Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations. Retrieval-augmented generation provided a solution for these models to update knowledge and enhance their performance. In contrast to previous retrieval-augmented LMs, which utilize specialized cross-attention mechanisms to help LLM encode retrieved text, BiomedRAG adopts a simpler approach by directly inputting the retrieved chunk-based documents into the LLM. This straightforward design is easily applicable to existing retrieval and language models, effectively bypassing noise information in retrieved documents, particularly in noise-intensive tasks. Moreover, we demonstrate the potential for utilizing the LLM to supervise the retrieval model in the biomedical domain, enabling it to retrieve the document that assists the LM in improving its predictions. Our experiments reveal that with the tuned scorer,\textsc{ BiomedRAG} attains superior performance across 5 biomedical NLP tasks, encompassing information extraction (triple extraction, relation extraction), text classification, link prediction, and question-answering, leveraging over 9 datasets. For instance, in the triple extraction task, \textsc{BiomedRAG} outperforms other triple extraction systems with micro-F1 scores of 81.42 and 88.83 on GIT and ChemProt corpora, respectively.
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ACM/IEEE第23屆模型驅動工程語言和系統國際會議，是模型驅動軟件和系統工程的首要會議系列，由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來，模型涵蓋了建模的各個方面，從語言和方法到工具和應用程序。模特的參加者來自不同的背景，包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇，參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會，并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。
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Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at //github.com/NYUSHCS/GraphFM.
Segmentation has become a crucial pre-processing step to many refined downstream tasks, and particularly so in the medical domain. Even with recent improvements in segmentation models, many segmentation tasks remain difficult. When multiple organs are segmented simultaneously, difficulties are due not only to the limited availability of labelled data, but also to class imbalance. In this work we propose dynamic class-based loss strategies to mitigate the effects of highly imbalanced training data. We show how our approach improves segmentation performance on a challenging Multi-Class 3D Abdominal Organ dataset.
Conditional Independence (CI) graphs are a type of probabilistic graphical models that are primarily used to gain insights about feature relationships. Each edge represents the partial correlation between the connected features which gives information about their direct dependence. In this survey, we list out different methods and study the advances in techniques developed to recover CI graphs. We cover traditional optimization methods as well as recently developed deep learning architectures along with their recommended implementations. To facilitate wider adoption, we include preliminaries that consolidate associated operations, for example techniques to obtain covariance matrix for mixed datatypes.
Recently, brain-inspired spiking neural networks (SNNs) have attracted great research attention owing to their inherent bio-interpretability, event-triggered properties and powerful perception of spatiotemporal information, which is beneficial to handling event-based neuromorphic datasets. In contrast to conventional static image datasets, event-based neuromorphic datasets present heightened complexity in feature extraction due to their distinctive time series and sparsity characteristics, which influences their classification accuracy. To overcome this challenge, a novel approach termed Neuromorphic Momentum Contrast Learning (NeuroMoCo) for SNNs is introduced in this paper by extending the benefits of self-supervised pre-training to SNNs to effectively stimulate their potential. This is the first time that self-supervised learning (SSL) based on momentum contrastive learning is realized in SNNs. In addition, we devise a novel loss function named MixInfoNCE tailored to their temporal characteristics to further increase the classification accuracy of neuromorphic datasets, which is verified through rigorous ablation experiments. Finally, experiments on DVS-CIFAR10, DVS128Gesture and N-Caltech101 have shown that NeuroMoCo of this paper establishes new state-of-the-art (SOTA) benchmarks: 83.6% (Spikformer-2-256), 98.62% (Spikformer-2-256), and 84.4% (SEW-ResNet-18), respectively.
Large Language Models are prone to biased predictions and hallucinations, underlining the paramount importance of understanding their model-internal reasoning process. However, achieving faithful attributions for the entirety of a black-box transformer model and maintaining computational efficiency is an unsolved challenge. By extending the Layer-wise Relevance Propagation attribution method to handle attention layers, we address these challenges effectively. While partial solutions exist, our method is the first to faithfully and holistically attribute not only input but also latent representations of transformer models with the computational efficiency similar to a single backward pass. Through extensive evaluations against existing methods on LLaMa 2, Mixtral 8x7b, Flan-T5 and vision transformer architectures, we demonstrate that our proposed approach surpasses alternative methods in terms of faithfulness and enables the understanding of latent representations, opening up the door for concept-based explanations. We provide an LRP library at //github.com/rachtibat/LRP-eXplains-Transformers.
Artificial intelligence-enhanced identification of organs, lesions, and other structures in medical imaging is typically done using convolutional neural networks (CNNs) designed to make voxel-accurate segmentations of the region of interest. However, the labels required to train these CNNs are time-consuming to generate and require attention from subject matter experts to ensure quality. For tasks where voxel-level precision is not required, object detection models offer a viable alternative that can reduce annotation effort. Despite this potential application, there are few options for general purpose object detection frameworks available for 3-D medical imaging. We report on MedYOLO, a 3-D object detection framework using the one-shot detection method of the YOLO family of models and designed for use with medical imaging. We tested this model on four different datasets: BRaTS, LIDC, an abdominal organ Computed Tomography (CT) dataset, and an ECG-gated heart CT dataset. We found our models achieve high performance on commonly present medium and large-sized structures such as the heart, liver, and pancreas even without hyperparameter tuning. However, the models struggle with very small or rarely present structures.
