+            torch_dtype="auto",
+        )
+        self._model.eval()
+
+    def generate(self, question: str, passages: List[str]) -> str:
+        """Generate an answer given a question and retrieved passages.
+
+        Args:
+            question: the user question
+            passages: list of retrieved passage texts
+
+        Returns:
+            Generated answer string.
+        """
+        if self._model is None:
+            self._load_model()
+
+        context = "\n\n".join(
+            f"[{i+1}] {p}" for i, p in enumerate(passages)
+        )
+        prompt = PROMPT_TEMPLATE.format(context=context, question=question)
+
+        inputs = self._tokenizer(prompt, return_tensors="pt")
+        outputs = self._model.generate(
+            **inputs,
+            max_new_tokens=self.config.max_new_tokens,
+            temperature=self.config.temperature if self.config.temperature > 0 else None,
+            do_sample=self.config.temperature > 0,
+        )
+        # Decode only the generated tokens (skip the prompt)
+        generated = outputs[0][inputs["input_ids"].shape[1]:]
+        return self._tokenizer.decode(generated, skip_special_tokens=True).strip()
+
+
+class FakeGenerator:
+    """Deterministic mock generator for testing. No model download needed."""
+
+    def generate(self, question: str, passages: List[str]) -> str:
+        """Return a mock answer.
+
+        Args:
+            question: the user question
+            passages: list of retrieved passages
+
+        Returns:
+            Mock answer string.
+        """
+        return "mock answer"
diff --git a/hag/hopfield.py b/hag/hopfield.py
new file mode 100644
index 0000000..287e4af
--- /dev/null
+++ b/hag/hopfield.py
@@ -0,0 +1,124 @@
+"""Core Modern Continuous Hopfield Network retrieval module.
+
+Implements the iterative retrieval dynamics from:
+    Ramsauer et al., "Hopfield Networks is All You Need" (ICLR 2021)
+
+Update rule: q_{t+1} = M * softmax(beta * M^T * q_t)
+Energy:      E(q) = -1/beta * log(sum_i exp(beta * q^T m_i)) + 1/2 * ||q||^2
+"""
+
+import logging
+from typing import Optional
+
+import torch
+
+from hag.config import HopfieldConfig
+from hag.datatypes import HopfieldResult
+
+logger = logging.getLogger(__name__)
+
+
+class HopfieldRetrieval:
+    """Modern Continuous Hopfield Network for memory retrieval.
+
+    Given memory bank M in R^{d x N} and query q in R^d:
+    1. Compute attention: alpha = softmax(beta * M^T @ q)
+    2. Update query: q_new = M @ alpha
+    3. Repeat until convergence or max_iter
+
+    The energy function is:
+        E(q) = -1/beta * log(sum_i exp(beta * q^T m_i)) + 1/2 * ||q||^2
+
+    Key property: E(q_{t+1}) <= E(q_t) (monotonic decrease)
+    """
+
+    def __init__(self, config: HopfieldConfig) -> None:
+        self.config = config
+
+    @torch.no_grad()
+    def retrieve(
+        self,
+        query: torch.Tensor,
+        memory: torch.Tensor,
+        return_trajectory: bool = False,
+        return_energy: bool = False,
+    ) -> HopfieldResult:
+        """Run iterative Hopfield retrieval.
+
+        Args:
+            query: (d,) or (batch, d) — query embedding(s)
+            memory: (d, N) — memory bank of passage embeddings
+            return_trajectory: if True, store q_t at each step
+            return_energy: if True, store E(q_t) at each step
+
+        Returns:
+            HopfieldResult with attention_weights, converged_query, num_steps,
+            and optionally trajectory and energy_curve.
