arXiv subjects

Yi Zhang

Publications and source records attributed to Yi Zhang.

At least 883 records · Page 49Linked to original sources

arXiv2022

Fine-Tuning BERT for Automatic ADME Semantic Labeling in FDA Drug Labeling to Enhance Product-Specific Guidance Assessment

Product-specific guidances (PSGs) recommended by the United States Food and Drug Administration (FDA) are instrumental to promote and guide generic drug product development. To assess a PSG, the FDA assessor needs to take extensive time and effort to manually retrieve supportive drug information of absorption, distribution, metabolism, and excretion (ADME) from the reference listed drug labeling. In this work, we leveraged the state-of-the-art pre-trained language models to automatically label the ADME paragraphs in the pharmacokinetics section from the FDA-approved drug labeling to facilitate PSG assessment. We applied a transfer learning approach by fine-tuning the pre-trained Bidirectional Encoder Representations from Transformers (BERT) model to develop a novel application of ADME semantic labeling, which can automatically retrieve ADME paragraphs from drug labeling instead of manual work. We demonstrated that fine-tuning the pre-trained BERT model can outperform the conventional machine learning techniques, achieving up to 11.6% absolute F1 improvement. To our knowledge, we were the first to successfully apply BERT to solve the ADME semantic labeling task. We further assessed the relative contribution of pre-training and fine-tuning to the overall performance of the BERT model in the ADME semantic labeling task using a series of analysis methods such as attention similarity and layer-based ablations. Our analysis revealed that the information learned via fine-tuning is focused on task-specific knowledge in the top layers of the BERT, whereas the benefit from the pre-trained BERT model is from the bottom layers.

cs.CL↗

arXiv2022

Two-Stage Fine-Tuning: A Novel Strategy for Learning Class-Imbalanced Data

Classification on long-tailed distributed data is a challenging problem, which suffers from serious class-imbalance and hence poor performance on tail classes with only a few samples. Owing to this paucity of samples, learning on the tail classes is especially challenging for the fine-tuning when transferring a pretrained model to a downstream task. In this work, we present a simple modification of standard fine-tuning to cope with these challenges. Specifically, we propose a two-stage fine-tuning: we first fine-tune the final layer of the pretrained model with class-balanced reweighting loss, and then we perform the standard fine-tuning. Our modification has several benefits: (1) it leverages pretrained representations by only fine-tuning a small portion of the model parameters while keeping the rest untouched; (2) it allows the model to learn an initial representation of the specific task; and importantly (3) it protects the learning of tail classes from being at a disadvantage during the model updating. We conduct extensive experiments on synthetic datasets of both two-class and multi-class tasks of text classification as well as a real-world application to ADME (i.e., absorption, distribution, metabolism, and excretion) semantic labeling. The experimental results show that the proposed two-stage fine-tuning outperforms both fine-tuning with conventional loss and fine-tuning with a reweighting loss on the above datasets.

cs.CL↗

arXiv2022

Adaptive Testing for Connected and Automated Vehicles with Sparse Control Variates in Overtaking Scenarios

Testing and evaluation is a critical step in the development and deployment of connected and automated vehicles (CAVs). Due to the black-box property and various types of CAVs, how to test and evaluate CAVs adaptively remains a major challenge. Many approaches have been proposed to adaptively generate testing scenarios during the testing process. However, most existing approaches cannot be applied to complex scenarios, where the variables needed to define such scenarios are high dimensional. Towards filling this gap, the adaptive testing with sparse control variates method is proposed in this paper. Instead of adaptively generating testing scenarios, our approach evaluates CAVs' performances by adaptively utilizing the testing results. Specifically, each testing result is adjusted using multiple linear regression techniques based on control variates. As the regression coefficients can be adaptively optimized for the CAV under test, using the adjusted results can reduce the estimation variance, compared with using the testing results directly. To overcome the high dimensionality challenge, sparse control variates are utilized only for the critical variables of testing scenarios. To validate the proposed method, the high-dimensional overtaking scenarios are investigated, and the results demonstrate that our approach can further accelerate the evaluation process by about 30 times.

