Peptides are formed by the dehydration condensation of multiple amino acids. The primary structure of a peptide can be represented either as an amino acid sequence or as a molecular graph consisting of atoms and chemical bonds. Previous studies have indicated that deep learning routes specific to sequential and graphical peptide forms exhibit comparable performance on downstream tasks. Despite the fact that these models learn representations of the same modality of peptides, we find that they explain their predictions differently. Considering sequential and graphical models as two experts making inferences from different perspectives, we work on fusing expert knowledge to enrich the learned representations for improving the discriminative performance. To achieve this, we propose a peptide co-modeling method, RepCon, which employs a contrastive learning-based framework to enhance the mutual information of representations from decoupled sequential and graphical end-to-end models. It considers representations from the sequential encoder and the graphical encoder for the same peptide sample as a positive pair and learns to enhance the consistency of representations between positive sample pairs and to repel representations between negative pairs. Empirical studies of RepCon and other co-modeling methods are conducted on open-source discriminative datasets, including aggregation propensity, retention time, antimicrobial peptide prediction, and family classification from Peptide Database. Our results demonstrate the superiority of the co-modeling approach over independent modeling, as well as the superiority of RepCon over other methods under the co-modeling framework. In addition, the attribution on RepCon further corroborates the validity of the approach at the level of model explanation.
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Cluster-randomized trials often involve units that are irregularly distributed in space without well-separated communities. In these settings, cluster construction is a critical aspect of the design due to the potential for cross-cluster interference. The existing literature relies on partial interference models, which take clusters as given and assume no cross-cluster interference. We relax this assumption by allowing interference to decay with geographic distance between units. This induces a bias-variance trade-off: constructing fewer, larger clusters reduces bias due to interference but increases variance. We propose new estimators that exclude units most potentially impacted by cross-cluster interference and show that this substantially reduces asymptotic bias relative to conventional difference-in-means estimators. We provide formal justification for a new design that chooses the number of clusters to balance the asymptotic bias and variance of our estimators and uses unsupervised learning to automate cluster construction.
Coronary Artery Disease (CAD) is one of the most common forms of heart disease, which is caused by a buildup of atherosclerotic plaque (known as stenosis) in the coronary arteries, leading to insufficient supplement of blood, oxygen, and nutrients to the heart. Fractional Flow Reserve (FFR), measuring the pressure ratio between the aorta and distal coronary artery, is an invasive physiologic gold standard for assessing the severity of coronary artery stenosis. Despite its benefits, invasive FFR assessment is still underutilized due to its high cost, time-consuming, experimental variability, and increased risk to patients. In this study, an attention-based multi-fidelity machine learning model (AttMulFid) is proposed for computationally efficient and accurate FFR assessment with uncertainty measurement. Within AttMulFid, an autoencoder is utilized to intelligently select geometric features from coronary arteries, with additional attention on the key area. Results show that the geometric features are able to represent the entirety of the geometric information and intelligently allocate attention based on crucial properties of geometry. Furthermore, the AttMulFid is a feasible approach for non-invasive, rapid, and accurate FFR assessment (with 0.002s/simulation).
We examine the extent to which sublinear-sample property testing and estimation applies to settings where samples are independently but not identically distributed. Specifically, we consider the following distributional property testing framework: Suppose there is a set of distributions over a discrete support of size $k$, $\textbf{p}_1, \textbf{p}_2,\ldots,\textbf{p}_T$, and we obtain $c$ independent draws from each distribution. Suppose the goal is to learn or test a property of the average distribution, $\textbf{p}_{\mathrm{avg}}$. This setup models a number of important practical settings where the individual distributions correspond to heterogeneous entities -- either individuals, chronologically distinct time periods, spatially separated data sources, etc. From a learning standpoint, even with $c=1$ samples from each distribution, $\Theta(k/\varepsilon^2)$ samples are necessary and sufficient to learn $\textbf{p}_{\mathrm{avg}}$ to within error $\varepsilon$ in TV distance. To test uniformity or identity -- distinguishing the case that $\textbf{p}_{\mathrm{avg}}$ is equal to some reference distribution, versus has $\ell_1$ distance at least $\varepsilon$ from the reference distribution, we show that a linear number of samples in $k$ is necessary given $c=1$ samples from each distribution. In contrast, for $c \ge 2$, we recover the usual sublinear sample testing of the i.i.d. setting: we show that $O(\sqrt{k}/\varepsilon^2 + 1/\varepsilon^4)$ samples are sufficient, matching the optimal sample complexity in the i.i.d. case in the regime where $\varepsilon \ge k^{-1/4}$. Additionally, we show that in the $c=2$ case, there is a constant $\rho > 0$ such that even in the linear regime with $\rho k$ samples, no tester that considers the multiset of samples (ignoring which samples were drawn from the same $\textbf{p}_i$) can perform uniformity testing.
Categorical semantics of type theories are often characterized as structure-preserving functors. This is because in category theory both the syntax and the domain of interpretation are uniformly treated as structured categories, so that we can express interpretations as structure-preserving functors between them. This mathematical characterization of semantics makes it convenient to manipulate and to reason about relationships between interpretations. Motivated by this success of functorial semantics, we address the question of finding a functorial analogue in abstract interpretation, a general framework for comparing semantics, so that we can bring similar benefits of functorial semantics to semantic abstractions used in abstract interpretation. Major differences concern the notion of interpretation that is being considered. Indeed, conventional semantics are value-based whereas abstract interpretation typically deals with more complex properties. In this paper, we propose a functorial approach to abstract interpretation and study associated fundamental concepts therein. In our approach, interpretations are expressed as oplax functors in the category of posets, and abstraction relations between interpretations are expressed as lax natural transformations representing concretizations. We present examples of these formal concepts from monadic semantics of programming languages and discuss soundness.
