Xiaochen Zheng

Dehua Zheng, Xiaochen Zheng, Laurence T. Yang et al.

Recent research about camouflaged object detection (COD) aims to segment highly concealed objects hidden in complex surroundings. The tiny, fuzzy camouflaged objects result in visually indistinguishable properties. However, current single-view COD detectors are sensitive to background distractors. Therefore, blurred boundaries and variable shapes of the camouflaged objects are challenging to be fully captured with a single-view detector. To overcome these obstacles, we propose a behavior-inspired framework, called Multi-view Feature Fusion Network (MFFN), which mimics the human behaviors of finding indistinct objects in images, i.e., observing from multiple angles, distances, perspectives. Specifically, the key idea behind it is to generate multiple ways of observation (multi-view) by data augmentation and apply them as inputs. MFFN captures critical boundary and semantic information by comparing and fusing extracted multi-view features. In addition, our MFFN exploits the dependence and interaction between views and channels. Specifically, our methods leverage the complementary information between different views through a two-stage attention module called Co-attention of Multi-view (CAMV). And we design a local-overall module called Channel Fusion Unit (CFU) to explore the channel-wise contextual clues of diverse feature maps in an iterative manner. The experiment results show that our method performs favorably against existing state-of-the-art methods via training with the same data. The code will be available at https://github.com/dwardzheng/MFFN_COD.

Yinghao Zhu, Zixiang Wang, Long He et al.

Electronic Health Records (EHRs) contain a wealth of patient data; however, the sparsity of EHRs data often presents significant challenges for predictive modeling. Conventional imputation methods inadequately distinguish between real and imputed data, leading to potential inaccuracies of patient representations. To address these issues, we introduce PRISM, a framework that indirectly imputes data by leveraging prototype representations of similar patients, thus ensuring compact representations that preserve patient information. PRISM also includes a feature confidence learner module, which evaluates the reliability of each feature considering missing statuses. Additionally, PRISM introduces a new patient similarity metric that accounts for feature confidence, avoiding over-reliance on imprecise imputed values. Our extensive experiments on the MIMIC-III, MIMIC-IV, PhysioNet Challenge 2012, eICU datasets demonstrate PRISM's superior performance in predicting in-hospital mortality and 30-day readmission tasks, showcasing its effectiveness in handling EHR data sparsity. For the sake of reproducibility and further research, we have publicly released the code at https://github.com/yhzhu99/PRISM.

Yinghao Zhu, Junyi Gao, Zixiang Wang et al.

Large Language Models (LLMs) are increasingly deployed in medicine. However, their utility in non-generative clinical prediction, often presumed inferior to specialized models, remains under-evaluated, leading to ongoing debate within the field and potential for misuse, misunderstanding, or over-reliance due to a lack of systematic benchmarking. Our ClinicRealm study addresses this by benchmarking 15 GPT-style LLMs, 5 BERT-style models, and 11 traditional methods on unstructured clinical notes and structured Electronic Health Records (EHR), while also assessing their reasoning, reliability, and fairness. Key findings reveal a significant shift: for clinical note predictions, leading LLMs (e.g., DeepSeek-V3.1-Think, GPT-5) in zero-shot settings now decisively outperform finetuned BERT models. On structured EHRs, while specialized models excel with ample data, advanced LLMs (e.g., GPT-5, DeepSeek-V3.1-Think) show potent zero-shot capabilities, often surpassing conventional models in data-scarce settings. Notably, leading open-source LLMs can match or exceed proprietary counterparts. These results provide compelling evidence that modern LLMs are competitive tools for non-generative clinical prediction, particularly with unstructured text and offering data-efficient structured data options, thus necessitating a re-evaluation of model selection strategies. This research should serve as an important insight for medical informaticists, AI developers, and clinical researchers, potentially prompting a reassessment of current assumptions and inspiring new approaches to LLM application in predictive healthcare.

Xiaochen Zheng, Xingyu Chen, Manuel Schürch et al.

Contrastive learning methods have shown an impressive ability to learn meaningful representations for image or time series classification. However, these methods are less effective for time series forecasting, as optimization of instance discrimination is not directly applicable to predicting the future state from the historical context. To address these limitations, we propose SimTS, a simple representation learning approach for improving time series forecasting by learning to predict the future from the past in the latent space. SimTS exclusively uses positive pairs and does not depend on negative pairs or specific characteristics of a given time series. In addition, we show the shortcomings of the current contrastive learning framework used for time series forecasting through a detailed ablation study. Overall, our work suggests that SimTS is a promising alternative to other contrastive learning approaches for time series forecasting.