eess.SY↗

arXiv2022

Probing Electronic States in Monolayer Semiconductors through Static and Transient Third-Harmonic Spectroscopy

Electronic states and their dynamics are of critical importance for electronic and optoelectronic applications. Here, we probe various relevant electronic states in monolayer MoS2, such as multiple excitonic Rydberg states and free-particle energy bands, with a high relative contrast of up to >200 via broadband (from ~1.79 to 3.10 eV) static third-harmonic spectroscopy, which is further supported by theoretical calculations. Moreover, we introduce transient third-harmonic spectroscopy to demonstrate that third-harmonic generation can be all-optically modulated with a modulation depth exceeding ~94% at ~2.18 eV, providing direct evidence of dominant carrier relaxation processes, associated with carrier-exciton and carrier-phonon interactions. Our results indicate that static and transient third-harmonic spectroscopies are not only promising techniques for the characterization of monolayer semiconductors and their heterostructures, but also a potential platform for disruptive photonic and optoelectronic applications, including all-optical modulation and imaging.

physics.optics↗

arXiv2022

Counterfactually Measuring and Eliminating Social Bias in Vision-Language Pre-training Models

Vision-Language Pre-training (VLP) models have achieved state-of-the-art performance in numerous cross-modal tasks. Since they are optimized to capture the statistical properties of intra- and inter-modality, there remains risk to learn social biases presented in the data as well. In this work, we (1) introduce a counterfactual-based bias measurement \emph{CounterBias} to quantify the social bias in VLP models by comparing the [MASK]ed prediction probabilities of factual and counterfactual samples; (2) construct a novel VL-Bias dataset including 24K image-text pairs for measuring gender bias in VLP models, from which we observed that significant gender bias is prevalent in VLP models; and (3) propose a VLP debiasing method \emph{FairVLP} to minimize the difference in the [MASK]ed prediction probabilities between factual and counterfactual image-text pairs for VLP debiasing. Although CounterBias and FairVLP focus on social bias, they are generalizable to serve as tools and provide new insights to probe and regularize more knowledge in VLP models.

cs.CV↗

arXiv2022

Vision-based Uneven BEV Representation Learning with Polar Rasterization and Surface Estimation

In this work, we propose PolarBEV for vision-based uneven BEV representation learning. To adapt to the foreshortening effect of camera imaging, we rasterize the BEV space both angularly and radially, and introduce polar embedding decomposition to model the associations among polar grids. Polar grids are rearranged to an array-like regular representation for efficient processing. Besides, to determine the 2D-to-3D correspondence, we iteratively update the BEV surface based on a hypothetical plane, and adopt height-based feature transformation. PolarBEV keeps real-time inference speed on a single 2080Ti GPU, and outperforms other methods for both BEV semantic segmentation and BEV instance segmentation. Thorough ablations are presented to validate the design. The code will be released at \url{https://github.com/SuperZ-Liu/PolarBEV}.

cs.CV↗

arXiv2022

Explanation-based Counterfactual Retraining(XCR): A Calibration Method for Black-box Models

With the rapid development of eXplainable Artificial Intelligence (XAI), a long line of past work has shown concerns about the Out-of-Distribution (OOD) problem in perturbation-based post-hoc XAI models and explanations are socially misaligned. We explore the limitations of post-hoc explanation methods that use approximators to mimic the behavior of black-box models. Then we propose eXplanation-based Counterfactual Retraining (XCR), which extracts feature importance fastly. XCR applies the explanations generated by the XAI model as counterfactual input to retrain the black-box model to address OOD and social misalignment problems. Evaluation of popular image datasets shows that XCR can improve model performance when only retaining 12.5% of the most crucial features without changing the black-box model structure. Furthermore, the evaluation of the benchmark of corruption datasets shows that the XCR is very helpful for improving model robustness and positively impacts the calibration of OOD problems. Even though not calibrated in the validation set like some OOD calibration methods, the corrupted data metric outperforms existing methods. Our method also beats current OOD calibration methods on the OOD calibration metric if calibration on the validation set is applied.

