Jue Hou

Yucong Lin, Jinhua Su, Yuhang Li et al.

Deep learning methods have contributed substantially to the rapid advancement of medical image segmentation, the quality of which relies on the suitable design of loss functions. Popular loss functions, including the cross-entropy and dice losses, often fall short of boundary detection, thereby limiting high-resolution downstream applications such as automated diagnoses and procedures. We developed a novel loss function that is tailored to reflect the boundary information to enhance the boundary detection. As the contrast between segmentation and background regions along the classification boundary naturally induces heterogeneity over the pixels, we propose the piece-wise two-sample t-test augmented (PTA) loss that is infused with the statistical test for such heterogeneity. We demonstrate the improved boundary detection power of the PTA loss compared to benchmark losses without a t-test component.

Jue Hou, Anisia Katinskaia, Anh-Duc Vu et al.

Assessment of proficiency of the learner is an essential part of Intelligent Tutoring Systems (ITS). We use Item Response Theory (IRT) in computer-aided language learning for assessment of student ability in two contexts: in test sessions, and in exercises during practice sessions. Exhaustive testing across a wide range of skills can provide a detailed picture of proficiency, but may be undesirable for a number of reasons. Therefore, we first aim to replace exhaustive tests with efficient but accurate adaptive tests. We use learner data collected from exhaustive tests under imperfect conditions, to train an IRT model to guide adaptive tests. Simulations and experiments with real learner data confirm that this approach is efficient and accurate. Second, we explore whether we can accurately estimate learner ability directly from the context of practice with exercises, without testing. We transform learner data collected from exercise sessions into a form that can be used for IRT modeling. This is done by linking the exercises to {\em linguistic constructs}; the constructs are then treated as "items" within IRT. We present results from large-scale studies with thousands of learners. Using teacher assessments of student ability as "ground truth," we compare the estimates obtained from tests vs. those from exercises. The experiments confirm that the IRT models can produce accurate ability estimation based on exercises.

Anisia Katinskaia, Jue Hou, Anh-Duc Vu et al.

This paper presents the development of an AI-based language learning platform Revita. It is a freely available intelligent online tutor, developed to support learners of multiple languages, from low-intermediate to advanced levels. It has been in pilot use by hundreds of students at several universities, whose feedback and needs are shaping the development. One of the main emerging features of Revita is the introduction of a system of linguistic constructs as the representation of domain knowledge. The system of constructs is developed in close collaboration with experts in language teaching. Constructs define the types of exercises, the content of the feedback, and enable the detailed modeling and evaluation of learning progress.

Mingjun Xu, Jinhan Dong, Jue Hou et al.

Multimodal document retrieval systems enable information access across text, images, and layouts, benefiting various domains like document-based question answering, report analysis, and interactive content summarization. Rerankers improve retrieval precision by reordering retrieved candidates. However, current multimodal reranking methods remain underexplored, with significant room for improvement in both training strategies and overall effectiveness. Moreover, the lack of explicit reasoning makes it difficult to analyze and optimize these methods further. In this paper, We propose MM-R5, a MultiModal Reasoning-Enhanced ReRanker via Reinforcement Learning for Document Retrieval, aiming to provide a more effective and reliable solution for multimodal reranking tasks. MM-R5 is trained in two stages: supervised fine-tuning (SFT) and reinforcement learning (RL). In the SFT stage, we focus on improving instruction-following and guiding the model to generate complete and high-quality reasoning chains. To support this, we introduce a novel data construction strategy that produces rich, high-quality reasoning data. In the RL stage, we design a task-specific reward framework, including a reranking reward tailored for multimodal candidates and a composite template-based reward to further refine reasoning quality. We conduct extensive experiments on MMDocIR, a challenging public benchmark spanning multiple domains. MM-R5 achieves state-of-the-art performance on most metrics and delivers comparable results to much larger models on the remaining ones. Moreover, compared to the best retrieval-only method, MM-R5 improves recall@1 by over 4%. These results validate the effectiveness of our reasoning-enhanced training pipeline. Our code is available at https://github.com/i2vec/MM-R5 .

Jiaxi Zhuang, Yaorui Shi, Jue Hou et al.

