arXiv subjects

Tengfei Ma

Publications and source records attributed to Tengfei Ma.

At least 109 records · Page 6Linked to original sources

arXiv2020

Long-lived and multiplexed atom-photon entanglement interface with feed-forward-controlled readouts

The quantum interface (QI) that generates entanglement between photonic and spin-wave (atomic memory) qubits is a basic building block for quantum repeaters. Realizing ensemble-based repeaters in practice requires quantum memory providing long lifetime and multimode capacity. Significant progresses have been achieved on these separate goals. The remaining challenge is to combine long-lived and multimode memories into a single QI. Here, by establishing multimode, magnetic-field-insensitive and long-wavelength spin-wave storage in laser-cooled atoms that are placed inside a phase-passively-stabilized polarization interferometer, we constructed a multiplexed QI that stores up to three long-lived spin-wave qubits. Using a feed-forward-controlled system, we demonstrated that the multiplexed QI gives rise to a 3-fold increase in the atom-photon (photon-photon) entanglement-generation probability compared to single-mode QIs. The measured Bell parameter is 2.5+/-0.1 combined with a memory lifetime up to 1ms. The presented work represents a key step forward in realizing fiber-based long-distance quantum communications.

quant-ph↗

arXiv2020

Repurpose Open Data to Discover Therapeutics for COVID-19 using Deep Learning

There have been more than 850,000 confirmed cases and over 48,000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there are currently no proven effective medications against COVID-19. Drug repurposing offers a promising way for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, genes, pathways, and expressions, from a large scientific corpus of 24 million PubMed publications. Using Amazon AWS computing resources, we identified 41 repurposable drugs (including indomethacin, toremifene and niclosamide) whose therapeutic association with COVID-19 were validated by transcriptomic and proteomic data in SARS-CoV-2 infected human cells and data from ongoing clinical trials. While this study, by no means recommends specific drugs, it demonstrates a powerful deep learning methodology to prioritize existing drugs for further investigation, which holds the potential of accelerating therapeutic development for COVID-19.

q-bio.QM↗

arXiv2020

CHEER: Rich Model Helps Poor Model via Knowledge Infusion

There is a growing interest in applying deep learning (DL) to healthcare, driven by the availability of data with multiple feature channels in rich-data environments (e.g., intensive care units). However, in many other practical situations, we can only access data with much fewer feature channels in a poor-data environments (e.g., at home), which often results in predictive models with poor performance. How can we boost the performance of models learned from such poor-data environment by leveraging knowledge extracted from existing models trained using rich data in a related environment? To address this question, we develop a knowledge infusion framework named CHEER that can succinctly summarize such rich model into transferable representations, which can be incorporated into the poor model to improve its performance. The infused model is analyzed theoretically and evaluated empirically on several datasets. Our empirical results showed that CHEER outperformed baselines by 5.60% to 46.80% in terms of the macro-F1 score on multiple physiological datasets.

cs.LG↗

arXiv2019

Pre-training of Graph Augmented Transformers for Medication Recommendation

Medication recommendation is an important healthcare application. It is commonly formulated as a temporal prediction task. Hence, most existing works only utilize longitudinal electronic health records (EHRs) from a small number of patients with multiple visits ignoring a large number of patients with a single visit (selection bias). Moreover, important hierarchical knowledge such as diagnosis hierarchy is not leveraged in the representation learning process. To address these challenges, we propose G-BERT, a new model to combine the power of Graph Neural Networks (GNNs) and BERT (Bidirectional Encoder Representations from Transformers) for medical code representation and medication recommendation. We use GNNs to represent the internal hierarchical structures of medical codes. Then we integrate the GNN representation into a transformer-based visit encoder and pre-train it on EHR data from patients only with a single visit. The pre-trained visit encoder and representation are then fine-tuned for downstream predictive tasks on longitudinal EHRs from patients with multiple visits. G-BERT is the first to bring the language model pre-training schema into the healthcare domain and it achieved state-of-the-art performance on the medication recommendation task.

