Liping Liu

Vikram Gavini, Liping Liu

Using the orbital-free density functional theory as a model theory, we present an analysis of the field theoretic approach to quasi-continuum method. In particular, by perturbation method and multiple scale analysis, we provide a formal justification for the validity of the coarse-graining of various fields, which is central to the quasi-continuum reduction of field theories. Further, we derive the homogenized equations that govern the behavior of electronic fields in regions of smooth deformations. Using Fourier analysis, we determine the far-field solutions for these fields in the presence of local defects, and subsequently estimate cell-size effects in computed defect energies.

Thomas Schnelldorfer, Janil Castro, Atoussa Goldar-Najafi et al.

For several cancer patients, operative resection with curative intent can end up in early recurrence of the cancer. Current limitations in peri-operative cancer staging and especially intra-operative misidentification of visible metastases is likely the main reason leading to unnecessary operative interventions in the affected individuals. Here, we evaluate whether an artificial intelligence (AI) system can improve recognition of peritoneal surface metastases on routine staging laparoscopy images from patients with gastrointestinal malignancies. In a simulated setting evaluating biopsied peritoneal lesions, a prototype deep learning surgical guidance system outperformed oncologic surgeons in identifying peritoneal surface metastases. In this environment the developed AI model would have improved the identification of metastases by 5% while reducing the number of unnecessary biopsies by 28% compared to current standard practice. Evaluating non-biopsied peritoneal lesions, the findings support the possibility that the AI system could identify peritoneal surface metastases that were falsely deemed benign in clinical practice. Our findings demonstrate the technical feasibility of an AI system for intra-operative identification of peritoneal surface metastases, but require future assessment in a multi-institutional clinical setting.

Xiaohui Chen, Xi Chen, Liping Liu

Variational Graph Autoencoders (VGAEs) are powerful models for unsupervised learning of node representations from graph data. In this work, we systematically analyze modeling node attributes in VGAEs and show that attribute decoding is important for node representation learning. We further propose a new learning model, interpretable NOde Representation with Attribute Decoding (NORAD). The model encodes node representations in an interpretable approach: node representations capture community structures in the graph and the relationship between communities and node attributes. We further propose a rectifying procedure to refine node representations of isolated notes, improving the quality of these nodes' representations. Our empirical results demonstrate the advantage of the proposed model when learning graph data in an interpretable approach.

Xiaohui Chen, Xu Han, Jiajing Hu et al.

A graph generative model defines a distribution over graphs. One type of generative model is constructed by autoregressive neural networks, which sequentially add nodes and edges to generate a graph. However, the likelihood of a graph under the autoregressive model is intractable, as there are numerous sequences leading to the given graph; this makes maximum likelihood estimation challenging. Instead, in this work we derive the exact joint probability over the graph and the node ordering of the sequential process. From the joint, we approximately marginalize out the node orderings and compute a lower bound on the log-likelihood using variational inference. We train graph generative models by maximizing this bound, without using the ad-hoc node orderings of previous methods. Our experiments show that the log-likelihood bound is significantly tighter than the bound of previous schemes. Moreover, the models fitted with the proposed algorithm can generate high-quality graphs that match the structures of target graphs not seen during training. We have made our code publicly available at \hyperref[https://github.com/tufts-ml/graph-generation-vi]{https://github.com/tufts-ml/graph-generation-vi}.

Yukun Li, Liping Liu

Diffusion models have been popular for point cloud generation tasks. Existing works utilize the forward diffusion process to convert the original point distribution into a noise distribution and then learn the reverse diffusion process to recover the point distribution from the noise distribution. However, the reverse diffusion process can produce samples with non-smooth points on the surface because of the ignorance of the point cloud geometric properties. We propose alleviating the problem by incorporating the local smoothness constraint into the diffusion framework for point cloud generation. Experiments demonstrate the proposed model can generate realistic shapes and smoother point clouds, outperforming multiple state-of-the-art methods.

Yinkai Wang, Xiaohui Chen, Liping Liu et al.

