CRAFT: LLM-Based Iterative Refinement for Temporal Reasoning over Clinical Narratives

In mental health care, reasoning over patient journeys is a key task for clinicians. Yet these journeys, encompassing a longitudinal progression of biological, psychological, and social events, are often spread across disparate unstructured text narratives, making temporal recovery challenging. We present CliniCIRCA, a multi-stage LLM framework for Calendar-anchored, Imprecision-aware Reconstruction of Clinical Annals. To our knowledge, CliniCIRCA is the first to temporally classify clinical events across unstructured discharge summaries without event-level timestamps. From 14,882 MIMIC-III mental health admissions, we first construct a benchmark of 52 discharge summaries on which CliniCIRCA produces 15,891 temporally tagged events. After correcting 629 errors based on a clinician-in-the-loop evaluation, we produce verified gold-standard labels. Finally, the corrected timelines drive a temporally grounded summarization stage that compresses each source 1.52 times into a date-grouped chronological record. We then scale the framework to generate 1,000 silver-standard timelines and evaluate them as training data. Compared with zero- and few-shot prompting, instruction tuning generally improves five open-weight models on event extraction, temporal tagging, and summarization across silver and clinician-verified evaluations.

Reconstructing precise clinical timelines is essential for modeling patient trajectories and forecasting risk in complex, heterogeneous conditions like sepsis. While unstructured clinical narratives offer semantically rich and contextually complete descriptions of a patient's course, they often lack temporal precision and contain ambiguous event timing. Conversely, structured electronic health record (EHR) data provides precise temporal anchors but misses a substantial portion of clinically meaningful events. We introduce a retrieval-augmented multimodal alignment framework that bridges this gap to improve the temporal precision of absolute clinical timelines extracted from text. Our approach formulates timeline reconstruction as a graph-based multistep process: it first extracts central anchor events from narratives to build an initial temporal scaffold, places non-central events relative to this backbone, and then calibrates the timeline using retrieved structured EHR rows as external temporal evidence. Evaluated using instruction-tuned large language models on the i2m4 benchmark spanning MIMIC-III and MIMIC-IV, our multimodal pipeline consistently improves absolute timestamp accuracy (AULTC) and improves temporal concordance across nearly all evaluated models over unimodal text-only reconstruction, without compromising event match rates. Furthermore, our empirical gap analysis reveals that 34.8% of text-derived events are entirely absent from tabular records, demonstrating that aligning these modalities can produce a more temporally faithful and clinically informative reconstruction of patient trajectories than either source alone.

Retrieval-Augmented Generation (RAG) systems retrieve and integrate external knowledge to ground large language model (LLM) outputs. However, current RAG architectures treat all retrieved facts as equally valid regardless of temporal provenance, leading to temporal hallucination, where plausible but obsolete facts corrupt the output. A clinical lab reading from yesterday is actionable; the same reading from six months ago is noise. We present Chronofy, a three-layer neuro-symbolic framework implementing the Temporal-Logical Decay Architecture (TLDA) that embeds temporal validity directly into the representation, retrieval, and reasoning layers of RAG systems. Layer 1 reserves a dedicated temporal subspace within Matryoshka embeddings to make fact age structurally irremovable from the representation. Layer 2 integrates learnable exponential decay functions into graph-based retrieval, where the decay coefficient $β_j$ is grounded in Bayesian decision theory as an approximation of twice the latent process mean-reversion rate. Layer 3 applies Signal Temporal Logic (STL) robustness functions to evaluate the temporal validity of retrieved knowledge, not LLM output confidence, and enforces the possibilistic weakest-link principle to bound output confidence by the most decayed evidence in the reasoning chain. We evaluate Chronofy on temporal knowledge graph forecasting benchmarks, the TimE temporal QA benchmark, and a domain-specific sensitivity analysis, demonstrating that explicit temporal decay modeling improves retrieval precision, reduces temporal hallucination, and enables principled data re-acquisition triggers when temporal context is insufficient.