Despite their general capabilities, LLMs still struggle on biomedical NER tasks, which are difficult due to the presence of specialized terminology and lack of training data. In this work we set out to improve LLM performance on biomedical NER in limited data settings via a new knowledge augmentation approach which incorporates definitions of relevant concepts on-the-fly. During this process, to provide a test bed for knowledge augmentation, we perform a comprehensive exploration of prompting strategies. Our experiments show that definition augmentation is useful for both open source and closed LLMs. For example, it leads to a relative improvement of 15\% (on average) in GPT-4 performance (F1) across all (six) of our test datasets. We conduct extensive ablations and analyses to demonstrate that our performance improvements stem from adding relevant definitional knowledge. We find that careful prompting strategies also improve LLM performance, allowing them to outperform fine-tuned language models in few-shot settings. To facilitate future research in this direction, we release our code at //github.com/allenai/beacon.
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Nutrition estimation is crucial for effective dietary management and overall health and well-being. Existing methods often struggle with sub-optimal accuracy and can be time-consuming. In this paper, we propose NuNet, a transformer-based network designed for nutrition estimation that utilizes both RGB and depth information from food images. We have designed and implemented a multi-scale encoder and decoder, along with two types of feature fusion modules, specialized for estimating five nutritional factors. These modules effectively balance the efficiency and effectiveness of feature extraction with flexible usage of our customized attention mechanisms and fusion strategies. Our experimental study shows that NuNet outperforms its variants and existing solutions significantly for nutrition estimation. It achieves an error rate of 15.65%, the lowest known to us, largely due to our multi-scale architecture and fusion modules. This research holds practical values for dietary management with huge potential for transnational research and deployment and could inspire other applications involving multiple data types with varying degrees of importance.
Symmetries exist abundantly in the loss function of neural networks. We characterize the learning dynamics of stochastic gradient descent (SGD) when exponential symmetries, a broad subclass of continuous symmetries, exist in the loss function. We establish that when gradient noises do not balance, SGD has the tendency to move the model parameters toward a point where noises from different directions are balanced. Here, a special type of fixed point in the constant directions of the loss function emerges as a candidate for solutions for SGD. As the main theoretical result, we prove that every parameter $\theta$ connects without loss function barrier to a unique noise-balanced fixed point $\theta^*$. The theory implies that the balancing of gradient noise can serve as a novel alternative mechanism for relevant phenomena such as progressive sharpening and flattening and can be applied to understand common practical problems such as representation normalization, matrix factorization, warmup, and formation of latent representations.
With the continuous development and improvement of medical services, there is a growing demand for improving diabetes diagnosis. Exhaled breath analysis, characterized by its speed, convenience, and non-invasive nature, is leading the trend in diagnostic development. Studies have shown that the acetone levels in the breath of diabetes patients are higher than normal, making acetone a basis for diabetes breath analysis. This provides a more readily accepted method for early diabetes prevention and monitoring. Addressing issues such as the invasive nature, disease transmission risks, and complexity of diabetes testing, this study aims to design a diabetes gas biomarker acetone detection system centered around a sensor array using gas sensors and pattern recognition algorithms. The research covers sensor selection, sensor preparation, circuit design, data acquisition and processing, and detection model establishment to accurately identify acetone. Titanium dioxide was chosen as the nano gas-sensitive material to prepare the acetone gas sensor, with data collection conducted using STM32. Filtering was applied to process the raw sensor data, followed by feature extraction using principal component analysis. A recognition model based on support vector machine algorithm was used for qualitative identification of gas samples, while a recognition model based on backpropagation neural network was employed for quantitative detection of gas sample concentrations. Experimental results demonstrated recognition accuracies of 96% and 97.5% for acetone-ethanol and acetone-methanol mixed gases, and 90% for ternary acetone, ethanol, and methanol mixed gases.
