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Sheng Zhang

Publications and source records attributed to Sheng Zhang.

At least 145 records · Page 8Linked to original sources

MedFuzz: Exploring the Robustness of Large Language Models in Medical Question Answering

Large language models (LLM) have achieved impressive performance on medical question-answering benchmarks. However, high benchmark accuracy does not imply that the performance generalizes to real-world clinical settings. Medical question-answering benchmarks rely on assumptions consistent with quantifying LLM performance but that may not hold in the open world of the clinic. Yet LLMs learn broad knowledge that can help the LLM generalize to practical conditions regardless of unrealistic assumptions in celebrated benchmarks. We seek to quantify how well LLM medical question-answering benchmark performance generalizes when benchmark assumptions are violated. Specifically, we present an adversarial method that we call MedFuzz (for medical fuzzing). MedFuzz attempts to modify benchmark questions in ways aimed at confounding the LLM. We demonstrate the approach by targeting strong assumptions about patient characteristics presented in the MedQA benchmark. Successful "attacks" modify a benchmark item in ways that would be unlikely to fool a medical expert but nonetheless "trick" the LLM into changing from a correct to an incorrect answer. Further, we present a permutation test technique that can ensure a successful attack is statistically significant. We show how to use performance on a "MedFuzzed" benchmark, as well as individual successful attacks. The methods show promise at providing insights into the ability of an LLM to operate robustly in more realistic settings.

cs.CL↗

Probing Perfection: The Relentless Art of Meddling for Pulmonary Airway Segmentation from HRCT via a Human-AI Collaboration Based Active Learning Method

In pulmonary tracheal segmentation, the scarcity of annotated data is a prevalent issue in medical segmentation. Additionally, Deep Learning (DL) methods face challenges: the opacity of 'black box' models and the need for performance enhancement. Our Human-Computer Interaction (HCI) based models (RS_UNet, LC_UNet, UUNet, and WD_UNet) address these challenges by combining diverse query strategies with various DL models. We train four HCI models and repeat these steps: (1) Query Strategy: The HCI models select samples that provide the most additional representative information when labeled in each iteration and identify unlabeled samples with the greatest predictive disparity using Wasserstein Distance, Least Confidence, Entropy Sampling, and Random Sampling. (2) Central line correction: Selected samples are used for expert correction of system-generated tracheal central lines in each training round. (3) Update training dataset: Experts update the training dataset after each DL model's training epoch, enhancing the trustworthiness and performance of the models. (4) Model training: The HCI model is trained using the updated dataset and an enhanced UNet version. Experimental results confirm the effectiveness of these HCI-based approaches, showing that WD-UNet, LC-UNet, UUNet, and RS-UNet achieve comparable or superior performance to state-of-the-art DL models. Notably, WD-UNet achieves this with only 15%-35% of the training data, reducing physician annotation time by 65%-85%.

eess.IV↗

MuirBench: A Comprehensive Benchmark for Robust Multi-image Understanding

We introduce MuirBench, a comprehensive benchmark that focuses on robust multi-image understanding capabilities of multimodal LLMs. MuirBench consists of 12 diverse multi-image tasks (e.g., scene understanding, ordering) that involve 10 categories of multi-image relations (e.g., multiview, temporal relations). Comprising 11,264 images and 2,600 multiple-choice questions, MuirBench is created in a pairwise manner, where each standard instance is paired with an unanswerable variant that has minimal semantic differences, in order for a reliable assessment. Evaluated upon 20 recent multi-modal LLMs, our results reveal that even the best-performing models like GPT-4o and Gemini Pro find it challenging to solve MuirBench, achieving 68.0% and 49.3% in accuracy. Open-source multimodal LLMs trained on single images can hardly generalize to multi-image questions, hovering below 33.3% in accuracy. These results highlight the importance of MuirBench in encouraging the community to develop multimodal LLMs that can look beyond a single image, suggesting potential pathways for future improvements.

