Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension

Although deep learning techniques have shown significant achievements, they frequently depend on extensive amounts of hand-labeled data and tend to perform inadequately in few-shot scenarios. The objective of this study is to devise a strategy that can improve the model's capability to recognize biomedical entities in scenarios of few-shot learning. By redefining biomedical named entity recognition (BioNER) as a machine reading comprehension (MRC) problem, we propose a demonstration-based learning method to address few-shot BioNER, which involves constructing appropriate task demonstrations. In assessing our proposed method, we compared the proposed method with existing advanced methods using six benchmark datasets, including BC4CHEMD, BC5CDR-Chemical, BC5CDR-Disease, NCBI-Disease, BC2GM, and JNLPBA. We examined the models' efficacy by reporting F1 scores from both the 25-shot and 50-shot learning experiments. In 25-shot learning, we observed 1.1% improvements in the average F1 scores compared to the baseline method, reaching 61.7%, 84.1%, 69.1%, 70.1%, 50.6%, and 59.9% on six datasets, respectively. In 50-shot learning, we further improved the average F1 scores by 1.0% compared to the baseline method, reaching 73.1%, 86.8%, 76.1%, 75.6%, 61.7%, and 65.4%, respectively. We reported that in the realm of few-shot learning BioNER, MRC-based language models are much more proficient in recognizing biomedical entities compared to the sequence labeling approach. Furthermore, our MRC-language models can compete successfully with fully-supervised learning methodologies that rely heavily on the availability of abundant annotated data. These results highlight possible pathways for future advancements in few-shot BioNER methodologies.

A Motion Assessment Method for Reference Stack Selection in Fetal Brain MRI Reconstruction Based on Tensor Rank Approximation

Purpose: Slice-to-volume registration and super-resolution reconstruction (SVR-SRR) is commonly used to generate 3D volumes of the fetal brain from 2D stacks of slices acquired in multiple orientations. A critical initial step in this pipeline is to select one stack with the minimum motion as a reference for registration. An accurate and unbiased motion assessment (MA) is thus crucial for successful selection. Methods: We presented a MA method that determines the minimum motion stack based on 3D low-rank approximation using CANDECOMP/PARAFAC (CP) decomposition. Compared to the current 2D singular value decomposition (SVD) based method that requires flattening stacks into matrices to obtain ranks, in which the spatial information is lost, the CP-based method can factorize 3D stack into low-rank and sparse components in a computationally efficient manner. The difference between the original stack and its low-rank approximation was proposed as the motion indicator. Results: Compared to SVD-based methods, our proposed CP-based MA demonstrated higher sensitivity in detecting small motion with a lower baseline bias. Experiments on randomly simulated motion illustrated that the proposed CP method achieved a higher success rate of 95.45% in identifying the minimum motion stack, compared to SVD-based method with a success rate of 58.18%. We further demonstrated that combining CP-based MA with existing SRR-SVR pipeline significantly improved 3D volume reconstruction. Conclusion: The proposed CP-based MA method showed superior performance compared to SVD-based methods with higher sensitivity to motion, success rate, and lower baseline bias, and can be used as a prior step to improve fetal brain reconstruction.

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.

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%.

Resource allocation for reconfigurable intelligent surface aided broadcast channels

A two-user downlink network aided by a reconfigurable intelligent surface is considered. The weighted sum signal to interference plus noise ratio maximization and the sum rate maximization models are presented, where the precoding vectors and the RIS matrix are jointly optimized. Since the optimization problem is non-convex and difficult, new approximation models are proposed. The upper bounds of the corresponding objective functions are derived and maximized. Two new algorithms based on the alternating direction method of multiplier are proposed. It is proved that the proposed algorithms converge to the KKT points of the approximation models as long as the iteration points converge. Simulation results show the good performances of the proposed models compared to state of the art algorithms.

