arXiv subjects

Hanwen Xu

Publications and source records attributed to Hanwen Xu.

28 records · Page 2Linked to original sources

arXiv2024

Panacea: A foundation model for clinical trial search, summarization, design, and recruitment

Clinical trials are fundamental in developing new drugs, medical devices, and treatments. However, they are often time-consuming and have low success rates. Although there have been initial attempts to create large language models (LLMs) for clinical trial design and patient-trial matching, these models remain task-specific and not adaptable to diverse clinical trial tasks. To address this challenge, we propose a clinical trial foundation model named Panacea, designed to handle multiple tasks, including trial search, trial summarization, trial design, and patient-trial matching. We also assemble a large-scale dataset, named TrialAlign, of 793,279 trial documents and 1,113,207 trial-related scientific papers, to infuse clinical knowledge into the model by pre-training. We further curate TrialInstruct, which has 200,866 of instruction data for fine-tuning. These resources enable Panacea to be widely applicable for a range of clinical trial tasks based on user requirements. We evaluated Panacea on a new benchmark, named TrialPanorama, which covers eight clinical trial tasks. Our method performed the best on seven of the eight tasks compared to six cutting-edge generic or medicine-specific LLMs. Specifically, Panacea showed great potential to collaborate with human experts in crafting the design of eligibility criteria, study arms, and outcome measures, in multi-round conversations. In addition, Panacea achieved 14.42% improvement in patient-trial matching, 41.78% to 52.02% improvement in trial search, and consistently ranked at the top for five aspects of trial summarization. Our approach demonstrates the effectiveness of Panacea in clinical trials and establishes a comprehensive resource, including training data, model, and benchmark, for developing clinical trial foundation models, paving the path for AI-based clinical trial development.

cs.CL↗

arXiv2024

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↗

arXiv2024

A multi-objective optimization framework for terrain modification based on a combined hydrological and earthwork cost-benefit

The escalating risk of urban inundation has drawn increased attention to urban stormwater management. This study proposes a multi-objective optimization for terrain modification, combining the Non-dominated Sorting Genetic Algorithm II (NSGA-II) with digital elevation model (DEM)-based hydrological cost factor analysis. To reduce the precipitation erosive forces and runoff kinetic energy, the resulting framework offers the possibility of efficiently searching numerous solutions for trade-off sets that meet three conflicting objectives: minimizing maximum flow velocity, maximizing runoff path length and minimizing earthwork costs. Our application case study in Høje Taastrup, Denmark, demonstrates the ability of the optimization framework to iteratively generate diversified modification scenarios, which form the reference for topography planning. The three individual objective preferred solutions, a balanced solution, and twenty solutions under regular ordering are selected and visualized to determine the limits of the optimization and the cost-effectiveness tendency. Integrating genetic algorithms with DEM-based hydrological analysis demonstrates the potential to consider more complicated hydrological benefit objectives with open-ended characteristics. It provides a novel and efficient way to optimize topographic characteristics for improving holistic stormwater management strategies.

cs.CE↗

arXiv2023

When an Image is Worth 1,024 x 1,024 Words: A Case Study in Computational Pathology

This technical report presents LongViT, a vision Transformer that can process gigapixel images in an end-to-end manner. Specifically, we split the gigapixel image into a sequence of millions of patches and project them linearly into embeddings. LongNet is then employed to model the extremely long sequence, generating representations that capture both short-range and long-range dependencies. The linear computation complexity of LongNet, along with its distributed algorithm, enables us to overcome the constraints of both computation and memory. We apply LongViT in the field of computational pathology, aiming for cancer diagnosis and prognosis within gigapixel whole-slide images. Experimental results demonstrate that LongViT effectively encodes gigapixel images and outperforms previous state-of-the-art methods on cancer subtyping and survival prediction. Code and models will be available at https://aka.ms/LongViT.

