pwc-archive/papers-with-abstracts huggingface dataset:
AUTOCT: Automating Interpretable Clinical Trial Prediction with LLM Agents
Authors: Fengze Liu, Haoyu Wang, Joonhyuk Cho, Dan Roth, Andrew W. Lo
Date: 2025-06-04 00:00:00
Tasks: Drug Discovery, Prediction

Clinical trials are critical for advancing medical treatments but remain prohibitively expensive and time-consuming. Accurate prediction of clinical trial outcomes can significantly reduce research and development costs and accelerate drug discovery. While recent deep learning models have shown promise by leveraging unstructured data, their black-box nature, lack of interpretability, and vulnerability to label leakage limit their practical use in high-stakes biomedical contexts. In this work, we propose AutoCT, a novel framework that combines the reasoning capabilities of large language models with the explainability of classical machine learning. AutoCT autonomously generates, evaluates, and refines tabular features based on public information without human input. Our method uses Monte Carlo Tree Search to iteratively optimize predictive performance. Experimental results show that AutoCT performs on par with or better than SOTA methods on clinical trial prediction tasks within only a limited number of self-refinement iterations, establishing a new paradigm for scalable, interpretable, and cost-efficient clinical trial prediction.
Knowledge-guided Contextual Gene Set Analysis Using Large Language Models
Authors: Zhizheng Wang, Chi-Ping Day, Chih-Hsuan Wei, Qiao Jin, Robert Leaman, Yifan Yang, Shubo Tian, Aodong Qiu, Yin Fang, Qingqing Zhu, Xinghua Lu, Zhiyong Lu
Date: 2025-06-04 00:00:00
Tasks: Benchmarking

Gene set analysis (GSA) is a foundational approach for interpreting genomic data of diseases by linking genes to biological processes. However, conventional GSA methods overlook clinical context of the analyses, often generating long lists of enriched pathways with redundant, nonspecific, or irrelevant results. Interpreting these requires extensive, ad-hoc manual effort, reducing both reliability and reproducibility. To address this limitation, we introduce cGSA, a novel AI-driven framework that enhances GSA by incorporating context-aware pathway prioritization. cGSA integrates gene cluster detection, enrichment analysis, and large language models to identify pathways that are not only statistically significant but also biologically meaningful. Benchmarking on 102 manually curated gene sets across 19 diseases and ten disease-related biological mechanisms shows that cGSA outperforms baseline methods by over 30%, with expert validation confirming its increased precision and interpretability. Two independent case studies in melanoma and breast cancer further demonstrate its potential to uncover context-specific insights and support targeted hypothesis generation.
Bridging the Performance Gap Between Target-Free and Target-Based Reinforcement Learning With Iterated Q-Learning
Authors: Théo Vincent, Yogesh Tripathi, Tim Faust, Yaniv Oren, Jan Peters, Carlo D'Eramo
Date: 2025-06-04 00:00:00
Tasks: Q-Learning

In value-based reinforcement learning, removing the target network is tempting as the boostrapped target would be built from up-to-date estimates, and the spared memory occupied by the target network could be reallocated to expand the capacity of the online network. However, eliminating the target network introduces instability, leading to a decline in performance. Removing the target network also means we cannot leverage the literature developed around target networks. In this work, we propose to use a copy of the last linear layer of the online network as a target network, while sharing the remaining parameters with the up-to-date online network, hence stepping out of the binary choice between target-based and target-free methods. It enables us to leverage the concept of iterated Q-learning, which consists of learning consecutive Bellman iterations in parallel, to reduce the performance gap between target-free and target-based approaches. Our findings demonstrate that this novel method, termed iterated Shared Q-Learning (iS-QL), improves the sample efficiency of target-free approaches across various settings. Importantly, iS-QL requires a smaller memory footprint and comparable training time to classical target-based algorithms, highlighting its potential to scale reinforcement learning research.
Diffusion Transformer-based Universal Dose Denoising for Pencil Beam Scanning Proton Therapy
Authors: Yuzhen Ding, Jason Holmes, Hongying Feng, Martin Bues, Lisa A. McGee, Jean-Claude M. Rwigema, Nathan Y. Yu, Terence S. Sio, Sameer R. Keole, William W. Wong, Steven E. Schild, Jonathan B. Ashman, Sujay A. Vora, Daniel J. Ma, Samir H. Patel, Wei Liu
Date: 2025-06-04 00:00:00
Tasks: Denoising

