Jonathan Liu

Jonathan Liu, Haoling Qiu, Jonathan Lasko et al.

Recent research has shown that hallucinations, omissions, and biases are prevalent in everyday use-cases of LLMs. However, chatbots used in medical contexts must provide consistent advice in situations where non-medical factors are involved, such as when demographic information is present. In order to understand the conditions under which medical chatbots fail to perform as expected, we develop an infrastructure that 1) automatically generates queries to probe LLMs and 2) evaluates answers to these queries using multiple LLM-as-a-judge setups and prompts. For 1), our prompt creation pipeline samples the space of patient demographics, histories, disorders, and writing styles to create realistic questions that we subsequently use to prompt LLMs. In 2), our evaluation pipeline provides hallucination and omission detection using LLM-as-a-judge as well as agentic workflows, in addition to LLM-as-a-judge treatment category detectors. As a baseline study, we perform two case studies on inter-LLM agreement and the impact of varying the answering and evaluation LLMs. We find that LLM annotators exhibit low agreement scores (average Cohen's Kappa $κ=0.118$), and only specific (answering, evaluation) LLM pairs yield statistically significant differences across writing styles, genders, and races. We recommend that studies using LLM evaluation use multiple LLMs as evaluators in order to avoid arriving at statistically significant but non-generalizable results, particularly in the absence of ground-truth data. We also suggest publishing inter-LLM agreement metrics for transparency. Our code and dataset are available here: https://github.com/BBN-E/medic-neurips-2025-demo.

Jonathan Liu, Kia Ghods

We present a parameter-efficient Diffusion Transformer (DiT) for generating 200bp cell-type-specific regulatory DNA sequences. By replacing the U-Net backbone of DNA-Diffusion with a transformer denoiser equipped with a 2D CNN input encoder, our model matches the U-Net's best validation loss in 13 epochs (60$\times$ fewer) and converges 39% lower, while reducing memorization from 5.3% to 1.7% of generated sequences aligning to training data via BLAT. Ablations show the CNN encoder is essential: without it, validation loss increases 70% regardless of positional embedding choice. We further apply DDPO finetuning using Enformer as a reward model, achieving a 38$\times$ improvement in predicted regulatory activity. Cross-validation against DRAKES on an independent prediction task confirms that improvements reflect genuine regulatory signal rather than reward model overfitting.

Yifan Liu, Xishun Liao, Haoxuan Ma et al.

Understanding and modeling human mobility patterns is crucial for effective transportation planning and urban development. Despite significant advances in mobility research, there remains a critical gap in simulation platforms that allow for algorithm development, policy implementation, and comprehensive evaluation at scale. Traditional activity-based models require extensive data collection and manual calibration, machine learning approaches struggle with adaptation to dynamic conditions, and treding agent-based Large Language Models (LLMs) implementations face computational constraints with large-scale simulations. To address these challenges, we propose MobiVerse, a hybrid framework leverages the efficiency of lightweight domain-specific generator for generating base activity chains with the adaptability of LLMs for context-aware modifications. A case study was conducted in Westwood, Los Angeles, where we efficiently generated and dynamically adjusted schedules for the whole population of approximately 53,000 agents on a standard PC. Our experiments demonstrate that MobiVerse successfully enables agents to respond to environmental feedback, including road closures, large gathering events like football games, and congestion, through our hybrid framework. Its modular design facilitates testing various mobility algorithms at both transportation system and agent levels. Results show our approach maintains computational efficiency while enhancing behavioral realism. MobiVerse bridges the gap in mobility simulation by providing a customizable platform for mobility systems planning and operations with benchmark algorithms. Code and videos are available at https://github.com/ucla-mobility/MobiVerse.

Sindhuja Madabushi, Arda Dogan, Jonathan Liu et al.

Existing XAI metrics measure faithfulness for a single model, ignoring model multiplicity where near-optimal classifiers rely on different or spurious acoustic cues. In noisy farm environments, stationary artifacts such as ventilation noise can produce explanations that are faithful yet unreliable, as masking-based metrics fail to penalize redundant shortcuts. We propose AGRI-Fidelity, a reliability-oriented evaluation framework for listenable explanations in poultry disease detection without spatial ground truth. The method combines cross-model consensus with cyclic temporal permutation to construct null distributions and compute a False Discovery Rate (FDR), suppressing stationary artifacts while preserving time-localized bioacoustic markers. Across real and controlled datasets, AGRI-Fidelity effectively provides reliability-aware discrimination for all data points versus masking-based metrics.