Semantic Reasoning in Medicine: The Role of Knowledge Graphs Across Five Key Domains

Knowledge graphs (KGs) have emerged as a promising solution for integrating and reasoning over complex biomedical and clinical data in healthcare. By representing structured relationships among entities such as diseases, drugs, symptoms, and patient records, KGs provide a semantic backbone for decision-making, prediction, recommendation, and personalized care. Recent advances have demonstrated their utility across diverse medical applications--including clinical decision support systems, disease and treatment outcome prediction, health recommender systems, precision medicine, and medical question answering--where KGs often enhance interpretability, semantic coherence, and patient-specific reasoning. In parallel, a growing body of work focuses on medical KG generation itself, proposing frameworks that construct graphs from EHRs, clinical narratives, biomedical literature, and web resources using ontologies, semantic web technologies, deep-learning-based information extraction, and hybrid neuro-symbolic pipelines. Despite this progress, significant challenges remain, including limited and fragmented knowledge coverage, difficulties in aligning heterogeneous data sources, the fragility of current reasoning and representation-learning methods on dense multi-relational graphs, and unresolved issues related to privacy, bias, and accountability. This survey reviews and categorizes current research on KGs in medicine along both application-oriented and methodology-oriented dimensions, discusses their benefits and technical foundations, and outlines key limitations and open research directions. By analyzing trends, architectures, and evaluation practices, this work aims to guide future developments in KG-driven medical AI systems and support their safe and effective integration into healthcare environments.

Where Black-box Drug-Target Interaction Prediction Models Look: Cross-Method Explainability

Drug-target interaction (DTI) and affinity (DTA) predictors increasingly achieve strong benchmark scores, yet their internal use of sequence, fingerprint, and graph features often remains opaque. We present an interpretability audit of BridgeDPI architecture on three different datasets including Gao, Human, and C.elegans. This study combines gradient-based attributions -- integrated gradients, saliency, layer-wise relevance propagation, SmoothGrad, and SmoothGrad-IG -- with feature-wise occlusion ablation and strict intersection consensus across methods to reduce single-explainer bias. We summarize sensitivity and signed effects at raw inputs, at the bridge similarity scaffold, and through the graph convolution, including edge-level sensitivities and targeted edge removals. The results show that explainability is most informative when treated as model criticism: it reveals modality dominance, padding and special-token artifacts, dataset-dependent cooperative versus suppressive effects across layers, and chemistry-consistent fragment and composition motifs where methods agree. These analyses do not substitute for structural or experimental ground truth, yet they can provide testable hypotheses for downstream validation in computational drug discovery pipelines. More broadly, applying modern XAI to contemporary DTI/DTA models is still an early pass over the rich structure implicit in trained weights and data -- yet even this first layer of scrutiny already helps researchers relate predictions to drug- and target-side representations and to prioritize external validation.

CPPO: Contrastive Perception for Vision Language Policy Optimization

We introduce CPPO, a Contrastive Perception Policy Optimization method for finetuning vision-language models (VLMs). While reinforcement learning (RL) has advanced reasoning in language models, extending it to multimodal reasoning requires improving both the perception and reasoning aspects. Prior works tackle this challenge mainly with explicit perception rewards, but disentangling perception tokens from reasoning tokens is difficult, requiring extra LLMs, ground-truth data, forced separation of perception from reasoning by policy model, or applying rewards indiscriminately to all output tokens. CPPO addresses this problem by detecting perception tokens via entropy shifts in the model outputs under perturbed input images. CPPO then extends the RL objective function with a Contrastive Perception Loss (CPL) that enforces consistency under information-preserving perturbations and sensitivity under information-removing ones. Experiments show that CPPO surpasses previous perception-rewarding methods, while avoiding extra models, making training more efficient and scalable.

OAM-Assisted Self-Healing Is Directional, Proportional and Persistent

In this paper we demonstrate the postulated mechanism of self-healing specifically due to orbital-angular-momentum (OAM) in radio vortex beams having equal beam-widths. In previous work we experimentally demonstrated self-healing effects in OAM beams at 28 GHz and postulated a theoretical mechanism to account for them. In this work we further characterize the OAM self-healing mechanism theoretically and confirm those characteristics with systematic and controlled experimental measurements on a 28 GHz outdoor link. Specifically, we find that the OAM self-healing mechanism is an additional self-healing mechanism in structured electromagnetic beams which is directional with respect to the displacement of an obstruction relative to the beam axis. We also confirm our previous findings that the amount of OAM self-healing is proportional to the OAM order, and additionally find that it persists beyond the focusing region into the far field. As such, OAM-assisted self-healing brings an advantage over other so-called non-diffracting beams both in terms of the minimum distance for onset of self-healing and the amount of self-healing obtainable. We relate our findings by extending theoretical models in the literature and develop a unifying electromagnetic analysis to account for self-healing of OAM-bearing non-diffracting beams more rigorously.

CASP: Compression of Large Multimodal Models Based on Attention Sparsity

In this work, we propose an extreme compression technique for Large Multimodal Models (LMMs). While previous studies have explored quantization as an efficient post-training compression method for Large Language Models (LLMs), low-bit compression for multimodal models remains under-explored. The redundant nature of inputs in multimodal models results in a highly sparse attention matrix. We theoretically and experimentally demonstrate that the attention matrix's sparsity bounds the compression error of the Query and Key weight matrices. Based on this, we introduce CASP, a model compression technique for LMMs. Our approach performs a data-aware low-rank decomposition on the Query and Key weight matrix, followed by quantization across all layers based on an optimal bit allocation process. CASP is compatible with any quantization technique and enhances state-of-the-art 2-bit quantization methods (AQLM and QuIP#) by an average of 21% on image- and video-language benchmarks.

