Objective: High-throughput phenotyping will accelerate the use of electronic health records (EHRs) for translational research. A critical roadblock is the extensive medical supervision required for phenotyping algorithm (PA) estimation and evaluation. To address this challenge, numerous weakly-supervised learning methods have been proposed. However, there is a paucity of methods for reliably evaluating the predictive performance of PAs when a very small proportion of the data is labeled. To fill this gap, we introduce a semi-supervised approach (ssROC) for estimation of the receiver operating characteristic (ROC) parameters of PAs (e.g., sensitivity, specificity). Materials and Methods: ssROC uses a small labeled dataset to nonparametrically impute missing labels. The imputations are then used for ROC parameter estimation to yield more precise estimates of PA performance relative to classical supervised ROC analysis (supROC) using only labeled data. We evaluated ssROC with synthetic, semi-synthetic, and EHR data from Mass General Brigham (MGB). Results: ssROC produced ROC parameter estimates with minimal bias and significantly lower variance than supROC in the simulated and semi-synthetic data. For the five PAs from MGB, the estimates from ssROC are 30% to 60% less variable than supROC on average. Discussion: ssROC enables precise evaluation of PA performance without demanding large volumes of labeled data. ssROC is also easily implementable in open-source R software. Conclusion: When used in conjunction with weakly-supervised PAs, ssROC facilitates the reliable and streamlined phenotyping necessary for EHR-based research.
Spiking neural networks (SNNs) have been thriving on numerous tasks to leverage their promising energy efficiency and exploit their potentialities as biologically plausible intelligence. Meanwhile, the Neural Radiance Fields (NeRF) render high-quality 3D scenes with massive energy consumption, but few works delve into the energy-saving solution with a bio-inspired approach. In this paper, we propose SpikingNeRF, which aligns the radiance ray with the temporal dimension of SNN, to naturally accommodate the SNN to the reconstruction of Radiance Fields. Thus, the computation turns into a spike-based, multiplication-free manner, reducing the energy consumption. In SpikingNeRF, each sampled point on the ray is matched onto a particular time step, and represented in a hybrid manner where the voxel grids are maintained as well. Based on the voxel grids, sampled points are determined whether to be masked for better training and inference. However, this operation also incurs irregular temporal length. We propose the temporal padding strategy to tackle the masked samples to maintain regular temporal length, i.e., regular tensors, and the temporal condensing strategy to form a denser data structure for hardware-friendly computation. Extensive experiments on various datasets demonstrate that our method reduces the 70.79% energy consumption on average and obtains comparable synthesis quality with the ANN baseline.
Fairness in Language Models (LMs) remains a longstanding challenge, given the inherent biases in training data that can be perpetuated by models and affect the downstream tasks. Recent methods employ expensive retraining or attempt debiasing during inference by constraining model outputs to contrast from a reference set of biased templates or exemplars. Regardless, they dont address the primary goal of fairness to maintain equitability across different demographic groups. In this work, we posit that inferencing LMs to generate unbiased output for one demographic under a context ensues from being aware of outputs for other demographics under the same context. To this end, we propose Counterfactually Aware Fair InferencE (CAFIE), a framework that dynamically compares the model understanding of diverse demographics to generate more equitable sentences. We conduct an extensive empirical evaluation using base LMs of varying sizes and across three diverse datasets and found that CAFIE outperforms strong baselines. CAFIE produces fairer text and strikes the best balance between fairness and language modeling capability
Large language models (LLMs) have shown impressive capabilities across various natural language tasks. However, evaluating their alignment with human preferences remains a challenge. To this end, we propose a comprehensive human evaluation framework to assess LLMs' proficiency in following instructions on diverse real-world tasks. We construct a hierarchical task tree encompassing 7 major areas covering over 200 categories and over 800 tasks, which covers diverse capabilities such as question answering, reasoning, multiturn dialogue, and text generation, to evaluate LLMs in a comprehensive and in-depth manner. We also design detailed evaluation standards and processes to facilitate consistent, unbiased judgments from human evaluators. A test set of over 3,000 instances is released, spanning different difficulty levels and knowledge domains. Our work provides a standardized methodology to evaluate human alignment in LLMs for both English and Chinese. We also analyze the feasibility of automating parts of evaluation with a strong LLM (GPT-4). Our framework supports a thorough assessment of LLMs as they are integrated into real-world applications. We have made publicly available the task tree, TencentLLMEval dataset, and evaluation methodology which have been demonstrated as effective in assessing the performance of Tencent Hunyuan LLMs. By doing so, we aim to facilitate the benchmarking of advances in the development of safe and human-aligned LLMs.
