We introduce Neural Organ Transplantation (NOT), a modular adaptation framework that enables trained transformer layers to function as reusable transferable checkpoints for domain adaptation. Unlike conventional fine-tuning approaches that tightly couple trained parameters to specific model instances and training data, NOT extracts contiguous layer subsets ("donor organs") from pre-trained models, trains them independently on domain-specific data, and saves them as standalone checkpoint files that can be transplanted into compatible recipient models without access to the original training data. Through experiments on three decoder-only transformer architectures spanning 124M to 20B parameters (GPT-2, TinyLlama, and GPT-OSS), we demonstrate that donor transplantation substantially outperforms existing adaptation methods, achieving an order-of-magnitude improvement in perplexity over LoRA while training significantly faster. The method exhibits position dependence, with early insertion positions yielding optimal results. Cross-domain transfer at billion-parameter scale reveals unexpected regularization benefits. These findings demonstrate that transformer middle layers can support ef
Reinforcement learning with verifiable rewards (RLVR) has recently advanced the reasoning capabilities of large language models (LLMs). While prior work has emphasized algorithmic design, data curation, and reward shaping, we investigate RLVR from a sample-centric perspective and introduce LPPO (Learning-Progress and Prefix-guided Optimization), a framework of progressive optimization techniques. Our work addresses a critical question: how to best leverage a small set of trusted, high-quality demonstrations, rather than simply scaling up data volume. First, motivated by how hints aid human problem-solving, we propose prefix-guided sampling, an online data augmentation method that incorporates partial solution prefixes from expert demonstrations to guide the policy, particularly for challenging instances. Second, inspired by how humans focus on important questions aligned with their current capabilities, we introduce learning-progress weighting, a dynamic strategy that adjusts each training sample's influence based on model progression. We estimate sample-level learning progress via an exponential moving average of per-sample pass rates, promoting samples that foster learning and de
Graph Retrieval-Augmented Generation (GraphRAG) has emerged as a promising paradigm that organizes external knowledge into structured graphs of entities and relations, enabling large language models (LLMs) to perform complex reasoning beyond text-chunk retrieval. Recent advances have integrated reinforcement learning (RL) into agentic GraphRAG approaches, enabling iterative interactions with knowledge graphs during training. However, existing RL-based methods suffer from two key limitations: (1) they primarily depend on semantic similarity for retrieval, often overlooking the underlying graph topology, and (2) they rely on sparse, outcome-level rewards that fail to capture the quality of intermediate retrieval steps and their dependencies. To address these limitations, we propose HyperGraphPro, a progress-aware agentic framework for graph-based retrieval and multi-step reasoning. HyperGraphPro introduces a structure-aware hypergraph retrieval mechanism that jointly considers semantic relevance and graph connectivity, promoting coherent traversal along multi-hop reasoning paths. Furthermore, we design a progress-based stepwise policy optimization that provides dense learning signals
This study presents an Initial Data Analysis (IDA) of the German Transplantation Registry (TxReg) data for a better data understanding and to inform future data analyses. The IDA is focusing on data on first-time kidney-only transplantations in adult recipients from deceased donors between 2006 and 2016 and refers to data from 14,954 recipients and 9,964 donors across 25 tables. Investigated aspects include missing data patterns and structure, data consistency, and availability of event time data. Results show that missing data proportions vary widely, with some tables nearly complete while others have over 50% missing values. Missing data patterns are identified using a decision tree approach. An influx and outflux analysis demonstrates that some variables have high potential for imputing missing data, while others were less suitable for imputation. We identified 168 multi-sourced variables that are reported by multiple data providers in parallel leading to discrepancies for some variables but also providing opportunities for missing data imputation. Our findings on event time data demonstrate the importance of carefully selecting the variables used for event time analyses as resu
Ensemble learning is a widespread technique to improve the prediction performance of neural networks. However, it comes at the price of increased memory and inference time. In this work we propose a novel model fusion technique called \emph{Neuron Transplantation (NT)} in which we fuse an ensemble of models by transplanting important neurons from all ensemble members into the vacant space obtained by pruning insignificant neurons. An initial loss in performance post-transplantation can be quickly recovered via fine-tuning, consistently outperforming individual ensemble members of the same model capacity and architecture. Furthermore, NT enables all the ensemble members to be jointly pruned and jointly trained in a combined model. Comparing it to alignment-based averaging (like Optimal-Transport-fusion), it requires less fine-tuning than the corresponding OT-fused model, the fusion itself is faster and requires less memory, while the resulting model performance is comparable or better. The code is available under the following link: https://github.com/masterbaer/neuron-transplantation.
