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Heli Qi

Heli Qi contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computation and LanguageMachine LearningArtificial Intelligenceeess.ASComputational Engineering, Finance, and ScienceSound

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Published work

6 published item(s)

preprint2026arXiv

Can LLM Agents Respond to Disasters? Benchmarking Heterogeneous Geospatial Reasoning in Emergency Operations

Operational disaster response goes beyond damage assessment, requiring responders to integrate multi-sensor signals, reason over road networks, populations and key facilities, plan evacuations, and produce actionable reports. However, prior work largely isolates remote-sensing perception or evaluates generic tool use, leaving the end-to-end workflows of emergency operations underexplored. In this paper, we introduce Disaster Operational Response Agent benchmark (DORA), the first agentic benchmark for end-to-end disaster response: 515 expert-authored tasks across 45 real-world disaster events spanning 10 types, paired with expert-verified, replayable gold trajectories totaling 3,500 tool-call steps. Tasks span five dimensions that cover the operational disaster-response pipeline: disaster perception, spatial relational analysis, rescue and evacuation planning, temporal evolution reasoning, and multi-modal report synthesis. Agents compose calls from a 108-tool MCP library over heterogeneous geospatial data: optical, SAR, and multi-spectral imagery across single-, bi-, and multi-temporal sequences (0.015-10m GSD), complemented by elevation and social vector layers. We comprehensively evaluate 13 frontier LLMs on our benchmark, revealing three persistent challenges: 1) disaster-domain grounding exposes unique failure modes (damage-semantic grounding, sensor-modality mismatch, and disaster-pipeline composition); 2) agents are doubly bottlenecked by tool selection and argument grounding, where gold tool-order hints improve accuracy by only 1.08-4.40%, and alternative scaffolds yield at most a 3.24% gain; 3) compositional fragility scales with trajectory length, the agent-to-gold gap widening from 7% to 56% on long pipelines. DORA establishes a rigorous testbed for operationally reliable disaster-response agents.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Proteo-R1: Reasoning Foundation Models for De Novo Protein Design

Deep learning in \emph{de novo} protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce \textbf{Proteo-R1}, a reasoning-guided protein design framework that explicitly decouples \emph{molecular understanding} from \emph{geometric generation}. Proteo-R1 adopts a dual-expert architecture in which a multimodal large language model (MLLM) serves as an \emph{understanding expert}, analyzing protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed as hard constraints to a separate diffusion-based \emph{generation expert}, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with state-of-the-art geometric generative models. Code, data, and demos are available at https://smiles724.github.io/r1/.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

The Confidence Dichotomy: Analyzing and Mitigating Miscalibration in Tool-Use Agents

Autonomous agents based on large language models (LLMs) are rapidly evolving to handle multi-turn tasks, but ensuring their trustworthiness remains a critical challenge. A fundamental pillar of this trustworthiness is calibration, which refers to an agent's ability to express confidence that reliably reflects its actual performance. While calibration is well-established for static models, its dynamics in tool-integrated agentic workflows remain underexplored. In this work, we systematically investigate verbalized calibration in tool-use agents, revealing a fundamental confidence dichotomy driven by tool type. Specifically, our pilot study identifies that evidence tools (e.g., web search) systematically induce severe overconfidence due to inherent noise in retrieved information, while verification tools (e.g., code interpreters) can ground reasoning through deterministic feedback and mitigate miscalibration. To robustly improve calibration across tool types, we propose a reinforcement learning (RL) fine-tuning framework that jointly optimizes task accuracy and calibration, supported by a holistic benchmark of reward designs. We demonstrate that our trained agents not only achieve superior calibration but also exhibit robust generalization from local training environments to noisy web settings and to distinct domains such as mathematical reasoning. Our results highlight the necessity of domain-specific calibration strategies for tool-use agents. More broadly, this work establishes a foundation for building self-aware agents that can reliably communicate uncertainty in high-stakes, real-world deployments.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Toward Global Large Language Models in Medicine

Despite continuous advances in medical technology, the global distribution of health care resources remains uneven. The development of large language models (LLMs) has transformed the landscape of medicine and holds promise for improving health care quality and expanding access to medical information globally. However, existing LLMs are primarily trained on high-resource languages, limiting their applicability in global medical scenarios. To address this gap, we constructed GlobMed, a large multilingual medical dataset, containing over 500,000 entries spanning 12 languages, including four low-resource languages. Building on this, we established GlobMed-Bench, which systematically assesses 56 state-of-the-art proprietary and open-weight LLMs across multiple multilingual medical tasks, revealing significant performance disparities across languages, particularly for low-resource languages. Additionally, we introduced GlobMed-LLMs, a suite of multilingual medical LLMs trained on GlobMed, with parameters ranging from 1.7B to 8B. GlobMed-LLMs achieved an average performance improvement of over 40% relative to baseline models, with a more than threefold increase in performance on low-resource languages. Together, these resources provide an important foundation for advancing the equitable development and application of LLMs globally, enabling broader language communities to benefit from technological advances.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

SpeeChain: A Speech Toolkit for Large-Scale Machine Speech Chain

This paper introduces SpeeChain, an open-source Pytorch-based toolkit designed to develop the machine speech chain for large-scale use. This first release focuses on the TTS-to-ASR chain, a core component of the machine speech chain, that refers to the TTS data augmentation by unspoken text for ASR. To build an efficient pipeline for the large-scale TTS-to-ASR chain, we implement easy-to-use multi-GPU batch-level model inference, multi-dataloader batch generation, and on-the-fly data selection techniques. In this paper, we first explain the overall procedure of the TTS-to-ASR chain and the difficulties of each step. Then, we present a detailed ablation study on different types of unlabeled data, data filtering thresholds, batch composition, and real-synthetic data ratios. Our experimental results on train_clean_460 of LibriSpeech demonstrate that our TTS-to-ASR chain can significantly improve WER in a semi-supervised setting.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Improved Consistency Training for Semi-Supervised Sequence-to-Sequence ASR via Speech Chain Reconstruction and Self-Transcribing

Consistency regularization has recently been applied to semi-supervised sequence-to-sequence (S2S) automatic speech recognition (ASR). This principle encourages an ASR model to output similar predictions for the same input speech with different perturbations. The existing paradigm of semi-supervised S2S ASR utilizes SpecAugment as data augmentation and requires a static teacher model to produce pseudo transcripts for untranscribed speech. However, this paradigm fails to take full advantage of consistency regularization. First, the masking operations of SpecAugment may damage the linguistic contents of the speech, thus influencing the quality of pseudo labels. Second, S2S ASR requires both input speech and prefix tokens to make the next prediction. The static prefix tokens made by the offline teacher model cannot match dynamic pseudo labels during consistency training. In this work, we propose an improved consistency training paradigm of semi-supervised S2S ASR. We utilize speech chain reconstruction as the weak augmentation to generate high-quality pseudo labels. Moreover, we demonstrate that dynamic pseudo transcripts produced by the student ASR model benefit the consistency training. Experiments on LJSpeech and LibriSpeech corpora show that compared to supervised baselines, our improved paradigm achieves a 12.2% CER improvement in the single-speaker setting and 38.6% in the multi-speaker setting.

0 citations0 reviewsNo code linkedOpen access