arXiv subjects

Han Liu

Publications and source records attributed to Han Liu.

At least 235 records · Page 13Linked to original sources

arXiv2023

Learning Multiple Coordinated Agents under Directed Acyclic Graph Constraints

This paper proposes a novel multi-agent reinforcement learning (MARL) method to learn multiple coordinated agents under directed acyclic graph (DAG) constraints. Unlike existing MARL approaches, our method explicitly exploits the DAG structure between agents to achieve more effective learning performance. Theoretically, we propose a novel surrogate value function based on a MARL model with synthetic rewards (MARLM-SR) and prove that it serves as a lower bound of the optimal value function. Computationally, we propose a practical training algorithm that exploits new notion of leader agent and reward generator and distributor agent to guide the decomposed follower agents to better explore the parameter space in environments with DAG constraints. Empirically, we exploit four DAG environments including a real-world scheduling for one of Intel's high volume packaging and test factory to benchmark our methods and show it outperforms the other non-DAG approaches.

cs.LG↗

arXiv2023

Aligning Offline Metrics and Human Judgments of Value for Code Generation Models

Large language models have demonstrated great potential to assist programmers in generating code. For such human-AI pair programming scenarios, we empirically demonstrate that while generated code is most often evaluated in terms of their functional correctness (i.e., whether generations pass available unit tests), correctness does not fully capture (e.g., may underestimate) the productivity gains these models may provide. Through a user study with N = 49 experienced programmers, we show that while correctness captures high-value generations, programmers still rate code that fails unit tests as valuable if it reduces the overall effort needed to complete a coding task. Finally, we propose a hybrid metric that combines functional correctness and syntactic similarity and show that it achieves a 14% stronger correlation with value and can therefore better represent real-world gains when evaluating and comparing models.

cs.SE↗

arXiv2023

Feature Programming for Multivariate Time Series Prediction

We introduce the concept of programmable feature engineering for time series modeling and propose a feature programming framework. This framework generates large amounts of predictive features for noisy multivariate time series while allowing users to incorporate their inductive bias with minimal effort. The key motivation of our framework is to view any multivariate time series as a cumulative sum of fine-grained trajectory increments, with each increment governed by a novel spin-gas dynamical Ising model. This fine-grained perspective motivates the development of a parsimonious set of operators that summarize multivariate time series in an abstract fashion, serving as the foundation for large-scale automated feature engineering. Numerically, we validate the efficacy of our method on several synthetic and real-world noisy time series datasets.

cs.LG↗

arXiv2023

A Comprehensive Study on Quality Assurance Tools for Java

Quality assurance (QA) tools are receiving more and more attention and are widely used by developers. Given the wide range of solutions for QA technology, it is still a question of evaluating QA tools. Most existing research is limited in the following ways: (i) They compare tools without considering scanning rules analysis. (ii) They disagree on the effectiveness of tools due to the study methodology and benchmark dataset. (iii) They do not separately analyze the role of the warnings. (iv) There is no large-scale study on the analysis of time performance. To address these problems, in the paper, we systematically select 6 free or open-source tools for a comprehensive study from a list of 148 existing Java QA tools. To carry out a comprehensive study and evaluate tools in multi-level dimensions, we first mapped the scanning rules to the CWE and analyze the coverage and granularity of the scanning rules. Then we conducted an experiment on 5 benchmarks, including 1,425 bugs, to investigate the effectiveness of these tools. Furthermore, we took substantial effort to investigate the effectiveness of warnings by comparing the real labeled bugs with the warnings and investigating their role in bug detection. Finally, we assessed these tools' time performance on 1,049 projects. The useful findings based on our comprehensive study can help developers improve their tools and provide users with suggestions for selecting QA tools.