+        """
+        # Ensure query is 2D: (batch, d)
+        if query.dim() == 1:
+            query = query.unsqueeze(0)  # (1, d)
+
+        q = query.clone()  # (batch, d)
+
+        trajectory = [q.clone()] if return_trajectory else None
+        energies = [self.compute_energy(q, memory)] if return_energy else None
+
+        num_steps = 0
+        for t in range(self.config.max_iter):
+            # Core Hopfield update
+            logits = self.config.beta * (q @ memory)  # (batch, N)
+            alpha = torch.softmax(logits, dim=-1)  # (batch, N)
+            q_new = alpha @ memory.T  # (batch, d)
+
+            # Check convergence
+            delta = torch.norm(q_new - q, dim=-1).max()  # scalar
+            q = q_new
+
+            if return_trajectory:
+                trajectory.append(q.clone())
+            if return_energy:
+                energies.append(self.compute_energy(q, memory))
+
+            num_steps = t + 1
+
+            if delta < self.config.conv_threshold:
+                break
+
+        # Final attention weights (recompute to ensure consistency)
+        logits = self.config.beta * (q @ memory)  # (batch, N)
+        alpha = torch.softmax(logits, dim=-1)  # (batch, N)
+
+        return HopfieldResult(
+            attention_weights=alpha,
+            converged_query=q,
+            num_steps=num_steps,
+            trajectory=trajectory,
+            energy_curve=energies,
+        )
+
+    def compute_energy(
+        self,
+        query: torch.Tensor,
+        memory: torch.Tensor,
+    ) -> torch.Tensor:
+        """Compute the Hopfield energy function.
+
+        E(q) = -1/beta * log(sum_i exp(beta * q^T m_i)) + 1/2 * ||q||^2
+
+        Args:
+            query: (batch, d) or (d,) — query embedding(s)
+            memory: (d, N) — memory bank
+
+        Returns:
+            Energy scalar or (batch,) tensor.
+        """
+        if query.dim() == 1:
+            query = query.unsqueeze(0)  # (1, d)
+
+        logits = self.config.beta * (query @ memory)  # (batch, N)
+        lse = torch.logsumexp(logits, dim=-1)  # (batch,)
+        norm_sq = 0.5 * (query**2).sum(dim=-1)  # (batch,)
+        energy = -1.0 / self.config.beta * lse + norm_sq  # (batch,)
+
+        return energy
diff --git a/hag/memory_bank.py b/hag/memory_bank.py
new file mode 100644
index 0000000..42dcc73
--- /dev/null
+++ b/hag/memory_bank.py
@@ -0,0 +1,93 @@
+"""Memory bank construction and management for passage embeddings."""
+
+import logging
+from typing import Dict, List, Optional
+
+import torch
+import torch.nn.functional as F
+
+from hag.config import MemoryBankConfig
+
+logger = logging.getLogger(__name__)
+
+
+class MemoryBank:
+    """Stores passage embeddings and provides lookup from indices back to text.
+
+    The memory bank is M in R^{d x N} where each column is a passage embedding.
+    Also maintains a mapping from column index to passage text for final retrieval.
+    """
+
+    def __init__(self, config: MemoryBankConfig) -> None:
+        self.config = config
+        self.embeddings: Optional[torch.Tensor] = None  # (d, N)
+        self.passages: List[str] = []
+
+    def build_from_embeddings(
+        self, embeddings: torch.Tensor, passages: List[str]
+    ) -> None:
+        """Build memory bank from precomputed embeddings.
+
+        Args:
+            embeddings: (N, d) — passage embeddings (note: input is N x d)
+            passages: list of N passage strings
+        """
+        assert embeddings.shape[0] == len(passages), (
+            f"Number of embeddings ({embeddings.shape[0]}) must match "
+            f"number of passages ({len(passages)})"
+        )
+        if self.config.normalize:
+            embeddings = F.normalize(embeddings, dim=-1)
+        self.embeddings = embeddings.T  # Store as (d, N) for efficient matmul
+        self.passages = list(passages)
+        logger.info("Built memory bank with %d passages, dim=%d", self.size, self.dim)
+
+    def get_passages_by_indices(self, indices: torch.Tensor) -> List[str]:
+        """Given top-k indices, return corresponding passage texts.
+
+        Args:
+            indices: (k,) or (batch, k) tensor of integer indices
+
+        Returns:
+            List of passage strings.
+        """
+        flat_indices = indices.flatten().tolist()
+        return [self.passages[i] for i in flat_indices]
+
+    def save(self, path: str) -> None:
+        """Save memory bank to disk.
+
+        Args:
+            path: file path for saving (e.g., 'memory_bank.pt')
+        """
+        data: Dict = {
+            "embeddings": self.embeddings,
+            "passages": self.passages,
+            "config": {
+                "embedding_dim": self.config.embedding_dim,
+                "normalize": self.config.normalize,
+            },
+        }
+        torch.save(data, path)
+        logger.info("Saved memory bank to %s", path)
+
+    def load(self, path: str) -> None:
+        """Load memory bank from disk.