cs.CV↗

Fuzzy Attention-based Border Rendering Network for Lung Organ Segmentation

Automatic lung organ segmentation on CT images is crucial for lung disease diagnosis. However, the unlimited voxel values and class imbalance of lung organs can lead to false-negative/positive and leakage issues in advanced methods. Additionally, some slender lung organs are easily lost during the recycled down/up-sample procedure, e.g., bronchioles & arterioles, causing severe discontinuity issue. Inspired by these, this paper introduces an effective lung organ segmentation method called Fuzzy Attention-based Border Rendering (FABR) network. Since fuzzy logic can handle the uncertainty in feature extraction, hence the fusion of deep networks and fuzzy sets should be a viable solution for better performance. Meanwhile, unlike prior top-tier methods that operate on all regular dense points, our FABR depicts lung organ regions as cube-trees, focusing only on recycle-sampled border vulnerable points, rendering the severely discontinuous, false-negative/positive organ regions with a novel Global-Local Cube-tree Fusion (GLCF) module. All experimental results, on four challenging datasets of airway & artery, demonstrate that our method can achieve the favorable performance significantly.

eess.IV↗

Towards a clinically accessible radiology foundation model: open-access and lightweight, with automated evaluation

The scaling laws and extraordinary performance of large foundation models motivate the development and utilization of such models in biomedicine. However, despite early promising results on some biomedical benchmarks, there are still major challenges that need to be addressed before these models can be used in real-world clinics. Frontier general-domain models such as GPT-4V still have significant performance gaps in multimodal biomedical applications. More importantly, less-acknowledged pragmatic issues, including accessibility, model cost, and tedious manual evaluation make it hard for clinicians to use state-of-the-art large models directly on private patient data. Here, we explore training open-source small multimodal models (SMMs) to bridge competency gaps for unmet clinical needs in radiology. To maximize data efficiency, we adopt a modular approach by incorporating state-of-the-art pre-trained models for image and text modalities, and focusing on training a lightweight adapter to ground each modality to the text embedding space, as exemplified by LLaVA-Med. For training, we assemble a large dataset of over 697 thousand radiology image-text pairs. For evaluation, we propose CheXprompt, a GPT-4-based metric for factuality evaluation, and demonstrate its parity with expert evaluation. For best practice, we conduct a systematic ablation study on various choices in data engineering and multimodal training. The resulting LlaVA-Rad (7B) model attains state-of-the-art results on standard radiology tasks such as report generation and cross-modal retrieval, even outperforming much larger models such as GPT-4V and Med-PaLM M (84B). The inference of LlaVA-Rad is fast and can be performed on a single V100 GPU in private settings, offering a promising state-of-the-art tool for real-world clinical applications.

cs.CL↗

Enabling Large-Scale and High-Precision Fluid Simulations on Near-Term Quantum Computers

Quantum computational fluid dynamics (QCFD) offers a promising alternative to classical computational fluid dynamics (CFD) by leveraging quantum algorithms for higher efficiency. This paper introduces a comprehensive QCFD method, including an iterative method "Iterative-QLS" that suppresses error in quantum linear solver, and a subspace method to scale the solution to a larger size. We implement our method on a superconducting quantum computer, demonstrating successful simulations of steady Poiseuille flow and unsteady acoustic wave propagation. The Poiseuille flow simulation achieved a relative error of less than $0.2\%$, and the unsteady acoustic wave simulation solved a 5043-dimensional matrix. We emphasize the utilization of the quantum-classical hybrid approach in applications of near-term quantum computers. By adapting to quantum hardware constraints and offering scalable solutions for large-scale CFD problems, our method paves the way for practical applications of near-term quantum computers in computational science.

physics.comp-ph↗

Enabling Efficient Batch Serving for LMaaS via Generation Length Prediction

Nowadays, large language models (LLMs) are published as a service and can be accessed by various applications via APIs, also known as language-model-as-a-service (LMaaS). Without knowing the generation length of requests, existing serving systems serve requests in a first-come, first-served (FCFS) manner with a fixed batch size, which leads to two problems that affect batch serving efficiency. First, the generation lengths of requests in a batch vary, and requests with short generation lengths must wait for requests with long generation lengths to finish during the batch serving procedure. Second, requests with longer generation lengths consume more memory during serving. Without knowing the generation lengths of batched requests, the batch size is always set small to avoid the out-of-memory (OOM) error, thus preventing the GPU from being fully utilized. In this paper, we find that a significant number of popular applications in the LMaaS scenario have a positive correlation between the generation length and the length of raw user input. Based on this observation, we propose Magnus, which can accurately predict the request generation length with the user input length, application-level, and user-level semantic features. Accordingly, Magnus can achieve high request throughput by batching requests of similar generation lengths together with adaptive batch sizes. Besides, Magnus can also schedule batches with the highest response ratio next (HRRN) policy to reduce request response time. Experiments conducted on our testbed show that Magnus improves request throughput by up to 234\% and reduces response time by up to 89.7\% compared to baselines.