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional machine learning models struggle with task transferability, while specialized molecular language models provide little insight into their decision-making processes. To address these limitations, we propose \textbf{MPPReasoner}, a multimodal large language model that incorporates chemical reasoning for molecular property prediction. Our approach, built upon Qwen2.5-VL-7B-Instruct, integrates molecular images with SMILES strings to enable comprehensive molecular understanding. We develop a two-stage training strategy: supervised fine-tuning (SFT) using 16,000 high-quality reasoning trajectories generated through expert knowledge and multiple teacher models, followed by Reinforcement Learning from Principle-Guided Rewards (RLPGR). RLPGR employs verifiable, rule-based rewards that systematically evaluate chemical principle application, molecular structure analysis, and logical consistency through computational verification. Extensive experiments across 8 datasets demonstrate significant performance improvements, with MPPReasoner outperforming the best baselines by 7.91\% and 4.53\% on in-distribution and out-of-distribution tasks respectively. MPPReasoner exhibits exceptional cross-task generalization and generates chemically sound reasoning paths that provide valuable insights into molecular property analysis, substantially enhancing both interpretability and practical utility for chemists. Code is available at https://anonymous.4open.science/r/MPPReasoner-12687.

Jue Hou, Anisia Katinskaia, Lari Kotilainen et al.

This paper investigates what insights about linguistic features and what knowledge about the structure of natural language can be obtained from the encodings in transformer language models.In particular, we explore how BERT encodes the government relation between constituents in a sentence. We use several probing classifiers, and data from two morphologically rich languages. Our experiments show that information about government is encoded across all transformer layers, but predominantly in the early layers of the model. We find that, for both languages, a small number of attention heads encode enough information about the government relations to enable us to train a classifier capable of discovering new, previously unknown types of government, never seen in the training data. Currently, data is lacking for the research community working on grammatical constructions, and government in particular. We release the Government Bank -- a dataset defining the government relations for thousands of lemmas in the languages in our experiments.

Jiaxi Zhuang, Kangning Li, Jue Hou et al.

Extracting molecular structure-activity relationships (SARs) from scientific literature and patents is essential for drug discovery and materials research. However, this task remains challenging due to heterogeneous document formats and limitations of existing methods. Specifically, rule-based approaches relying on rigid templates fail to generalize across diverse document layouts, while general-purpose multimodal large language models (MLLMs) lack sufficient accuracy and reliability for specialized tasks, such as layout detection and optical chemical structure recognition (OCSR). To address these challenges, we introduce DocSAR-200, a rigorously annotated benchmark of 200 scientific documents designed specifically for evaluating SAR extraction methods. Additionally, we propose Doc2SAR, a novel synergistic framework that integrates domain-specific tools with MLLMs enhanced via supervised fine-tuning (SFT). Extensive experiments demonstrate that Doc2SAR achieves state-of-the-art performance across various document types, significantly outperforming leading end-to-end baselines. Specifically, Doc2SAR attains an overall Table Recall of 80.78% on DocSAR-200, exceeding end2end GPT-4o by 51.48%. Furthermore, Doc2SAR demonstrates practical usability through efficient inference and is accompanied by a web app.

Yongkang Xiao, Sinian Zhang, Yi Dai et al.

Knowledge graph completion (KGC) aims to predict missing triples in knowledge graphs (KGs) by leveraging existing triples and textual information. Recently, generative large language models (LLMs) have been increasingly employed for graph tasks. However, current approaches typically encode graph context in textual form, which fails to fully exploit the potential of LLMs for perceiving and reasoning about graph structures. To address this limitation, we propose DrKGC (Dynamic Subgraph Retrieval-Augmented LLMs for Knowledge Graph Completion). DrKGC employs a flexible lightweight model training strategy to learn structural embeddings and logical rules within the KG. It then leverages a novel bottom-up graph retrieval method to extract a subgraph for each query guided by the learned rules. Finally, a graph convolutional network (GCN) adapter uses the retrieved subgraph to enhance the structural embeddings, which are then integrated into the prompt for effective LLM fine-tuning. Experimental results on two general domain benchmark datasets and two biomedical datasets demonstrate the superior performance of DrKGC. Furthermore, a realistic case study in the biomedical domain highlights its interpretability and practical utility.

Jun Wen, Jue Hou, Clara-Lea Bonzel et al.

Electronic health record (EHR) data are increasingly used to support real-world evidence (RWE) studies. Yet its ability to generate reliable RWE is limited by the lack of readily available precise information on the timing of clinical events such as the onset time of heart failure. We propose a LAbel-efficienT incidenT phEnotyping (LATTE) algorithm to accurately annotate the timing of clinical events from longitudinal EHR data. By leveraging the pre-trained semantic embedding vectors from large-scale EHR data as prior knowledge, LATTE selects predictive EHR features in a concept re-weighting module by mining their relationship to the target event and compresses their information into longitudinal visit embeddings through a visit attention learning network. LATTE employs a recurrent neural network to capture the sequential dependency between the target event and visit embeddings before/after it. To improve label efficiency, LATTE constructs highly informative longitudinal silver-standard labels from large-scale unlabeled patients to perform unsupervised pre-training and semi-supervised joint training. Finally, LATTE enhances cross-site portability via contrastive representation learning. LATTE is evaluated on three analyses: the onset of type-2 diabetes, heart failure, and the onset and relapses of multiple sclerosis. We use various evaluation metrics present in the literature including the $ABC_{gain}$, the proportion of reduction in the area between the observed event indicator and the predicted cumulative incidences in reference to the prediction per incident prevalence. LATTE consistently achieves substantial improvement over benchmark methods such as SAMGEP and RETAIN in all settings.