cs.AI↗

arXiv2019

Online Planner Selection with Graph Neural Networks and Adaptive Scheduling

Automated planning is one of the foundational areas of AI. Since no single planner can work well for all tasks and domains, portfolio-based techniques have become increasingly popular in recent years. In particular, deep learning emerges as a promising methodology for online planner selection. Owing to the recent development of structural graph representations of planning tasks, we propose a graph neural network (GNN) approach to selecting candidate planners. GNNs are advantageous over a straightforward alternative, the convolutional neural networks, in that they are invariant to node permutations and that they incorporate node labels for better inference. Additionally, for cost-optimal planning, we propose a two-stage adaptive scheduling method to further improve the likelihood that a given task is solved in time. The scheduler may switch at halftime to a different planner, conditioned on the observed performance of the first one. Experimental results validate the effectiveness of the proposed method against strong baselines, both deep learning and non-deep learning based. The code is available at \url{https://github.com/matenure/GNN_planner}.

cs.AI↗

arXiv2019

EvolveGCN: Evolving Graph Convolutional Networks for Dynamic Graphs

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at \url{https://github.com/IBM/EvolveGCN}.

cs.LG↗

arXiv2019

DeepDrawing: A Deep Learning Approach to Graph Drawing

Node-link diagrams are widely used to facilitate network explorations. However, when using a graph drawing technique to visualize networks, users often need to tune different algorithm-specific parameters iteratively by comparing the corresponding drawing results in order to achieve a desired visual effect. This trial and error process is often tedious and time-consuming, especially for non-expert users. Inspired by the powerful data modelling and prediction capabilities of deep learning techniques, we explore the possibility of applying deep learning techniques to graph drawing. Specifically, we propose using a graph-LSTM-based approach to directly map network structures to graph drawings. Given a set of layout examples as the training dataset, we train the proposed graph-LSTM-based model to capture their layout characteristics. Then, the trained model is used to generate graph drawings in a similar style for new networks. We evaluated the proposed approach on two special types of layouts (i.e., grid layouts and star layouts) and two general types of layouts (i.e., ForceAtlas2 and PivotMDS) in both qualitative and quantitative ways. The results provide support for the effectiveness of our approach. We also conducted a time cost assessment on the drawings of small graphs with 20 to 50 nodes. We further report the lessons we learned and discuss the limitations and future work.

cs.HC↗

arXiv2019

GENN: Predicting Correlated Drug-drug Interactions with Graph Energy Neural Networks

Gaining more comprehensive knowledge about drug-drug interactions (DDIs) is one of the most important tasks in drug development and medical practice. Recently graph neural networks have achieved great success in this task by modeling drugs as nodes and drug-drug interactions as links and casting DDI predictions as link prediction problems. However, correlations between link labels (e.g., DDI types) were rarely considered in existing works. We propose the graph energy neural network (GENN) to explicitly model link type correlations. We formulate the DDI prediction task as a structure prediction problem and introduce a new energy-based model where the energy function is defined by graph neural networks. Experiments on two real-world DDI datasets demonstrated that GENN is superior to many baselines without consideration of link type correlations and achieved $13.77\%$ and $5.01\%$ PR-AUC improvement on the two datasets, respectively. We also present a case study in which \mname can better capture meaningful DDI correlations compared with baseline models.

cs.LG↗

arXiv2019

RDPD: Rich Data Helps Poor Data via Imitation

In many situations, we need to build and deploy separate models in related environments with different data qualities. For example, an environment with strong observation equipments (e.g., intensive care units) often provides high-quality multi-modal data, which are acquired from multiple sensory devices and have rich-feature representations. On the other hand, an environment with poor observation equipment (e.g., at home) only provides low-quality, uni-modal data with poor-feature representations. To deploy a competitive model in a poor-data environment without requiring direct access to multi-modal data acquired from a rich-data environment, this paper develops and presents a knowledge distillation (KD) method (RDPD) to enhance a predictive model trained on poor data using knowledge distilled from a high-complexity model trained on rich, private data. We evaluated RDPD on three real-world datasets and shown that its distilled model consistently outperformed all baselines across all datasets, especially achieving the greatest performance improvement over a model trained only on low-quality data by 24.56% on PR-AUC and 12.21% on ROC-AUC, and over that of a state-of-the-art KD model by 5.91% on PR-AUC and 4.44% on ROC-AUC.

cs.LG↗

arXiv2019

MINA: Multilevel Knowledge-Guided Attention for Modeling Electrocardiography Signals

