arXiv subjects

Mohammad Akbari

Publications and source records attributed to Mohammad Akbari.

At least 19 recordsLinked to original sources

arXiv2026

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.

cs.LG↗

arXiv2026

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.

cs.LG↗

arXiv2026

From Segments to Scenes: Temporal Understanding for Agentic Autonomous Driving via Vision-Language Models

Vision-Language Models (VLMs) are increasingly deployed as the perception and reasoning backbone of autonomous agents acting in the wild, with autonomous driving (AD) being one of the most safety-critical instances. Reliable temporal understanding is essential for such agents to anticipate events, attribute causes, and act safely in dynamic environments, yet this remains a significant challenge even for state-of-the-art (SoTA) VLMs. Prior video benchmarks have emphasized other content (sports, cooking, etc.), yet no existing benchmark focuses exclusively on temporal understanding for both short- and long-form AD footage. To fill this gap, we present the Temporal Understanding in Autonomous Driving (TAD) benchmark, comprising nearly 6000 question-answer (QA) pairs across 7 tasks, and evaluate 9 closed- and open-source generalist as well as AD-specialist models. Current SoTA models perform substantially below human accuracy on TAD. To improve the temporal reasoning of VLM-based driving agents, we propose two novel training-free solutions: Scene-CoT, which uses Chain-of-Thought (CoT) reasoning, and TCogMap, which incorporates an ego-centric temporal cognitive map produced by a trajectory-analysis module that operates as an agentic tool around the VLM. Integrated with existing VLMs, our methods improve average accuracy on TAD by up to $17.72\%$ and by up to $10.35\%$ on STSBench. By introducing TAD, benchmarking SoTA models, and proposing effective enhancements, this work aims to catalyze further progress on temporal understanding for agentic AD systems operating in the wild. The benchmark and evaluation code are available at ${\href{https://huggingface.co/datasets/vbdai/TAD}{\text{Hugging Face}}}$ and ${\href{https://github.com/vbdi/tad_bench}{\text{GitHub}}}$, respectively.

cs.CV↗

arXiv2026

CPPO: Contrastive Perception Policy Optimization for VLM Agents

We introduce CPPO, a Contrastive Perception Policy Optimization method for finetuning vision--language models (VLMs). Reliable perception is a core requirement for VLM-based agents that must reason and act in open-ended environments: faulty visual grounding cascades directly into faulty actions, hallucinated tool calls, and unsafe decisions. While reinforcement learning (RL) has significantly improved reasoning in language models, extending these advances to multimodal agents requires improving both perception and reasoning. Prior works address this challenge mainly through explicit perception rewards, which often require extra LLM judges, ground-truth annotations, or forced separation of perception from reasoning. CPPO addresses this limitation in a self-supervised manner by extending the RL objective with a Contrastive Perception Loss (CPL) that provides a direct learning signal for visual grounding. The contrastive objective encourages the model to become more sensitive to input visual information. To apply this signal effectively, CPPO identifies perception tokens using an entropy-shift mechanism in the model's output distributions under perturbed images and applies the contrastive loss selectively to those tokens during training. Experiments show that CPPO surpasses prior methods while avoiding extra models, making training more efficient and scalable, and yielding policies that are better suited to perception-critical agentic tasks.

cs.CV↗

arXiv2025

Spatial Reasoning with Vision-Language Models in Ego-Centric Multi-View Scenes

Understanding 3D spatial relationships remains a major limitation of current Vision-Language Models (VLMs). Prior work has addressed this issue by creating spatial question-answering (QA) datasets based on single images or indoor videos. However, real-world embodied AI agents such as robots and self-driving cars typically rely on ego-centric, multi-view observations. To this end, we introduce Ego3D-Bench, a new benchmark designed to evaluate the spatial reasoning abilities of VLMs using ego-centric, multi-view outdoor data. Ego3D-Bench comprises over 8,600 QA pairs, created with significant involvement from human annotators to ensure quality and diversity. We benchmark 16 SOTA VLMs, including GPT-4o, Gemini1.5-Pro, InternVL3, and Qwen2.5-VL. Our results reveal a notable performance gap between human level scores and VLM performance, highlighting that current VLMs still fall short of human level spatial understanding. To bridge this gap, we propose Ego3D-VLM, a post-training framework that enhances 3D spatial reasoning of VLMs. Ego3D-VLM generates cognitive map based on estimated global 3D coordinates, resulting in 12% average improvement on multi-choice QA and 56% average improvement on absolute distance estimation. Ego3D-VLM is modular and can be integrated with any existing VLM. Together, Ego3D-Bench and Ego3D-VLM offer valuable tools for advancing toward human level spatial understanding in real-world, multi-view environments.