cs.DC↗

Kinetics of orbital ordering in cooperative Jahn-Teller models: Machine-learning enabled large-scale simulations

We present a scalable machine learning (ML) force-field model for the adiabatic dynamics of cooperative Jahn-Teller (JT) systems. Large scale dynamical simulations of the JT model also shed light on the orbital ordering dynamics in colossal magnetoresistance manganites. The JT effect in these materials describes the distortion of local oxygen octahedra driven by a coupling to the orbital degrees of freedom of $e_g$ electrons. An effective electron-mediated interaction between the local JT modes leads to a structural transition and the emergence of long-range orbital order at low temperatures. Assuming the principle of locality, a deep-learning neural-network model is developed to accurately and efficiently predict the electron-induced forces that drive the dynamical evolution of JT phonons. A group-theoretical method is utilized to develop a descriptor that incorporates the combined orbital and lattice symmetry into the ML model. Large-scale Langevin dynamics simulations, enabled by the ML force-field models, are performed to investigate the coarsening dynamics of the composite JT distortion and orbital order after a thermal quench. The late-stage coarsening of orbital domains exhibits pronounced freezing behaviors which are likely related to the unusual morphology of the domain structures. Our work highlights a promising avenue for multi-scale dynamical modeling of correlated electron systems.

cond-mat.str-el↗

Realization of a programmable multi-purpose photonic quantum memory with over-thousand qubit manipulations

Quantum networks can enable various applications such as distributed quantum computing, long-distance quantum communication, and network-based quantum sensing with unprecedented performances. One of the most important building blocks for a quantum network is a photonic quantum memory which serves as the interface between the communication channel and the local functional unit. A programmable quantum memory which can process a large stream of flying qubits and fulfill the requirements of multiple core functions in a quantum network is still to-be-realized. Here we report a high-performance quantum memory which can simultaneously store 72 optical qubits carried by 144 spatially separated atomic ensembles and support up to a thousand consecutive write or read operations in a random access way, two orders of magnitude larger than the previous record. Due to the built-in programmability, this quantum memory can be adapted on-demand for several functions. As example applications, we realize quantum queue, stack, and buffer which closely resemble the counterpart devices for classical information processing. We further demonstrate the synchronization and reshuffle of 4 entangled pairs of photonic pulses with probabilistic arrival time and arbitrary release order via the memory, which is an essential requirement for the realization of quantum repeaters and efficient routing in quantum networks. Realization of this multi-purpose programmable quantum memory thus constitutes a key enabling building block for future large-scale fully-functional quantum networks.

quant-ph↗

Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge

Airway-related quantitative imaging biomarkers are crucial for examination, diagnosis, and prognosis in pulmonary diseases. However, the manual delineation of airway trees remains prohibitively time-consuming. While significant efforts have been made towards enhancing airway modelling, current public-available datasets concentrate on lung diseases with moderate morphological variations. The intricate honeycombing patterns present in the lung tissues of fibrotic lung disease patients exacerbate the challenges, often leading to various prediction errors. To address this issue, the 'Airway-Informed Quantitative CT Imaging Biomarker for Fibrotic Lung Disease 2023' (AIIB23) competition was organized in conjunction with the official 2023 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). The airway structures were meticulously annotated by three experienced radiologists. Competitors were encouraged to develop automatic airway segmentation models with high robustness and generalization abilities, followed by exploring the most correlated QIB of mortality prediction. A training set of 120 high-resolution computerised tomography (HRCT) scans were publicly released with expert annotations and mortality status. The online validation set incorporated 52 HRCT scans from patients with fibrotic lung disease and the offline test set included 140 cases from fibrosis and COVID-19 patients. The results have shown that the capacity of extracting airway trees from patients with fibrotic lung disease could be enhanced by introducing voxel-wise weighted general union loss and continuity loss. In addition to the competitive image biomarkers for prognosis, a strong airway-derived biomarker (Hazard ratio>1.5, p<0.0001) was revealed for survival prognostication compared with existing clinical measurements, clinician assessment and AI-based biomarkers.

eess.IV↗

Fast delivery of heralded atom-photon quantum correlation over 12km fiber through multiplexing enhancement

