Zahra Ahmadi

Hoang H. Nguyen, Nhat-Minh Nguyen, Chunyao Xie et al.

Learning heterogeneous graphs consisting of different types of nodes and edges enhances the results of homogeneous graph techniques. An interesting example of such graphs is control-flow graphs representing possible software code execution flows. As such graphs represent more semantic information of code, developing techniques and tools for such graphs can be highly beneficial for detecting vulnerabilities in software for its reliability. However, existing heterogeneous graph techniques are still insufficient in handling complex graphs where the number of different types of nodes and edges is large and variable. This paper concentrates on the Ethereum smart contracts as a sample of software codes represented by heterogeneous contract graphs built upon both control-flow graphs and call graphs containing different types of nodes and links. We propose MANDO, a new heterogeneous graph representation to learn such heterogeneous contract graphs' structures. MANDO extracts customized metapaths, which compose relational connections between different types of nodes and their neighbors. Moreover, it develops a multi-metapath heterogeneous graph attention network to learn multi-level embeddings of different types of nodes and their metapaths in the heterogeneous contract graphs, which can capture the code semantics of smart contracts more accurately and facilitate both fine-grained line-level and coarse-grained contract-level vulnerability detection. Our extensive evaluation of large smart contract datasets shows that MANDO improves the vulnerability detection results of other techniques at the coarse-grained contract level. More importantly, it is the first learning-based approach capable of identifying vulnerabilities at the fine-grained line-level, and significantly improves the traditional code analysis-based vulnerability detection approaches by 11.35% to 70.81% in terms of F1-score.

Raneen Younis, Abdul Hakmeh, Zahra Ahmadi

Conventional time series classification approaches based on bags of patterns or shapelets face significant challenges in dealing with a vast amount of feature candidates from high-dimensional multivariate data. In contrast, deep neural networks can learn low-dimensional features efficiently, and in particular, Convolutional Neural Networks (CNN) have shown promising results in classifying Multivariate Time Series (MTS) data. A key factor in the success of deep neural networks is this astonishing expressive power. However, this power comes at the cost of complex, black-boxed models, conflicting with the goals of building reliable and human-understandable models. An essential criterion in understanding such predictive deep models involves quantifying the contribution of time-varying input variables to the classification. Hence, in this work, we introduce a new framework for interpreting multivariate time series data by extracting and clustering the input representative patterns that highly activate CNN neurons. This way, we identify each signal's role and dependencies, considering all possible combinations of signals in the MTS input. Then, we construct a graph that captures the temporal relationship between the extracted patterns for each layer. An effective graph merging strategy finds the connection of each node to the previous layer's nodes. Finally, a graph embedding algorithm generates new representations of the created interpretable time-series features. To evaluate the performance of our proposed framework, we run extensive experiments on eight datasets of the UCR/UEA archive, along with HAR and PAM datasets. The experiments indicate the benefit of our time-aware graph-based representation in MTS classification while enriching them with more interpretability.

Abeer Mostafa, Thi Huyen Nguyen, Zahra Ahmadi

Assessing originality in AI research is arguably the most consequential yet least reliable step in peer review. Reviewer judgments of originality remain opaque, inconsistent, and dependent on comparisons to prior work that are often incomplete. In this paper, we present a large-scale, data-driven qualitative and quantitative analysis of research originality based on over 100,000 peer-review reports from leading AI venues, spanning a period of rapid growth in the field. Leveraging structured, semantically retrieved prior work and signals embedded in expert reviewer assessments, we systematically characterize how originality is perceived in practice and identify the key dimensions that most strongly influence novelty judgments. Our analysis yields a fine-grained, evidence-based framework that equips both authors and reviewers with actionable insights into how originality is evaluated. In addition, we evaluate the reliability of current large language model (LLM) agents in assessing originality. We find that these models tend to systematically overestimate novelty and struggle to detect conceptual plagiarism, particularly in the presence of paraphrasing. We release our dataset, trained models, and code at: https://anonymous.4open.science/r/Novelty-Reviewer-365C/.