The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast majority of spectral measurements remain in the "dark chemical space" without structural annotations. To improve annotation, we propose MADGEN (Mass-spec Attends to De Novo Molecular GENeration), a scaffold-based method for de novo molecular structure generation guided by mass spectrometry data. MADGEN operates in two stages: scaffold retrieval and spectra-conditioned molecular generation starting with the scaffold. In the first stage, given an MS/MS spectrum, we formulate scaffold retrieval as a ranking problem and employ contrastive learning to align mass spectra with candidate molecular scaffolds. In the second stage, starting from the retrieved scaffold, we employ the MS/MS spectrum to guide an attention-based generative model to generate the final molecule. Our approach constrains the molecular generation search space, reducing its complexity and improving generation accuracy. We evaluate MADGEN on three datasets (NIST23, CANOPUS, and MassSpecGym) and evaluate MADGEN's performance with a predictive scaffold retriever and with an oracle retriever. We demonstrate the effectiveness of using attention to integrate spectral information throughout the generation process to achieve strong results with the oracle retriever.

Liping Liu, Chunhong Zhang, Likang Wu et al.

Self-reflection for Large Language Models (LLMs) has gained significant attention. Existing approaches involve models iterating and improving their previous responses based on LLMs' internal reflection ability or external feedback. However, recent research has raised doubts about whether intrinsic self-correction without external feedback may even degrade performance. Based on our empirical evidence, we find that current static reflection methods may lead to redundant, drift, and stubborn issues. To mitigate this, we introduce Instruct-of-Reflection (IoRT), a novel and general reflection framework that leverages dynamic-meta instruction to enhance the iterative reflection capability of LLMs. Specifically, we propose the instructor driven by the meta-thoughts and self-consistency classifier, generates various instructions, including refresh, stop, and select, to guide the next reflection iteration. Our experiments demonstrate that IoRT achieves an average improvement of 10.1% over established baselines in mathematical and commonsense reasoning tasks, highlighting its efficacy and applicability.

Panagiotis Lymperopoulos, Liping Liu

Finding Minimal Unsatisfiable Subsets (MUSes) of binary constraints is a common problem in infeasibility analysis of over-constrained systems. However, because of the exponential search space of the problem, enumerating MUSes is extremely time-consuming in real applications. In this work, we propose to prune formulas using a learned model to speed up MUS enumeration. We represent formulas as graphs and then develop a graph-based learning model to predict which part of the formula should be pruned. Importantly, our algorithm does not require data labeling by only checking the satisfiability of pruned formulas. It does not even require training data from the target application because it extrapolates to data with different distributions. In our experiments we combine our algorithm with existing MUS enumerators and validate its effectiveness in multiple benchmarks including a set of real-world problems outside our training distribution. The experiment results show that our method significantly accelerates MUS enumeration on average on these benchmark problems.

Junxuan Yu, Yaofei Duan, Yuhao Huang et al.

Echocardiography is routine for cardiac examination. However, 2D ultrasound (US) struggles with accurate metric calculation and direct observation of 3D cardiac structures. Moreover, 3D US is limited by low resolution, small field of view and scarce availability in practice. Constructing the cardiac anatomical twin from 2D images is promising to provide precise treatment planning and clinical quantification. However, it remains challenging due to the rare paired data, complex structures, and US noises. In this study, we introduce a novel generative framework UltraTwin, to obtain cardiac anatomical twin from sparse multi-view 2D US. Our contribution is three-fold. First, pioneered the construction of a real-world and high-quality dataset containing strictly paired multi-view 2D US and CT, and pseudo-paired data. Second, we propose a coarse-to-fine scheme to achieve hierarchical reconstruction optimization. Last, we introduce an implicit autoencoder for topology-aware constraints. Extensive experiments show that UltraTwin reconstructs high-quality anatomical twins versus strong competitors. We believe it advances anatomical twin modeling for potential applications in personalized cardiac care.

Hang Yin, Yao Su, Liping Liu et al.