cs.CV↗

arXiv2025

An Ensemble Embedding Approach for Improving Semantic Caching Performance in LLM-based Systems

Semantic caching enhances the efficiency of large language model (LLM) systems by identifying semantically similar queries, storing responses once, and serving them for subsequent equivalent requests. However, existing semantic caching frameworks rely on single embedding models for query representation, which limits their ability to capture the diverse semantic relationships present in real-world query distributions. This paper presents an ensemble embedding approach that combines multiple embedding models through a trained meta-encoder to improve semantic similarity detection in LLM caching systems. We evaluate our method using the Quora Question Pairs (QQP) dataset, measuring cache hit ratios, cache miss ratios, token savings, and response times. Our ensemble approach achieves a 92\% cache hit ratio for semantically equivalent queries while maintaining an 85\% accuracy in correctly rejecting non-equivalent queries as cache misses. These results demonstrate that ensemble embedding methods significantly outperform single-model approaches in distinguishing between semantically similar and dissimilar queries, leading to more effective caching performance and reduced computational overhead in LLM-based systems.

cs.LG↗

arXiv2025

EnrichEvent: Enriching Social Data with Contextual Information for Emerging Event Extraction

Social platforms have emerged as crucial platforms for distributing information and discussing social events, offering researchers an excellent opportunity to design and implement novel event detection frameworks. Identifying unspecified events and detecting events without prior knowledge enables governments, aid agencies, and experts to respond swiftly and effectively to unfolding situations, such as natural disasters, by assessing severity and optimizing aid delivery. Social data is characterized by misspellings, incompleteness, word sense ambiguation, and irregular language. While discussing an ongoing event, users share different opinions and perspectives based on their prior experience, background, and knowledge. Prior works primarily leverage tweets' lexical and structural patterns to capture users' opinions and views about events. In this study, we propose an end-to-end novel framework, EnrichEvent, to identify unspecified events from streaming social data. In addition to lexical and structural patterns, we leverage contextual knowledge of the tweets to enrich their representation and gain a better perspective on users' opinions about events. Compared to our baselines, the EnrichEvent framework achieves the highest values for Consolidation outcome with an average of 87% vs. 67% and the lowest for Discrimination outcome with an average of 10% vs. 16%. Moreover, the Trending Data Extraction module in the EnrichEvent framework improves efficiency by reducing Runtime by up to 50% by identifying and discarding irrelevant tweets within message blocks, making the framework highly scalable for processing streaming data. Our source code and dataset are available in our official replication package.

cs.CL↗

arXiv2025

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.

cs.CV↗

arXiv2025

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.

physics.optics↗

arXiv2025

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 $\href{https://github.com/vbdi/divprune}{\text{here}}$.

cs.CV↗

arXiv2025

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.

cs.CV↗

arXiv2025

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.

q-bio.QM↗

arXiv2024

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.

cs.CL↗

arXiv2024

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.

cs.CV↗

arXiv2024

AMUSE: Adaptive Multi-Segment Encoding for Dataset Watermarking

Curating high quality datasets that play a key role in the emergence of new AI applications requires considerable time, money, and computational resources. So, effective ownership protection of datasets is becoming critical. Recently, to protect the ownership of an image dataset, imperceptible watermarking techniques are used to store ownership information (i.e., watermark) into the individual image samples. Embedding the entire watermark into all samples leads to significant redundancy in the embedded information which damages the watermarked dataset quality and extraction accuracy. In this paper, a multi-segment encoding-decoding method for dataset watermarking (called AMUSE) is proposed to adaptively map the original watermark into a set of shorter sub-messages and vice versa. Our message encoder is an adaptive method that adjusts the length of the sub-messages according to the protection requirements for the target dataset. Existing image watermarking methods are then employed to embed the sub-messages into the original images in the dataset and also to extract them from the watermarked images. Our decoder is then used to reconstruct the original message from the extracted sub-messages. The proposed encoder and decoder are plug-and-play modules that can easily be added to any watermarking method. To this end, extensive experiments are preformed with multiple watermarking solutions which show that applying AMUSE improves the overall message extraction accuracy upto 28% for the same given dataset quality. Furthermore, the image dataset quality is enhanced by a PSNR of $\approx$2 dB on average, while improving the extraction accuracy for one of the tested image watermarking methods.