cs.CV↗

arXiv2023

GraphPrompt: Graph-Based Prompt Templates for Biomedical Synonym Prediction

In the expansion of biomedical dataset, the same category may be labeled with different terms, thus being tedious and onerous to curate these terms. Therefore, automatically mapping synonymous terms onto the ontologies is desirable, which we name as biomedical synonym prediction task. Unlike biomedical concept normalization (BCN), no clues from context can be used to enhance synonym prediction, making it essential to extract graph features from ontology. We introduce an expert-curated dataset OBO-syn encompassing 70 different types of concepts and 2 million curated concept-term pairs for evaluating synonym prediction methods. We find BCN methods perform weakly on this task for not making full use of graph information. Therefore, we propose GraphPrompt, a prompt-based learning approach that creates prompt templates according to the graphs. GraphPrompt obtained 37.2\% and 28.5\% improvement on zero-shot and few-shot settings respectively, indicating the effectiveness of these graph-based prompt templates. We envision that our method GraphPrompt and OBO-syn dataset can be broadly applied to graph-based NLP tasks, and serve as the basis for analyzing diverse and accumulating biomedical data. All the data and codes are avalible at: https://github.com/HanwenXuTHU/GraphPrompt

cs.CL↗

arXiv2023

Towards Large-scale Single-shot Millimeter-wave Imaging for Low-cost Security Inspection

Millimeter-wave (MMW) imaging is emerging as a promising technique for safe security inspection. It achieves a delicate balance between imaging resolution, penetrability and human safety, resulting in higher resolution compared to low-frequency microwave, stronger penetrability compared to visible light, and stronger safety compared to X ray. Despite of recent advance in the last decades, the high cost of requisite large-scale antenna array hinders widespread adoption of MMW imaging in practice. To tackle this challenge, we report a large-scale single-shot MMW imaging framework using sparse antenna array, achieving low-cost but high-fidelity security inspection under an interpretable learning scheme. We first collected extensive full-sampled MMW echoes to study the statistical ranking of each element in the large-scale array. These elements are then sampled based on the ranking, building the experimentally optimal sparse sampling strategy that reduces the cost of antenna array by up to one order of magnitude. Additionally, we derived an untrained interpretable learning scheme, which realizes robust and accurate image reconstruction from sparsely sampled echoes. Last, we developed a neural network for automatic object detection, and experimentally demonstrated successful detection of concealed centimeter-sized targets using 10% sparse array, whereas all the other contemporary approaches failed at the same sample sampling ratio. The performance of the reported technique presents higher than 50% superiority over the existing MMW imaging schemes on various metrics including precision, recall, and mAP50. With such strong detection ability and order-of-magnitude cost reduction, we anticipate that this technique provides a practical way for large-scale single-shot MMW imaging, and could advocate its further practical applications.

eess.IV↗

arXiv2023

Large-scale Global Low-rank Optimization for Computational Compressed Imaging

Computational reconstruction plays a vital role in computer vision and computational photography. Most of the conventional optimization and deep learning techniques explore local information for reconstruction. Recently, nonlocal low-rank (NLR) reconstruction has achieved remarkable success in improving accuracy and generalization. However, the computational cost has inhibited NLR from seeking global structural similarity, which consequentially keeps it trapped in the tradeoff between accuracy and efficiency and prevents it from high-dimensional large-scale tasks. To address this challenge, we report here the global low-rank (GLR) optimization technique, realizing highly-efficient large-scale reconstruction with global self-similarity. Inspired by the self-attention mechanism in deep learning, GLR extracts exemplar image patches by feature detection instead of conventional uniform selection. This directly produces key patches using structural features to avoid burdensome computational redundancy. Further, it performs patch matching across the entire image via neural-based convolution, which produces the global similarity heat map in parallel, rather than conventional sequential block-wise matching. As such, GLR improves patch grouping efficiency by more than one order of magnitude. We experimentally demonstrate GLR's effectiveness on temporal, frequency, and spectral dimensions, including different computational imaging modalities of compressive temporal imaging, magnetic resonance imaging, and multispectral filter array demosaicing. This work presents the superiority of inherent fusion of deep learning strategies and iterative optimization, and breaks the persistent dilemma of the tradeoff between accuracy and efficiency for various large-scale reconstruction tasks.