+
+        Args:
+            path: file path to load from
+        """
+        data = torch.load(path, weights_only=False)
+        self.embeddings = data["embeddings"]
+        self.passages = data["passages"]
+        logger.info("Loaded memory bank from %s (%d passages)", path, self.size)
+
+    @property
+    def size(self) -> int:
+        """Number of passages in the memory bank."""
+        return self.embeddings.shape[1] if self.embeddings is not None else 0
+
+    @property
+    def dim(self) -> int:
+        """Embedding dimensionality."""
+        return self.embeddings.shape[0] if self.embeddings is not None else 0
diff --git a/hag/metrics.py b/hag/metrics.py
new file mode 100644
index 0000000..6a196df
--- /dev/null
+++ b/hag/metrics.py
@@ -0,0 +1,113 @@
+"""Evaluation metrics for HAG: exact match, F1, retrieval recall."""
+
+import logging
+import re
+import string
+from collections import Counter
+from typing import Dict, List
+
+from hag.datatypes import PipelineResult
+
+logger = logging.getLogger(__name__)
+
+
+def _normalize_answer(text: str) -> str:
+    """Normalize answer text: lowercase, strip, remove articles and punctuation."""
+    text = text.lower().strip()
+    # Remove articles
+    text = re.sub(r"\b(a|an|the)\b", " ", text)
+    # Remove punctuation
+    text = text.translate(str.maketrans("", "", string.punctuation))
+    # Collapse whitespace
+    text = " ".join(text.split())
+    return text
+
+
+def exact_match(prediction: str, ground_truth: str) -> float:
+    """Normalized exact match.
+
+    Args:
+        prediction: predicted answer string
+        ground_truth: gold answer string
+
+    Returns:
+        1.0 if normalized strings match, 0.0 otherwise.
+    """
+    return float(_normalize_answer(prediction) == _normalize_answer(ground_truth))
+
+
+def f1_score(prediction: str, ground_truth: str) -> float:
+    """Token-level F1 between prediction and ground truth.
+
+    Args:
+        prediction: predicted answer string
+        ground_truth: gold answer string
+
+    Returns:
+        F1 score between 0.0 and 1.0.
+    """
+    pred_tokens = _normalize_answer(prediction).split()
+    gold_tokens = _normalize_answer(ground_truth).split()
+
+    if not pred_tokens and not gold_tokens:
+        return 1.0
+    if not pred_tokens or not gold_tokens:
+        return 0.0
+
+    common = Counter(pred_tokens) & Counter(gold_tokens)
+    num_same = sum(common.values())
+
+    if num_same == 0:
+        return 0.0
+
+    precision = num_same / len(pred_tokens)
+    recall = num_same / len(gold_tokens)
+    f1 = 2 * precision * recall / (precision + recall)
+    return f1
+
+
+def retrieval_recall_at_k(
+    retrieved_indices: List[int], gold_indices: List[int], k: int
+) -> float:
+    """What fraction of gold passages appear in the retrieved top-k?
+
+    Args:
+        retrieved_indices: list of retrieved passage indices (top-k)
+        gold_indices: list of gold/relevant passage indices
+        k: number of retrieved passages to consider
+
+    Returns:
+        Recall score between 0.0 and 1.0.
+    """
+    if not gold_indices:
+        return 1.0
+    retrieved_set = set(retrieved_indices[:k])
+    gold_set = set(gold_indices)
+    return len(retrieved_set & gold_set) / len(gold_set)
+
+
+def evaluate_dataset(
+    results: List[PipelineResult], gold_answers: List[str]
+) -> Dict[str, float]:
+    """Compute aggregate metrics over a dataset.
+
+    Args:
+        results: list of PipelineResult from the pipeline
+        gold_answers: list of gold answer strings
+
+    Returns:
+        Dict with keys 'em', 'f1' containing averaged scores.
+    """
+    assert len(results) == len(gold_answers)
+
+    em_scores = []
+    f1_scores = []
+
+    for result, gold in zip(results, gold_answers):
+        em_scores.append(exact_match(result.answer, gold))
+        f1_scores.append(f1_score(result.answer, gold))
+
+    return {
+        "em": sum(em_scores) / len(em_scores) if em_scores else 0.0,
+        "f1": sum(f1_scores) / len(f1_scores) if f1_scores else 0.0,
+    }
diff --git a/hag/pipeline.py b/hag/pipeline.py
new file mode 100644
index 0000000..1fefb84
--- /dev/null
+++ b/hag/pipeline.py
@@ -0,0 +1,107 @@
+"""End-to-end RAG/HAG pipeline: query -> encode -> retrieve -> generate."""