Reconfigurable Intelligent Surface Enabled Spatial Multiplexing with Fully Convolutional Network

Reconfigurable intelligent surface (RIS) is an emerging technology for future wireless communication systems. In this work, we consider downlink spatial multiplexing enabled by the RIS for weighted sum-rate (WSR) maximization. In the literature, most solutions use alternating gradient-based optimization, which has moderate performance, high complexity, and limited scalability. We propose to apply a fully convolutional network (FCN) to solve this problem, which was originally designed for semantic segmentation of images. The rectangular shape of the RIS and the spatial correlation of channels with adjacent RIS antennas due to the short distance between them encourage us to apply it for the RIS configuration. We design a set of channel features that includes both cascaded channels via the RIS and the direct channel. In the base station (BS), the differentiable minimum mean squared error (MMSE) precoder is used for pretraining and the weighted minimum mean squared error (WMMSE) precoder is then applied for fine-tuning, which is nondifferentiable, more complex, but achieves a better performance. Evaluation results show that the proposed solution has higher performance and allows for a faster evaluation than the baselines. Hence it scales better to a large number of antennas, advancing the RIS one step closer to practical deployment.

Control Parameters Considered Harmful: Detecting Range Specification Bugs in Drone Configuration Modules via Learning-Guided Search

In order to support a variety of missions and deal with different flight environments, drone control programs typically provide configurable control parameters. However, such a flexibility introduces vulnerabilities. One such vulnerability, referred to as range specification bugs, has been recently identified. The vulnerability originates from the fact that even though each individual parameter receives a value in the recommended value range, certain combinations of parameter values may affect the drone physical stability. In this paper we develop a novel learning-guided search system to find such combinations, that we refer to as incorrect configurations. Our system applies metaheuristic search algorithms mutating configurations to detect the configuration parameters that have values driving the drone to unstable physical states. To guide the mutations, our system leverages a machine learning predictor as the fitness evaluator. Finally, by utilizing multi-objective optimization, our system returns the feasible ranges based on the mutation search results. Because in our system the mutations are guided by a predictor, evaluating the parameter configurations does not require realistic/simulation executions. Therefore, our system supports a comprehensive and yet efficient detection of incorrect configurations. We have carried out an experimental evaluation of our system. The evaluation results show that the system successfully reports potentially incorrect configurations, of which over 85% lead to actual unstable physical states.

Biomedical named entity recognition using BERT in the machine reading comprehension framework

Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence labeling framework to implement biomedical named entity recognition (BioNER) is currently a conventional method. This method, however, often cannot take full advantage of the semantic information in the dataset, and the performance is not always satisfactory. In this work, instead of treating the BioNER task as a sequence labeling problem, we formulate it as a machine reading comprehension (MRC) problem. This formulation can introduce more prior knowledge utilizing well-designed queries, and no longer need decoding processes such as conditional random fields (CRF). We conduct experiments on six BioNER datasets, and the experimental results demonstrate the effectiveness of our method. Our method achieves state-of-the-art (SOTA) performance on the BC4CHEMD, BC5CDR-Chem, BC5CDR-Disease, NCBI Disease, BC2GM and JNLPBA datasets, with F1-scores of 92.38%, 94.19%, 87.36%, 90.04%, 84.98% and 78.93%, respectively.

Chemical-protein Interaction Extraction via Gaussian Probability Distribution and External Biomedical Knowledge

The biomedical literature contains a wealth of chemical-protein interactions (CPIs). Automatically extracting CPIs described in biomedical literature is essential for drug discovery, precision medicine, as well as basic biomedical research. However, the existing methods do not consider the impact of overlapping relations on CPI extraction. This leads to the extraction of sentences with overlapping relations becoming the bottleneck of CPI extraction. In this paper, we propose a novel neural network-based approach to improve the CPI extraction performance of sentences with overlapping relations. Specifically, the approach first employs BERT to generate high-quality contextual representations of the title sequence, instance sequence, and knowledge sequence. Then, the Gaussian probability distribution is introduced to capture the local structure of the instance. Meanwhile, the attention mechanism is applied to fuse the title information and biomedical knowledge, respectively. Finally, the related representations are concatenated and fed into the softmax function to extract CPIs. We evaluate our proposed model on the CHEMPROT corpus. Our proposed model is superior in performance as compared with other state-of-the-art models. The experimental results show that the Gaussian probability distribution and external knowledge are complementary to each other. Integrating them can effectively improve the CPI extraction performance. Furthermore, the Gaussian probability distribution can significantly improve the extraction performance of sentences with overlapping relations in biomedical relation extraction tasks. Data and code are available at https://github.com/CongSun-dlut/CPI_extraction.