Distributing quantum entanglement between distant parties is a significant but difficult task in quantum information science, as it can enable numerous applications but suffers from exponential decay in the quantum channel. Quantum repeater is one of the most promising approaches towards this goal. In a quantum repeater protocol, it is essential that the entanglement generation speed within each elementary link is faster than the memory decoherence rate, to enable the scale-up of the quantum repeater by connecting neighboring repeater segments. This stringent requirement has not been implemented over a fiber of metropolitan scale so far. As a step towards this challenging goal, in this work we experimentally realize multiplexing-enhanced generation of heralded atom-photon quantum correlation over a 12km fiber. We excite the memory modes in a multiplexed quantum memory successively to generate 280 pairs of atom-photon quantum correlations with a train of photonic time-bin pulses filling the long fiber. After successful detection of a heralding signal, the excited memory mode can be identified and retrieved into idler photons on demand with either fixed or variable storage time. With the multiplexing enhancement, the heralding rate of atom-photon correlation can reach 1.95kHz, and the ratio between the quantum correlation generation rate to memory decoherence rate can be improved to 0.46 for a fiber length of 12km, which is so far the best for long fiber length (>10km) to our knowledge. This work therefore constitutes an important step towards the realization of a large-scale quantum repeater network.

quant-ph↗

Coarsening of chiral domains in itinerant electron magnets: A machine learning force field approach

Frustrated itinerant magnets often exhibit complex noncollinear or noncoplanar magnetic orders which support topological electronic structures. A canonical example is the anomalous quantum Hall state with a chiral spin order stabilized by electron-spin interactions on a triangular lattice. While a long-range magnetic order cannot survive thermal fluctuations in two dimensions, the chiral order which results from the breaking of a discrete Ising symmetry persists even at finite temperatures. We present a scalable machine learning (ML) framework to model the complex electron-mediated spin-spin interactions that stabilize the chiral magnetic domains in a triangular lattice. Large-scale dynamical simulations, enabled by the ML force-field models, are performed to investigate the coarsening of chiral domains after a thermal quench. While the chiral phase is described by a broken $Z_2$ Ising-type symmetry, we find that the characteristic size of chiral domains increases linearly with time, in stark contrast to the expected Allen-Cahn domain growth law for a non-conserved Ising order parameter field. The linear growth of the chiral domains is attributed to the orientational anisotropy of domain boundaries. Our work also demonstrates the promising potential of ML models for large-scale spin dynamics of itinerant magnets.

cond-mat.str-el↗

Code Search Debiasing:Improve Search Results beyond Overall Ranking Performance

Code search engine is an essential tool in software development. Many code search methods have sprung up, focusing on the overall ranking performance of code search. In this paper, we study code search from another perspective by analyzing the bias of code search models. Biased code search engines provide poor user experience, even though they show promising overall performance. Due to different development conventions (e.g., prefer long queries or abbreviations), some programmers will find the engine useful, while others may find it hard to get desirable search results. To mitigate biases, we develop a general debiasing framework that employs reranking to calibrate search results. It can be easily plugged into existing engines and handle new code search biases discovered in the future. Experiments show that our framework can effectively reduce biases. Meanwhile, the overall ranking performance of code search gets improved after debiasing.

cs.CL↗

Make it more specific: A novel uncertainty based airway segmentation application on 3D U-Net and its variants

Each medical segmentation task should be considered with a specific AI algorithm based on its scenario so that the most accurate prediction model can be obtained. The most popular algorithms in medical segmentation, 3D U-Net and its variants, can directly implement the task of lung trachea segmentation, but its failure to consider the special tree-like structure of the trachea suggests that there is much room for improvement in its segmentation accuracy. Therefore, a research gap exists because a great amount of state-of-the-art DL algorithms are vanilla 3D U-Net structures, which do not introduce the various performance-enhancing modules that come with special natural image modality in lung airway segmentation. In this paper, we proposed two different network structures Branch-Level U-Net (B-UNet) and Branch-Level CE-UNet (B-CE-UNet) which are based on U-Net structure and compared the prediction results with the same dataset. Specially, both of the two networks add branch loss and central line loss to learn the feature of fine branch endings of the airways. Uncertainty estimation algorithms are also included to attain confident predictions and thereby, increase the overall trustworthiness of our whole model. In addition, predictions of the lung trachea based on the maximum connectivity rate were calculated and extracted during post-processing for segmentation refinement and pruning.