Reading fluency assessment is a critical component of literacy programmes, serving to guide and monitor early education interventions. Given the resource intensive nature of the exercise when conducted by teachers, the development of automatic tools that can operate on audio recordings of oral reading is attractive as an objective and highly scalable solution. Multiple complex aspects such as accuracy, rate and expressiveness underlie human judgements of reading fluency. In this work, we investigate end-to-end modeling on a training dataset of children's audio recordings of story texts labeled by human experts. The pre-trained wav2vec2.0 model is adopted due its potential to alleviate the challenges from the limited amount of labeled data. We report the performance of a number of system variations on the relevant measures, and also probe the learned embeddings for lexical and acoustic-prosodic features known to be important to the perception of reading fluency.
Branch-and-bound (BaB) is among the most effective methods for neural network (NN) verification. However, existing works on BaB have mostly focused on NNs with piecewise linear activations, especially ReLU networks. In this paper, we develop a general framework, named GenBaB, to conduct BaB for general nonlinearities in general computational graphs based on linear bound propagation. To decide which neuron to branch, we design a new branching heuristic which leverages linear bounds as shortcuts to efficiently estimate the potential improvement after branching. To decide nontrivial branching points for general nonlinear functions, we propose to optimize branching points offline, which can be efficiently leveraged during verification with a lookup table. We demonstrate the effectiveness of our GenBaB on verifying a wide range of NNs, including networks with activation functions such as Sigmoid, Tanh, Sine and GeLU, as well as networks involving multi-dimensional nonlinear operations such as multiplications in LSTMs and Vision Transformers. Our framework also allows the verification of general nonlinear computation graphs and enables verification applications beyond simple neural networks, particularly for AC Optimal Power Flow (ACOPF). GenBaB is part of the latest $\alpha,\!\beta$-CROWN, the winner of the 4th International Verification of Neural Networks Competition (VNN-COMP 2023).
The Sequential Sentence Classification task within the domain of medical abstracts, termed as SSC, involves the categorization of sentences into pre-defined headings based on their roles in conveying critical information in the abstract. In the SSC task, sentences are sequentially related to each other. For this reason, the role of sentence embeddings is crucial for capturing both the semantic information between words in the sentence and the contextual relationship of sentences within the abstract, which then enhances the SSC system performance. In this paper, we propose a LSTM-based deep learning network with a focus on creating comprehensive sentence representation at the sentence level. To demonstrate the efficacy of the created sentence representation, a system utilizing these sentence embeddings is also developed, which consists of a Convolutional-Recurrent neural network (C-RNN) at the abstract level and a multi-layer perception network (MLP) at the segment level. Our proposed system yields highly competitive results compared to state-of-the-art systems and further enhances the F1 scores of the baseline by 1.0%, 2.8%, and 2.6% on the benchmark datasets PudMed 200K RCT, PudMed 20K RCT and NICTA-PIBOSO, respectively. This indicates the significant impact of improving sentence representation on boosting model performance.
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.
Due to their increasing spread, confidence in neural network predictions became more and more important. However, basic neural networks do not deliver certainty estimates or suffer from over or under confidence. Many researchers have been working on understanding and quantifying uncertainty in a neural network's prediction. As a result, different types and sources of uncertainty have been identified and a variety of approaches to measure and quantify uncertainty in neural networks have been proposed. This work gives a comprehensive overview of uncertainty estimation in neural networks, reviews recent advances in the field, highlights current challenges, and identifies potential research opportunities. It is intended to give anyone interested in uncertainty estimation in neural networks a broad overview and introduction, without presupposing prior knowledge in this field. A comprehensive introduction to the most crucial sources of uncertainty is given and their separation into reducible model uncertainty and not reducible data uncertainty is presented. The modeling of these uncertainties based on deterministic neural networks, Bayesian neural networks, ensemble of neural networks, and test-time data augmentation approaches is introduced and different branches of these fields as well as the latest developments are discussed. For a practical application, we discuss different measures of uncertainty, approaches for the calibration of neural networks and give an overview of existing baselines and implementations. Different examples from the wide spectrum of challenges in different fields give an idea of the needs and challenges regarding uncertainties in practical applications. Additionally, the practical limitations of current methods for mission- and safety-critical real world applications are discussed and an outlook on the next steps towards a broader usage of such methods is given.
We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.
Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.
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