cs.SE↗

arXiv2023

Crystal Structure and Phonon Density of States of FeSi up to 120 GPa

The strongly correlated material FeSi exhibits several unusual thermal, magnetic, and structural properties under varying pressure-temperature (P-T) conditions. It is a potential thermoelectric alloy and a materials of several geological implications as a possible constituent at the Earth's core mantle boundary (CMB). The phase transition behavior and lattice dynamics of FeSi under different P-T conditions remain elusive. A previous theoretical work predicted a pressure induced B20-B2 transition at ambient temperature, yet the transition is only observed at high P-T conditions in the experiments. Furthermore, the closing of the electronic gap due to a dramatic renormalization of the electronic structure and phonon anomalies has been reported based on density function calculations. In this study we have performed high pressure powder diffraction and Nuclear Resonant Inelastic X-ray Scattering (NRIXS) measurements up to 120 GPa to understand the phase stability and the lattice dynamics. Our study shows evidence for a nonhydrostatic stress induced B20-B2 transition in FeSi around 36 GPa for the first time. The Fe partial phonon density of states (PDOS) and thermal parameters were derived from NRIXS up to 120 GPa with the density function theoretical (DFT) calculations. These calculations further predict and are consistent with pressure-induced metallization and band gap closing around 12 GPa.

cond-mat.mtrl-sci↗

arXiv2023

KGML-xDTD: A Knowledge Graph-based Machine Learning Framework for Drug Treatment Prediction and Mechanism Description

Background: Computational drug repurposing is a cost- and time-efficient approach that aims to identify new therapeutic targets or diseases (indications) of existing drugs/compounds. It is especially critical for emerging and/or orphan diseases due to its cheaper investment and shorter research cycle compared with traditional wet-lab drug discovery approaches. However, the underlying mechanisms of action (MOAs) between repurposed drugs and their target diseases remain largely unknown, which is still a main obstacle for computational drug repurposing methods to be widely adopted in clinical settings. Results: In this work, we propose KGML-xDTD: a Knowledge Graph-based Machine Learning framework for explainably predicting Drugs Treating Diseases. It is a two-module framework that not only predicts the treatment probabilities between drugs/compounds and diseases but also biologically explains them via knowledge graph (KG) path-based, testable mechanisms of action (MOAs). We leverage knowledge-and-publication based information to extract biologically meaningful "demonstration paths" as the intermediate guidance in the Graph-based Reinforcement Learning (GRL) path-finding process. Comprehensive experiments and case study analyses show that the proposed framework can achieve state-of-the-art performance in both predictions of drug repurposing and recapitulation of human-curated drug MOA paths. Conclusions: KGML-xDTD is the first model framework that can offer KG-path explanations for drug repurposing predictions by leveraging the combination of prediction outcomes and existing biological knowledge and publications. We believe it can effectively reduce "black-box" concerns and increase prediction confidence for drug repurposing based on predicted path-based explanations, and further accelerate the process of drug discovery for emerging diseases.

q-bio.QM↗

arXiv2023

Boosting Few-Shot Text Classification via Distribution Estimation

Distribution estimation has been demonstrated as one of the most effective approaches in dealing with few-shot image classification, as the low-level patterns and underlying representations can be easily transferred across different tasks in computer vision domain. However, directly applying this approach to few-shot text classification is challenging, since leveraging the statistics of known classes with sufficient samples to calibrate the distributions of novel classes may cause negative effects due to serious category difference in text domain. To alleviate this issue, we propose two simple yet effective strategies to estimate the distributions of the novel classes by utilizing unlabeled query samples, thus avoiding the potential negative transfer issue. Specifically, we first assume a class or sample follows the Gaussian distribution, and use the original support set and the nearest few query samples to estimate the corresponding mean and covariance. Then, we augment the labeled samples by sampling from the estimated distribution, which can provide sufficient supervision for training the classification model. Extensive experiments on eight few-shot text classification datasets show that the proposed method outperforms state-of-the-art baselines significantly.

cs.CL↗

arXiv2023

SSL^2: Self-Supervised Learning meets Semi-Supervised Learning: Multiple Sclerosis Segmentation in 7T-MRI from large-scale 3T-MRI