+
+import logging
+from typing import List, Optional, Protocol, Union
+
+import numpy as np
+import torch
+
+from hag.config import PipelineConfig
+from hag.datatypes import PipelineResult, RetrievalResult
+from hag.hopfield import HopfieldRetrieval
+from hag.memory_bank import MemoryBank
+from hag.retriever_faiss import FAISSRetriever
+from hag.retriever_hopfield import HopfieldRetriever
+
+logger = logging.getLogger(__name__)
+
+
+class EncoderProtocol(Protocol):
+    """Protocol for encoder interface."""
+
+    def encode(self, texts: Union[str, List[str]]) -> torch.Tensor: ...
+
+
+class GeneratorProtocol(Protocol):
+    """Protocol for generator interface."""
+
+    def generate(self, question: str, passages: List[str]) -> str: ...
+
+
+class RAGPipeline:
+    """End-to-end pipeline: query -> encode -> retrieve -> generate.
+
+    Supports both FAISS (baseline) and Hopfield (ours) retrieval.
+    """
+
+    def __init__(
+        self,
+        config: PipelineConfig,
+        encoder: EncoderProtocol,
+        generator: GeneratorProtocol,
+        memory_bank: Optional[MemoryBank] = None,
+        faiss_retriever: Optional[FAISSRetriever] = None,
+    ) -> None:
+        self.config = config
+        self.encoder = encoder
+        self.generator = generator
+
+        if config.retriever_type == "faiss":
+            assert faiss_retriever is not None, "FAISSRetriever required for faiss mode"
+            self.retriever_type = "faiss"
+            self.faiss_retriever = faiss_retriever
+            self.hopfield_retriever: Optional[HopfieldRetriever] = None
+        elif config.retriever_type == "hopfield":
+            assert memory_bank is not None, "MemoryBank required for hopfield mode"
+            hopfield = HopfieldRetrieval(config.hopfield)
+            self.retriever_type = "hopfield"
+            self.hopfield_retriever = HopfieldRetriever(
+                hopfield, memory_bank, top_k=config.hopfield.top_k
+            )
+            self.faiss_retriever = None
+        else:
+            raise ValueError(f"Unknown retriever_type: {config.retriever_type}")
+
+    def run(self, question: str) -> PipelineResult:
+        """Run the full pipeline on a single question.
+
+        1. Encode question -> query embedding
+        2. Retrieve passages (FAISS or Hopfield)
+        3. Generate answer with LLM
+
+        Args:
+            question: input question string
+
+        Returns:
+            PipelineResult with answer and retrieval metadata.
+        """
+        # Encode
+        query_emb = self.encoder.encode(question)  # (1, d)
+
+        # Retrieve
+        if self.retriever_type == "hopfield":
+            retrieval_result = self.hopfield_retriever.retrieve(query_emb)
+        else:
+            query_np = query_emb.detach().numpy().astype(np.float32)
+            retrieval_result = self.faiss_retriever.retrieve(query_np)
+
+        # Generate
+        answer = self.generator.generate(question, retrieval_result.passages)
+
+        return PipelineResult(
+            question=question,
+            answer=answer,
+            retrieved_passages=retrieval_result.passages,
+            retrieval_result=retrieval_result,
+        )
+
+    def run_batch(self, questions: List[str]) -> List[PipelineResult]:
+        """Run pipeline on a batch of questions.
+
+        Args:
+            questions: list of question strings
+
+        Returns:
+            List of PipelineResult, one per question.
+        """
+        return [self.run(q) for q in questions]
diff --git a/hag/retriever_faiss.py b/hag/retriever_faiss.py
new file mode 100644
index 0000000..cd54a85
--- /dev/null
+++ b/hag/retriever_faiss.py
@@ -0,0 +1,73 @@
+"""Baseline FAISS top-k retriever for vanilla RAG."""
+
+import logging
+from typing import List, Optional
+
+import faiss
+import numpy as np
+import torch
+
+from hag.datatypes import RetrievalResult
+
+logger = logging.getLogger(__name__)
+
+
+class FAISSRetriever:
+    """Standard top-k retrieval using FAISS inner product search.
+
+    This is the baseline to compare against Hopfield retrieval.
+    """
+
+    def __init__(self, top_k: int = 5) -> None:
+        self.index: Optional[faiss.IndexFlatIP] = None
+        self.passages: List[str] = []
+        self.top_k = top_k
+
+    def build_index(self, embeddings: np.ndarray, passages: List[str]) -> None:
+        """Build FAISS IndexFlatIP from embeddings.