Purpose: Intensity-modulated proton therapy (IMPT) offers precise tumor coverage while sparing organs at risk (OARs) in head and neck (H&N) cancer. However, its sensitivity to anatomical changes requires frequent adaptation through online adaptive radiation therapy (oART), which depends on fast, accurate dose calculation via Monte Carlo (MC) simulations. Reducing particle count accelerates MC but degrades accuracy. To address this, denoising low-statistics MC dose maps is proposed to enable fast, high-quality dose generation. Methods: We developed a diffusion transformer-based denoising framework. IMPT plans and 3D CT images from 80 H&N patients were used to generate noisy and high-statistics dose maps using MCsquare (1 min and 10 min per plan, respectively). Data were standardized into uniform chunks with zero-padding, normalized, and transformed into quasi-Gaussian distributions. Testing was done on 10 H&N, 10 lung, 10 breast, and 10 prostate cancer cases, preprocessed identically. The model was trained with noisy dose maps and CT images as input and high-statistics dose maps as ground truth, using a combined loss of mean square error (MSE), residual loss, and regional MAE (focusing on top/bottom 10% dose voxels). Performance was assessed via MAE, 3D Gamma passing rate, and DVH indices. Results: The model achieved MAEs of 0.195 (H&N), 0.120 (lung), 0.172 (breast), and 0.376 Gy[RBE] (prostate). 3D Gamma passing rates exceeded 92% (3%/2mm) across all sites. DVH indices for clinical target volumes (CTVs) and OARs closely matched the ground truth. Conclusion: A diffusion transformer-based denoising framework was developed and, though trained only on H&N data, generalizes well across multiple disease sites.
Classifying Dental Care Providers Through Machine Learning with Features Ranking
Authors: Mohammad Subhi Al-Batah, Mowafaq Salem Alzboon, Muhyeeddin Alqaraleh, Mohammed Hasan Abu-Arqoub, Rashiq Rafiq Marie
Date: 2025-06-04 00:00:00
Tasks: feature selection, Missing Values

This study investigates the application of machine learning (ML) models for classifying dental providers into two categories - standard rendering providers and safety net clinic (SNC) providers - using a 2018 dataset of 24,300 instances with 20 features. The dataset, characterized by high missing values (38.1%), includes service counts (preventive, treatment, exams), delivery systems (FFS, managed care), and beneficiary demographics. Feature ranking methods such as information gain, Gini index, and ANOVA were employed to identify critical predictors, revealing treatment-related metrics (TXMT_USER_CNT, TXMT_SVC_CNT) as top-ranked features. Twelve ML models, including k-Nearest Neighbors (kNN), Decision Trees, Support Vector Machines (SVM), Stochastic Gradient Descent (SGD), Random Forest, Neural Networks, and Gradient Boosting, were evaluated using 10-fold cross-validation. Classification accuracy was tested across incremental feature subsets derived from rankings. The Neural Network achieved the highest accuracy (94.1%) using all 20 features, followed by Gradient Boosting (93.2%) and Random Forest (93.0%). Models showed improved performance as more features were incorporated, with SGD and ensemble methods demonstrating robustness to missing data. Feature ranking highlighted the dominance of treatment service counts and annotation codes in distinguishing provider types, while demographic variables (AGE_GROUP, CALENDAR_YEAR) had minimal impact. The study underscores the importance of feature selection in enhancing model efficiency and accuracy, particularly in imbalanced healthcare datasets. These findings advocate for integrating feature-ranking techniques with advanced ML algorithms to optimize dental provider classification, enabling targeted resource allocation for underserved populations.
Comparative performance of ensemble models in predicting dental provider types: insights from fee-for-service data
Authors: Mohammad Subhi Al-Batah, Muhyeeddin Alqaraleh, Mowafaq Salem Alzboon, Abdullah Alourani
Date: 2025-06-04 00:00:00