Jue Hou, Anisia Katinskaia, Anh-Duc Vu et al.

Language modeling is a fundamental task in natural language processing, which has been thoroughly explored with various architectures and hyperparameters. However, few studies focus on the effect of sub-word segmentation on the performance of language models (LMs). In this paper, we compare GPT and BERT models trained with the statistical segmentation algorithm BPE vs. two unsupervised algorithms for morphological segmentation -- Morfessor and StateMorph. We train the models for several languages -- including ones with very rich morphology -- and compare their performance with different segmentation algorithms, vocabulary sizes, and model sizes. The results show that training with morphological segmentation allows the LMs to: 1. achieve lower perplexity, 2. converge more efficiently in terms of training time, and 3. achieve equivalent or better evaluation scores on downstream tasks. Lastly, we show 4. that LMs of smaller size using morphological segmentation can perform comparably to models of larger size trained with BPE -- both in terms of (1) perplexity and (3) scores on downstream tasks. Points (2) and (4) impact on sustainability of LMs, since they reduce the model cost: size and computation time. While (2) reduces cost only in the training phase, (4) does so also in the inference phase.

Jue Hou, Zijian Guo, Tianxi Cai

Risk modeling with EHR data is challenging due to a lack of direct observations on the disease outcome, and the high dimensionality of the candidate predictors. In this paper, we develop a surrogate assisted semi-supervised-learning (SAS) approach to risk modeling with high dimensional predictors, leveraging a large unlabeled data on candidate predictors and surrogates of outcome, as well as a small labeled data with annotated outcomes. The SAS procedure borrows information from surrogates along with candidate predictors to impute the unobserved outcomes via a sparse working imputation model with moment conditions to achieve robustness against mis-specification in the imputation model and a one-step bias correction to enable interval estimation for the predicted risk. We demonstrate that the SAS procedure provides valid inference for the predicted risk derived from a high dimensional working model, even when the underlying risk prediction model is dense and the risk model is mis-specified. We present an extensive simulation study to demonstrate the superiority of our SSL approach compared to existing supervised methods. We apply the method to derive genetic risk prediction of type-2 diabetes mellitus using a EHR biobank cohort.

Jue Hou, Jelena Bradic, Ronghui Xu

Estimating causal effects for survival outcomes in the high-dimensional setting is an extremely important topic for many biomedical applications as well as areas of social sciences. We propose a new orthogonal score method for treatment effect estimation and inference that results in asymptotically valid confidence intervals assuming only good estimation properties of the hazard outcome model and the conditional probability of treatment. This guarantee allows us to provide valid inference for the conditional treatment effect under the high-dimensional additive hazards model under considerably more generality than existing approaches. In addition, we develop a new Hazards Difference (HDi), estimator. We showcase that our approach has double-robustness properties in high dimensions: with cross-fitting, the HDi estimate is consistent under a wide variety of treatment assignment models; the HDi estimate is also consistent when the hazards model is misspecified and instead the true data generating mechanism follows a partially linear additive hazards model. We further develop a novel sparsity doubly robust result, where either the outcome or the treatment model can be a fully dense high-dimensional model. We apply our methods to study the treatment effect of radical prostatectomy versus conservative management for prostate cancer patients using the SEER-Medicare Linked Data.

Jue Hou, Jelena Bradic, Ronghui Xu

The purpose of this paper is to construct confidence intervals for the regression coefficients in the Fine-Gray model for competing risks data with random censoring, where the number of covariates can be larger than the sample size. Despite strong motivation from biomedical applications, a high-dimensional Fine-Gray model has attracted relatively little attention among the methodological or theoretical literature. We fill in this gap by developing confidence intervals based on a one-step bias-correction for a regularized estimation. We develop a theoretical framework for the partial likelihood, which does not have independent and identically distributed entries and therefore presents many technical challenges. We also study the approximation error from the weighting scheme under random censoring for competing risks and establish new concentration results for time-dependent processes. In addition to the theoretical results and algorithms, we present extensive numerical experiments and an application to a study of non-cancer mortality among prostate cancer patients using the linked Medicare-SEER data.