Binarization is a powerful compression technique for neural networks, significantly reducing FLOPs, but often results in a significant drop in model performance. To address this issue, partial binarization techniques have been developed, but a systematic approach to mixing binary and full-precision parameters in a single network is still lacking. In this paper, we propose a controlled approach to partial binarization, creating a budgeted binary neural network (B2NN) with our MixBin strategy. This method optimizes the mixing of binary and full-precision components, allowing for explicit selection of the fraction of the network to remain binary. Our experiments show that B2NNs created using MixBin outperform those from random or iterative searches and state-of-the-art layer selection methods by up to 3% on the ImageNet-1K dataset. We also show that B2NNs outperform the structured pruning baseline by approximately 23% at the extreme FLOP budget of 15%, and perform well in object tracking, with up to a 12.4% relative improvement over other baselines. Additionally, we demonstrate that B2NNs developed by MixBin can be transferred across datasets, with some cases showing improved performance over directly applying MixBin on the downstream data.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
Recently, Mutual Information (MI) has attracted attention in bounding the generalization error of Deep Neural Networks (DNNs). However, it is intractable to accurately estimate the MI in DNNs, thus most previous works have to relax the MI bound, which in turn weakens the information theoretic explanation for generalization. To address the limitation, this paper introduces a probabilistic representation of DNNs for accurately estimating the MI. Leveraging the proposed MI estimator, we validate the information theoretic explanation for generalization, and derive a tighter generalization bound than the state-of-the-art relaxations.
With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.
Many tasks in natural language processing can be viewed as multi-label classification problems. However, most of the existing models are trained with the standard cross-entropy loss function and use a fixed prediction policy (e.g., a threshold of 0.5) for all the labels, which completely ignores the complexity and dependencies among different labels. In this paper, we propose a meta-learning method to capture these complex label dependencies. More specifically, our method utilizes a meta-learner to jointly learn the training policies and prediction policies for different labels. The training policies are then used to train the classifier with the cross-entropy loss function, and the prediction policies are further implemented for prediction. Experimental results on fine-grained entity typing and text classification demonstrate that our proposed method can obtain more accurate multi-label classification results.
We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.
Many natural language processing tasks solely rely on sparse dependencies between a few tokens in a sentence. Soft attention mechanisms show promising performance in modeling local/global dependencies by soft probabilities between every two tokens, but they are not effective and efficient when applied to long sentences. By contrast, hard attention mechanisms directly select a subset of tokens but are difficult and inefficient to train due to their combinatorial nature. In this paper, we integrate both soft and hard attention into one context fusion model, "reinforced self-attention (ReSA)", for the mutual benefit of each other. In ReSA, a hard attention trims a sequence for a soft self-attention to process, while the soft attention feeds reward signals back to facilitate the training of the hard one. For this purpose, we develop a novel hard attention called "reinforced sequence sampling (RSS)", selecting tokens in parallel and trained via policy gradient. Using two RSS modules, ReSA efficiently extracts the sparse dependencies between each pair of selected tokens. We finally propose an RNN/CNN-free sentence-encoding model, "reinforced self-attention network (ReSAN)", solely based on ReSA. It achieves state-of-the-art performance on both Stanford Natural Language Inference (SNLI) and Sentences Involving Compositional Knowledge (SICK) datasets.