KALE: Enhancing Knowledge Manipulation in Large Language Models via Knowledge-aware Learning

Despite the impressive performance of large language models (LLMs) pretrained on vast knowledge corpora, advancing their knowledge manipulation-the ability to effectively recall, reason, and transfer relevant knowledge-remains challenging. Existing methods mainly leverage Supervised Fine-Tuning (SFT) on labeled datasets to enhance LLMs' knowledge manipulation ability. However, we observe that SFT models still exhibit the known&incorrect phenomenon, where they explicitly possess relevant knowledge for a given question but fail to leverage it for correct answers. To address this challenge, we propose KALE (Knowledge-Aware LEarning)-a post-training framework that leverages knowledge graphs (KGs) to generate high-quality rationales and enhance LLMs' knowledge manipulation ability. Specifically, KALE first introduces a Knowledge-Induced (KI) data synthesis method that efficiently extracts multi-hop reasoning paths from KGs to generate high-quality rationales for question-answer pairs. Then, KALE employs a Knowledge-Aware (KA) fine-tuning paradigm that enhances knowledge manipulation by internalizing rationale-guided reasoning through minimizing the KL divergence between predictions with and without rationales. Extensive experiments on eight popular benchmarks across six different LLMs demonstrate the effectiveness of KALE, achieving accuracy improvements of up to 11.72% and an average of 4.18%.

Spatial Multi-Task Learning for Breast Cancer Molecular Subtype Prediction from Single-Phase DCE-MRI

Accurate molecular subtype classification is essential for personalized breast cancer treatment, yet conventional immunohistochemical analysis relies on invasive biopsies and is prone to sampling bias. Although dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) enables non-invasive tumor characterization, clinical workflows typically acquire only single-phase post-contrast images to reduce scan time and contrast agent dose. In this study, we propose a spatial multi-task learning framework for breast cancer molecular subtype prediction from clinically practical single-phase DCE-MRI. The framework simultaneously predicts estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) status, and the Ki-67 proliferation index -- biomarkers that collectively define molecular subtypes. The architecture integrates a deep feature extraction network with multi-scale spatial attention to capture intratumoral and peritumoral characteristics, together with a region-of-interest weighting module that emphasizes the tumor core, rim, and surrounding tissue. Multi-task learning exploits biological correlations among biomarkers through shared representations with task-specific prediction branches. Experiments on a dataset of 960 cases (886 internal cases split 7:1:2 for training/validation/testing, and 74 external cases evaluated via five-fold cross-validation) demonstrate that the proposed method achieves an AUC of 0.893, 0.824, and 0.857 for ER, PR, and HER2 classification, respectively, and a mean absolute error of 8.2\% for Ki-67 regression, significantly outperforming radiomics and single-task deep learning baselines. These results indicate the feasibility of accurate, non-invasive molecular subtype prediction using standard imaging protocols.

Decision Feedback-Aided Known-Interference Cancellation

Known-interference cancellation (KIC) in combination with cooperative jamming can be used to provide covertness and security to wireless communications at the physical layer. However, since the signal of interest (SI) of a wireless communication system acts as estimation noise, i.e., interference, to KIC, the SI limits the extent to which the known interference (KI) can be canceled and that in turn limits the throughput of the wireless communication system that is being hidden or secured. In this letter, we analyze a decision feedback-aided known-interference cancellation (DF-KIC) structure in which both the KI and SI are canceled iteratively and successively. Measurement results demonstrate that introducing decision feedback to KIC improves its KI cancellation capability and hence increases the wireless communication system's useful throughput, albeit at the expense of a higher computational load.

SR-KI: Scalable and Real-Time Knowledge Integration into LLMs via Supervised Attention

This paper proposes SR-KI, a novel approach for integrating real-time and large-scale structured knowledge bases (KBs) into large language models (LLMs). SR-KI begins by encoding KBs into key-value pairs using a pretrained encoder, and injects them into LLMs' KV cache. Building on this representation, we employ a two-stage training paradigm: first locating a dedicated retrieval layer within the LLM, and then applying an attention-based loss at this layer to explicitly supervise attention toward relevant KB entries. Unlike traditional retrieval-augmented generation methods that rely heavily on the performance of external retrievers and multi-stage pipelines, SR-KI supports end-to-end inference by performing retrieval entirely within the models latent space. This design enables efficient compression of injected knowledge and facilitates dynamic knowledge updates. Comprehensive experiments demonstrate that SR-KI enables the integration of up to 40K KBs into a 7B LLM on a single A100 40GB GPU, and achieves strong retrieval performance, maintaining over 98% Recall@10 on the best-performing task and exceeding 88% on average across all tasks. Task performance on question answering and KB ID generation also demonstrates that SR-KI maintains strong performance while achieving up to 99.75% compression of the injected KBs.