Automated segmentation of multiple sclerosis (MS) lesions from MRI scans is important to quantify disease progression. In recent years, convolutional neural networks (CNNs) have shown top performance for this task when a large amount of labeled data is available. However, the accuracy of CNNs suffers when dealing with few and/or sparsely labeled datasets. A potential solution is to leverage the information available in large public datasets in conjunction with a target dataset which only has limited labeled data. In this paper, we propose a training framework, SSL2 (self-supervised-semi-supervised), for multi-modality MS lesion segmentation with limited supervision. We adopt self-supervised learning to leverage the knowledge from large public 3T datasets to tackle the limitations of a small 7T target dataset. To leverage the information from unlabeled 7T data, we also evaluate state-of-the-art semi-supervised methods for other limited annotation settings, such as small labeled training size and sparse annotations. We use the shifted-window (Swin) transformer1 as our backbone network. The effectiveness of self-supervised and semi-supervised training strategies is evaluated in our in-house 7T MRI dataset. The results indicate that each strategy improves lesion segmentation for both limited training data size and for sparse labeling scenarios. The combined overall framework further improves the performance substantially compared to either of its components alone. Our proposed framework thus provides a promising solution for future data/label-hungry 7T MS studies.

cs.CV↗

arXiv2023

Learning Human-Compatible Representations for Case-Based Decision Support

Algorithmic case-based decision support provides examples to help human make sense of predicted labels and aid human in decision-making tasks. Despite the promising performance of supervised learning, representations learned by supervised models may not align well with human intuitions: what models consider as similar examples can be perceived as distinct by humans. As a result, they have limited effectiveness in case-based decision support. In this work, we incorporate ideas from metric learning with supervised learning to examine the importance of alignment for effective decision support. In addition to instance-level labels, we use human-provided triplet judgments to learn human-compatible decision-focused representations. Using both synthetic data and human subject experiments in multiple classification tasks, we demonstrate that such representation is better aligned with human perception than representation solely optimized for classification. Human-compatible representations identify nearest neighbors that are perceived as more similar by humans and allow humans to make more accurate predictions, leading to substantial improvements in human decision accuracies (17.8% in butterfly vs. moth classification and 13.2% in pneumonia classification).

cs.LG↗

arXiv2023

Cloak: Transitioning States on Legacy Blockchains Using Secure and Publicly Verifiable Off-Chain Multi-Party Computation

In recent years, the confidentiality of smart contracts has become a fundamental requirement for practical applications. While many efforts have been made to develop architectural capabilities for enforcing confidential smart contracts, a few works arise to extend confidential smart contracts to Multi-Party Computation (MPC), i.e., multiple parties jointly evaluate a transaction off-chain and commit the outputs on-chain without revealing their secret inputs/outputs to each other. However, existing solutions lack public verifiability and require O(n) transactions to enable negotiation or resist adversaries, thus suffering from inefficiency and compromised security. In this paper, we propose Cloak, a framework for enabling Multi-Party Transaction (MPT) on existing blockchains. An MPT refers to transitioning blockchain states by an publicly verifiable off-chain MPC. We identify and handle the challenges of securing MPT by harmonizing TEE and blockchain. Consequently, Cloak secures the off-chain nondeterministic negotiation process (a party joins an MPT without knowing identities or the total number of parties until the MPT proposal settles), achieves public verifiability (the public can validate that the MPT correctly handles the secret inputs/outputs from multiple parties and reads/writes states on-chain), and resists Byzantine adversaries. According to our proof, Cloak achieves better security with only 2 transactions, superior to previous works that achieve compromised security at O(n) transactions cost. By evaluating examples and real-world MPTs, the gas cost of Cloak reduces by 32.4% on average.

cs.CR↗

arXiv2023

Real-Time Image Demoireing on Mobile Devices

Moire patterns appear frequently when taking photos of digital screens, drastically degrading the image quality. Despite the advance of CNNs in image demoireing, existing networks are with heavy design, causing redundant computation burden for mobile devices. In this paper, we launch the first study on accelerating demoireing networks and propose a dynamic demoireing acceleration method (DDA) towards a real-time deployment on mobile devices. Our stimulus stems from a simple-yet-universal fact that moire patterns often unbalancedly distribute across an image. Consequently, excessive computation is wasted upon non-moire areas. Therefore, we reallocate computation costs in proportion to the complexity of image patches. In order to achieve this aim, we measure the complexity of an image patch by designing a novel moire prior that considers both colorfulness and frequency information of moire patterns. Then, we restore image patches with higher-complexity using larger networks and the ones with lower-complexity are assigned with smaller networks to relieve the computation burden. At last, we train all networks in a parameter-shared supernet paradigm to avoid additional parameter burden. Extensive experiments on several benchmarks demonstrate the efficacy of our proposed DDA. In addition, the acceleration evaluated on the VIVO X80 Pro smartphone equipped with a chip of Snapdragon 8 Gen 1 shows that our method can drastically reduce the inference time, leading to a real-time image demoireing on mobile devices. Source codes and models are released at https://github.com/zyxxmu/DDA

