State-of-the-Art Evidence Retriever for Precision Medicine: Algorithm Development and Validation.

BACKGROUND: Under the paradigm of precision medicine (PM), patients with the same disease can receive different personalized therapies according to their clinical and genetic features. These therapies are determined by the totality of all available clinical evidence, including results from case reports, clinical trials, and systematic reviews. However, it is increasingly difficult for physicians to find such evidence from scientific publications, whose size is growing at an unprecedented pace. OBJECTIVE: In this work, we propose the PM-Search system to facilitate the retrieval of clinical literature that contains critical evidence for or against giving specific therapies to certain cancer patients. METHODS: The PM-Search system combines a baseline retriever that selects document candidates at a large scale and an evidence reranker that finely reorders the candidates based on their evidence quality. The baseline retriever uses query expansion and keyword matching with the ElasticSearch retrieval engine, and the evidence reranker fits pretrained language models to expert annotations that are derived from an active learning strategy. RESULTS: The PM-Search system achieved the best performance in the retrieval of high-quality clinical evidence at the Text Retrieval Conference PM Track 2020, outperforming the second-ranking systems by large margins (0.4780 vs 0.4238 for standard normalized discounted cumulative gain at rank 30 and 0.4519 vs 0.4193 for exponential normalized discounted cumulative gain at rank 30). CONCLUSIONS: We present PM-Search, a state-of-the-art search engine to assist the practicing of evidence-based PM. PM-Search uses a novel Bidirectional Encoder Representations from Transformers for Biomedical Text Mining-based active learning strategy that models evidence quality and improves the model performance. Our analyses show that evidence quality is a distinct aspect from general relevance, and specific modeling of evidence quality beyond general relevance is required for a PM search engine.

Cross-Modal Knowledge Adaptation for Language-Based Person Search.

In this paper, we present a method named Cross-Modal Knowledge Adaptation (CMKA) for language-based person search. We argue that the image and text information are not equally important in determining a person's identity. In other words, image carries image-specific information such as lighting condition and background, while text contains more modal agnostic information that is more beneficial to cross-modal matching. Based on this consideration, we propose CMKA to adapt the knowledge of image to the knowledge of text. Specially, text-to-image guidance is obtained at different levels: individuals, lists, and classes. By combining these levels of knowledge adaptation, the image-specific information is suppressed, and the common space of image and text is better constructed. We conduct experiments on the CUHK-PEDES dataset. The experimental results show that the proposed CMKA outperforms the state-of-the-art methods.

Feature Pyramid Reconfiguration with Consistent Loss for Object Detection.

Taking the feature pyramids into account has become a crucial way to boost the object detection performance. While various pyramid representations have been developed, previous works are still inefficient to integrate the semantical information over different scales. Moreover, recent object detectors are suffering from accurate object location applications, mainly due to the coarse definition of the "positive" examples at training and predicting phases. In this paper, we begin by analyzing current pyramid solutions, and then propose a novel architecture by reconfiguring the feature hierarchy in a flexible yet effective way. In particular, our architecture consists of two lightweight and trainable processes: global attention and local reconfiguration. The global attention is to emphasize the global information of each feature scale, while the local reconfiguration is to capture the local correlations across different scales. Both the global attention and local reconfiguration are non-linear and thus exhibit more expressive ability. Then, we discover that the loss function for object detectors during training is the central cause of the inaccurate location problem. We propose to address this issue by reshaping the standard cross entropy loss such that it focuses more on accurate predictions. Both the feature reconfiguration and the consistent loss could be utilized in popular one-stage (SSD, RetinaNet) and two-stage (Faster R-CNN) detection frameworks. Extensive experimental evaluations on PASCAL VOC 2007, PASCAL VOC 2012 and MS COCO datasets demonstrate that, our models achieve consistent and significant boosts compared with other state-of-the-art methods.

Electroencephalography Classification in Brain-Computer Interface with Manifold Constraints Transfer.

Insufficient training data is a serious problem in all domains related to bioinformatics. Transfer learning is a promising tool to solve this problem, which relaxes the hypothesis that training data must be independent and identically distributed with the test data. We construct a sophisticated electroencephalography (EEG) signal representation and obtain an efficient EEG feature extractor through manifold constraints-based joint adversarial training with training data from other domains. EEG signal is more easily distinguished in the feature space mapped by the feature extractor. Negative transfer is one of the most challenging problems in transfer learning. In our approach, we apply manifold constraints to overcome this problem, which can avoid the geometric manifolds in the target domain being destroyed. The experiments demonstrate that our approach has many advantages when applied to EEG classification tasks.

Low-Rank Linear Dynamical Systems for Motor Imagery EEG.

The common spatial pattern (CSP) and other spatiospectral feature extraction methods have become the most effective and successful approaches to solve the problem of motor imagery electroencephalography (MI-EEG) pattern recognition from multichannel neural activity in recent years. However, these methods need a lot of preprocessing and postprocessing such as filtering, demean, and spatiospectral feature fusion, which influence the classification accuracy easily. In this paper, we utilize linear dynamical systems (LDSs) for EEG signals feature extraction and classification. LDSs model has lots of advantages such as simultaneous spatial and temporal feature matrix generation, free of preprocessing or postprocessing, and low cost. Furthermore, a low-rank matrix decomposition approach is introduced to get rid of noise and resting state component in order to improve the robustness of the system. Then, we propose a low-rank LDSs algorithm to decompose feature subspace of LDSs on finite Grassmannian and obtain a better performance. Extensive experiments are carried out on public dataset from "BCI Competition III Dataset IVa" and "BCI Competition IV Database 2a." The results show that our proposed three methods yield higher accuracies compared with prevailing approaches such as CSP and CSSP.