NeuroRAD-FM: A Foundation Model for Neuro-Oncology with Distributionally Robust Training

Neuro-oncology poses unique challenges for machine learning due to heterogeneous data and tumor complexity, limiting the ability of foundation models (FMs) to generalize across cohorts. Existing FMs also perform poorly in predicting uncommon molecular markers, which are essential for treatment response and risk stratification. To address these gaps, we developed a neuro-oncology specific FM with a distributionally robust loss function, enabling accurate estimation of tumor phenotypes while maintaining cross-institution generalization. We pretrained self-supervised backbones (BYOL, DINO, MAE, MoCo) on multi-institutional brain tumor MRI and applied distributionally robust optimization (DRO) to mitigate site and class imbalance. Downstream tasks included molecular classification of common markers (MGMT, IDH1, 1p/19q, EGFR), uncommon alterations (ATRX, TP53, CDKN2A/2B, TERT), continuous markers (Ki-67, TP53), and overall survival prediction in IDH1 wild-type glioblastoma at UCSF, UPenn, and CUIMC. Our method improved molecular prediction and reduced site-specific embedding differences. At CUIMC, mean balanced accuracy rose from 0.744 to 0.785 and AUC from 0.656 to 0.676, with the largest gains for underrepresented endpoints (CDKN2A/2B accuracy 0.86 to 0.92, AUC 0.73 to 0.92; ATRX AUC 0.69 to 0.82; Ki-67 accuracy 0.60 to 0.69). For survival, c-index improved at all sites: CUIMC 0.592 to 0.597, UPenn 0.647 to 0.672, UCSF 0.600 to 0.627. Grad-CAM highlighted tumor and peri-tumoral regions, confirming interpretability. Overall, coupling FMs with DRO yields more site-invariant representations, improves prediction of common and uncommon markers, and enhances survival discrimination, underscoring the need for prospective validation and integration of longitudinal and interventional signals to advance precision neuro-oncology.

SciCom Wiki: Fact-Checking and FAIR Knowledge Distribution for Scientific Videos and Podcasts

Democratic societies need accessible, reliable information. Videos and Podcasts have established themselves as the medium of choice for civic dissemination, but also as carriers of misinformation. The emerging Science Communication Knowledge Infrastructure (SciCom KI) curating non-textual media is still fragmented and not adequately equipped to scale against the content flood. Our work sets out to support the SciCom KI with a central, collaborative platform, the SciCom Wiki, to facilitate FAIR (findable, accessible, interoperable, reusable) media representation and the fact-checking of their content, particularly for videos and podcasts. Building an open-source service system centered around Wikibase, we survey requirements from 53 stakeholders, refine these in 11 interviews, and evaluate our prototype based on these requirements with another 14 participants. To address the most requested feature, fact-checking, we developed a neurosymbolic computational fact-checking approach, converting heterogenous media into knowledge graphs. This increases machine-readability and allows comparing statements against equally represented ground-truth. Our computational fact-checking tool was iteratively evaluated through 10 expert interviews, a public user survey with 43 participants verified the necessity and usability of our tool. Overall, our findings identified several needs to systematically support the SciCom KI. The SciCom Wiki, as a FAIR digital library complementing our neurosymbolic computational fact-checking framework, was found suitable to address the raised requirements. Further, we identified that the SciCom KI is severely underdeveloped regarding FAIR knowledge and related systems facilitating its collaborative creation and curation. Our system can provide a central knowledge node, yet a collaborative effort is required to scale against the imminent (mis-)information flood.

