Amir Akbarnejad

Amir Akbarnejad, Nilanjan Ray, Penny J. Barnes et al.

Despite the advances in machine learning and digital pathology, it is not yet clear if machine learning methods can accurately predict molecular information merely from histomorphology. In a quest to answer this question, we built a large-scale dataset (185538 images) with reliable measurements for Ki67, ER, PR, and HER2 statuses. The dataset is composed of mirrored images of H\&E and corresponding images of immunohistochemistry (IHC) assays (Ki67, ER, PR, and HER2. These images are mirrored through registration. To increase reliability, individual pairs were inspected and discarded if artifacts were present (tissue folding, bubbles, etc). Measurements for Ki67, ER and PR were determined by calculating H-Score from image analysis. HER2 measurement is based on binary classification: 0 and 1+ (IHC scores representing a negative subset) vs 3+ (IHC score positive subset). Cases with IHC equivocal score (2+) were excluded. We show that a standard ViT-based pipeline can achieve prediction performances around 90% in terms of Area Under the Curve (AUC) when trained with a proper labeling protocol. Finally, we shed light on the ability of the trained classifiers to localize relevant regions, which encourages future work to improve the localizations. Our proposed dataset is publicly available: https://ihc4bc.github.io/

Andrea Rubbi, Amir Akbarnejad, Mohammad Vali Sanian et al.

Robust generalization under distribution shift remains a key challenge for conditional generative modeling: conditional flow-based methods often fit the training conditions well but fail to extrapolate to unseen ones. We introduce SP-FM, a shortest-path flow-matching framework that improves out-of-distribution (OOD) generalization by conditioning both the base distribution and the flow field on the condition. Specifically, SP-FM learns a condition-dependent base distribution parameterized as a flexible, learnable mixture, together with a condition-dependent vector field trained via shortest-path flow matching. Conditioning the base allows the model to adapt its starting distribution across conditions, enabling smooth interpolation and more reliable extrapolation beyond the observed training range. We provide theoretical insights into the resulting conditional transport and show how mixture-conditioned bases enhance robustness under shift. Empirically, SP-FM is effective across heterogeneous domains, including predicting responses to unseen perturbations in single-cell transcriptomics and modeling treatment effects in high-content microscopy--based drug screening. Overall, SP-FM provides a simple yet effective plug-in strategy for improving conditional generative modeling and OOD generalization across diverse domains.

Andrea Rubbi, Arpit Merchant, Samuel Ogden et al.

High-throughput gene perturbation experiments can test several genetic interventions in parallel, yet experimental budgets remain limited. A central goal is hit discovery: identifying as many perturbations as possible whose phenotypic effect exceeds a predefined threshold. Pure exploration strategies are statistically inefficient, wasting budget on low-value regions. Bayesian optimization methods offer a principled alternative but target a single global optimum, over-exploiting dominant modes while neglecting other high-value regions. We formalize hit discovery as a sequential experimental design problem and propose Probability-of-Hit, an acquisition function that directly targets threshold exceedance by ranking candidates according to their posterior probability of being a hit. We prove asymptotic optimality of this approach and demonstrate strong empirical performance on both synthetic benchmarks and real biological immunology datasets, including up to 6.4% improvement over baselines on the Schmidt IL-2 dataset.

Amir Akbarnejad, Gilbert Bigras, Nilanjan Ray

The analogy between Gaussian processes (GPs) and deep artificial neural networks (ANNs) has received a lot of interest, and has shown promise to unbox the blackbox of deep ANNs. Existing theoretical works put strict assumptions on the ANN (e.g. requiring all intermediate layers to be wide, or using specific activation functions). Accommodating those theoretical assumptions is hard in recent deep architectures, and those theoretical conditions need refinement as new deep architectures emerge. In this paper we derive an evidence lower-bound that encourages the GP's posterior to match the ANN's output without any requirement on the ANN. Using our method we find out that on 5 datasets, only a subset of those theoretical assumptions are sufficient. Indeed, in our experiments we used a normal ResNet-18 or feed-forward backbone with a single wide layer in the end. One limitation of training GPs is the lack of scalability with respect to the number of inducing points. We use novel computational techniques that allow us to train GPs with hundreds of thousands of inducing points and with GPU acceleration. As shown in our experiments, doing so has been essential to get a close match between the GPs and the ANNs on 5 datasets. We implement our method as a publicly available tool called GPEX: https://github.com/amirakbarnejad/gpex. On 5 datasets (4 image datasets, and 1 biological dataset) and ANNs with 2 types of functionality (classifier or attention-mechanism) we were able to find GPs whose outputs closely match those of the corresponding ANNs. After matching the GPs to the ANNs, we used the GPs' kernel functions to explain the ANNs' decisions. We provide more than 200 explanations (around 30 explanations in the paper and the rest in the supplementary) which are highly interpretable by humans and show the ability of the obtained GPs to unbox the ANNs' decisions.

Daniel Zügner, Amir Akbarnejad, Stephan Günnemann

Deep learning models for graphs have achieved strong performance for the task of node classification. Despite their proliferation, currently there is no study of their robustness to adversarial attacks. Yet, in domains where they are likely to be used, e.g. the web, adversaries are common. Can deep learning models for graphs be easily fooled? In this work, we introduce the first study of adversarial attacks on attributed graphs, specifically focusing on models exploiting ideas of graph convolutions. In addition to attacks at test time, we tackle the more challenging class of poisoning/causative attacks, which focus on the training phase of a machine learning model. We generate adversarial perturbations targeting the node's features and the graph structure, thus, taking the dependencies between instances in account. Moreover, we ensure that the perturbations remain unnoticeable by preserving important data characteristics. To cope with the underlying discrete domain we propose an efficient algorithm Nettack exploiting incremental computations. Our experimental study shows that accuracy of node classification significantly drops even when performing only few perturbations. Even more, our attacks are transferable: the learned attacks generalize to other state-of-the-art node classification models and unsupervised approaches, and likewise are successful even when only limited knowledge about the graph is given.