Maximilian Idahl, Zahra Ahmadi

We present OpenReviewer, an open-source system for generating high-quality peer reviews of machine learning and AI conference papers. At its core is Llama-OpenReviewer-8B, an 8B parameter language model specifically fine-tuned on 79,000 expert reviews from top conferences. Given a PDF paper submission and review template as input, OpenReviewer extracts the full text, including technical content like equations and tables, and generates a structured review following conference-specific guidelines. Our evaluation on 400 test papers shows that OpenReviewer produces considerably more critical and realistic reviews compared to general-purpose LLMs like GPT-4 and Claude-3.5. While other LLMs tend toward overly positive assessments, OpenReviewer's recommendations closely match the distribution of human reviewer ratings. The system provides authors with rapid, constructive feedback to improve their manuscripts before submission, though it is not intended to replace human peer review. OpenReviewer is available as an online demo and open-source tool.

Carolin Cissee, Raneen Younis, Zahra Ahmadi

Multimodal learning seeks to integrate information from heterogeneous sources, where signals may be shared across modalities, specific to individual modalities, or emerge only through their interaction. While self-supervised multimodal contrastive learning has achieved remarkable progress, most existing methods predominantly capture redundant cross-modal signals, often neglecting modality-specific (unique) and interaction-driven (synergistic) information. Recent extensions broaden this perspective, yet they either fail to explicitly model synergistic interactions or learn different information components in an entangled manner, leading to incomplete representations and potential information leakage. We introduce \textbf{COrAL}, a principled framework that explicitly and simultaneously preserves redundant, unique, and synergistic information within multimodal representations. COrAL employs a dual-path architecture with orthogonality constraints to disentangle shared and modality-specific features, ensuring a clean separation of information components. To promote synergy modeling, we introduce asymmetric masking with complementary view-specific patterns, compelling the model to infer cross-modal dependencies rather than rely solely on redundant cues. Extensive experiments on synthetic benchmarks and diverse MultiBench datasets demonstrate that COrAL consistently matches or outperforms state-of-the-art methods while exhibiting low performance variance across runs. These results indicate that explicitly modeling the full spectrum of multimodal information yields more stable, reliable, and comprehensive embeddings.

Raneen Younis, Louay Hamdi, Lukas Chavez et al.

Whole-slide images are central to digital pathology, yet their extreme size and scarce annotations make self-supervised learning essential. Masked Autoencoders (MAEs) with Vision Transformer backbones have recently shown strong potential for histopathology representation learning. However, conventional random patch sampling during MAE pretraining often includes irrelevant or noisy regions, limiting the model's ability to capture meaningful tissue patterns. In this paper, we present a lightweight and domain-adapted framework that brings structure and biological relevance into MAE-based learning through a wavelet-informed patch selection strategy. WISE-MAE applies a two-step coarse-to-fine process: wavelet-based screening at low magnification to locate structurally rich regions, followed by high-resolution extraction for detailed modeling. This approach mirrors the diagnostic workflow of pathologists and improves the quality of learned representations. Evaluations across multiple cancer datasets, including lung, renal, and colorectal tissues, show that WISE-MAE achieves competitive representation quality and downstream classification performance while maintaining efficiency under weak supervision.

Ali Rasekh, Reza Heidari, Amir Hosein Haji Mohammad Rezaie et al.

With the increasing availability of diverse data types, particularly images and time series data from medical experiments, there is a growing demand for techniques designed to combine various modalities of data effectively. Our motivation comes from the important areas of predicting mortality and phenotyping where using different modalities of data could significantly improve our ability to predict. To tackle this challenge, we introduce a new method that uses two separate encoders, one for each type of data, allowing the model to understand complex patterns in both visual and time-based information. Apart from the technical challenges, our goal is to make the predictive model more robust in noisy conditions and perform better than current methods. We also deal with imbalanced datasets and use an uncertainty loss function, yielding improved results while simultaneously providing a principled means of modeling uncertainty. Additionally, we include attention mechanisms to fuse different modalities, allowing the model to focus on what's important for each task. We tested our approach using the comprehensive multimodal MIMIC dataset, combining MIMIC-IV and MIMIC-CXR datasets. Our experiments show that our method is effective in improving multimodal deep learning for clinical applications. The code will be made available online.