cs.MM↗

arXiv2024

GOLD: Generalized Knowledge Distillation via Out-of-Distribution-Guided Language Data Generation

Knowledge distillation from LLMs is essential for the efficient deployment of language models. Prior works have proposed data generation using LLMs for preparing distilled models. We argue that generating data with LLMs is prone to sampling mainly from the center of original content distribution. This limitation hinders the distilled model from learning the true underlying data distribution and to forget the tails of the distributions (samples with lower probability). To this end, we propose GOLD, a task-agnostic data generation and knowledge distillation framework, which employs an iterative out-of-distribution-guided feedback mechanism for the LLM. As a result, the generated data improves the generalizability of distilled models. An energy-based OOD evaluation approach is also introduced to deal with noisy generated data. Our extensive experiments on 10 different classification and sequence-to-sequence tasks in NLP show that GOLD respectively outperforms prior arts and the LLM with an average improvement of 5% and 14%. We will also show that the proposed method is applicable to less explored and novel tasks. The code is available.

cs.CL↗

arXiv2024

Learned Image Compression with Gaussian-Laplacian-Logistic Mixture Model and Concatenated Residual Modules

Recently deep learning-based image compression methods have achieved significant achievements and gradually outperformed traditional approaches including the latest standard Versatile Video Coding (VVC) in both PSNR and MS-SSIM metrics. Two key components of learned image compression are the entropy model of the latent representations and the encoding/decoding network architectures. Various models have been proposed, such as autoregressive, softmax, logistic mixture, Gaussian mixture, and Laplacian. Existing schemes only use one of these models. However, due to the vast diversity of images, it is not optimal to use one model for all images, even different regions within one image. In this paper, we propose a more flexible discretized Gaussian-Laplacian-Logistic mixture model (GLLMM) for the latent representations, which can adapt to different contents in different images and different regions of one image more accurately and efficiently, given the same complexity. Besides, in the encoding/decoding network design part, we propose a concatenated residual blocks (CRB), where multiple residual blocks are serially connected with additional shortcut connections. The CRB can improve the learning ability of the network, which can further improve the compression performance. Experimental results using the Kodak, Tecnick-100 and Tecnick-40 datasets show that the proposed scheme outperforms all the leading learning-based methods and existing compression standards including VVC intra coding (4:4:4 and 4:2:0) in terms of the PSNR and MS-SSIM. The source code is available at \url{https://github.com/fengyurenpingsheng}

eess.IV↗

arXiv2024

Self-Healing Effects in OAM Beams Observed on a 28 GHz Experimental Link

In this paper we document for the first time some of the effects of self-healing, a property of orbital-angular-momentum (OAM) or vortex beams, as observed on a millimeter-wave experimental communications link in an outdoors line-of-sight (LOS) scenario. The OAM beams have a helical phase and polarization structure and have conical amplitude shape in the far field. The Poynting vectors of the OAM beams also possess helical structures, orthogonal to the corresponding helical phase-fronts. Due to such non-planar structure in the direction orthogonal to the beam axis, OAM beams are a subset of structured light beams. Such structured beams are known to possess self-healing properties when partially obstructed along their propagation axis, especially in their near fields, resulting in partial reconstruction of their structures at larger distances along their beam axis. Various theoretical rationales have been proposed to explain, model and experimentally verify the self-healing physical effects in structured optical beams, using various types of obstructions and experimental techniques. Based on these models, we hypothesize that any self-healing observed will be greater as the OAM order increases. Here we observe the self-healing effects for the first time in structured OAM radio beams, in terms of communication signals and channel parameters rather than beam structures. We capture the effects of partial near-field obstructions of OAM beams of different orders on the communications signals and provide a physical rationale to substantiate that the self-healing effect was observed to increase with the order of OAM, agreeing with our hypothesis.

eess.SP↗