The recently unprecedented advancements in Large Language Models (LLMs) have propelled the medical community by establishing advanced medical-domain models. However, due to the limited collection of medical datasets, there are only a few comprehensive benchmarks available to gauge progress in this area. In this paper, we introduce a new medical question-answering (QA) dataset that contains massive manual instruction for solving Traditional Chinese Medicine examination tasks, called TCMD. Specifically, our TCMD collects massive questions across diverse domains with their annotated medical subjects and thus supports us in comprehensively assessing the capability of LLMs in the TCM domain. Extensive evaluation of various general LLMs and medical-domain-specific LLMs is conducted. Moreover, we also analyze the robustness of current LLMs in solving TCM QA tasks by introducing randomness. The inconsistency of the experimental results also reveals the shortcomings of current LLMs in solving QA tasks. We also expect that our dataset can further facilitate the development of LLMs in the TCM area.
Graph Neural Networks (GNNs) have advanced the field of machine learning by utilizing graph-structured data, which is ubiquitous in the real world. GNNs have applications in various fields, ranging from social network analysis to drug discovery. GNN training is strenuous, requiring significant computational resources and human expertise. It makes a trained GNN an indispensable Intellectual Property (IP) for its owner. Recent studies have shown GNNs to be vulnerable to model-stealing attacks, which raises concerns over IP rights protection. Watermarking has been shown to be effective at protecting the IP of a GNN model. Existing efforts to develop a watermarking scheme for GNNs have only focused on the node classification and the graph classification tasks. To the best of our knowledge, we introduce the first-ever watermarking scheme for GNNs tailored to the Link Prediction (LP) task. We call our proposed watermarking scheme GENIE (watermarking Graph nEural Networks for lInk prEdiction). We design GENIE using a novel backdoor attack to create a trigger set for two key methods of LP: (1) node representation-based and (2) subgraph-based. In GENIE, the watermark is embedded into the GNN model by training it on both the trigger set and a modified training set, resulting in a watermarked GNN model. To assess a suspect model, we verify the watermark against the trigger set. We extensively evaluate GENIE across 3 model architectures (i.e., SEAL, GCN, and GraphSAGE) and 7 real-world datasets. Furthermore, we validate the robustness of GENIE against 11 state-of-the-art watermark removal techniques and 3 model extraction attacks. We also demonstrate that GENIE is robust against ownership piracy attack. Our ownership demonstration scheme statistically guarantees both False Positive Rate (FPR) and False Negative Rate (FNR) to be less than $10^{-6}$.
Large Language Models (LLMs) are being used for a wide variety of tasks. While they are capable of generating human-like responses, they can also produce undesirable output including potentially harmful information, racist or sexist language, and hallucinations. Alignment methods are designed to reduce such undesirable output, via techniques such as fine-tuning, prompt engineering, and representation engineering. However, existing methods face several challenges: some require costly fine-tuning for every alignment task; some do not adequately remove undesirable concepts, failing alignment; some remove benign concepts, lowering the linguistic capabilities of LLMs. To address these issues, we propose Parsimonious Concept Engineering (PaCE), a novel activation engineering framework for alignment. First, to sufficiently model the concepts, we construct a large-scale concept dictionary in the activation space, in which each atom corresponds to a semantic concept. Then, given any alignment task, we instruct a concept partitioner to efficiently annotate the concepts as benign or undesirable. Finally, at inference time, we decompose the LLM activations along the concept dictionary via sparse coding, to accurately represent the activation as a linear combination of the benign and undesirable components. By removing the latter ones from the activation, we reorient the behavior of LLMs towards alignment goals. We conduct experiments on tasks such as response detoxification, faithfulness enhancement, and sentiment revising, and show that PaCE achieves state-of-the-art alignment performance while maintaining linguistic capabilities.
Convolutional Neural Networks (CNNs) have gained significant traction in the field of machine learning, particularly due to their high accuracy in visual recognition. Recent works have pushed the performance of GPU implementations of CNNs to significantly improve their classification and training times. With these improvements, many frameworks have become available for implementing CNNs on both CPUs and GPUs, with no support for FPGA implementations. In this work we present a modified version of the popular CNN framework Caffe, with FPGA support. This allows for classification using CNN models and specialized FPGA implementations with the flexibility of reprogramming the device when necessary, seamless memory transactions between host and device, simple-to-use test benches, and the ability to create pipelined layer implementations. To validate the framework, we use the Xilinx SDAccel environment to implement an FPGA-based Winograd convolution engine and show that the FPGA layer can be used alongside other layers running on a host processor to run several popular CNNs (AlexNet, GoogleNet, VGG A, Overfeat). The results show that our framework achieves 50 GFLOPS across 3x3 convolutions in the benchmarks. This is achieved within a practical framework, which will aid in future development of FPGA-based CNNs.
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