Traditional feature engineering approaches for molecular sequence classification suffer from sparsity issues and computational complexity, while deep learning models often underperform on tabular biological data. This paper introduces a novel topological approach that transforms molecular sequences into images by combining Chaos Game Representation (CGR) with Rips complex construction from algebraic topology. Our method maps sequence elements to 2D coordinates via CGR, computes pairwise distances, and constructs Rips complexes to capture both local structural and global topological features. We provide formal guarantees on representation uniqueness, topological stability, and information preservation. Extensive experiments on anticancer peptide datasets demonstrate superior performance over vector-based, sequence language models, and existing image-based methods, achieving 86.8\% and 94.5\% accuracy on breast and lung cancer datasets, respectively. The topological representation preserves critical sequence information while enabling effective utilization of vision-based deep learning architectures for molecular sequence analysis.

Computed tomography (CT) is a key imaging modality for diagnosis, yet its clinical utility is marred by high radiation exposure and long turnaround times, restricting its use for larger-scale screening. Although chest radiography (CXR) is more accessible and safer, existing CXR foundation models focus primarily on detecting diseases that are readily visible on the CXR. Recently, works have explored training disease classification models on simulated CXRs, but they remain limited to recognizing a single disease type from CT. CT foundation models have also emerged with significantly improved detection of pathologies in CT. However, the generalized application of CT-derived labels on CXR has remained illusive. In this study, we propose X2CT-CLIP, a tri-modal knowledge transfer learning framework that bridges the modality gap between CT and CXR while reducing the computational burden of model training. Our approach is the first work to enable multi-abnormality classification in CT, using CXR, by transferring knowledge from 3D CT volumes and associated radiology reports to a CXR encoder via a carefully designed tri-modal alignment mechanism in latent space. Extensive evaluations on three multi-label CT datasets demonstrate that our method outperforms state-of-the-art baselines in cross-modal retrieval, few-shot adaptation, and external validation. These results highlight the potential of CXR, enriched with knowledge derived from CT, as a viable efficient alternative for disease detection in resource-limited settings.

First formulated by Sir Isaac Newton in his work "Philosophiae Naturalis Principia Mathematica", the concept of the Three-Body Problem was put forth as a study of the motion of the three celestial bodies within the Earth-Sun-Moon system. In a generalized definition, it seeks to predict the motion for an isolated system composed of three point masses freely interacting under Newton's law of universal attraction. This proves to be analogous to a multitude of interactions between celestial bodies, and thus, the problem finds applicability within the studies of celestial mechanics. Despite numerous attempts by renowned physicists to solve it throughout the last three centuries, no general closed-form solutions have been reached due to its inherently chaotic nature for most initial conditions. Current state-of-the-art solutions are based on two approaches, either numerical high-precision integration or machine learning-based. Notwithstanding the breakthroughs of neural networks, these present a significant limitation, which is their ignorance of any prior knowledge of the chaotic systems presented. Thus, in this work, we propose a novel method that utilizes Physics-Informed Neural Networks (PINNs). These deep neural networks are able to incorporate any prior system knowledge expressible as an Ordinary Differential Equation (ODE) into their learning processes as a regularizing agent. Our findings showcase that PINNs surpass current state-of-the-art machine learning methods with comparable prediction quality. Despite a better prediction quality, the usability of numerical integrators suffers due to their prohibitively high computational cost. These findings confirm that PINNs are both effective and time-efficient open-form solvers of the Three-Body Problem that capitalize on the extensive knowledge we hold of classical mechanics.

