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Simply Stabilizing the Loop via Fully Looped Transformer

arXiv:2605.18797v2 Announce Type: replace-cross Abstract: Scaling model performance typically requires increasing model size. Looped Transformer offers a compelling alternative by iteratively reusing the same Transformer blocks, trading additional computation for improved performance without increasing parameter count or context length. Because the number of loop iterations can be adjusted at inference, it also provides a natural mechanism for balancing performance and test-time compute. However, Looped Transformer still suffers from training instability when the number of loop iterations increases. Our analysis reveals that this instability stems from two sources: gradient oscillation and residual explosion. To address these two problems, we propose the Fully Looped Transformer, which introduces two parameter-free modifications: (1) Fully Looped Architecture, which distributes inter-loop signals across all layers to mitigate residual explosion; (2) Attention Injection, which reuses the existing attention block to suppress gradient oscillation. These modifications stabilize training dynamics, enabling the Fully Looped Transformer to be trained stably up to 12 loop iterations, whereas other baseline looped models collapse in this regime. In milder settings where Looped Transformer does not collapse, Fully Looped Transformer still improves average downstream-task performance by up to 13.2\%. Overall, our experiments demonstrate that Fully Looped Transformer improves training stability, enhances downstream performance, and provides preliminary adaptability under different test-time compute budgets by varying loop iterations at inference.
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Multimodal data-driven prediction of postoperative recurrence and survival in hepatocellular carcinoma: a narrative review

J Gastrointest Oncol. 2026 Apr 30;17(2):96. doi: 10.21037/jgo-2025-aw-848. Epub 2026 Mar 27.

ABSTRACT

BACKGROUND AND OBJECTIVE: Hepatocellular carcinoma (HCC) is characterized by high postoperative recurrence rates and poor long-term survival despite advances in surgical and systemic therapies. Accurate prediction of postoperative recurrence and survival risk is critical for individualized surveillance, adjuvant treatment selection, and precision management. With the rapid development of artificial intelligence (AI) and medical informatics, multimodal data-driven models integrating clinical, imaging, pathological, and omics information have emerged as a promising paradigm. This narrative review aims to systematically summarize recent advances in multimodal prediction models for postoperative recurrence and survival in HCC, compare modeling strategies and fusion approaches, and discuss current challenges and future directions for clinical translation.

METHODS: A narrative literature review was conducted by searching PubMed, Web of Science, and Google Scholar for studies published between 2020 and 2025. Articles focusing on postoperative recurrence or survival prediction in HCC using single-modal or multimodal data were included. Relevant studies were identified using keywords related to HCC, multimodal data, AI, machine learning, deep learning, recurrence, and prognosis.

KEY CONTENT AND FINDINGS: This review summarizes commonly used data modalities, including clinical variables, medical imaging, pathological features, and multi-omics data, and outlines their respective strengths and limitations. Conventional statistical models and AI-based approaches, including non-deep learning and deep learning algorithms, are compared. Particular emphasis is placed on multimodal fusion strategies at the feature level and decision level, with discussion of their methodological characteristics and suitable clinical scenarios. Overall, multimodal models consistently demonstrate superior predictive performance compared with single-modality approaches. However, key challenges remain, including data heterogeneity, limited interpretability of complex models, insufficient external validation, and the predominance of static baseline modeling.

CONCLUSIONS: Multimodal data-driven prediction models represent a promising strategy for improving postoperative risk stratification and personalized management in HCC. While current evidence highlights their potential advantages over traditional prognostic tools, broader clinical adoption is hindered by methodological limitations and a lack of standardized frameworks. Future research should focus on longitudinal multimodal modeling, multi-center prospective validation, and enhanced model interpretability to facilitate integration into clinical workflows and inform precision oncology-oriented decision-making.

PMID:42169935 | PMC:PMC13187996 | DOI:10.21037/jgo-2025-aw-848

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Interpreting Omics Data Analysis with Large Language Models for Disease Target and Drug Discovery

bioRxiv [Preprint]. 2026 May 5:2026.04.30.721768. doi: 10.64898/2026.04.30.721768.

ABSTRACT

In biomedical scientific discovery, synthesizing prior knowledge from the literature is an essential component of interpreting numerical omics data analyses for disease target identification and drug discovery. Large language models (LLMs) alone can rapidly retrieve disease mechanisms from biomedical text, but text-only outputs are general and unreliable for target and drug prioritization without cohort-specific quantitative evidence. Herein, we propose a provenance-aware Text-to-Target framework that couples schema-constrained multi-model LLM retrieval with numeric omics data analysis. The key design is a modality-aware fusion step: candidates are partitioned into overlap-supported anchors, retrieval-only hidden hubs, and network-emergent novelty nodes, then propagated into staged hypothesis and strategy generation under topology constraints. We evaluate the model in Alzheimer's disease (AD) and pancreatic ductal adenocarcinoma (PDAC). In PDAC, the workflow produced a balanced 75-gene candidate universe and a 23-strategy portfolio, with significant DepMap support at both target level and strategy level. In AD, stricter candidate controls yielded a compact 34-gene universe and 14 strategies; under an expanded CRISPRbrain registry, both target-level axes were significant, with strong strategy-level enrichment. Across both diseases, final strategies preserved full provenance closure to the candidate pool, enabling end-to-end auditability from retrieval artifacts to validation outputs. These results support a transferable discovery architecture in which omics evidence constrains biological activity, LLM retrieval expands mechanistic search space, and network-aware fusion preserves interpretability. The framework provides a reproducible basis for dual-disease target prioritization and motivates continuous literature-mechanism concordance with agentic evidence-refresh loops.

PMID:42146439 | PMC:PMC13174328 | DOI:10.64898/2026.04.30.721768

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Characterization of dysbiosis patterns in gut microbiota of digestive system cancers: an umbrella review

Front Microbiol. 2026 Apr 28;17:1782471. doi: 10.3389/fmicb.2026.1782471. eCollection 2026.

ABSTRACT

Digestive system cancers (DSCs) represent a substantial global health burden. In recent years, the role of gut microbiota in the DSCs has garnered considerable attention, but its change pattern during tumor progression and the specific mechanisms are still not fully understood. We conducted a comprehensive systematic review to characterize patterns of gut microbiota dysbiosis across different DSC types and assess their clinical significance. We systematically searched four English and three Chinese databases up to January 2025 to identify systematic reviews focused on the dynamic characteristics of the gut microbiota during gastrointestinal tumorigenesis. Microbiota biodiversity and taxonomic composition were extracted to identify specific signatures associated with DSCs. The ROBIS tool was used to evaluate the methodological quality of the included studies. Ultimately, 59 studies involving six distinct DSC types were included. Data synthesis and comparison revealed distinct microbiota profiles across DSCs. At the phylum level, Bacillota was decreased in esophageal cancer (EC) and pancreatic ductal adenocarcinoma (PDAC), Pseudomonadota was augmented in EC but exhibited divergent trajectories in colorectal cancer (CRC) and PDAC. Genus-level analyses revealed Veillonella enrichment in EC and PDAC, and Fusobacterium outgrowth in EC, gastric cancer (GC) and CRC. Parvimonas and Streptococcus showed a concordant ascending trend in GC and CRC. Prevotella was overrepresented in EC and GC. This synthesis delineates a qualitative landscape of gut microbiota imbalances associated with various DSCs, highlighting the potential for these microbial shifts to serve as markers for early detection and targeted therapy. Multiomics integration and prospective cohort studies should be prioritized to accelerate clinical translation.

PMID:42131199 | PMC:PMC13161176 | DOI:10.3389/fmicb.2026.1782471

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