The discovery of drug-target interactions (DTIs) is a pivotal process in pharmaceutical development. Computational approaches are a promising and efficient alternative to tedious and costly wet-lab experiments for predicting novel DTIs from numerous candidates. Recently, with the availability of abundant heterogeneous biological information from diverse data sources, computational methods have been able to leverage multiple drug and target similarities to boost the performance of DTI prediction. Similarity integration is an effective and flexible strategy to extract crucial information across complementary similarity views, providing a compressed input for any similarity-based DTI prediction model. However, existing similarity integration methods filter and fuse similarities from a global perspective, neglecting the utility of similarity views for each drug and target. In this study, we propose a Fine-Grained Selective similarity integration approach, called FGS, which employs a local interaction consistency-based weight matrix to capture and exploit the importance of similarities at a finer granularity in both similarity selection and combination steps. We evaluate FGS on five DTI prediction datasets under various prediction settings. Experimental results show that our method not only outperforms similarity integration competitors with comparable computational costs, but also achieves better prediction performance than state-of-the-art DTI prediction approaches by collaborating with conventional base models. Furthermore, case studies on the analysis of similarity weights and on the verification of novel predictions confirm the practical ability of FGS.
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One of the main challenges in modern recommendation systems is how to effectively utilize multimodal content to achieve more personalized recommendations. Despite various proposed solutions, most of them overlook the mismatch between the knowledge gained from independent feature extraction processes and downstream recommendation tasks. Specifically, multimodal feature extraction processes do not incorporate prior knowledge relevant to recommendation tasks, while recommendation tasks often directly use these multimodal features as side information. This mismatch can lead to model fitting biases and performance degradation, which this paper refers to as the \textit{curse of knowledge} problem. To address this issue, we propose using knowledge soft integration to balance the utilization of multimodal features and the curse of knowledge problem it brings about. To achieve this, we put forward a Knowledge Soft Integration framework for the multimodal recommendation, abbreviated as KSI, which is composed of the Structure Efficiently Injection (SEI) module and the Semantic Soft Integration (SSI) module. In the SEI module, we model the modality correlation between items using Refined Graph Neural Network (RGNN), and introduce a regularization term to reduce the redundancy of user/item representations. In the SSI module, we design a self-supervised retrieval task to further indirectly integrate the semantic knowledge of multimodal features, and enhance the semantic discrimination of item representations. Extensive experiments on three benchmark datasets demonstrate the superiority of KSI and validate the effectiveness of its two modules.
This paper presents Squid, a new conjunctive query synthesis algorithm for searching code with target patterns. Given positive and negative examples along with a natural language description, Squid analyzes the relations derived from the examples by a Datalog-based program analyzer and synthesizes a conjunctive query expressing the search intent. The synthesized query can be further used to search for desired grammatical constructs in the editor. To achieve high efficiency, we prune the huge search space by removing unnecessary relations and enumerating query candidates via refinement. We also introduce two quantitative metrics for query prioritization to select the queries from multiple candidates, yielding desired queries for code search. We have evaluated Squid on over thirty code search tasks. It is shown that Squid successfully synthesizes the conjunctive queries for all the tasks, taking only 2.56 seconds on average.
We develop the first active learning method in the predict-then-optimize framework. Specifically, we develop a learning method that sequentially decides whether to request the "labels" of feature samples from an unlabeled data stream, where the labels correspond to the parameters of an optimization model for decision-making. Our active learning method is the first to be directly informed by the decision error induced by the predicted parameters, which is referred to as the Smart Predict-then-Optimize (SPO) loss. Motivated by the structure of the SPO loss, our algorithm adopts a margin-based criterion utilizing the concept of distance to degeneracy and minimizes a tractable surrogate of the SPO loss on the collected data. In particular, we develop an efficient active learning algorithm with both hard and soft rejection variants, each with theoretical excess risk (i.e., generalization) guarantees. We further derive bounds on the label complexity, which refers to the number of samples whose labels are acquired to achieve a desired small level of SPO risk. Under some natural low-noise conditions, we show that these bounds can be better than the naive supervised learning approach that labels all samples. Furthermore, when using the SPO+ loss function, a specialized surrogate of the SPO loss, we derive a significantly smaller label complexity under separability conditions. We also present numerical evidence showing the practical value of our proposed algorithms in the settings of personalized pricing and the shortest path problem.
Modern advances in machine learning (ML) and wearable medical sensors (WMSs) in edge devices have enabled ML-driven disease detection for smart healthcare. Conventional ML-driven disease detection methods rely on customizing individual models for each disease and its corresponding WMS data. However, such methods lack adaptability to distribution shifts and new task classification classes. Also, they need to be rearchitected and retrained from scratch for each new disease. Moreover, installing multiple ML models in an edge device consumes excessive memory, drains the battery faster, and complicates the detection process. To address these challenges, we propose DOCTOR, a multi-disease detection continual learning (CL) framework based on WMSs. It employs a multi-headed deep neural network (DNN) and an exemplar-replay-style CL algorithm. The CL algorithm enables the framework to continually learn new missions where different data distributions, classification classes, and disease detection tasks are introduced sequentially. It counteracts catastrophic forgetting with a data preservation method and a synthetic data generation module. The data preservation method efficiently preserves the most informative subset of training data from previous missions based on the average training loss of each data instance. The synthetic data generation module models the probability distribution of the real training data and then generates as much synthetic data as needed for replays while maintaining data privacy. The multi-headed DNN enables DOCTOR to detect multiple diseases simultaneously based on user WMS data. We demonstrate DOCTOR's efficacy in maintaining high multi-disease classification accuracy with a single DNN model in various CL experiments. DOCTOR achieves very competitive performance across all CL scenarios relative to the ideal joint-training framework while maintaining a small model size.