In surgical procedures, correct instrument counting is essential. Instance segmentation is a location method that locates not only an object's bounding box but also each pixel's specific details. However, obtaining mask-level annotations is labor-intensive in instance segmentation. To address this issue, we propose a novel yet effective weakly-supervised surgical instrument instance segmentation approach, named Point-based Weakly-supervised Instance Segmentation (PWISeg). PWISeg adopts an FCN-based architecture with point-to-box and point-to-mask branches to model the relationships between feature points and bounding boxes, as well as feature points and segmentation masks on FPN, accomplishing instrument detection and segmentation jointly in a single model. Since mask level annotations are hard to available in the real world, for point-to-mask training, we introduce an unsupervised projection loss, utilizing the projected relation between predicted masks and bboxes as supervision signal. On the other hand, we annotate a few pixels as the key pixel for each instrument. Based on this, we further propose a key pixel association loss and a key pixel distribution loss, driving the point-to-mask branch to generate more accurate segmentation predictions. To comprehensively evaluate this task, we unveil a novel surgical instrument dataset with manual annotations, setting up a benchmark for further research. Our comprehensive research trial validated the superior performance of our PWISeg. The results show that the accuracy of surgical instrument segmentation is improved, surpassing most methods of instance segmentation via weakly supervised bounding boxes. This improvement is consistently observed in our proposed dataset and when applied to the public HOSPI-Tools dataset.
With increasing complexity of Automated Driving Systems (ADS), ensuring their safety and reliability has become a critical challenge. The Verification and Validation (V&V) of these systems are particularly demanding when AI components are employed to implement perception and/or control functions. In ESA-funded project VIVAS, we developed a generic framework for system-level simulation-based V&V of autonomous systems. The approach is based on a simulation model of the system, an abstract model that describes symbolically the system behavior, and formal methods to generate scenarios and verify the simulation executions. Various coverage criteria can be defined to guide the automated generation of the scenarios. In this paper, we describe the instantiation of the VIVAS framework for an ADS case study. This is based on the integration of CARLA, a widely-used driving simulator, and its ScenarioRunner tool, which enables the creation of diverse and complex driving scenarios. This is also used in the CARLA Autonomous Driving Challenge to validate different ADS agents for perception and control based on AI, shared by the CARLA community. We describe the development of an abstract ADS model and the formulation of a coverage criterion that focuses on the behaviors of vehicles relative to the vehicle with ADS under verification. Leveraging the VIVAS framework, we generate and execute various driving scenarios, thus testing the capabilities of the AI components. The results show the effectiveness of VIVAS in automatically generating scenarios for system-level simulation-based V&V of an automated driving system using CARLA and ScenarioRunner. Therefore, they highlight the potential of the approach as a powerful tool in the future of ADS V&V methodologies.
Computerized cognitive training (CCT) is a scalable, well-tolerated intervention that has promise for slowing cognitive decline. Outcomes from CCT are limited by a lack of effective engagement, which is decreased by factors such as mental fatigue, particularly in older adults at risk for dementia. There is a need for scalable, automated measures that can monitor mental fatigue during CCT. Here, we develop and validate a novel Recurrent Video Transformer (RVT) method for monitoring real-time mental fatigue in older adults with mild cognitive impairment from video-recorded facial gestures during CCT. The RVT model achieved the highest balanced accuracy(78%) and precision (0.82) compared to the prior state-of-the-art models for binary and multi-class classification of mental fatigue and was additionally validated via significant association (p=0.023) with CCT reaction time. By leveraging dynamic temporal information, the RVT model demonstrates the potential to accurately measure real-time mental fatigue, laying the foundation for future personalized CCT that increase effective engagement.
Defensive deception is a promising approach for cyberdefense. Although defensive deception is increasingly popular in the research community, there has not been a systematic investigation of its key components, the underlying principles, and its tradeoffs in various problem settings. This survey paper focuses on defensive deception research centered on game theory and machine learning, since these are prominent families of artificial intelligence approaches that are widely employed in defensive deception. This paper brings forth insights, lessons, and limitations from prior work. It closes with an outline of some research directions to tackle major gaps in current defensive deception research.
The recent proliferation of knowledge graphs (KGs) coupled with incomplete or partial information, in the form of missing relations (links) between entities, has fueled a lot of research on knowledge base completion (also known as relation prediction). Several recent works suggest that convolutional neural network (CNN) based models generate richer and more expressive feature embeddings and hence also perform well on relation prediction. However, we observe that these KG embeddings treat triples independently and thus fail to cover the complex and hidden information that is inherently implicit in the local neighborhood surrounding a triple. To this effect, our paper proposes a novel attention based feature embedding that captures both entity and relation features in any given entity's neighborhood. Additionally, we also encapsulate relation clusters and multihop relations in our model. Our empirical study offers insights into the efficacy of our attention based model and we show marked performance gains in comparison to state of the art methods on all datasets.
Attention mechanism has been used as an ancillary means to help RNN or CNN. However, the Transformer (Vaswani et al., 2017) recently recorded the state-of-the-art performance in machine translation with a dramatic reduction in training time by solely using attention. Motivated by the Transformer, Directional Self Attention Network (Shen et al., 2017), a fully attention-based sentence encoder, was proposed. It showed good performance with various data by using forward and backward directional information in a sentence. But in their study, not considered at all was the distance between words, an important feature when learning the local dependency to help understand the context of input text. We propose Distance-based Self-Attention Network, which considers the word distance by using a simple distance mask in order to model the local dependency without losing the ability of modeling global dependency which attention has inherent. Our model shows good performance with NLI data, and it records the new state-of-the-art result with SNLI data. Additionally, we show that our model has a strength in long sentences or documents.
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