Efficient sampling of the Boltzmann distribution of molecular systems is a long-standing challenge. Recently, instead of generating long molecular dynamics simulations, generative machine learning methods such as normalizing flows have been used to learn the Boltzmann distribution directly, without samples. However, this approach is susceptible to mode collapse and thus often does not explore the full configurational space. In this work, we address this challenge by separating the problem into two levels, the fine-grained and coarse-grained degrees of freedom. A normalizing flow conditioned on the coarse-grained space yields a probabilistic connection between the two levels. To explore the configurational space, we employ coarse-grained simulations with active learning which allows us to update the flow and make all-atom potential energy evaluations only when necessary. Using alanine dipeptide as an example, we show that our methods obtain a speedup to molecular dynamics simulations of approximately 15.9 to 216.2 compared to the speedup of 4.5 of the current state-of-the-art machine learning approach.
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Deep Learning (DL) models have gained popularity in neuroimaging studies for predicting psychological behaviors, cognitive traits, and brain pathologies. However, these models can be biased by confounders such as age, sex, or imaging artifacts from the acquisition process. To address this, we introduce 'DeepRepViz', a two-part framework designed to identify confounders in DL model predictions. The first component is a visualization tool that can be used to qualitatively examine the final latent representation of the DL model. The second component is a metric called 'Con-score' that quantifies the confounder risk associated with a variable, using the final latent representation of the DL model. We demonstrate the effectiveness of the Con-score using a simple simulated setup by iteratively altering the strength of a simulated confounder and observing the corresponding change in the Con-score. Next, we validate the DeepRepViz framework on a large-scale neuroimaging dataset (n=12000) by performing three MRI-phenotype prediction tasks that include (a) predicting chronic alcohol users, (b) classifying participant sex, and (c) predicting performance speed on a cognitive task called 'trail making'. DeepRepViz identifies sex as a significant confounder in the DL model predicting chronic alcohol users (Con-score=0.35) and age as a confounder in the model predicting cognitive task performance (Con-score=0.3). In conclusion, the DeepRepViz framework provides a systematic approach to test for potential confounders such as age, sex, and imaging artifacts and improves the transparency of DL models for neuroimaging studies.
Machine Learning (ML) is becoming increasingly important for IoT-based applications. However, the dynamic and ad-hoc nature of many IoT ecosystems poses unique challenges to the efficacy of ML algorithms. One such challenge is data incompleteness, which is manifested as missing sensor readings. Many factors, including sensor failures and/or network disruption, can cause data incompleteness. Furthermore, most IoT systems are severely power-constrained. It is important that we build IoT-based ML systems that are robust against data incompleteness while simultaneously being energy efficient. This paper presents an empirical study of SECOE - a recent technique for alleviating data incompleteness in IoT - with respect to its energy bottlenecks. Towards addressing the energy bottlenecks of SECOE, we propose ENAMLE - a proactive, energy-aware technique for mitigating the impact of concurrent missing data. ENAMLE is unique in the sense that it builds an energy-aware ensemble of sub-models, each trained with a subset of sensors chosen carefully based on their correlations. Furthermore, at inference time, ENAMLE adaptively alters the number of the ensemble of models based on the amount of missing data rate and the energy-accuracy trade-off. ENAMLE's design includes several novel mechanisms for minimizing energy consumption while maintaining accuracy. We present extensive experimental studies on two distinct datasets that demonstrate the energy efficiency of ENAMLE and its ability to alleviate sensor failures.
EEG-based brainprint recognition with deep learning models has garnered much attention in biometric identification. Yet, studies have indicated vulnerability to adversarial attacks in deep learning models with EEG inputs. In this paper, we introduce a novel adversarial attack method that jointly attacks time-domain and frequency-domain EEG signals by employing wavelet transform. Different from most existing methods which only target time-domain EEG signals, our method not only takes advantage of the time-domain attack's potent adversarial strength but also benefits from the imperceptibility inherent in frequency-domain attack, achieving a better balance between attack performance and imperceptibility. Extensive experiments are conducted in both white- and grey-box scenarios and the results demonstrate that our attack method achieves state-of-the-art attack performance on three datasets and three deep-learning models. In the meanwhile, the perturbations in the signals attacked by our method are barely perceptible to the human visual system.
Background and aims Generalizability of AI colonoscopy algorithms is important for wider adoption in clinical practice. However, current techniques for evaluating performance on unseen data require expensive and time-intensive labels. Methods We use a "Masked Siamese Network" (MSN) to identify novel phenomena in unseen data and predict polyp detector performance. MSN is trained to predict masked out regions of polyp images, without any labels. We test MSN's ability to be trained on data only from Israel and detect unseen techniques, narrow-band imaging (NBI) and chromendoscoy (CE), on colonoscopes from Japan (354 videos, 128 hours). We also test MSN's ability to predict performance of Computer Aided Detection (CADe) of polyps on colonoscopies from both countries, even though MSN is not trained on data from Japan. Results MSN correctly identifies NBI and CE as less similar to Israel whitelight than Japan whitelight (bootstrapped z-test, |z| > 496, p < 10-8 for both) using the label-free Frechet distance. MSN detects NBI with 99% accuracy, predicts CE better than our heuristic (90% vs 79% accuracy) despite being trained only on whitelight, and is the only method that is robust to noisy labels. MSN predicts CADe polyp detector performance on in-domain Israel and out-of-domain Japan colonoscopies (r=0.79, 0.37 respectively). With few examples of Japan detector performance to train on, MSN prediction of Japan performance improves (r=0.56). Conclusion Our technique can identify distribution shifts in clinical data and can predict CADe detector performance on unseen data, without labels. Our self-supervised approach can aid in detecting when data in practice is different from training, such as between hospitals or data has meaningfully shifted from training. MSN has potential for application to medical image domains beyond colonoscopy.