Raneen Younis, Suvinava Basak, Lukas Chavez et al.

The rapid growth of biomedical literature and curated databases has made it increasingly difficult for researchers to systematically connect biomarker mechanisms to actionable drug combination hypotheses. We present AI Co-Scientist (CoDHy), an interactive, human-in-the-loop system for biomarker-guided drug combination hypothesis generation in cancer research. CoDHy integrates structured biomedical databases and unstructured literature evidence into a task-specific knowledge graph, which serves as the basis for graph-based reasoning and hypothesis construction. The system combines knowledge graph embeddings with agent-based reasoning to generate, validate, and rank candidate drug combinations, while explicitly grounding each hypothesis in retrievable evidence. Through a web-based interface, users can configure the scientific context, inspect intermediate results, and iteratively refine hypotheses, enabling transparent and researcher-steerable exploration rather than automated decision-making. We demonstrate CoDHy as a system for exploratory hypothesis generation and decision support in translational oncology, highlighting its design, interaction workflow, and practical use cases.

Patrick Abels, Zahra Ahmadi, Sophie Burkhardt et al.

Decision-making usually takes five steps: identifying the problem, collecting data, extracting evidence, identifying pro and con arguments, and making decisions. Focusing on extracting evidence, this paper presents a hybrid model that combines latent Dirichlet allocation and word embeddings to obtain external knowledge from structured and unstructured data. We study the task of sentence-level argument mining, as arguments mostly require some degree of world knowledge to be identified and understood. Given a topic and a sentence, the goal is to classify whether a sentence represents an argument in regard to the topic. We use a topic model to extract topic- and sentence-specific evidence from the structured knowledge base Wikidata, building a graph based on the cosine similarity between the entity word vectors of Wikidata and the vector of the given sentence. Also, we build a second graph based on topic-specific articles found via Google to tackle the general incompleteness of structured knowledge bases. Combining these graphs, we obtain a graph-based model which, as our evaluation shows, successfully capitalizes on both structured and unstructured data.

Sophie Burkhardt, Jannis Brugger, Nicolas Wagner et al.

Most deep neural networks are considered to be black boxes, meaning their output is hard to interpret. In contrast, logical expressions are considered to be more comprehensible since they use symbols that are semantically close to natural language instead of distributed representations. However, for high-dimensional input data such as images, the individual symbols, i.e. pixels, are not easily interpretable. We introduce the concept of first-order convolutional rules, which are logical rules that can be extracted using a convolutional neural network (CNN), and whose complexity depends on the size of the convolutional filter and not on the dimensionality of the input. Our approach is based on rule extraction from binary neural networks with stochastic local search. We show how to extract rules that are not necessarily short, but characteristic of the input, and easy to visualize. Our experiments show that the proposed approach is able to model the functionality of the neural network while at the same time producing interpretable logical rules.

Zahra Ahmadi, Stefan Kramer

Many modern applications deal with multi-label data, such as functional categorizations of genes, image labeling and text categorization. Classification of such data with a large number of labels and latent dependencies among them is a challenging task, and it becomes even more challenging when the data is received online and in chunks. Many of the current multi-label classification methods require a lot of time and memory, which make them infeasible for practical real-world applications. In this paper, we propose a fast linear label space dimension reduction method that transforms the labels into a reduced encoded space and trains models on the obtained pseudo labels. Additionally, it provides an analytical method to update the decoding matrix which maps the labels into the original space and is used during the test phase. Experimental results show the effectiveness of this approach in terms of running times and the prediction performance over different measures.