Renal transplantation emerges as the most effective solution for end-stage renal disease. Occurring from complex causes, a substantial risk of transplant chronic dysfunction persists and may lead to graft loss. Medical imaging plays a substantial role in renal transplant monitoring in clinical practice. However, graft supervision is multi-disciplinary, notably joining nephrology, urology, and radiology, while identifying robust biomarkers from such high-dimensional and complex data for prognosis is challenging. In this work, taking inspiration from the recent success of Large Language Models (LLMs), we propose MEDIMP -- Medical Images with clinical Prompts -- a model to learn meaningful multi-modal representations of renal transplant Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE MRI) by incorporating structural clinicobiological data after translating them into text prompts. MEDIMP is based on contrastive learning from joint text-image paired embeddings to perform this challenging task. Moreover, we propose a framework that generates medical prompts using automatic textual data augmentations from LLMs. Our goal is to learn meaningful manifolds of renal transplant DCE MR
In clinical studies, the risk of the primary (terminal) event may be modified by intermediate events, resulting in semicompeting risks. To study the treatment effect on the terminal event mediated by the intermediate event, researchers wish to decompose the total effect into direct and indirect effects. In this article, we extend the randomized interventional approach to time-to-event outcomes, where both intermediate and terminal events are subject to right censoring. We envision a random draw for the intermediate event process from a reference distribution, either marginally over time-varying confounders or conditionally given the observed history. We present the identification formula for interventional effects. We also discuss some variants of the identification assumptions. We estimate the treatment effects using nonparametric maximum likelihood estimation and propose a sensitivity analysis that incorporates a latent frailty. As an illustration, we study the effect of matched unrelated donor versus haploidentical donor on death mediated by relapse in a hematopoietic cell transplantation study with graft-versus-host disease (GVHD) as the time-varying confounder. We find that ma
Liver transplantation continues to be the gold standard for treating patients with end-stage liver diseases. However, despite the huge success of liver transplantation in improving patient outcomes, long term graft survival continues to be a major problem. The current clinical practice in the management of liver transplant patients is centered around immunosuppressive multidrug regimens. Current research has been focusing on phenotypic personalized medicine as a novel approach in the optimization of immunosuppression, a regressional math modeling focusing on individual patient dose and response using specific markers like transaminases. A prospective area of study includes the development of a mechanistic computational math modeling for optimizing immunosuppression to improve patient outcomes and increase long-term graft survival by exploring the intricate immune/drug interactions to help us further our understanding and management of medical problems like transplants, autoimmunity, and cancer therapy. Thus, by increasing long-term graft survival, the need for redo transplants will decrease, which will free up organs and potentially help with the organ shortage problem promoting eq
Multi-step multimodal reasoning tasks pose significant challenges for multimodal large language models (MLLMs), and finding effective ways to enhance their performance in such scenarios remains an unresolved issue. In this paper, we propose AR-MCTS, a universal framework designed to progressively improve the reasoning capabilities of MLLMs through Active Retrieval (AR) and Monte Carlo Tree Search (MCTS). Our approach begins with the development of a unified retrieval module that retrieves key supporting insights for solving complex reasoning problems from a hybrid-modal retrieval corpus. To bridge the gap in automated multimodal reasoning verification, we employ the MCTS algorithm combined with an active retrieval mechanism, which enables the automatic generation of step-wise annotations. This strategy dynamically retrieves key insights for each reasoning step, moving beyond traditional beam search sampling to improve the diversity and reliability of the reasoning space. Additionally, we introduce a process reward model that aligns progressively to support the automatic verification of multimodal reasoning tasks. Experimental results across three complex multimodal reasoning benchm
Recent work takes both philosophical and scientific progress to consist in acquiring factive epistemic states such as knowledge. However, much of this work leaves unclear what entity is the subject of these epistemic states. Furthermore, by focusing only on states like knowledge, we overlook progress in intermediate cases between ignorance and knowledge -- for example, many now celebrated theories were initially so controversial that they were not known. This paper develops an improved framework for thinking about intellectual progress. Firstly, I argue that we should think of progress relative to the epistemic position of an intellectual community rather than individual inquirers. Secondly, I show how focusing on the extended process of inquiry (rather than the mere presence or absence of states like knowledge) provides a better evaluation of different types of progress. This includes progress through formulating worthwhile questions, acquiring new evidence, and increasing credence on the right answers to these questions. I close by considering the ramifications for philosophical progress, suggesting that my account supports rejecting the most negative views while allowing us to a