cs.CV↗

arXiv2023

HS-GCN: Hamming Spatial Graph Convolutional Networks for Recommendation

An efficient solution to the large-scale recommender system is to represent users and items as binary hash codes in the Hamming space. Towards this end, existing methods tend to code users by modeling their Hamming similarities with the items they historically interact with, which are termed as the first-order similarities in this work. Despite their efficiency, these methods suffer from the suboptimal representative capacity, since they forgo the correlation established by connecting multiple first-order similarities, i.e., the relation among the indirect instances, which could be defined as the high-order similarity. To tackle this drawback, we propose to model both the first- and the high-order similarities in the Hamming space through the user-item bipartite graph. Therefore, we develop a novel learning to hash framework, namely Hamming Spatial Graph Convolutional Networks (HS-GCN), which explicitly models the Hamming similarity and embeds it into the codes of users and items. Extensive experiments on three public benchmark datasets demonstrate that our proposed model significantly outperforms several state-of-the-art hashing models, and obtains performance comparable with the real-valued recommendation models.

cs.IR↗

arXiv2022

CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwannoma and Cochlea Segmentation

Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice - VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice - VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.

eess.IV↗

arXiv2022

Interdisciplinary Discovery of Nanomaterials Based on Convolutional Neural Networks

The material science literature contains up-to-date and comprehensive scientific knowledge of materials. However, their content is unstructured and diverse, resulting in a significant gap in providing sufficient information for material design and synthesis. To this end, we used natural language processing (NLP) and computer vision (CV) techniques based on convolutional neural networks (CNN) to discover valuable experimental-based information about nanomaterials and synthesis methods in energy-material-related publications. Our first system, TextMaster, extracts opinions from texts and classifies them into challenges and opportunities, achieving 94% and 92% accuracy, respectively. Our second system, GraphMaster, realizes data extraction of tables and figures from publications with 98.3\% classification accuracy and 4.3% data extraction mean square error. Our results show that these systems could assess the suitability of materials for a certain application by evaluation of synthesis insights and case analysis with detailed references. This work offers a fresh perspective on mining knowledge from scientific literature, providing a wide swatch to accelerate nanomaterial research through CNN.

cond-mat.mtrl-sci↗

arXiv2022

Drug repositioning for Alzheimer's disease with transfer learning

Deep Learning and DRUG-seq (Digital RNA with perturbation of genes) have attracted attention in drug discovery. However, the public DRUG-seq dataset is too small to be used for directly training a deep learning neural network from scratch. Inspired by the transfer learning technique, we pretrain a drug efficacy prediction neural network model with the Library of Integrated Network-based Cell-Signature (LINCS) L1000 data and then use human neural cell DRUG-seq data to fine-tune it. After training, the model is used for virtual screening to find potential drugs for Alzheimer's disease (AD) treatment. Finally, we find 27 potential drugs for AD treatment including Irsogladine (PDE4 inhibitor), Tasquinimod (HDAC4 selective inhibitor), Suprofen (dual COX-1/COX-2 inhibitor) et al.

q-bio.QM↗

arXiv2022

Enhancing Data Diversity for Self-training Based Unsupervised Cross-modality Vestibular Schwannoma and Cochlea Segmentation