Electrocardiography (ECG) signals are commonly used to diagnose various cardiac abnormalities. Recently, deep learning models showed initial success on modeling ECG data, however they are mostly black-box, thus lack interpretability needed for clinical usage. In this work, we propose MultIlevel kNowledge-guided Attention networks (MINA) that predict heart diseases from ECG signals with intuitive explanation aligned with medical knowledge. By extracting multilevel (beat-, rhythm- and frequency-level) domain knowledge features separately, MINA combines the medical knowledge and ECG data via a multilevel attention model, making the learned models highly interpretable. Our experiments showed MINA achieved PR-AUC 0.9436 (outperforming the best baseline by 5.51%) in real world ECG dataset. Finally, MINA also demonstrated robust performance and strong interpretability against signal distortion and noise contamination.

eess.SP↗

arXiv2019

IPC: A Benchmark Data Set for Learning with Graph-Structured Data

Benchmark data sets are an indispensable ingredient of the evaluation of graph-based machine learning methods. We release a new data set, compiled from International Planning Competitions (IPC), for benchmarking graph classification, regression, and related tasks. Apart from the graph construction (based on AI planning problems) that is interesting in its own right, the data set possesses distinctly different characteristics from popularly used benchmarks. The data set, named IPC, consists of two self-contained versions, grounded and lifted, both including graphs of large and skewedly distributed sizes, posing substantial challenges for the computation of graph models such as graph kernels and graph neural networks. The graphs in this data set are directed and the lifted version is acyclic, offering the opportunity of benchmarking specialized models for directed (acyclic) structures. Moreover, the graph generator and the labeling are computer programmed; thus, the data set may be extended easily if a larger scale is desired. The data set is accessible from \url{https://github.com/IBM/IPC-graph-data}.

cs.LG↗

arXiv2019

GAMENet: Graph Augmented MEmory Networks for Recommending Medication Combination

Recent progress in deep learning is revolutionizing the healthcare domain including providing solutions to medication recommendations, especially recommending medication combination for patients with complex health conditions. Existing approaches either do not customize based on patient health history, or ignore existing knowledge on drug-drug interactions (DDI) that might lead to adverse outcomes. To fill this gap, we propose the Graph Augmented Memory Networks (GAMENet), which integrates the drug-drug interactions knowledge graph by a memory module implemented as a graph convolutional networks, and models longitudinal patient records as the query. It is trained end-to-end to provide safe and personalized recommendation of medication combination. We demonstrate the effectiveness and safety of GAMENet by comparing with several state-of-the-art methods on real EHR data. GAMENet outperformed all baselines in all effectiveness measures, and also achieved 3.60% DDI rate reduction from existing EHR data.

cs.AI↗

arXiv2018

Reaching Data Confidentiality and Model Accountability on the CalTrain

Distributed collaborative learning (DCL) paradigms enable building joint machine learning models from distrusting multi-party participants. Data confidentiality is guaranteed by retaining private training data on each participant's local infrastructure. However, this approach to achieving data confidentiality makes today's DCL designs fundamentally vulnerable to data poisoning and backdoor attacks. It also limits DCL's model accountability, which is key to backtracking the responsible "bad" training data instances/contributors. In this paper, we introduce CALTRAIN, a Trusted Execution Environment (TEE) based centralized multi-party collaborative learning system that simultaneously achieves data confidentiality and model accountability. CALTRAIN enforces isolated computation on centrally aggregated training data to guarantee data confidentiality. To support building accountable learning models, we securely maintain the links between training instances and their corresponding contributors. Our evaluation shows that the models generated from CALTRAIN can achieve the same prediction accuracy when compared to the models trained in non-protected environments. We also demonstrate that when malicious training participants tend to implant backdoors during model training, CALTRAIN can accurately and precisely discover the poisoned and mislabeled training data that lead to the runtime mispredictions.

cs.CR↗

arXiv2018

Scalable Graph Learning for Anti-Money Laundering: A First Look

Organized crime inflicts human suffering on a genocidal scale: the Mexican drug cartels have murdered 150,000 people since 2006, upwards of 700,000 people per year are "exported" in a human trafficking industry enslaving an estimated 40 million people. These nefarious industries rely on sophisticated money laundering schemes to operate. Despite tremendous resources dedicated to anti-money laundering (AML) only a tiny fraction of illicit activity is prevented. The research community can help. In this brief paper, we map the structural and behavioral dynamics driving the technical challenge. We review AML methods, current and emergent. We provide a first look at scalable graph convolutional neural networks for forensic analysis of financial data, which is massive, dense, and dynamic. We report preliminary experimental results using a large synthetic graph (1M nodes, 9M edges) generated by a data simulator we created called AMLSim. We consider opportunities for high performance efficiency, in terms of computation and memory, and we share results from a simple graph compression experiment. Our results support our working hypothesis that graph deep learning for AML bears great promise in the fight against criminal financial activity.