Unsupervised domain adaptation has recently emerged as an effective paradigm for generalizing deep neural networks to new target domains. However, there is still enormous potential to be tapped to reach the fully supervised performance. In this paper, we present a novel active learning strategy to assist knowledge transfer in the target domain, dubbed active domain adaptation. We start from an observation that energy-based models exhibit free energy biases when training (source) and test (target) data come from different distributions. Inspired by this inherent mechanism, we empirically reveal that a simple yet efficient energy-based sampling strategy sheds light on selecting the most valuable target samples than existing approaches requiring particular architectures or computation of the distances. Our algorithm, Energy-based Active Domain Adaptation (EADA), queries groups of targe data that incorporate both domain characteristic and instance uncertainty into every selection round. Meanwhile, by aligning the free energy of target data compact around the source domain via a regularization term, domain gap can be implicitly diminished. Through extensive experiments, we show that EADA surpasses state-of-the-art methods on well-known challenging benchmarks with substantial improvements, making it a useful option in the open world. Code is available at //github.com/BIT-DA/EADA.
Link prediction on knowledge graphs (KGs) is a key research topic. Previous work mainly focused on binary relations, paying less attention to higher-arity relations although they are ubiquitous in real-world KGs. This paper considers link prediction upon n-ary relational facts and proposes a graph-based approach to this task. The key to our approach is to represent the n-ary structure of a fact as a small heterogeneous graph, and model this graph with edge-biased fully-connected attention. The fully-connected attention captures universal inter-vertex interactions, while with edge-aware attentive biases to particularly encode the graph structure and its heterogeneity. In this fashion, our approach fully models global and local dependencies in each n-ary fact, and hence can more effectively capture associations therein. Extensive evaluation verifies the effectiveness and superiority of our approach. It performs substantially and consistently better than current state-of-the-art across a variety of n-ary relational benchmarks. Our code is publicly available.
Drug-drug interaction(DDI) prediction is an important task in the medical health machine learning community. This study presents a new method, multi-view graph contrastive representation learning for drug-drug interaction prediction, MIRACLE for brevity, to capture inter-view molecule structure and intra-view interactions between molecules simultaneously. MIRACLE treats a DDI network as a multi-view graph where each node in the interaction graph itself is a drug molecular graph instance. We use GCNs and bond-aware attentive message passing networks to encode DDI relationships and drug molecular graphs in the MIRACLE learning stage, respectively. Also, we propose a novel unsupervised contrastive learning component to balance and integrate the multi-view information. Comprehensive experiments on multiple real datasets show that MIRACLE outperforms the state-of-the-art DDI prediction models consistently.
Recently pre-trained language representation models such as BERT have shown great success when fine-tuned on downstream tasks including information retrieval (IR). However, pre-training objectives tailored for ad-hoc retrieval have not been well explored. In this paper, we propose Pre-training with Representative wOrds Prediction (PROP) for ad-hoc retrieval. PROP is inspired by the classical statistical language model for IR, specifically the query likelihood model, which assumes that the query is generated as the piece of text representative of the "ideal" document. Based on this idea, we construct the representative words prediction (ROP) task for pre-training. Given an input document, we sample a pair of word sets according to the document language model, where the set with higher likelihood is deemed as more representative of the document. We then pre-train the Transformer model to predict the pairwise preference between the two word sets, jointly with the Masked Language Model (MLM) objective. By further fine-tuning on a variety of representative downstream ad-hoc retrieval tasks, PROP achieves significant improvements over baselines without pre-training or with other pre-training methods. We also show that PROP can achieve exciting performance under both the zero- and low-resource IR settings. The code and pre-trained models are available at //github.com/Albert-Ma/PROP.
With the rapid increase of large-scale, real-world datasets, it becomes critical to address the problem of long-tailed data distribution (i.e., a few classes account for most of the data, while most classes are under-represented). Existing solutions typically adopt class re-balancing strategies such as re-sampling and re-weighting based on the number of observations for each class. In this work, we argue that as the number of samples increases, the additional benefit of a newly added data point will diminish. We introduce a novel theoretical framework to measure data overlap by associating with each sample a small neighboring region rather than a single point. The effective number of samples is defined as the volume of samples and can be calculated by a simple formula $(1-\beta^{n})/(1-\beta)$, where $n$ is the number of samples and $\beta \in [0,1)$ is a hyperparameter. We design a re-weighting scheme that uses the effective number of samples for each class to re-balance the loss, thereby yielding a class-balanced loss. Comprehensive experiments are conducted on artificially induced long-tailed CIFAR datasets and large-scale datasets including ImageNet and iNaturalist. Our results show that when trained with the proposed class-balanced loss, the network is able to achieve significant performance gains on long-tailed datasets.
The cross-domain recommendation technique is an effective way of alleviating the data sparsity in recommender systems by leveraging the knowledge from relevant domains. Transfer learning is a class of algorithms underlying these techniques. In this paper, we propose a novel transfer learning approach for cross-domain recommendation by using neural networks as the base model. We assume that hidden layers in two base networks are connected by cross mappings, leading to the collaborative cross networks (CoNet). CoNet enables dual knowledge transfer across domains by introducing cross connections from one base network to another and vice versa. CoNet is achieved in multi-layer feedforward networks by adding dual connections and joint loss functions, which can be trained efficiently by back-propagation. The proposed model is evaluated on two real-world datasets and it outperforms baseline models by relative improvements of 3.56\% in MRR and 8.94\% in NDCG, respectively.
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