Zeyu Yang, Zhao Meng, Xiaochen Zheng et al. · eth-zurich

Large Language Models (LLMs) have revolutionized natural language processing, but their robustness against adversarial attacks remains a critical concern. We presents a novel white-box style attack approach that exposes vulnerabilities in leading open-source LLMs, including Llama, OPT, and T5. We assess the impact of model size, structure, and fine-tuning strategies on their resistance to adversarial perturbations. Our comprehensive evaluation across five diverse text classification tasks establishes a new benchmark for LLM robustness. The findings of this study have far-reaching implications for the reliable deployment of LLMs in real-world applications and contribute to the advancement of trustworthy AI systems.

Yinghao Zhu, Ziyi He, Haoran Hu et al.

The rapid advancement of Large Language Models (LLMs) has stimulated interest in multi-agent collaboration for addressing complex medical tasks. However, the practical advantages of multi-agent collaboration approaches remain insufficiently understood. Existing evaluations often lack generalizability, failing to cover diverse tasks reflective of real-world clinical practice, and frequently omit rigorous comparisons against both single-LLM-based and established conventional methods. To address this critical gap, we introduce MedAgentBoard, a comprehensive benchmark for the systematic evaluation of multi-agent collaboration, single-LLM, and conventional approaches. MedAgentBoard encompasses four diverse medical task categories: (1) medical (visual) question answering, (2) lay summary generation, (3) structured Electronic Health Record (EHR) predictive modeling, and (4) clinical workflow automation, across text, medical images, and structured EHR data. Our extensive experiments reveal a nuanced landscape: while multi-agent collaboration demonstrates benefits in specific scenarios, such as enhancing task completeness in clinical workflow automation, it does not consistently outperform advanced single LLMs (e.g., in textual medical QA) or, critically, specialized conventional methods that generally maintain better performance in tasks like medical VQA and EHR-based prediction. MedAgentBoard offers a vital resource and actionable insights, emphasizing the necessity of a task-specific, evidence-based approach to selecting and developing AI solutions in medicine. It underscores that the inherent complexity and overhead of multi-agent collaboration must be carefully weighed against tangible performance gains. All code, datasets, detailed prompts, and experimental results are open-sourced at https://medagentboard.netlify.app/.

Xiaochen Zheng

Automated animal censuses with aerial imagery are a vital ingredient towards wildlife conservation. Recent models are generally based on supervised learning and thus require vast amounts of training data. Due to their scarcity and minuscule size, annotating animals in aerial imagery is a highly tedious process. In this project, we present a methodology to reduce the amount of required training data by resorting to self-supervised pretraining. In detail, we examine a combination of recent contrastive learning methodologies like Momentum Contrast (MoCo) and Cross-Level Instance-Group Discrimination (CLD) to condition our model on the aerial images without the requirement for labels. We show that a combination of MoCo, CLD, and geometric augmentations outperforms conventional models pretrained on ImageNet by a large margin. Meanwhile, strategies for smoothing label or prediction distribution in supervised learning have been proven useful in preventing the model from overfitting. We combine the self-supervised contrastive models with image mixup strategies and find that it is useful for learning more robust visual representations. Crucially, our methods still yield favorable results even if we reduce the number of training animals to just 10%, at which point our best model scores double the recall of the baseline at similar precision. This effectively allows reducing the number of required annotations to a fraction while still being able to train high-accuracy models in such highly challenging settings.

Xingyu Chen, Xiaochen Zheng, Amina Mollaysa et al.

Irregular multivariate time series data is characterized by varying time intervals between consecutive observations of measured variables/signals (i.e., features) and varying sampling rates (i.e., recordings/measurement) across these features. Modeling time series while taking into account these irregularities is still a challenging task for machine learning methods. Here, we introduce TADA, a Two-stageAggregation process with Dynamic local Attention to harmonize time-wise and feature-wise irregularities in multivariate time series. In the first stage, the irregular time series undergoes temporal embedding (TE) using all available features at each time step. This process preserves the contribution of each available feature and generates a fixed-dimensional representation per time step. The second stage introduces a dynamic local attention (DLA) mechanism with adaptive window sizes. DLA aggregates time recordings using feature-specific windows to harmonize irregular time intervals capturing feature-specific sampling rates. Then hierarchical MLP mixer layers process the output of DLA through multiscale patching to leverage information at various scales for the downstream tasks. TADA outperforms state-of-the-art methods on three real-world datasets, including the latest MIMIC IV dataset, and highlights its effectiveness in handling irregular multivariate time series and its potential for various real-world applications.

Xiaochen Zheng, Zhiwen Jiang, Melanie Guerard et al.