Dental provider classification plays a crucial role in optimizing healthcare resource allocation and policy planning. Effective categorization of providers, such as standard rendering providers and safety net clinic (SNC) providers, enhances service delivery to underserved populations. This study aimed to evaluate the performance of machine learning models in classifying dental providers using a 2018 dataset. A dataset of 24,300 instances with 20 features was analyzed, including beneficiary and service counts across fee-for-service (FFS), Geographic Managed Care, and Pre-Paid Health Plans. Providers were categorized by delivery system and patient age groups (0-20 and 21+). Despite 38.1% missing data, multiple machine learning algorithms were tested, including k-Nearest Neighbors (kNN), Decision Trees, Support Vector Machines (SVM), Stochastic Gradient Descent (SGD), Random Forest, Neural Networks, and Gradient Boosting. A 10-fold cross-validation approach was applied, and models were evaluated using AUC, classification accuracy (CA), F1-score, precision, and recall. Neural Networks achieved the highest AUC (0.975) and CA (94.1%), followed by Random Forest (AUC: 0.948, CA: 93.0%). These models effectively handled imbalanced data and complex feature interactions, outperforming traditional classifiers like Logistic Regression and SVM. Advanced machine learning techniques, particularly ensemble and deep learning models, significantly enhance dental workforce classification. Their integration into healthcare analytics can improve provider identification and resource distribution, benefiting underserved populations.
The Latent Space Hypothesis: Toward Universal Medical Representation Learning
Authors: Salil Patel
Date: 2025-06-04 00:00:00
Tasks: Continual Learning, Representation Learning

Medical data range from genomic sequences and retinal photographs to structured laboratory results and unstructured clinical narratives. Although these modalities appear disparate, many encode convergent information about a single underlying physiological state. The Latent Space Hypothesis frames each observation as a projection of a unified, hierarchically organized manifold -- much like shadows cast by the same three-dimensional object. Within this learned geometric representation, an individual's health status occupies a point, disease progression traces a trajectory, and therapeutic intervention corresponds to a directed vector. Interpreting heterogeneous evidence in a shared space provides a principled way to re-examine eponymous conditions -- such as Parkinson's or Crohn's -- that often mask multiple pathophysiological entities and involve broader anatomical domains than once believed. By revealing sub-trajectories and patient-specific directions of change, the framework supplies a quantitative rationale for personalised diagnosis, longitudinal monitoring, and tailored treatment, moving clinical practice away from grouping by potentially misleading labels toward navigation of each person's unique trajectory. Challenges remain -- bias amplification, data scarcity for rare disorders, privacy, and the correlation-causation divide -- but scale-aware encoders, continual learning on longitudinal data streams, and perturbation-based validation offer plausible paths forward.
NOBLE -- Neural Operator with Biologically-informed Latent Embeddings to Capture Experimental Variability in Biological Neuron Models
Authors: Luca Ghafourpour, Valentin Duruisseaux, Bahareh Tolooshams, Philip H. Wong, Costas A. Anastassiou, Anima Anandkumar
Date: 2025-06-05 00:00:00