cs.LG↗

arXiv2022

Hands-on Wireless Sensing with Wi-Fi: A Tutorial

With the rapid development of wireless communication technology, wireless access points (AP) and internet of things (IoT) devices have been widely deployed in our surroundings. Various types of wireless signals (e.g., Wi-Fi, LoRa, LTE) are filling out our living and working spaces. Previous researches reveal the fact that radio waves are modulated by the spatial structure during the propagation process (e.g., reflection, diffraction, and scattering) and superimposed on the receiver. This observation allows us to reconstruct the surrounding environment based on received wireless signals, called "wireless sensing". Wireless sensing is an emerging technology that enables a wide range of applications, such as gesture recognition for human-computer interaction, vital signs monitoring for health care, and intrusion detection for security management. Compared with other sensing paradigms, such as vision-based and IMU-based sensing, wireless sensing solutions have unique advantages such as high coverage, pervasiveness, low cost, and robustness under adverse light and texture scenarios. Besides, wireless sensing solutions are generally lightweight in terms of both computation overhead and device size. This tutorial takes Wi-Fi sensing as an example. It introduces both the theoretical principles and the code implementation of data collection, signal processing, features extraction, and model design. In addition, this tutorial highlights state-of-the-art deep learning models (e.g., CNN, RNN, and adversarial learning models) and their applications in wireless sensing systems. We hope this tutorial will help people in other research fields to break into wireless sensing research and learn more about its theories, designs, and implementation skills, promoting prosperity in the wireless sensing research field.

eess.SP↗

arXiv2022

Design Challenges for a Multi-Perspective Search Engine

Many users turn to document retrieval systems (e.g. search engines) to seek answers to controversial questions. Answering such user queries usually require identifying responses within web documents, and aggregating the responses based on their different perspectives. Classical document retrieval systems fall short at delivering a set of direct and diverse responses to the users. Naturally, identifying such responses within a document is a natural language understanding task. In this paper, we examine the challenges of synthesizing such language understanding objectives with document retrieval, and study a new perspective-oriented document retrieval paradigm. We discuss and assess the inherent natural language understanding challenges in order to achieve the goal. Following the design challenges and principles, we demonstrate and evaluate a practical prototype pipeline system. We use the prototype system to conduct a user survey in order to assess the utility of our paradigm, as well as understanding the user information needs for controversial queries.

cs.CL↗

arXiv2022

Hypernetwork-based Personalized Federated Learning for Multi-Institutional CT Imaging

Computed tomography (CT) is of great importance in clinical practice due to its powerful ability to provide patients' anatomical information without any invasive inspection, but its potential radiation risk is raising people's concerns. Deep learning-based methods are considered promising in CT reconstruction, but these network models are usually trained with the measured data obtained from specific scanning protocol and need to centralizedly collect large amounts of data, which will lead to serious data domain shift, and privacy concerns. To relieve these problems, in this paper, we propose a hypernetwork-based federated learning method for personalized CT imaging, dubbed as HyperFed. The basic assumption of HyperFed is that the optimization problem for each institution can be divided into two parts: the local data adaption problem and the global CT imaging problem, which are implemented by an institution-specific hypernetwork and a global-sharing imaging network, respectively. The purpose of global-sharing imaging network is to learn stable and effective common features from different institutions. The institution-specific hypernetwork is carefully designed to obtain hyperparameters to condition the global-sharing imaging network for personalized local CT reconstruction. Experiments show that HyperFed achieves competitive performance in CT reconstruction compared with several other state-of-the-art methods. It is believed as a promising direction to improve CT imaging quality and achieve personalized demands of different institutions or scanners without privacy data sharing. The codes will be released at https://github.com/Zi-YuanYang/HyperFed.

