Eli Waxman

Onur Selim Kilic, Yeti Z. Gurbuz, Cem O. Yaldiz et al.

Clinical practice guidelines are long, multimodal documents whose branching recommendations are difficult to convert into executable clinical decision support (CDS), and one-shot parsing often breaks cross-page continuity. Recent LLM/VLM extractors are mostly local or text-centric, under-specifying section interfaces and failing to consolidate cross-page control flow across full documents into one coherent decision graph. We present a decomposition-first pipeline that converts full-guideline evidence into an executable clinical decision graph through topology-aware chunking, interface-constrained chunk graph generation, and provenance-preserving global aggregation. Rather than relying on single-pass generation, the pipeline uses explicit entry/terminal interfaces and semantic deduplication to preserve cross-page continuity while keeping the induced control flow auditable and structurally consistent. We evaluate on an adjudicated prostate-guideline benchmark with matched inputs and the same underlying VLM backbone across compared methods. On the complete merged graph, our approach improves edge and triplet precision/recall from $19.6\%/16.1\%$ in existing models to $69.0\%/87.5\%$, while node recall rises from $78.1\%$ to $93.8\%$. These results support decomposition-first, auditable guideline-to-CDS conversion on this benchmark, while current evidence remains limited to one adjudicated prostate guideline and motivates broader multi-guideline validation.

Etrit Haxholli, Yeti Z. Gürbüz, Oğul Can et al.

While continuous diffusion models excel in modeling continuous distributions, their application to categorical data has been less effective. Recent work has shown that ratio-matching through score-entropy within a continuous-time discrete Markov chain (CTMC) framework serves as a competitive alternative to autoregressive models in language modeling. To enhance this framework, we first introduce three new theorems concerning the KL divergence between the data and learned distribution. Our results serve as the discrete counterpart to those established for continuous diffusion models and allow us to derive an improved upper bound of the perplexity. Second, we empirically show that ratio-matching performed by minimizing the denoising cross-entropy between the clean and corrupted data enables models to outperform those utilizing score-entropy with up to 10% lower perplexity/generative-perplexity, and 15% faster training steps. To further support our findings, we introduce and evaluate a novel CTMC transition-rate matrix that allows prediction refinement, and derive the analytic expression for its matrix exponential which facilitates the computation of conditional ratios thus enabling efficient training and generation.

Etrit Haxholli, Yeti Z. Gürbüz, Oğul Can et al.

Outperforming autoregressive models on categorical data distributions, such as textual data, remains challenging for continuous diffusion and flow models. Discrete flow matching, a recent framework for modeling categorical data, has shown competitive performance with autoregressive models. Despite its similarities with continuous flow matching, the rectification strategy applied in the continuous version does not directly extend to the discrete one due to the inherent stochasticity of discrete paths. This limitation necessitates exploring alternative methods to minimize state transitions during generation. To address this, we propose a dynamic-optimal-transport-like minimization objective for discrete flows with convex interpolants and derive its equivalent Kantorovich formulation. The latter defines transport cost solely in terms of inter-state similarity and is optimized using a minibatch strategy. Another limitation we address in the discrete flow framework is model evaluation. Unlike continuous flows, wherein the instantaneous change of variables enables density estimation, discrete models lack a similar mechanism due to the inherent non-determinism and discontinuity of their paths. To alleviate this issue, we propose an upper bound on the perplexity of discrete flow models, enabling performance evaluation and comparison with other methods.