This study aimed to investigate the effects of genetic polymorphisms on tacrolimus blood levels and intra-individual variability in recipients of heart transplants during the early post-transplantation period. Demographic information, concomitant medications, daily tacrolimus dose, trough concentration, and physiological and biochemical information of 87 Chinese recipients of heart transplants were collected. Trough concentrations were determined using a chemiluminescent micro-particle immunoassay, and 17 selected single nucleic acid polymorphisms were genotyped by direct sequencing. We assessed intra-individual variability by calculating the coefficient of variation of tacrolimus trough concentration and analyzed factors associated with tacrolimus concentration and intra-individual variability. Our study found that low body weight and a high percentage of neutrophils significantly influenced the coefficient of variation of tacrolimus. CYP3A5*1D and CYP3A7 rs776744 haplotypes correlated significantly with an intra-individual coefficient of variation of tacrolimus trough concentration during the early postoperative period. Patients with the CYP3A5*1D rs15524 and CYP3A7 rs776744 TT h
The study of disparities in the liver transplantation process may focus on quantifying causal effects, particularly the average, direct, or indirect effects of various social determinants of health on being listed as a candidate for transplant. Selection bias arises when the data sample does not represent the target population, defined here as all individuals referred to the transplant clinic. Listing decisions are made for the subset of patients who complete the evaluation process, who may differ systematically from the referred population. There is evidence that selection is associated with patient characteristics that also impact outcomes. Using data only from the selected population may yield biased causal effect estimates. However, incorporating data from the referred population allows for analytic correction. This correction leverages hypothesized causal relationships among selection, the outcome (getting listed), exposures, and mediators. Using directed acyclic graphs (DAGs), we establish graphical conditions under which a reweighted mediation formula identifies effect of interest - direct, indirect, and path-specific effects - in the presence of sample selection. In a clini
Graft-versus-host disease (GVHD) is a rare but often fatal complication in liver transplantation, with a very high mortality rate. By harnessing multi-modal deep learning methods to integrate heterogeneous and imbalanced electronic health records (EHR), we aim to advance early prediction of GVHD, paving the way for timely intervention and improved patient outcomes. In this study, we analyzed pre-transplant electronic health records (EHR) spanning the period before surgery for 2,100 liver transplantation patients, including 42 cases of graft-versus-host disease (GVHD), from a cohort treated at Mayo Clinic between 1992 and 2025. The dataset comprised four major modalities: patient demographics, laboratory tests, diagnoses, and medications. We developed a multi-modal deep learning framework that dynamically fuses these modalities, handles irregular records with missing values, and addresses extreme class imbalance through AUC-based optimization. The developed framework outperforms all single-modal and multi-modal machine learning baselines, achieving an AUC of 0.836, an AUPRC of 0.157, a recall of 0.768, and a specificity of 0.803. It also demonstrates the effectiveness of our approac
End-Stage Liver Disease (ESLD), a complex condition, has high rates of co-occurring comorbidities affecting multiple organ systems. There is no clear evidence-based practice (EBP) guidelines addressing the progression of comorbidities in ESLD patients awaiting liver transplantation (LT) and their impact on survival, both pre- and post-transplant. This study aimed to identify and quantify the trajectory of the most common and deteriorating comorbidities in ESLD patients awaiting LT and to analyze their effect on patient outcomes. An initial exploratory phase to identify frequent comorbidities in ESLD patients. Relevant EBP-driven data for diagnosing and measuring the progression of these conditions were collected and organized into five research matrices. In the quantitative phase, a retrospective analysis was conducted using longitudinal de-identified data from electronic health records (EHR) for patients who underwent LT between 2011-2021. Data included demographics, labs, procedures, and medications. Descriptive statistics and survival analysis assessed the association of comorbidities with post-transplant survival. The five most frequent comorbidities identified were Diabetes Me
Emergence of novel quantum ground states in correlated electron systems with strong spin-orbit coupling has been a recent subject of intensive studies. While it has been realized that spin-orbit coupling can provide non-trivial band topology in weakly interacting electron systems, as in topological insulators and semi-metals, the role of electron-electron interaction in strongly spin-orbit coupled systems has not been fully understood. The availability of new materials with significant electron correlation and strong spin-orbit coupling now makes such investigations possible. Many of these materials contain 5d or 4d transition metal elements; the prominent examples are iridium oxides or iridates. In this review, we succinctly discuss recent theoretical and experimental progress on this subject. After providing a brief overview, we focus on pyrochlore iridates and three-dimensional honeycomb iridates. In pyrochlore iridates, we discuss the quantum criticality of the bulk and surface states, and the relevance of the surface/boundary states in a number of topological and magnetic ground states, both in the bulk and thin film configurations. Experimental signatures of these boundary an
This manifesto outlines key principles for progress in the post-AI era, emphasizing non-linear yet cumulative advancement, deep understanding of purpose and context, multi-stakeholder collaboration, and system-level experimentation. It redefines progress as substantial, durable, and replicable advancement, highlighting the importance of balancing technological innovation with human-centric values. It acknowledges AI's potential to accelerate progress across industries while recognizing its limitations, such as creating illusions of understanding and potentially narrowing problem-solving approaches. It concludes that true progress in the AI age requires a symbiosis of artificial intelligence capabilities and human ingenuity, calling for a holistic, interdisciplinary approach to shape a future that serves all of humanity.