DivPrune: Diversity-based Visual Token Pruning for Large Multimodal Models

Large Multimodal Models (LMMs) have emerged as powerful models capable of understanding various data modalities, including text, images, and videos. LMMs encode both text and visual data into tokens that are then combined and processed by an integrated Large Language Model (LLM). Including visual tokens substantially increases the total token count, often by thousands. The increased input length for LLM significantly raises the complexity of inference, resulting in high latency in LMMs. To address this issue, token pruning methods, which remove part of the visual tokens, are proposed. The existing token pruning methods either require extensive calibration and fine-tuning or rely on suboptimal importance metrics which results in increased redundancy among the retained tokens. In this paper, we first formulate token pruning as Max-Min Diversity Problem (MMDP) where the goal is to select a subset such that the diversity among the selected {tokens} is maximized. Then, we solve the MMDP to obtain the selected subset and prune the rest. The proposed method, DivPrune, reduces redundancy and achieves the highest diversity of the selected tokens. By ensuring high diversity, the selected tokens better represent the original tokens, enabling effective performance even at high pruning ratios without requiring fine-tuning. Extensive experiments with various LMMs show that DivPrune achieves state-of-the-art accuracy over 16 image- and video-language datasets. Additionally, DivPrune reduces both the end-to-end latency and GPU memory usage for the tested models. The code is available $\href{https://github.com/vbdi/divprune}{\text{here}}$.

Drug-Target Interaction/Affinity Prediction: Deep Learning Models and Advances Review

Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate prediction of how drugs interact with their targets and the development of new drugs by using better methods and technologies have immense potential to speed up this process, ultimately leading to faster delivery of life-saving medications. Traditional methods used for drug-target interaction prediction show limitations, particularly in capturing complex relationships between drugs and their targets. As an outcome, deep learning models have been presented to overcome the challenges of interaction prediction through their precise and efficient end results. By outlining promising research avenues and models, each with a different solution but similar to the problem, this paper aims to give researchers a better idea of methods for even more accurate and efficient prediction of drug-target interaction, ultimately accelerating the development of more effective drugs. A total of 180 prediction methods for drug-target interactions were analyzed throughout the period spanning 2016 to 2025 using different frameworks based on machine learning, mainly deep learning and graph neural networks. Additionally, this paper discusses the novelty, architecture, and input representation of these models.

Task-Agnostic Language Model Watermarking via High Entropy Passthrough Layers

In the era of costly pre-training of large language models, ensuring the intellectual property rights of model owners, and insuring that said models are responsibly deployed, is becoming increasingly important. To this end, we propose model watermarking via passthrough layers, which are added to existing pre-trained networks and trained using a self-supervised loss such that the model produces high-entropy output when prompted with a unique private key, and acts normally otherwise. Unlike existing model watermarking methods, our method is fully task-agnostic, and can be applied to both classification and sequence-to-sequence tasks without requiring advanced access to downstream fine-tuning datasets. We evaluate the proposed passthrough layers on a wide range of downstream tasks, and show experimentally our watermarking method achieves a near-perfect watermark extraction accuracy and false-positive rate in most cases without damaging original model performance. Additionally, we show our method is robust to both downstream fine-tuning, fine-pruning, and layer removal attacks, and can be trained in a fraction of the time required to train the original model. Code is available in the paper.

Towards Secure and Usable 3D Assets: A Novel Framework for Automatic Visible Watermarking

3D models, particularly AI-generated ones, have witnessed a recent surge across various industries such as entertainment. Hence, there is an alarming need to protect the intellectual property and avoid the misuse of these valuable assets. As a viable solution to address these concerns, we rigorously define the novel task of automated 3D visible watermarking in terms of two competing aspects: watermark quality and asset utility. Moreover, we propose a method of embedding visible watermarks that automatically determines the right location, orientation, and number of watermarks to be placed on arbitrary 3D assets for high watermark quality and asset utility. Our method is based on a novel rigid-body optimization that uses back-propagation to automatically learn transforms for ideal watermark placement. In addition, we propose a novel curvature-matching method for fusing the watermark into the 3D model that further improves readability and security. Finally, we provide a detailed experimental analysis on two benchmark 3D datasets validating the superior performance of our approach in comparison to baselines. Code and demo are available.

LaWa: Using Latent Space for In-Generation Image Watermarking

With generative models producing high quality images that are indistinguishable from real ones, there is growing concern regarding the malicious usage of AI-generated images. Imperceptible image watermarking is one viable solution towards such concerns. Prior watermarking methods map the image to a latent space for adding the watermark. Moreover, Latent Diffusion Models (LDM) generate the image in the latent space of a pre-trained autoencoder. We argue that this latent space can be used to integrate watermarking into the generation process. To this end, we present LaWa, an in-generation image watermarking method designed for LDMs. By using coarse-to-fine watermark embedding modules, LaWa modifies the latent space of pre-trained autoencoders and achieves high robustness against a wide range of image transformations while preserving perceptual quality of the image. We show that LaWa can also be used as a general image watermarking method. Through extensive experiments, we demonstrate that LaWa outperforms previous works in perceptual quality, robustness against attacks, and computational complexity, while having very low false positive rate. Code is available here.