Characterizing the diverse computational properties of human neurons via multimodal electrophysiological, transcriptomic, and morphological data provides the foundation for constructing and validating bio-realistic neuron models that can advance our understanding of fundamental mechanisms underlying brain function. However, current modeling approaches remain constrained by the limited availability and intrinsic variability of experimental neuronal data. To capture variability, ensembles of deterministic models are often used, but are difficult to scale as model generation requires repeating computationally expensive optimization for each neuron. While deep learning is becoming increasingly relevant in this space, it fails to capture the full biophysical complexity of neurons, their nonlinear voltage dynamics, and variability. To address these shortcomings, we introduce NOBLE, a neural operator framework that learns a mapping from a continuous frequency-modulated embedding of interpretable neuron features to the somatic voltage response induced by current injection. Trained on data generated from biophysically realistic neuron models, NOBLE predicts distributions of neural dynamics accounting for the intrinsic experimental variability. Unlike conventional bio-realistic neuron models, interpolating within the embedding space offers models whose dynamics are consistent with experimentally observed responses. NOBLE is the first scaled-up deep learning framework validated on real experimental data, enabling efficient generation of synthetic neurons that exhibit trial-to-trial variability and achieve a $4200\times$ speedup over numerical solvers. To this end, NOBLE captures fundamental neural properties, opening the door to a better understanding of cellular composition and computations, neuromorphic architectures, large-scale brain circuits, and general neuroAI applications.
Towards Better Generalization via Distributional Input Projection Network
Authors: Yifan Hao, Yanxin Lu, Xinwei Shen, Tong Zhang
Date: 2025-06-05 00:00:00

As overparameterized models become increasingly prevalent, training loss alone offers limited insight into generalization performance. While smoothness has been linked to improved generalization across various settings, directly enforcing smoothness in neural networks remains challenging. To address this, we introduce Distributional Input Projection Networks (DIPNet), a novel framework that projects inputs into learnable distributions at each layer. This distributional representation induces a smoother loss landscape with respect to the input, promoting better generalization. We provide theoretical analysis showing that DIPNet reduces both local smoothness measures and the Lipschitz constant of the network, contributing to improved generalization performance. Empirically, we validate DIPNet across a wide range of architectures and tasks, including Vision Transformers (ViTs), Large Language Models (LLMs), ResNet and MLPs. Our method consistently enhances test performance under standard settings, adversarial attacks, out-of-distribution inputs, and reasoning benchmarks. We demonstrate that the proposed input projection strategy can be seamlessly integrated into existing models, providing a general and effective approach for boosting generalization performance in modern deep learning.
Influence Functions for Edge Edits in Non-Convex Graph Neural Networks
Authors: Jaeseung Heo, Kyeongheung Yun, Seokwon Yoon, Moonjeong Park, Jungseul Ok, Dongwoo Kim
Date: 2025-06-05 00:00:00
Tasks: Prediction

Understanding how individual edges influence the behavior of graph neural networks (GNNs) is essential for improving their interpretability and robustness. Graph influence functions have emerged as promising tools to efficiently estimate the effects of edge deletions without retraining. However, existing influence prediction methods rely on strict convexity assumptions, exclusively consider the influence of edge deletions while disregarding edge insertions, and fail to capture changes in message propagation caused by these modifications. In this work, we propose a proximal Bregman response function specifically tailored for GNNs, relaxing the convexity requirement and enabling accurate influence prediction for standard neural network architectures. Furthermore, our method explicitly accounts for message propagation effects and extends influence prediction to both edge deletions and insertions in a principled way. Experiments with real-world datasets demonstrate accurate influence predictions for different characteristics of GNNs. We further demonstrate that the influence function is versatile in applications such as graph rewiring and adversarial attacks.
UNO: Unlearning via Orthogonalization in Generative models
Authors: Pinak Mandal, Georg A. Gottwald
Date: 2025-06-05 00:00:00

As generative models become increasingly powerful and pervasive, the ability to unlearn specific data, whether due to privacy concerns, legal requirements, or the correction of harmful content, has become increasingly important. Unlike in conventional training, where data are accumulated and knowledge is reinforced, unlearning aims to selectively remove the influence of particular data points without costly retraining from scratch. To be effective and reliable, such algorithms need to achieve (i) forgetting of the undesired data, (ii) preservation of the quality of the generation, (iii) preservation of the influence of the desired training data on the model parameters, and (iv) small number of training steps. We propose fast unlearning algorithms based on loss gradient orthogonalization. We show that our algorithms are able to forget data while maintaining the fidelity of the original model. Using MNIST and CelebA data, we demonstrate that our algorithms achieve orders of magnitude faster unlearning times than their predecessors, such as gradient surgery.
Was Residual Penalty and Neural Operators All We Needed for Solving Optimal Control Problems?
Authors: Oliver G. S. Lundqvist, Fabricio Oliveira
Date: 2025-06-05 00:00:00
Tasks: All