eess.IV↗

arXiv2022

Depth Completion using Geometry-Aware Embedding

Exploiting internal spatial geometric constraints of sparse LiDARs is beneficial to depth completion, however, has been not explored well. This paper proposes an efficient method to learn geometry-aware embedding, which encodes the local and global geometric structure information from 3D points, e.g., scene layout, object's sizes and shapes, to guide dense depth estimation. Specifically, we utilize the dynamic graph representation to model generalized geometric relationship from irregular point clouds in a flexible and efficient manner. Further, we joint this embedding and corresponded RGB appearance information to infer missing depths of the scene with well structure-preserved details. The key to our method is to integrate implicit 3D geometric representation into a 2D learning architecture, which leads to a better trade-off between the performance and efficiency. Extensive experiments demonstrate that the proposed method outperforms previous works and could reconstruct fine depths with crisp boundaries in regions that are over-smoothed by them. The ablation study gives more insights into our method that could achieve significant gains with a simple design, while having better generalization capability and stability. The code is available at https://github.com/Wenchao-Du/GAENet.

cs.CV↗

arXiv2022

Stepping beyond your comfort zone: Diffusion-based network analytics for knowledge trajectory recommendation

Interest in tracing the research interests of scientific researchers is rising, and particularly that of predicting a researcher's knowledge trajectories beyond their current foci into potential inter-/cross-/multi-disciplinary interactions. Hence, in this study, we present a method of diffusion-based network analytics for knowledge trajectory recommendation. The method begins by constructing a heterogeneous bibliometric network consisting of a co-topic layer and a co-authorship layer. A novel link prediction approach with a diffusion strategy is then used to reflect real-world academic activity, such as knowledge sharing between co-authors or diffusing between similar research topics. This strategy differentiates the interactions occurring between homogeneous and heterogeneous nodes and weights the strengths of these interactions. Two sets of experiments - one with a local dataset and another with a global dataset - demonstrate that the proposed method is prior to selected baselines. In addition, to further examine the reliability of our method, we conducted a case study on recommending knowledge trajectories of selected information scientists and their research groups. The results demonstrate the empirical insights our method yields for individual researchers, communities, and research institutions in the information science discipline.

cs.SI↗

arXiv2022

Label Semantic Aware Pre-training for Few-shot Text Classification

In text classification tasks, useful information is encoded in the label names. Label semantic aware systems have leveraged this information for improved text classification performance during fine-tuning and prediction. However, use of label-semantics during pre-training has not been extensively explored. We therefore propose Label Semantic Aware Pre-training (LSAP) to improve the generalization and data efficiency of text classification systems. LSAP incorporates label semantics into pre-trained generative models (T5 in our case) by performing secondary pre-training on labeled sentences from a variety of domains. As domain-general pre-training requires large amounts of data, we develop a filtering and labeling pipeline to automatically create sentence-label pairs from unlabeled text. We perform experiments on intent (ATIS, Snips, TOPv2) and topic classification (AG News, Yahoo! Answers). LSAP obtains significant accuracy improvements over state-of-the-art models for few-shot text classification while maintaining performance comparable to state of the art in high-resource settings.

cs.CL↗

arXiv2022

PKUSEG: A Toolkit for Multi-Domain Chinese Word Segmentation

Chinese word segmentation (CWS) is a fundamental step of Chinese natural language processing. In this paper, we build a new toolkit, named PKUSEG, for multi-domain word segmentation. Unlike existing single-model toolkits, PKUSEG targets multi-domain word segmentation and provides separate models for different domains, such as web, medicine, and tourism. Besides, due to the lack of labeled data in many domains, we propose a domain adaptation paradigm to introduce cross-domain semantic knowledge via a translation system. Through this method, we generate synthetic data using a large amount of unlabeled data in the target domain and then obtain a word segmentation model for the target domain. We also further refine the performance of the default model with the help of synthetic data. Experiments show that PKUSEG achieves high performance on multiple domains. The new toolkit also supports POS tagging and model training to adapt to various application scenarios. The toolkit is now freely and publicly available for the usage of research and industry.

cs.CL↗

arXiv2022

HyperCI: A Higher Order Collective Influence Measure for Hypernetwork Dismantling