Target Safety Assessment (TSA) requires systematic integration of heterogeneous evidence, including genetic, transcriptomic, target homology, pharmacological, and clinical data, to evaluate potential safety liabilities of therapeutic targets. This process is inherently iterative and expert-driven, posing challenges in scalability and reproducibility. We present TSAssistant, a multi-agent framework designed to support TSA report drafting through a modular, section-based, and human-in-the-loop paradigm. The framework decomposes report generation into a coordinated pipeline of specialised subagents, each targeting a single TSA section. Specialised subagents retrieve structured and unstructured data as well as literature evidence from curated biomedical sources through standardised tool interfaces, producing individually citable, evidence-grounded sections. Agent behaviour is governed by a hierarchical instruction architecture comprising system prompts, domain-specific skill modules, and runtime user instructions. A key feature is an interactive refinement loop in which users may manually edit sections, append new information, upload additional sources, or re-invoke agents to revise specific sections, with the system maintaining conversational memory across iterations. TSAssistant is designed to reduce the mechanical burden of evidence synthesis and report drafting, supporting a hybrid model in which agentic AI augments evidence synthesis while toxicologists retain final decision authority.

Xiaochen Zheng, Alvaro Serra, Ilya Schneider Chernov et al.

Pharmaceutical research and development has accumulated vast and heterogeneous archives of data. Much of this knowledge stems from discontinued programs, and reusing these archives is invaluable for reverse translation. However, in practice, such reuse is often infeasible. In this work, we introduce DiscoVerse, a multi-agent co-scientist designed to support pharmaceutical research and development at Roche. Designed as a human-in-the-loop assistant, DiscoVerse enables domain-specific queries by delivering evidence-based answers: it retrieves relevant data, links across documents, summarises key findings and preserves institutional memory. We assess DiscoVerse through expert evaluation of source-linked outputs. Our evaluation spans a selected subset of 180 molecules from Roche's research and development repositories, encompassing over 0.87 billion BPE tokens and more than four decades of research. To our knowledge, this represents the first agentic framework to be systematically assessed on real pharmaceutical data for reverse translation, enabled by authorized access to confidential archives covering the full lifecycle of drug development. Our contributions include: role-specialized agent designs aligned with scientist workflows; human-in-the-loop support for reverse translation; expert evaluation; and a large-scale demonstration showing promising decision-making insights. In brief, across seven benchmark queries, DiscoVerse achieved near-perfect recall ($\geq 0.99$) with moderate precision ($0.71-0.91$). Qualitative assessments and three real-world pharmaceutical use cases further showed faithful, source-linked synthesis across preclinical and clinical evidence.

Yinghao Zhu, Xiaochen Zheng, Ahmed Allam et al.

We propose TAMER, a Test-time Adaptive MoE-driven framework for Electronic Health Record (EHR) Representation learning. TAMER introduces a framework where a Mixture-of-Experts (MoE) architecture is co-designed with Test-Time Adaptation (TTA) to jointly mitigate the intertwined challenges of patient heterogeneity and distribution shifts in EHR modeling. The MoE focuses on latent patient subgroups through domain-aware expert specialization, while TTA enables real-time adaptation to evolving health status distributions when new patient samples are introduced. Extensive experiments across four real-world EHR datasets demonstrate that TAMER consistently improves predictive performance for both mortality and readmission risk tasks when combined with diverse EHR modeling backbones. TAMER offers a promising approach for dynamic and personalized EHR-based predictions in practical clinical settings.

Xiaochen Zheng, Manuel Schürch, Xingyu Chen et al.

The identification of phenotypes within complex diseases or syndromes is a fundamental component of precision medicine, which aims to adapt healthcare to individual patient characteristics. Postoperative delirium (POD) is a complex neuropsychiatric condition with significant heterogeneity in its clinical manifestations and underlying pathophysiology. We hypothesize that POD comprises several distinct phenotypes, which cannot be directly observed in clinical practice. Identifying these phenotypes could enhance our understanding of POD pathogenesis and facilitate the development of targeted prevention and treatment strategies. In this paper, we propose an approach that combines supervised machine learning for personalized POD risk prediction with unsupervised clustering techniques to uncover potential POD phenotypes. We first demonstrate our approach using synthetic data, where we simulate patient cohorts with predefined phenotypes based on distinct sets of informative features. We aim to mimic any clinical disease with our synthetic data generation method. By training a predictive model and applying SHAP, we show that clustering patients in the SHAP feature importance space successfully recovers the true underlying phenotypes, outperforming clustering in the raw feature space. We then present a case study using real-world data from a cohort of elderly surgical patients. The results showcase the utility of our approach in uncovering clinically relevant subtypes of complex disorders like POD, paving the way for more precise and personalized treatment strategies.