Neural networks have been used to solve optimal control problems, typically by training neural networks using a combined loss function that considers data, differential equation residuals, and objective costs. We show that including cost functions in the training process is unnecessary, advocating for a simpler architecture and streamlined approach by decoupling the optimal control problem from the training process. Thus, our work shows that a simple neural operator architecture, such as DeepONet, coupled with an unconstrained optimization routine, can solve multiple optimal control problems with a single physics-informed training phase and a subsequent optimization phase. We achieve this by adding a penalty term based on the differential equation residual to the cost function and computing gradients with respect to the control using automatic differentiation through the trained neural operator within an iterative optimization routine. We showcase our method on nine distinct optimal control problems by training three separate DeepONet models, each corresponding to a different differential equation. For each model, we solve three problems with varying cost functions, demonstrating accurate and consistent performance across all cases.
TIMING: Temporality-Aware Integrated Gradients for Time Series Explanation
Authors: Hyeongwon Jang, Changhun Kim, Eunho Yang
Date: 2025-06-05 00:00:00
Tasks: Explainable artificial intelligence, Explainable Artificial Intelligence (XAI), Time Series

Recent explainable artificial intelligence (XAI) methods for time series primarily estimate point-wise attribution magnitudes, while overlooking the directional impact on predictions, leading to suboptimal identification of significant points. Our analysis shows that conventional Integrated Gradients (IG) effectively capture critical points with both positive and negative impacts on predictions. However, current evaluation metrics fail to assess this capability, as they inadvertently cancel out opposing feature contributions. To address this limitation, we propose novel evaluation metrics-Cumulative Prediction Difference (CPD) and Cumulative Prediction Preservation (CPP)-to systematically assess whether attribution methods accurately identify significant positive and negative points in time series XAI. Under these metrics, conventional IG outperforms recent counterparts. However, directly applying IG to time series data may lead to suboptimal outcomes, as generated paths ignore temporal relationships and introduce out-of-distribution samples. To overcome these challenges, we introduce TIMING, which enhances IG by incorporating temporal awareness while maintaining its theoretical properties. Extensive experiments on synthetic and real-world time series benchmarks demonstrate that TIMING outperforms existing time series XAI baselines. Our code is available at https://github.com/drumpt/TIMING.
TreeRPO: Tree Relative Policy Optimization
Authors: Zhicheng Yang, Zhijiang Guo, Yinya Huang, Xiaodan Liang, Yiwei Wang, Jing Tang
Date: 2025-06-05 00:00:00
Tasks: Math

Large Language Models (LLMs) have shown remarkable reasoning capabilities through Reinforcement Learning with Verifiable Rewards (RLVR) methods. However, a key limitation of existing approaches is that rewards defined at the full trajectory level provide insufficient guidance for optimizing the intermediate steps of a reasoning process. To address this, we introduce \textbf{\name}, a novel method that estimates the mathematical expectations of rewards at various reasoning steps using tree sampling. Unlike prior methods that rely on a separate step reward model, \name directly estimates these rewards through this sampling process. Building on the group-relative reward training mechanism of GRPO, \name innovatively computes rewards based on step-level groups generated during tree sampling. This advancement allows \name to produce fine-grained and dense reward signals, significantly enhancing the learning process and overall performance of LLMs. Experimental results demonstrate that our \name algorithm substantially improves the average Pass@1 accuracy of Qwen-2.5-Math on test benchmarks, increasing it from 19.0\% to 35.5\%. Furthermore, \name significantly outperforms GRPO by 2.9\% in performance while simultaneously reducing the average response length by 18.1\%, showcasing its effectiveness and efficiency. Our code will be available at \href{https://github.com/yangzhch6/TreeRPO}{https://github.com/yangzhch6/TreeRPO}.