eess.IV↗

arXiv2022

MetaFill: Text Infilling for Meta-Path Generation on Heterogeneous Information Networks

Heterogeneous Information Network (HIN) is essential to study complicated networks containing multiple edge types and node types. Meta-path, a sequence of node types and edge types, is the core technique to embed HINs. Since manually curating meta-paths is time-consuming, there is a pressing need to develop automated meta-path generation approaches. Existing meta-path generation approaches cannot fully exploit the rich textual information in HINs, such as node names and edge type names. To address this problem, we propose MetaFill, a text-infilling-based approach for meta-path generation. The key idea of MetaFill is to formulate meta-path identification problem as a word sequence infilling problem, which can be advanced by Pretrained Language Models (PLMs). We observed the superior performance of MetaFill against existing meta-path generation methods and graph embedding methods that do not leverage meta-paths in both link prediction and node classification on two real-world HIN datasets. We further demonstrated how MetaFill can accurately classify edges in the zero-shot setting, where existing approaches cannot generate any meta-paths. MetaFill exploits PLMs to generate meta-paths for graph embedding, opening up new avenues for language model applications in graph analysis.

cs.CL↗

arXiv2022

ProTranslator: zero-shot protein function prediction using textual description

Accurately finding proteins and genes that have a certain function is the prerequisite for a broad range of biomedical applications. Despite the encouraging progress of existing computational approaches in protein function prediction, it remains challenging to annotate proteins to a novel function that is not collected in the Gene Ontology and does not have any annotated proteins. This limitation, a side effect from the widely-used multi-label classification problem setting of protein function prediction, hampers the progress of studying new pathways and biological processes, and further slows down research in various biomedical areas. Here, we tackle this problem by annotating proteins to a function only based on its textual description so that we do not need to know any associated proteins for this function. The key idea of our method ProTranslator is to redefine protein function prediction as a machine translation problem, which translates the description word sequence of a function to the amino acid sequence of a protein. We can then transfer annotations from functions that have similar textual description to annotate a novel function. We observed substantial improvement in annotating novel functions and sparsely annotated functions on CAFA3, SwissProt and GOA datasets. We further demonstrated how our method accurately predicted gene members for a given pathway in Reactome, KEGG and MSigDB only based on the pathway description. Finally, we showed how ProTranslator enabled us to generate the textual description instead of the function label for a set of proteins, providing a new scheme for protein function prediction. We envision ProTranslator will give rise to a protein function "search engine" that returns a list of proteins based on the free text queried by the user.

q-bio.QM↗

arXiv2021

S3: Side-Channel Attack on Stylus Pencil through Sensors

With smart devices being an essential part of our everyday lives, unsupervised access to the mobile sensors' data can result in a multitude of side-channel attacks. In this paper, we study potential data leaks from Apple Pencil (2nd generation) supported by the Apple iPad Pro, the latest stylus pen which attaches to the iPad body magnetically for charging. We observe that the Pencil's body affects the magnetic readings sensed by the iPad's magnetometer when a user is using the Pencil. Therefore, we ask: Can we infer what a user is writing on the iPad screen with the Apple Pencil, given access to only the iPad's motion sensors' data? To answer this question, we present Side-channel attack on Stylus pencil through Sensors (S3), a system that identifies what a user is writing from motion sensor readings. We first use the sharp fluctuations in the motion sensors' data to determine when a user is writing on the iPad. We then introduce a high-dimensional particle filter to track the location and orientation of the Pencil during usage. Lastly, to guide particles, we build the Pencil's magnetic map serving as a bridge between the measured magnetic data and the Pencil location and orientation. We evaluate S3 with 10 subjects and demonstrate that we correctly identify 93.9%, 96%, 97.9%, and 93.33% of the letters, numbers, shapes, and words by only having access to the motion sensors' data.

cs.CR↗