+
+        Args:
+            embeddings: (N, d) numpy array of passage embeddings
+            passages: list of N passage strings
+        """
+        assert embeddings.shape[0] == len(passages)
+        d = embeddings.shape[1]
+        self.index = faiss.IndexFlatIP(d)
+        # Normalize for cosine similarity via inner product
+        faiss.normalize_L2(embeddings)
+        self.index.add(embeddings)
+        self.passages = list(passages)
+        logger.info("Built FAISS index with %d passages, dim=%d", len(passages), d)
+
+    def retrieve(self, query: np.ndarray) -> RetrievalResult:
+        """Retrieve top-k passages for a query.
+
+        Args:
+            query: (d,) or (batch, d) numpy array
+
+        Returns:
+            RetrievalResult with passages, scores, and indices.
+        """
+        assert self.index is not None, "Index not built. Call build_index first."
+
+        if query.ndim == 1:
+            query = query.reshape(1, -1)  # (1, d)
+
+        # Normalize query for cosine similarity
+        query_copy = query.copy()
+        faiss.normalize_L2(query_copy)
+
+        scores, indices = self.index.search(query_copy, self.top_k)  # (batch, k)
+
+        # Flatten for single query case
+        if scores.shape[0] == 1:
+            scores = scores[0]  # (k,)
+            indices = indices[0]  # (k,)
+
+        passages = [self.passages[i] for i in indices.flatten().tolist()]
+
+        return RetrievalResult(
+            passages=passages,
+            scores=torch.from_numpy(scores).float(),
+            indices=torch.from_numpy(indices).long(),
+        )
diff --git a/hag/retriever_hopfield.py b/hag/retriever_hopfield.py
new file mode 100644
index 0000000..1cb6968
--- /dev/null
+++ b/hag/retriever_hopfield.py
@@ -0,0 +1,77 @@
+"""Hopfield-based retriever wrapping HopfieldRetrieval + MemoryBank."""
+
+import logging
+from typing import List
+
+import torch
+
+from hag.datatypes import RetrievalResult
+from hag.hopfield import HopfieldRetrieval
+from hag.memory_bank import MemoryBank
+
+logger = logging.getLogger(__name__)
+
+
+class HopfieldRetriever:
+    """Wraps HopfieldRetrieval + MemoryBank into a retriever interface.
+
+    The bridge between Hopfield's continuous retrieval and the discrete
+    passage selection needed for LLM prompting.
+    """
+
+    def __init__(
+        self,
+        hopfield: HopfieldRetrieval,
+        memory_bank: MemoryBank,
+        top_k: int = 5,
+    ) -> None:
+        self.hopfield = hopfield
+        self.memory_bank = memory_bank
+        self.top_k = top_k
+
+    def retrieve(
+        self,
+        query_embedding: torch.Tensor,
+        return_analysis: bool = False,
+    ) -> RetrievalResult:
+        """Retrieve top-k passages using iterative Hopfield retrieval.
+
+        1. Run Hopfield iterative retrieval -> get attention weights alpha_T
+        2. Take top_k indices from alpha_T
+        3. Look up corresponding passage texts from memory bank
+        4. Optionally return trajectory and energy for analysis
+
+        Args:
+            query_embedding: (d,) or (batch, d) — query embedding
+            return_analysis: if True, include full HopfieldResult
+
+        Returns:
+            RetrievalResult with passages, scores, indices, and optionally
+            the full hopfield_result.
+        """
+        hopfield_result = self.hopfield.retrieve(
+            query_embedding,
+            self.memory_bank.embeddings,
+            return_trajectory=return_analysis,
+            return_energy=return_analysis,
+        )
+
+        alpha = hopfield_result.attention_weights  # (batch, N) or (1, N)
+
+        # Get top-k indices and scores
+        k = min(self.top_k, alpha.shape[-1])
+        scores, indices = torch.topk(alpha, k, dim=-1)  # (batch, k)
+
+        # Flatten for single-query case
+        if scores.shape[0] == 1:
+            scores = scores.squeeze(0)  # (k,)
+            indices = indices.squeeze(0)  # (k,)
+
+        passages = self.memory_bank.get_passages_by_indices(indices)
+
+        return RetrievalResult(
+            passages=passages,
+            scores=scores,
+            indices=indices,
+            hopfield_result=hopfield_result if return_analysis else None,
+        )