Spike train classification has recently become an important topic in the machine learning community, where each spike train is a binary event sequence with \emph{temporal-sparsity of signals of interest} and \emph{temporal-noise} properties. A promising model for it should follow the design principle of performing intensive computation only when signals of interest appear. So such tasks use mainly Spiking Neural Networks (SNNs) due to their consideration of temporal-sparsity of spike trains. However, the basic mechanism of SNNs ignore the temporal-noise issue, which makes them computationally expensive and thus high power consumption for analyzing spike trains on resource-constrained platforms. As an event-driven model, an SNN neuron makes a reaction given any input signals, making it difficult to quickly find signals of interest. In this paper, we introduce an event-attention mechanism that enables SNNs to dynamically highlight useful signals of the original spike trains. To this end, we propose SkipSNN, which extends existing SNN models by learning to mask out noise by skipping membrane potential updates and shortening the effective size of the computational graph. This process is analogous to how people choose to open and close their eyes to filter the information they see. We evaluate SkipSNN on various neuromorphic tasks and demonstrate that it achieves significantly better computational efficiency and classification accuracy than other state-of-the-art SNNs.

Dejie Chang, Mosha Chen, Chaozhen Liu et al.

Knowledge Graph has been proven effective in modeling structured information and conceptual knowledge, especially in the medical domain. However, the lack of high-quality annotated corpora remains a crucial problem for advancing the research and applications on this task. In order to accelerate the research for domain-specific knowledge graphs in the medical domain, we introduce DiaKG, a high-quality Chinese dataset for Diabetes knowledge graph, which contains 22,050 entities and 6,890 relations in total. We implement recent typical methods for Named Entity Recognition and Relation Extraction as a benchmark to evaluate the proposed dataset thoroughly. Empirical results show that the DiaKG is challenging for most existing methods and further analysis is conducted to discuss future research direction for improvements. We hope the release of this dataset can assist the construction of diabetes knowledge graphs and facilitate AI-based applications.

Hao Zhu, Liping Liu, Soha Hassoun

Detecting and quantifying products of cellular metabolism using Mass Spectrometry (MS) has already shown great promise in many biological and biomedical applications. The biggest challenge in metabolomics is annotation, where measured spectra are assigned chemical identities. Despite advances, current methods provide limited annotation for measured spectra. Here, we explore using graph neural networks (GNNs) to predict the spectra. The input to our model is a molecular graph. The model is trained and tested on the NIST 17 LC-MS dataset. We compare our results to NEIMS, a neural network model that utilizes molecular fingerprints as inputs. Our results show that GNN-based models offer higher performance than NEIMS. Importantly, we show that ranking results heavily depend on the candidate set size and on the similarity of the candidates to the target molecule, thus highlighting the need for consistent, well-characterized evaluation protocols for this domain.

Zhi Fengy, Haoyi Xiong, Chuanyuan Song et al.

Federated machine learning systems have been widely used to facilitate the joint data analytics across the distributed datasets owned by the different parties that do not trust each others. In this paper, we proposed a novel Gradient Boosting Machines (GBM) framework SecureGBM built-up with a multi-party computation model based on semi-homomorphic encryption, where every involved party can jointly obtain a shared Gradient Boosting machines model while protecting their own data from the potential privacy leakage and inferential identification. More specific, our work focused on a specific "dual--party" secure learning scenario based on two parties -- both party own an unique view (i.e., attributes or features) to the sample group of samples while only one party owns the labels. In such scenario, feature and label data are not allowed to share with others. To achieve the above goal, we firstly extent -- LightGBM -- a well known implementation of tree-based GBM through covering its key operations for training and inference with SEAL homomorphic encryption schemes. However, the performance of such re-implementation is significantly bottle-necked by the explosive inflation of the communication payloads, based on ciphertexts subject to the increasing length of plaintexts. In this way, we then proposed to use stochastic approximation techniques to reduced the communication payloads while accelerating the overall training procedure in a statistical manner. Our experiments using the real-world data showed that SecureGBM can well secure the communication and computation of LightGBM training and inference procedures for the both parties while only losing less than 3% AUC, using the same number of iterations for gradient boosting, on a wide range of benchmark datasets.

