Shiyu Jiang

Xuyin Qi, Zeyu Zhang, Aaron Berliano Handoko et al.

Prostate cancer, a growing global health concern, necessitates precise diagnostic tools, with Magnetic Resonance Imaging (MRI) offering high-resolution soft tissue imaging that significantly enhances diagnostic accuracy. Recent advancements in explainable AI and representation learning have significantly improved prostate cancer diagnosis by enabling automated and precise lesion classification. However, existing explainable AI methods, particularly those based on frameworks like generative adversarial networks (GANs), are predominantly developed for natural image generation, and their application to medical imaging often leads to suboptimal performance due to the unique characteristics and complexity of medical image. To address these challenges, our paper introduces three key contributions. First, we propose ProjectedEx, a generative framework that provides interpretable, multi-attribute explanations, effectively linking medical image features to classifier decisions. Second, we enhance the encoder module by incorporating feature pyramids, which enables multiscale feedback to refine the latent space and improves the quality of generated explanations. Additionally, we conduct comprehensive experiments on both the generator and classifier, demonstrating the clinical relevance and effectiveness of ProjectedEx in enhancing interpretability and supporting the adoption of AI in medical settings. Code will be released at https://github.com/Richardqiyi/ProjectedEx

Jianxiang Zang, Yongda Wei, Ruxue Bai et al.

Reliable reward models (RMs) are critical for ensuring the safe alignment of large language models (LLMs). However, current evaluation methods focus solely on preference perception accuracies in given specific scenarios, obscuring the critical vulnerabilities of RMs in real-world scenarios. We identify the true challenge lies in assessing a novel dimension: Suitability, defined as conditional reliability under specific real-world perturbations. To this end, we introduce Reward Auditor, a hypothesis-testing framework specifically designed for RM suitability inference. Rather than answering "How accurate is the RM's preference perception for given samples?", it employs scientific auditing to answer: "Can we infer RMs exhibit systematic vulnerabilities in specific real-world scenarios?". Under real-world perturbed scenarios, Reward Auditor quantifies statistical significance and effect size by auditing distribution degradation of RM preference perception confidence. This enables inference of both the certainty and severity of RM vulnerabilities across diverse real-world scenarios. This lays a solid foundation for building next-generation LLM alignment systems that are verifiably safe, more robust, and trustworthy.

Zirui Song, Guangxian Ouyang, Meng Fang et al.

Existing household robots have made significant progress in performing routine tasks, such as cleaning floors or delivering objects. However, a key limitation of these robots is their inability to recognize potential problems or dangers in home environments. For example, a child may pick up and ingest medication that has fallen on the floor, posing a serious risk. We argue that household robots should proactively detect such hazards or anomalies within the home, and propose the task of anomaly scenario generation. We leverage foundational models instead of relying on manually labeled data to build simulated environments. Specifically, we introduce a multi-agent brainstorming approach, where agents collaborate and generate diverse scenarios covering household hazards, hygiene management, and child safety. These textual task descriptions are then integrated with designed 3D assets to simulate realistic environments. Within these constructed environments, the robotic agent learns the necessary skills to proactively discover and handle the proposed anomalies through task decomposition, and optimal learning approach selection. We demonstrate that our generated environment outperforms others in terms of task description and scene diversity, ultimately enabling robotic agents to better address potential household hazards.

Xinzhe Zheng, Shiyu Jiang, Gustavo Seabra et al.

Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets. However, most current approaches assume a rigid protein binding pocket, neglecting the intrinsic flexibility of proteins and the conformational rearrangements induced by ligand binding, limiting their applicability in practical drug discovery. Here, we propose Apo2Mol, a diffusion-based generative framework for 3D molecule design that explicitly accounts for conformational flexibility in protein binding pockets. To support this, we curate a dataset of over 24,000 experimentally resolved apo-holo structure pairs from the Protein Data Bank, enabling the characterization of protein structure changes associated with ligand binding. Apo2Mol employs a full-atom hierarchical graph-based diffusion model that simultaneously generates 3D ligand molecules and their corresponding holo pocket conformations from input apo states. Empirical studies demonstrate that Apo2Mol can achieve state-of-the-art performance in generating high-affinity ligands and accurately capture realistic protein pocket conformational changes.

Shiyu Jiang, Xuyin Liu, Zitong Jerry Wang

Genomic language models (gLMs) hold promise for generating novel, functional DNA sequences for synthetic biology. However, realizing this potential requires models to go beyond evolutionary plausibility and understand how DNA sequence encodes gene expression and regulation. We introduce a benchmark called Nullsettes, which assesses how well models can predict in silico loss-of-function (LOF) mutations, in synthetic expression cassettes with little evolutionary precedent. Testing 12 state-of-the-art gLMs, we find that most fail to consistently detect these strong LOF mutations. All models show a sharp drop in predictive accuracy as the likelihood assigned to the original (nonmutant) sequence decreases, suggesting that gLMs rely heavily on pattern-matching to their evolutionary prior rather than on any mechanistic understanding of gene expression. Our findings highlight fundamental limitations in how gLMs generalize to engineered, non-natural sequences, and underscore the need for benchmarks and modeling strategies that prioritize functional understanding.