Deep Neural Networks (DNNs) have revolutionized artificial intelligence, achieving impressive results on diverse data types, including images, videos, and texts. However, DNNs still lag behind Gradient Boosting Decision Trees (GBDT) on tabular data, a format extensively utilized across various domains. In this paper, we propose DOFEN, short for \textbf{D}eep \textbf{O}blivious \textbf{F}orest \textbf{EN}semble, a novel DNN architecture inspired by oblivious decision trees. DOFEN constructs relaxed oblivious decision trees (rODTs) by randomly combining conditions for each column and further enhances performance with a two-level rODT forest ensembling process. By employing this approach, DOFEN achieves state-of-the-art results among DNNs and further narrows the gap between DNNs and tree-based models on the well-recognized benchmark: Tabular Benchmark \citep{grinsztajn2022tree}, which includes 73 total datasets spanning a wide array of domains. The code of DOFEN is available at: \url{https://github.com/Sinopac-Digital-Technology-Division/DOFEN}.

Quantifying robustness in a single measure for the purposes of model selection, development of adversarial training methods, and anticipating trends has so far been elusive. The simplest metric to consider is the number of trainable parameters in a model but this has previously been shown to be insufficient at explaining robustness properties. A variety of other metrics, such as ones based on boundary thickness and gradient flatness have been proposed but have been shown to be inadequate proxies for robustness. In this work, we investigate the relationship between a model's effective dimensionality, which can be thought of as model complexity, and its robustness properties. We run experiments on commercial-scale models that are often used in real-world environments such as YOLO and ResNet. We reveal a near-linear inverse relationship between effective dimensionality and adversarial robustness, that is models with a lower dimensionality exhibit better robustness. We investigate the effect of a variety of adversarial training methods on effective dimensionality and find the same inverse linear relationship present, suggesting that effective dimensionality can serve as a useful criterion for model selection and robustness evaluation, providing a more nuanced and effective metric than parameter count or previously-tested measures.

Several recent high-impact studies leverage large hospital-owned electrocardiographic (ECG) databases to model and predict patient mortality. MIMIC-IV, released September 2023, is the first comparable public dataset and includes 800,000 ECGs from a U.S. hospital system. Previously, the largest public ECG dataset was Code-15, containing 345,000 ECGs collected during routine care in Brazil. These datasets now provide an excellent resource for a broader audience to explore ECG survival modeling. Here, we benchmark survival model performance on Code-15 and MIMIC-IV with two neural network architectures, compare four deep survival modeling approaches to Cox regressions trained on classifier outputs, and evaluate performance at one to ten years. Our results yield AUROC and concordance scores comparable to past work (circa 0.8) and reasonable AUPRC scores (MIMIC-IV: 0.4-0.5, Code-15: 0.05-0.13) considering the fraction of ECG samples linked to a mortality (MIMIC-IV: 27\%, Code-15: 4\%). When evaluating models on the opposite dataset, AUROC and concordance values drop by 0.1-0.15, which may be due to cohort differences. All code and results are made public.

There is an increasing trend to mine vulnerabilities from software repositories and use machine learning techniques to automatically detect software vulnerabilities. A fundamental but unresolved research question is: how do different factors in the mining and learning process impact the accuracy of identifying vulnerabilities in software projects of varying characteristics? Substantial research has been dedicated in this area, including source code static analysis, software repository mining, and NLP-based machine learning. However, practitioners lack experience regarding the key factors for building a baseline model of the state-of-the-art. In addition, there lacks of experience regarding the transferability of the vulnerability signatures from project to project. This study investigates how the combination of different vulnerability features and three representative machine learning models impact the accuracy of vulnerability detection in 17 real-world projects. We examine two types of vulnerability representations: 1) code features extracted through NLP with varying tokenization strategies and three different embedding techniques (bag-of-words, word2vec, and fastText) and 2) a set of eight architectural metrics that capture the abstract design of the software systems. The three machine learning algorithms include a random forest model, a support vector machines model, and a residual neural network model. The analysis shows a recommended baseline model with signatures extracted through bag-of-words embedding, combined with the random forest, consistently increases the detection accuracy by about 4% compared to other combinations in all 17 projects. Furthermore, we observe the limitation of transferring vulnerability signatures across domains based on our experiments.