Single Shot AI-assisted quantification of KI-67 proliferation index in breast cancer

Reliable quantification of Ki-67, a key proliferation marker in breast cancer, is essential for molecular subtyping and informed treatment planning. Conventional approaches, including visual estimation and manual counting, suffer from interobserver variability and limited reproducibility. This study introduces an AI-assisted method using the YOLOv8 object detection framework for automated Ki-67 scoring. High-resolution digital images (40x magnification) of immunohistochemically stained tumor sections were captured from Ki-67 hotspot regions and manually annotated by a domain expert to distinguish Ki-67-positive and negative tumor cells. The dataset was augmented and divided into training (80%), validation (10%), and testing (10%) subsets. Among the YOLOv8 variants tested, the Medium model achieved the highest performance, with a mean Average Precision at 50% Intersection over Union (mAP50) exceeding 85% for Ki-67-positive cells. The proposed approach offers an efficient, scalable, and objective alternative to conventional scoring methods, supporting greater consistency in Ki-67 evaluation. Future directions include developing user-friendly clinical interfaces and expanding to multi-institutional datasets to enhance generalizability and facilitate broader adoption in diagnostic practice.

Open-Ended and Knowledge-Intensive Video Question Answering

Video question answering that requires external knowledge beyond the visual content remains a significant challenge in AI systems. While models can effectively answer questions based on direct visual observations, they often falter when faced with questions requiring broader contextual knowledge. To address this limitation, we investigate knowledge-intensive video question answering (KI-VideoQA) through the lens of multi-modal retrieval-augmented generation, with a particular focus on handling open-ended questions rather than just multiple-choice formats. Our comprehensive analysis examines various retrieval augmentation approaches using cutting-edge retrieval and vision language models, testing both zero-shot and fine-tuned configurations. We investigate several critical dimensions: the interplay between different information sources and modalities, strategies for integrating diverse multi-modal contexts, and the dynamics between query formulation and retrieval result utilization. Our findings reveal that while retrieval augmentation shows promise in improving model performance, its success is heavily dependent on the chosen modality and retrieval methodology. The study also highlights the critical role of query construction and retrieval depth optimization in effective knowledge integration. Through our proposed approach, we achieve a substantial 17.5% improvement in accuracy on multiple choice questions in the KnowIT VQA dataset, establishing new state-of-the-art performance levels.

Block Graph Neural Networks for tumor heterogeneity prediction

Accurate tumor classification is essential for selecting effective treatments, but current methods have limitations. Standard tumor grading, which categorizes tumors based on cell differentiation, is not recommended as a stand-alone procedure, as some well-differentiated tumors can be malignant. Tumor heterogeneity assessment via single-cell sequencing offers profound insights but can be costly and may still require significant manual intervention. Many existing statistical machine learning methods for tumor data still require complex pre-processing of MRI and histopathological data. In this paper, we propose to build on a mathematical model that simulates tumor evolution (O\.{z}a\'{n}ski (2017)) and generate artificial datasets for tumor classification. Tumor heterogeneity is estimated using normalized entropy, with a threshold to classify tumors as having high or low heterogeneity. Our contributions are threefold: (1) the cut and graph generation processes from the artificial data, (2) the design of tumor features, and (3) the construction of Block Graph Neural Networks (BGNN), a Graph Neural Network-based approach to predict tumor heterogeneity. The experimental results reveal that the combination of the proposed features and models yields excellent results on artificially generated data ($89.67\%$ accuracy on the test data). In particular, in alignment with the emerging trends in AI-assisted grading and spatial transcriptomics, our results suggest that enriching traditional grading methods with birth (e.g., Ki-67 proliferation index) and death markers can improve heterogeneity prediction and enhance tumor classification.

Patherea: Cell Detection and Classification for the 2020s

This paper presents a Patherea, a framework for point-based cell detection and classification that provides a complete solution for developing and evaluating state-of-the-art approaches. We introduce a large-scale dataset collected to directly replicate a clinical workflow for Ki-67 proliferation index estimation and use it to develop an efficient point-based approach that directly predicts point-based predictions, without the need for intermediate representations. The proposed approach effectively utilizes point proposal candidates with the hybrid Hungarian matching strategy and a flexible architecture that enables the usage of various backbones and (pre)training strategies. We report state-of-the-art results on existing public datasets - Lizard, BRCA-M2C, BCData, and the newly proposed Patherea dataset. We show that the performance on existing public datasets is saturated and that the newly proposed Patherea dataset represents a significantly harder challenge for the recently proposed approaches. We also demonstrate the effectiveness of recently proposed pathology foundational models that our proposed approach can natively utilize and benefit from. We also revisit the evaluation protocol that is used in the broader field of cell detection and classification and identify the erroneous calculation of performance metrics. Patherea provides a benchmarking utility that addresses the identified issues and enables a fair comparison of different approaches. The dataset and the code will be publicly released upon acceptance.