cs.SI↗

arXiv2018

Constrained Generation of Semantically Valid Graphs via Regularizing Variational Autoencoders

Deep generative models have achieved remarkable success in various data domains, including images, time series, and natural languages. There remain, however, substantial challenges for combinatorial structures, including graphs. One of the key challenges lies in the difficulty of ensuring semantic validity in context. For examples, in molecular graphs, the number of bonding-electron pairs must not exceed the valence of an atom; whereas in protein interaction networks, two proteins may be connected only when they belong to the same or correlated gene ontology terms. These constraints are not easy to be incorporated into a generative model. In this work, we propose a regularization framework for variational autoencoders as a step toward semantic validity. We focus on the matrix representation of graphs and formulate penalty terms that regularize the output distribution of the decoder to encourage the satisfaction of validity constraints. Experimental results confirm a much higher likelihood of sampling valid graphs in our approach, compared with others reported in the literature.

cs.LG↗

arXiv2018

AWE: Asymmetric Word Embedding for Textual Entailment

Textual entailment is a fundamental task in natural language processing. It refers to the directional relation between text fragments such that the "premise" can infer "hypothesis". In recent years deep learning methods have achieved great success in this task. Many of them have considered the inter-sentence word-word interactions between the premise-hypothesis pairs, however, few of them considered the "asymmetry" of these interactions. Different from paraphrase identification or sentence similarity evaluation, textual entailment is essentially determining a directional (asymmetric) relation between the premise and the hypothesis. In this paper, we propose a simple but effective way to enhance existing textual entailment algorithms by using asymmetric word embeddings. Experimental results on SciTail and SNLI datasets show that the learned asymmetric word embeddings could significantly improve the word-word interaction based textual entailment models. It is noteworthy that the proposed AWE-DeIsTe model can get 2.1% accuracy improvement over prior state-of-the-art on SciTail.

cs.CL↗

arXiv2018

Drug Similarity Integration Through Attentive Multi-view Graph Auto-Encoders

Drug similarity has been studied to support downstream clinical tasks such as inferring novel properties of drugs (e.g. side effects, indications, interactions) from known properties. The growing availability of new types of drug features brings the opportunity of learning a more comprehensive and accurate drug similarity that represents the full spectrum of underlying drug relations. However, it is challenging to integrate these heterogeneous, noisy, nonlinear-related information to learn accurate similarity measures especially when labels are scarce. Moreover, there is a trade-off between accuracy and interpretability. In this paper, we propose to learn accurate and interpretable similarity measures from multiple types of drug features. In particular, we model the integration using multi-view graph auto-encoders, and add attentive mechanism to determine the weights for each view with respect to corresponding tasks and features for better interpretability. Our model has flexible design for both semi-supervised and unsupervised settings. Experimental results demonstrated significant predictive accuracy improvement. Case studies also showed better model capacity (e.g. embed node features) and interpretability.

cs.LG↗

arXiv2018

FastGCN: Fast Learning with Graph Convolutional Networks via Importance Sampling

The graph convolutional networks (GCN) recently proposed by Kipf and Welling are an effective graph model for semi-supervised learning. This model, however, was originally designed to be learned with the presence of both training and test data. Moreover, the recursive neighborhood expansion across layers poses time and memory challenges for training with large, dense graphs. To relax the requirement of simultaneous availability of test data, we interpret graph convolutions as integral transforms of embedding functions under probability measures. Such an interpretation allows for the use of Monte Carlo approaches to consistently estimate the integrals, which in turn leads to a batched training scheme as we propose in this work---FastGCN. Enhanced with importance sampling, FastGCN not only is efficient for training but also generalizes well for inference. We show a comprehensive set of experiments to demonstrate its effectiveness compared with GCN and related models. In particular, training is orders of magnitude more efficient while predictions remain comparably accurate.

cs.LG↗