The Internet of Medical Things (IoMT) transcends traditional medical boundaries, enabling a transition from reactive treatment to proactive prevention. This innovative method revolutionizes healthcare by facilitating early disease detection and tailored care, particularly in chronic disease management, where IoMT automates treatments based on real-time health data collection. Nonetheless, its benefits are countered by significant security challenges that endanger the lives of its users due to the sensitivity and value of the processed data, thereby attracting malicious interests. Moreover, the utilization of wireless communication for data transmission exposes medical data to interception and tampering by cybercriminals. Additionally, anomalies may arise due to human errors, network interference, or hardware malfunctions. In this context, anomaly detection based on Machine Learning (ML) is an interesting solution, but it comes up against obstacles in terms of explicability and protection of privacy. To address these challenges, a new framework for Intrusion Detection Systems (IDS) is introduced, leveraging Artificial Neural Networks (ANN) for intrusion detection while utilizing Federated Learning (FL) for privacy preservation. Additionally, eXplainable Artificial Intelligence (XAI) methods are incorporated to enhance model explanation and interpretation. The efficacy of the proposed framework is evaluated and compared with centralized approaches using multiple datasets containing network and medical data, simulating various attack types impacting the confidentiality, integrity, and availability of medical and physiological data. The results obtained offer compelling evidence that the FL method performs comparably to the centralized method, demonstrating high performance. Additionally, it affords the dual advantage of safeguarding privacy and providing model explanation.
Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. Exploiting this structured information could potentially ease the detection of anomalies from radiography images. To this end, we propose a Simple Space-Aware Memory Matrix for In-painting and Detecting anomalies from radiography images (abbreviated as SimSID). We formulate anomaly detection as an image reconstruction task, consisting of a space-aware memory matrix and an in-painting block in the feature space. During the training, SimSID can taxonomize the ingrained anatomical structures into recurrent visual patterns, and in the inference, it can identify anomalies (unseen/modified visual patterns) from the test image. Our SimSID surpasses the state of the arts in unsupervised anomaly detection by +8.0%, +5.0%, and +9.9% AUC scores on ZhangLab, COVIDx, and CheXpert benchmark datasets, respectively. Code: //github.com/MrGiovanni/SimSID
Underlying data distributions of natural language, programming code, and mathematical symbols vary vastly, presenting a complex challenge for large language models (LLMs) that strive to achieve high performance across all three domains simultaneously. Achieving a very high level of proficiency for an LLM within a specific domain often requires extensive training with relevant corpora, which is typically accompanied by a sacrifice in performance in other domains. In this paper, we propose to fuse models that are already highly-specialized directly. The proposed fusing framework, UltraFuser, consists of three distinct specialists that are already sufficiently trained on language, coding, and mathematics. A token-level gating mechanism is introduced to blend the specialists' outputs. A two-stage training strategy accompanied by balanced sampling is designed to ensure stability. To effectively train the fused model, we further construct a high-quality supervised instruction tuning dataset, UltraChat 2, which includes text, code, and mathematical content. This dataset comprises approximately 300,000 instructions and covers a wide range of topics in each domain. Experiments show that our model could simultaneously achieve mastery of the three crucial domains.
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.
We introduce a multi-task setup of identifying and classifying entities, relations, and coreference clusters in scientific articles. We create SciERC, a dataset that includes annotations for all three tasks and develop a unified framework called Scientific Information Extractor (SciIE) for with shared span representations. The multi-task setup reduces cascading errors between tasks and leverages cross-sentence relations through coreference links. Experiments show that our multi-task model outperforms previous models in scientific information extraction without using any domain-specific features. We further show that the framework supports construction of a scientific knowledge graph, which we use to analyze information in scientific literature.
Object detection typically assumes that training and test data are drawn from an identical distribution, which, however, does not always hold in practice. Such a distribution mismatch will lead to a significant performance drop. In this work, we aim to improve the cross-domain robustness of object detection. We tackle the domain shift on two levels: 1) the image-level shift, such as image style, illumination, etc, and 2) the instance-level shift, such as object appearance, size, etc. We build our approach based on the recent state-of-the-art Faster R-CNN model, and design two domain adaptation components, on image level and instance level, to reduce the domain discrepancy. The two domain adaptation components are based on H-divergence theory, and are implemented by learning a domain classifier in adversarial training manner. The domain classifiers on different levels are further reinforced with a consistency regularization to learn a domain-invariant region proposal network (RPN) in the Faster R-CNN model. We evaluate our newly proposed approach using multiple datasets including Cityscapes, KITTI, SIM10K, etc. The results demonstrate the effectiveness of our proposed approach for robust object detection in various domain shift scenarios.
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