Virtual screening (VS) is a critical component of modern drug discovery, yet most existing methods--whether physics-based or deep learning-based--are developed around holo protein structures with known ligand-bound pockets. Consequently, their performance degrades significantly on apo or predicted structures such as those from AlphaFold2, which are more representative of real-world early-stage drug discovery, where pocket information is often missing. In this paper, we introduce an alignment-and-aggregation framework to enable accurate virtual screening under structural uncertainty. Our method comprises two core components: (1) a tri-modal contrastive learning module that aligns representations of the ligand, the holo pocket, and cavities detected from structures, thereby enhancing robustness to pocket localization error; and (2) a cross-attention based adapter for dynamically aggregating candidate binding sites, enabling the model to learn from activity data even without precise pocket annotations. We evaluated our method on a newly curated benchmark of apo structures, where it significantly outperforms state-of-the-art methods in blind apo setting, improving the early enrichment factor (EF1%) from 11.75 to 37.19. Notably, it also maintains strong performance on holo structures. These results demonstrate the promise of our approach in advancing first-in-class drug discovery, particularly in scenarios lacking experimentally resolved protein-ligand complexes. Our implementation is publicly available at https://github.com/Wiley-Z/AANet.

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We study the effect of adversarial perturbations of images on deep stereo matching networks for the disparity estimation task. We present a method to craft a single set of perturbations that, when added to any stereo image pair in a dataset, can fool a stereo network to significantly alter the perceived scene geometry. Our perturbation images are "universal" in that they not only corrupt estimates of the network on the dataset they are optimized for, but also generalize to stereo networks with different architectures across different datasets. We evaluate our approach on multiple public benchmark datasets and show that our perturbations can increase D1-error (akin to fooling rate) of state-of-the-art stereo networks from 1% to as much as 87%. We investigate the effect of perturbations on the estimated scene geometry and identify object classes that are most vulnerable. Our analysis on the activations of registered points between left and right images led us to find that certain architectural components, i.e. deformable convolution and explicit matching, can increase robustness against adversaries. We demonstrate that by simply designing networks with such components, one can reduce the effect of adversaries by up to 60.5%, which rivals the robustness of networks fine-tuned with costly adversarial data augmentation.

Data packet routing in aeronautical ad-hoc networks (AANETs) is challenging due to their high-dynamic topology. In this paper, we invoke deep learning (DL) to assist routing in AANETs. We set out from the single objective of minimizing the end-to-end (E2E) delay. Specifically, a deep neural network (DNN) is conceived for mapping the local geographic information observed by the forwarding node into the information required for determining the optimal next hop. The DNN is trained by exploiting the regular mobility pattern of commercial passenger airplanes from historical flight data. After training, the DNN is stored by each airplane for assisting their routing decisions during flight relying solely on local geographic information. Furthermore, we extend the DL-aided routing algorithm to a multi-objective scenario, where we aim for simultaneously minimizing the delay, maximizing the path capacity, and maximizing the path lifetime. Our simulation results based on real flight data show that the proposed DL-aided routing outperforms existing position-based routing protocols in terms of its E2E delay, path capacity as well as path lifetime, and it is capable of approaching the Pareto front that is obtained using global link information.

Current maritime communications mainly rely on satellites having meager transmission resources, hence suffering from poorer performance than modern terrestrial wireless networks. With the growth of transcontinental air traffic, the promising concept of aeronautical ad hoc networking relying on commercial passenger airplanes is potentially capable of enhancing satellite-based maritime communications via air-to-ground and multi-hop air-to-air links. In this article, we conceive space-air-ground integrated networks (SAGINs) for supporting ubiquitous maritime communications, where the low-earth-orbit satellite constellations, passenger airplanes, terrestrial base stations, ships, respectively, serve as the space-, air-, ground- and sea-layer. To meet heterogeneous service requirements, and accommodate the time-varying and self-organizing nature of SAGINs, we propose a deep learning (DL) aided multi-objective routing algorithm, which exploits the quasi-predictable network topology and operates in a distributed manner. Our simulation results based on real satellite, flight, and shipping data in the North Atlantic region show that the integrated network enhances the coverage quality by reducing the end-to-end (E2E) delay and by boosting the E2E throughput as well as improving the path-lifetime. The results demonstrate that our DL-aided multi-objective routing algorithm is capable of achieving near Pareto-optimal performance.

Data packet routing in aeronautical ad-hoc networks (AANETs) is challenging due to their high-dynamic topology. In this paper, we invoke deep reinforcement learning for routing in AANETs aiming at minimizing the end-to-end (E2E) delay. Specifically, a deep Q-network (DQN) is conceived for capturing the relationship between the optimal routing decision and the local geographic information observed by the forwarding node. The DQN is trained in an offline manner based on historical flight data and then stored by each airplane for assisting their routing decisions during flight. To boost the learning efficiency and the online adaptability of the proposed DQN-routing, we further exploit the knowledge concerning the system's dynamics by using a deep value network (DVN) conceived with a feedback mechanism. Our simulation results show that both DQN-routing and DVN-routing achieve lower E2E delay than the benchmark protocol, and DVN-routing performs similarly to the optimal routing that relies on perfect global information.

Archetypal analysis is a type of factor analysis where data is fit by a convex polytope whose corners are "archetypes" of the data, with the data represented as a convex combination of these archetypal points. While archetypal analysis has been used on biological data, it has not achieved widespread adoption because most data are not well fit by a convex polytope in either the ambient space or after standard data transformations. We propose a new approach to archetypal analysis. Instead of fitting a convex polytope directly on data or after a specific data transformation, we train a neural network (AAnet) to learn a transformation under which the data can best fit into a polytope. We validate this approach on synthetic data where we add nonlinearity. Here, AAnet is the only method that correctly identifies the archetypes. We also demonstrate AAnet on two biological datasets. In a T cell dataset measured with single cell RNA-sequencing, AAnet identifies several archetypal states corresponding to naive, memory, and cytotoxic T cells. In a dataset of gut microbiome profiles, AAnet recovers both previously described microbiome states and identifies novel extrema in the data. Finally, we show that AAnet has generative properties allowing us to uniformly sample from the data geometry even when the input data is not uniformly distributed.