Shengwen Yang, Bing Ren, Xuhui Zhou et al.

Federated Learning is a new distributed learning mechanism which allows model training on a large corpus of decentralized data owned by different data providers, without sharing or leakage of raw data. According to the characteristics of data dis-tribution, it could be usually classified into three categories: horizontal federated learning, vertical federated learning, and federated transfer learning. In this paper we present a solution for parallel dis-tributed logistic regression for vertical federated learning. As compared with existing works, the role of third-party coordinator is removed in our proposed solution. The system is built on the pa-rameter server architecture and aims to speed up the model training via utilizing a cluster of servers in case of large volume of training data. We also evaluate the performance of the parallel distributed model training and the experimental results show the great scalability of the system.

Qiang Huang, Jianhui Bu, Weijian Xie et al.

Question Answering (QA) systems are used to provide proper responses to users' questions automatically. Sentence matching is an essential task in the QA systems and is usually reformulated as a Paraphrase Identification (PI) problem. Given a question, the aim of the task is to find the most similar question from a QA knowledge base. In this paper, we propose a Multi-task Sentence Encoding Model (MSEM) for the PI problem, wherein a connected graph is employed to depict the relation between sentences, and a multi-task learning model is applied to address both the sentence matching and sentence intent classification problem. In addition, we implement a general semantic retrieval framework that combines our proposed model and the Approximate Nearest Neighbor (ANN) technology, which enables us to find the most similar question from all available candidates very quickly during online serving. The experiments show the superiority of our proposed method as compared with the existing sentence matching models.

Xingjian Li, Haoyi Xiong, Hanchao Wang et al.

Transfer learning through fine-tuning a pre-trained neural network with an extremely large dataset, such as ImageNet, can significantly accelerate training while the accuracy is frequently bottlenecked by the limited dataset size of the new target task. To solve the problem, some regularization methods, constraining the outer layer weights of the target network using the starting point as references (SPAR), have been studied. In this paper, we propose a novel regularized transfer learning framework DELTA, namely DEep Learning Transfer using Feature Map with Attention. Instead of constraining the weights of neural network, DELTA aims to preserve the outer layer outputs of the target network. Specifically, in addition to minimizing the empirical loss, DELTA intends to align the outer layer outputs of two networks, through constraining a subset of feature maps that are precisely selected by attention that has been learned in an supervised learning manner. We evaluate DELTA with the state-of-the-art algorithms, including L2 and L2-SP. The experiment results show that our proposed method outperforms these baselines with higher accuracy for new tasks.

Linfeng Liu, Liping Liu

Inference for GP models with non-Gaussian noises is computationally expensive when dealing with large datasets. Many recent inference methods approximate the posterior distribution with a simpler distribution defined on a small number of inducing points. The inference is accurate only when data points have strong correlation with these inducing points. In this paper, we consider the inference problem in a different direction: GP function values in the posterior are mostly correlated in short distance. We construct a variational distribution such that the inference for a data point considers only its neighborhood. With this construction, the variational lower bound is highly decomposible, hence we can run stochastic optimization with very small batches. We then train Graph Convolutional Networks as a reusable model to identify variational parameters for each data point. Model reuse greatly reduces the number of parameters and the number of iterations needed in optimization. The proposed method significantly speeds up the inference and often gets more accurate results than previous methods.

Liping Liu, Catherine Shenoy, Prakash P. Shenoy

By elaborating on the notion of linear belief functions (Dempster 1990; Liu 1996), we propose an elementary approach to knowledge representation for expert systems using linear belief functions. We show how to use basic matrices to represent market information and financial knowledge, including complete ignorance, statistical observations, subjective speculations, distributional assumptions, linear relations, and empirical asset pricing models. We then appeal to Dempster's rule of combination to integrate the knowledge for assessing an overall belief of portfolio performance, and updating the belief by incorporating additional information. We use an example of three gold stocks to illustrate the approach.