cs.CV↗

T-Rex: Text-assisted Retrosynthesis Prediction

As a fundamental task in computational chemistry, retrosynthesis prediction aims to identify a set of reactants to synthesize a target molecule. Existing template-free approaches only consider the graph structures of the target molecule, which often cannot generalize well to rare reaction types and large molecules. Here, we propose T-Rex, a text-assisted retrosynthesis prediction approach that exploits pre-trained text language models, such as ChatGPT, to assist the generation of reactants. T-Rex first exploits ChatGPT to generate a description for the target molecule and rank candidate reaction centers based both the description and the molecular graph. It then re-ranks these candidates by querying the descriptions for each reactants and examines which group of reactants can best synthesize the target molecule. We observed that T-Rex substantially outperformed graph-based state-of-the-art approaches on two datasets, indicating the effectiveness of considering text information. We further found that T-Rex outperformed the variant that only use ChatGPT-based description without the re-ranking step, demonstrate how our framework outperformed a straightforward integration of ChatGPT and graph information. Collectively, we show that text generated by pre-trained language models can substantially improve retrosynthesis prediction, opening up new avenues for exploiting ChatGPT to advance computational chemistry. And the codes can be found at https://github.com/lauyikfung/T-Rex.

cs.CL↗

Dephasing of Strong-Field-Driven Floquet States Revealed by Time- and Spectrum-Resolved Quantum-Path Interferometry

Floquet engineering, while a powerful tool for ultrafast quantum-state manipulation, faces challenges under strong-field conditions, as recent high harmonic generation studies unveil exceptionally short dephasing times. In this study, using time- and spectrum-resolved quantum-path interferometry, we investigate the dephasing mechanisms of terahertz-driven excitons. Our results reveal a dramatic increase in exciton dephasing rate beyond a threshold field strength, indicating exciton dissociation as the primary dephasing mechanism. Importantly, we demonstrate long dephasing times of strong-field-dressed excitons, supporting coherent strong-field manipulation of quantum materials.

physics.optics↗

UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition

Large language models (LLMs) have demonstrated remarkable generalizability, such as understanding arbitrary entities and relations. Instruction tuning has proven effective for distilling LLMs into more cost-efficient models such as Alpaca and Vicuna. Yet such student models still trail the original LLMs by large margins in downstream applications. In this paper, we explore targeted distillation with mission-focused instruction tuning to train student models that can excel in a broad application class such as open information extraction. Using named entity recognition (NER) for case study, we show how ChatGPT can be distilled into much smaller UniversalNER models for open NER. For evaluation, we assemble the largest NER benchmark to date, comprising 43 datasets across 9 diverse domains such as biomedicine, programming, social media, law, finance. Without using any direct supervision, UniversalNER attains remarkable NER accuracy across tens of thousands of entity types, outperforming general instruction-tuned models such as Alpaca and Vicuna by over 30 absolute F1 points in average. With a tiny fraction of parameters, UniversalNER not only acquires ChatGPT's capability in recognizing arbitrary entity types, but also outperforms its NER accuracy by 7-9 absolute F1 points in average. Remarkably, UniversalNER even outperforms by a large margin state-of-the-art multi-task instruction-tuned systems such as InstructUIE, which uses supervised NER examples. We also conduct thorough ablation studies to assess the impact of various components in our distillation approach. We release the distillation recipe, data, and UniversalNER models to facilitate future research on targeted distillation.

cs.CL↗

SpineCLUE: Automatic Vertebrae Identification Using Contrastive Learning and Uncertainty Estimation

Vertebrae identification in arbitrary fields-of-view plays a crucial role in diagnosing spine disease. Most spine CT contain only local regions, such as the neck, chest, and abdomen. Therefore, identification should not depend on specific vertebrae or a particular number of vertebrae being visible. Existing methods at the spine-level are unable to meet this challenge. In this paper, we propose a three-stage method to address the challenges in 3D CT vertebrae identification at vertebrae-level. By sequentially performing the tasks of vertebrae localization, segmentation, and identification, the anatomical prior information of the vertebrae is effectively utilized throughout the process. Specifically, we introduce a dual-factor density clustering algorithm to acquire localization information for individual vertebra, thereby facilitating subsequent segmentation and identification processes. In addition, to tackle the issue of interclass similarity and intra-class variability, we pre-train our identification network by using a supervised contrastive learning method. To further optimize the identification results, we estimated the uncertainty of the classification network and utilized the message fusion module to combine the uncertainty scores, while aggregating global information about the spine. Our method achieves state-of-the-art results on the VerSe19 and VerSe20 challenge benchmarks. Additionally, our approach demonstrates outstanding generalization performance on an collected dataset containing a wide range of abnormal cases.

cs.CV↗