Patient life circumstances, including social determinants of health (SDOH), shape both health outcomes and care access, contributing to persistent disparities across gender, race, and socioeconomic status. Liver transplantation exemplifies these challenges, requiring complex eligibility and allocation decisions where SDOH directly influence patient evaluation. We developed an artificial intelligence (AI)-driven framework to analyze how broadly defined SDOH -- encompassing both traditional social determinants and transplantation-related psychosocial factors -- influence patient care trajectories. Using large language models, we extracted 23 SDOH factors related to patient eligibility for liver transplantation from psychosocial evaluation notes. These SDOH ``snapshots'' significantly improve prediction of patient progression through transplantation evaluation stages and help explain liver transplantation decisions including the recommendation based on psychosocial evaluation and the listing of a patient for a liver transplantation. Our analysis helps identify patterns of SDOH prevalence across demographics that help explain racial disparities in liver transplantation decisions. We hi
Context. JavaScript is a popular programming language today with several implementations competing for market dominance. Although a specification document and a conformance test suite exist to guide engine development, bugs occur and have important practical consequences. Implementing correct engines is challenging because the spec is intentionally incomplete and evolves frequently. Objective. This paper investigates the use of test transplantation and differential testing for revealing functional bugs in JavaScript engines. The former technique runs the regression test suite of a given engine on another engine. The latter technique fuzzes existing inputs and then compares the output produced by different engines with a differential oracle. Method. We conducted experiments with engines from five major players-Apple, Facebook, Google, Microsoft, and Mozilla-to assess the effectiveness of test transplantation and differential testing. Results. Our results indicate that both techniques revealed several bugs, many of which confirmed by developers. We reported 35 bugs with test transplantation (23 of these bugs confirmed and 19 fixed) and reported 24 bugs with differential testing (17 o
Ensuring large language models (LLM) behave consistently with human goals, values, and intentions is crucial for their safety but yet computationally expensive. To reduce the computational cost of alignment training of LLMs, especially for those with a huge number of parameters, and to reutilize learned value alignment, we propose ConTrans, a novel framework that enables weak-to-strong alignment transfer via concept transplantation. From the perspective of representation engineering, ConTrans refines concept vectors in value alignment from a source LLM (usually a weak yet aligned LLM). The refined concept vectors are then reformulated to adapt to the target LLM (usually a strong yet unaligned base LLM) via affine transformation. In the third step, ConTrans transplants the reformulated concept vectors into the residual stream of the target LLM. Experiments demonstrate the successful transplantation of a wide range of aligned concepts from 7B models to 13B and 70B models across multiple LLMs and LLM families. Remarkably, ConTrans even surpasses instruction-tuned models in terms of truthfulness. Experiment results validate the effectiveness of both inter-LLM-family and intra-LLM-famil
Colonoscopic Polyp Re-Identification aims to match the same polyp from a large gallery with images from different views taken using different cameras, which plays an important role in the prevention and treatment of colorectal cancer in computer-aided diagnosis. However, the coarse resolution of high-level features of a specific polyp often leads to inferior results for small objects where detailed information is important. To address this challenge, we propose a novel architecture, named Gated Progressive Fusion network, to selectively fuse features from multiple levels using gates in a fully connected way for polyp ReID. On the basis of it, a gated progressive fusion strategy is introduced to achieve layer-wise refinement of semantic information through multi-level feature interactions. Experiments on standard benchmarks show the benefits of the multimodal setting over state-of-the-art unimodal ReID models, especially when combined with the specialized multimodal fusion strategy.