Automatic segmentation of vestibular schwannoma (VS) and cochlea from magnetic resonance imaging can facilitate VS treatment planning. Unsupervised segmentation methods have shown promising results without requiring the time-consuming and laborious manual labeling process. In this paper, we present an approach for VS and cochlea segmentation in an unsupervised domain adaptation setting. Specifically, we first develop a cross-site cross-modality unpaired image translation strategy to enrich the diversity of the synthesized data. Then, we devise a rule-based offline augmentation technique to further minimize the domain gap. Lastly, we adopt a self-configuring segmentation framework empowered by self-training to obtain the final results. On the CrossMoDA 2022 validation leaderboard, our method has achieved competitive VS and cochlea segmentation performance with mean Dice scores of 0.8178 $\pm$ 0.0803 and 0.8433 $\pm$ 0.0293, respectively.

cs.CV↗

arXiv2022

Evaluation of Synthetically Generated CT for use in Transcranial Focused Ultrasound Procedures

Transcranial focused ultrasound (tFUS) is a therapeutic ultrasound method that focuses sound through the skull to a small region noninvasively and often under MRI guidance. CT imaging is used to estimate the acoustic properties that vary between individual skulls to enable effective focusing during tFUS procedures, exposing patients to potentially harmful radiation. A method to estimate acoustic parameters in the skull without the need for CT would be desirable. Here, we synthesized CT images from routinely acquired T1-weighted MRI by using a 3D patch-based conditional generative adversarial network (cGAN) and evaluated the performance of synthesized CT (sCT) images for treatment planning with tFUS. We compared the performance of sCT to real CT (rCT) images for tFUS planning using Kranion and simulations using the acoustic toolbox, k-Wave. Simulations were performed for 3 tFUS scenarios: 1) no aberration correction, 2) correction with phases calculated from Kranion, and 3) phase shifts calculated from time-reversal. From Kranion, skull density ratio, skull thickness, and number of active elements between rCT and sCT had Pearson's Correlation Coefficients of 0.94, 0.92, and 0.98, respectively. Among 20 targets, differences in simulated peak pressure between rCT and sCT were largest without phase correction (12.4$\pm$8.1%) and smallest with Kranion phases (7.3$\pm$6.0%). The distance between peak focal locations between rCT and sCT was less than 1.3 mm for all simulation cases. Real and synthetically generated skulls had comparable image similarity, skull measurements, and acoustic simulation metrics. Our work demonstrates the feasibility of replacing real CTs with the MR-synthesized CT for tFUS planning. Source code and a docker image with the trained model are available at https://github.com/han-liu/SynCT_TcMRgFUS

eess.IV↗

arXiv2022

Adaptive Contrastive Learning with Dynamic Correlation for Multi-Phase Organ Segmentation

Recent studies have demonstrated the superior performance of introducing ``scan-wise" contrast labels into contrastive learning for multi-organ segmentation on multi-phase computed tomography (CT). However, such scan-wise labels are limited: (1) a coarse classification, which could not capture the fine-grained ``organ-wise" contrast variations across all organs; (2) the label (i.e., contrast phase) is typically manually provided, which is error-prone and may introduce manual biases of defining phases. In this paper, we propose a novel data-driven contrastive loss function that adapts the similar/dissimilar contrast relationship between samples in each minibatch at organ-level. Specifically, as variable levels of contrast exist between organs, we hypothesis that the contrast differences in the organ-level can bring additional context for defining representations in the latent space. An organ-wise contrast correlation matrix is computed with mean organ intensities under one-hot attention maps. The goal of adapting the organ-driven correlation matrix is to model variable levels of feature separability at different phases. We evaluate our proposed approach on multi-organ segmentation with both non-contrast CT (NCCT) datasets and the MICCAI 2015 BTCV Challenge contrast-enhance CT (CECT) datasets. Compared to the state-of-the-art approaches, our proposed contrastive loss yields a substantial and significant improvement of 1.41% (from 0.923 to 0.936, p-value$<$0.01) and 2.02% (from 0.891 to 0.910, p-value$<$0.01) on mean Dice scores across all organs with respect to NCCT and CECT cohorts. We further assess the trained model performance with the MICCAI 2021 FLARE Challenge CECT datasets and achieve a substantial improvement of mean Dice score from 0.927 to 0.934 (p-value$<$0.01). The code is available at: https://github.com/MASILab/DCC_CL

cs.CV↗