Tabular data plays a crucial role in various domains but often suffers from missing values, thereby curtailing its potential utility. Traditional imputation techniques frequently yield suboptimal results and impose substantial computational burdens, leading to inaccuracies in subsequent modeling tasks. To address these challenges, we propose DiffImpute, a novel Denoising Diffusion Probabilistic Model (DDPM). Specifically, DiffImpute is trained on complete tabular datasets, ensuring that it can produce credible imputations for missing entries without undermining the authenticity of the existing data. Innovatively, it can be applied to various settings of Missing Completely At Random (MCAR) and Missing At Random (MAR). To effectively handle the tabular features in DDPM, we tailor four tabular denoising networks, spanning MLP, ResNet, Transformer, and U-Net. We also propose Harmonization to enhance coherence between observed and imputed data by infusing the data back and denoising them multiple times during the sampling stage. To enable efficient inference while maintaining imputation performance, we propose a refined non-Markovian sampling process that works along with Harmonization. Empirical evaluations on seven diverse datasets underscore the prowess of DiffImpute. Specifically, when paired with the Transformer as the denoising network, it consistently outperforms its competitors, boasting an average ranking of 1.7 and the most minimal standard deviation. In contrast, the next best method lags with a ranking of 2.8 and a standard deviation of 0.9. The code is available at https://github.com/Dendiiiii/DiffImpute.

Recently, motivated by real applications, a major research direction in graph neural networks (GNNs) is to explore deeper structures. For instance, the graph connectivity is not always consistent with the label distribution (e.g., the closest neighbors of some nodes are not from the same category). In this case, GNNs need to stack more layers, in order to find the same categorical neighbors in a longer path for capturing the class-discriminative information. However, two major problems hinder the deeper GNNs to obtain satisfactory performance, i.e., vanishing gradient and over-smoothing. On one hand, stacking layers makes the neural network hard to train as the gradients of the first few layers vanish. Moreover, when simply addressing vanishing gradient in GNNs, we discover the shading neighbors effect (i.e., stacking layers inappropriately distorts the non-IID information of graphs and degrade the performance of GNNs). On the other hand, deeper GNNs aggregate much more information from common neighbors such that individual node representations share more overlapping features, which makes the final output representations not discriminative (i.e., overly smoothed). In this paper, for the first time, we address both problems to enable deeper GNNs, and propose Deeper-GXX, which consists of the Weight-Decaying Graph Residual Connection module (WDG-ResNet) and Topology-Guided Graph Contrastive Loss (TGCL). Extensive experiments on real-world data sets demonstrate that Deeper-GXX outperforms state-of-the-art deeper baselines. Graph neural networks (GNNs) have been proven successful at modeling graph data by extracting node hidden representations that are effective for many downstream tasks.

High-end vehicles have been furnished with a number of electronic control units (ECUs), which provide upgrading functions to enhance the driving experience. The controller area network (CAN) is a well-known protocol that connects these ECUs because of its modesty and efficiency. However, the CAN bus is vulnerable to various types of attacks. Although the intrusion detection system (IDS) is proposed to address the security problem of the CAN bus, most previous studies only provide alerts when attacks occur without knowing the specific type of attack. Moreover, an IDS is designed for a specific car model due to diverse car manufacturers. In this study, we proposed a novel deep learning model called supervised contrastive (SupCon) ResNet, which can handle multiple attack identification on the CAN bus. Furthermore, the model can be used to improve the performance of a limited-size dataset using a transfer learning technique. The capability of the proposed model is evaluated on two real car datasets. When tested with the car hacking dataset, the experiment results show that the SupCon ResNet model improves the overall false-negative rates of four types of attack by four times on average, compared to other models. In addition, the model achieves the highest F1 score at 0.9994 on the survival dataset by utilizing transfer learning. Finally, the model can adapt to hardware constraints in terms of memory size and running time.