The connectivity of networked systems is often dependent on a small portion of critical nodes. Network dismantling studies the strategy to identify a subset of nodes the removal of which will maximally destroy the connectivity of a network and fragment it into disconnected components. However, conventional network dismantling approaches focus on simple network which models only pairwise interaction between nodes while groupwise interactions among arbitrary number of nodes are ubiquitous in networked systems like integrated circuits. Groupwise interactions modeled by hypernetwork introduce higher order connectivity patterns, which limits the application of conventional network dismantling methods on hypernetwork. In this brief, we propose HyperCI, a higher order collective influence measure for hypernetwork dismantling. It considers the node co-occurrence characteristics and higher order influence ability both introduced by hyperedges in hypernetwork. We evaluate the effectiveness of our proposed HyperCI on six real world hypernetworks including integrated circuits and citation networks and the results indicate our proposed HyperCI outperforms baseline network dismantling methods for both simple network and hypernetwork.

cs.SI↗

arXiv2022

A microstructure estimation Transformer inspired by sparse representation for diffusion MRI

Diffusion magnetic resonance imaging (dMRI) is an important tool in characterizing tissue microstructure based on biophysical models, which are complex and highly non-linear. Resolving microstructures with optimization techniques is prone to estimation errors and requires dense sampling in the q-space. Deep learning based approaches have been proposed to overcome these limitations. Motivated by the superior performance of the Transformer, in this work, we present a learning-based framework based on Transformer, namely, a Microstructure Estimation Transformer with Sparse Coding (METSC) for dMRI-based microstructure estimation with downsampled q-space data. To take advantage of the Transformer while addressing its limitation in large training data requirements, we explicitly introduce an inductive bias - model bias into the Transformer using a sparse coding technique to facilitate the training process. Thus, the METSC is composed with three stages, an embedding stage, a sparse representation stage, and a mapping stage. The embedding stage is a Transformer-based structure that encodes the signal to ensure the voxel is represented effectively. In the sparse representation stage, a dictionary is constructed by solving a sparse reconstruction problem that unfolds the Iterative Hard Thresholding (IHT) process. The mapping stage is essentially a decoder that computes the microstructural parameters from the output of the second stage, based on the weighted sum of normalized dictionary coefficients where the weights are also learned. We tested our framework on two dMRI models with downsampled q-space data, including the intravoxel incoherent motion (IVIM) model and the neurite orientation dispersion and density imaging (NODDI) model. The proposed method achieved up to 11.25 folds of acceleration in scan time and outperformed the other state-of-the-art learning-based methods.

eess.SP↗

arXiv2022

On the quantisation and anomalies of antisymmetric tensor-spinors

We perform the quantisation of antisymmetric tensor-spinors (fermionic $p$-forms) $ψ^α_{μ_1 \dots μ_p}$ using the Batalin-Vilkovisky field-antifield formalism. Just as for the gravitino ($p=1$), an extra propagating Nielsen-Kallosh ghost appears in quadratic gauges containing a differential operator. The appearance of this `third ghost' is described within the BV formalism for arbitrary reducible gauge theories. We then use the resulting spectrum of ghosts and the Atiyah-Singer index theorem to compute gravitational anomalies.

hep-th↗

arXiv2022

AFFIRM: Affinity Fusion-based Framework for Iteratively Random Motion correction of multi-slice fetal brain MRI

Multi-slice magnetic resonance images of the fetal brain are usually contaminated by severe and arbitrary fetal and maternal motion. Hence, stable and robust motion correction is necessary to reconstruct high-resolution 3D fetal brain volume for clinical diagnosis and quantitative analysis. However, the conventional registration-based correction has a limited capture range and is insufficient for detecting relatively large motions. Here, we present a novel Affinity Fusion-based Framework for Iteratively Random Motion (AFFIRM) correction of the multi-slice fetal brain MRI. It learns the sequential motion from multiple stacks of slices and integrates the features between 2D slices and reconstructed 3D volume using affinity fusion, which resembles the iterations between slice-to-volume registration and volumetric reconstruction in the regular pipeline. The method accurately estimates the motion regardless of brain orientations and outperforms other state-of-the-art learning-based methods on the simulated motion-corrupted data, with a 48.4% reduction of mean absolute error for rotation and 61.3% for displacement. We then incorporated AFFIRM into the multi-resolution slice-to-volume registration and tested it on the real-world fetal MRI scans at different gestation stages. The results indicated that adding AFFIRM to the conventional pipeline improved the success rate of fetal brain super-resolution reconstruction from 77.2% to 91.9%.

eess.IV↗