Xiaochen Zheng, Benjamin Kellenberger, Rui Gong et al.

Automated animal censuses with aerial imagery are a vital ingredient towards wildlife conservation. Recent models are generally based on deep learning and thus require vast amounts of training data. Due to their scarcity and minuscule size, annotating animals in aerial imagery is a highly tedious process. In this project, we present a methodology to reduce the amount of required training data by resorting to self-supervised pretraining. In detail, we examine a combination of recent contrastive learning methodologies like Momentum Contrast (MoCo) and Cross-Level Instance-Group Discrimination (CLD) to condition our model on the aerial images without the requirement for labels. We show that a combination of MoCo, CLD, and geometric augmentations outperforms conventional models pre-trained on ImageNet by a large margin. Crucially, our method still yields favorable results even if we reduce the number of training animals to just 10%, at which point our best model scores double the recall of the baseline at similar precision. This effectively allows reducing the number of required annotations to a fraction while still being able to train high-accuracy models in such highly challenging settings.

Jože M. Rožanec, Jinzhi Lu, Jan Rupnik et al.

Actionable Cognitive Twins are the next generation Digital Twins enhanced with cognitive capabilities through a knowledge graph and artificial intelligence models that provide insights and decision-making options to the users. The knowledge graph describes the domain-specific knowledge regarding entities and interrelationships related to a manufacturing setting. It also contains information on possible decision-making options that can assist decision-makers, such as planners or logisticians. In this paper, we propose a knowledge graph modeling approach to construct actionable cognitive twins for capturing specific knowledge related to demand forecasting and production planning in a manufacturing plant. The knowledge graph provides semantic descriptions and contextualization of the production lines and processes, including data identification and simulation or artificial intelligence algorithms and forecasts used to support them. Such semantics provide ground for inferencing, relating different knowledge types: creative, deductive, definitional, and inductive. To develop the knowledge graph models for describing the use case completely, systems thinking approach is proposed to design and verify the ontology, develop a knowledge graph and build an actionable cognitive twin. Finally, we evaluate our approach in two use cases developed for a European original equipment manufacturer related to the automotive industry as part of the European Horizon 2020 project FACTLOG.

Lu Jinzhi, Ma Junda, Xiaochen Zheng et al.

Model-based systems engineering (MBSE) provides an important capability for managing the complexities of system development. MBSE empowers the formalisms of system architectures for supporting model-based requirement elicitation, specification, design, development, testing, fielding, etc. However, the modeling languages and techniques are quite heterogeneous, even within the same enterprise system, which creates difficulties for data interoperability. The discrepancies among data structures and language syntaxes make information exchange among MBSE models even more difficult, resulting in considerable information deviations when connecting data flows across the enterprise. For this reason, this paper presents an ontology based upon graphs, objects, points, properties, roles, and relationships with entensions (GOPPRRE), providing meta models that support the various lifecycle stages of MBSE formalisms. In particular, knowledge-graph models are developed to support unified model representations to further implement ontological data integration based on GOPPRRE throughout the entire lifecycle. The applicability of the MBSE formalism is verified using quantitative and qualitative approaches. Moreover, the GOPPRRE ontologies are generated from the MBSE language formalisms in a domain-specific modeling tool, \textit{MetaGraph} in order to evaluate its availiablity. The results demonstrate that the proposed ontology supports both formal structures and the descriptive logic of the systems engineering lifecycle.

Jinzhi Lu, Xiaochen Zheng, Zhenchao Hu et al.

Model-based Systems Engineering (MBSE) has been widely utilized to formalize system artifacts and facilitate their development throughout the entire lifecycle. During complex system development, MBSE models need to be frequently exchanged across stakeholders. Concerns about data security and tampering using traditional data exchange approaches obstruct the construction of a reliable marketplace for digital assets. The emerging Distributed Ledger Technology (DLT), represented by blockchain, provides a novel solution for this purpose owing to its unique advantages such as tamper-resistant and decentralization. In this paper, we integrate MBSE approaches with DLT aiming to create a decentralized marketplace to facilitate the exchange of digital engineering assets (DEAs). We first define DEAs from perspectives of digital engineering objects, development processes and system architectures. Based on this definition, the Graph-Object-Property-Point-Role-Relationship (GOPPRR) approach is used to formalize the DEAs. Then we propose a framework of a decentralized DEAs marketplace and specify the requirements, based on which we select a Directed Acyclic Graph (DAG) structured DLT solution. As a proof-of-concept, a prototype of the proposed DEAs marketplace is developed and a case study is conducted to verify its feasibility. The experiment results demonstrate that the proposed marketplace facilitates free DEAs exchange with a high level of security, efficiency and decentralization.