GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models consistently outperform random baselines and can exploit local sequence signals such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.

Symphony for Medical Coding: A Next-Generation Agentic System for Scalable and Explainable Medical Coding

Medical coding translates free-text clinical documentation into standardized codes drawn from classification systems that contain tens of thousands of entries and are updated annually. It is central to billing, clinical research, and quality reporting, yet remains largely manual, slow, and error-prone. Existing automated approaches learn to predict a fixed set of codes from labeled data, thereby preventing adaptation to new codes or different coding systems without retraining on different data. They also provide no explanation for their predictions, limiting trust in safety-critical settings. We introduce Symphony for Medical Coding, a system that approaches the task the way expert human coders do: by reasoning over the clinical narrative with direct access to the coding guidelines. This design allows Symphony to operate across any coding system and to provide span-level evidence linking each predicted code to the text that supports it. We evaluate on two public benchmarks and three real-world datasets spanning inpatient, outpatient, emergency, and subspecialty settings across the United States and the United Kingdom. Symphony achieves state-of-the-art results across all settings, establishing itself as a flexible, deployment-ready foundation for automated clinical coding.

TextReasoningBench: Does Reasoning Really Improve Text Classification in Large Language Models?

Eliciting explicit, step-by-step reasoning traces from large language models (LLMs) has emerged as a dominant paradigm for enhancing model capabilities. Although such reasoning strategies were originally designed for problems requiring explicit multi-step reasoning, they have increasingly been applied to a broad range of NLP tasks. This expansion implicitly assumes that deliberative reasoning uniformly benefits heterogeneous tasks. However, whether such reasoning mechanisms truly benefit classification tasks remains largely underexplored, especially considering their substantial token and time costs. To fill this gap, we introduce TextReasoningBench, a systematic benchmark designed to evaluate the effectiveness and efficiency of reasoning strategies for text classification with LLMs. We compare seven reasoning strategies, namely IO, CoT, SC-CoT, ToT, GoT, BoC, and long-CoT across ten LLMs on five text classification datasets. Beyond traditional metrics such as accuracy and macro-F1, we introduce two cost-aware evaluation metrics that quantify the performance gain per reasoning token and the efficiency of performance improvement relative to token cost growth. Experimental results reveal three notable findings: (1) Reasoning does not universally improve classification performance: while moderate strategies such as CoT and SC-CoT yield consistent but limited gains (typically +1% to +3% on big models), more complex methods (e.g., ToT and GoT) often fail to outperform simpler baselines and can even degrade performance, especially on small models; (2) Reasoning is often inefficient: many reasoning strategies increase token consumption by 10$\times$ to 100$\times$ (e.g., SC-CoT and ToT) while providing only marginal performance improvements.

Cross-Modal Prototype Alignment and Mixing for Training-Free Few-Shot Classification

Vision-language models (VLMs) like CLIP are trained with the objective of aligning text and image pairs. To improve CLIP-based few-shot image classification, recent works have observed that, along with text embeddings, image embeddings from the training set are an important source of information. In this work we investigate the impact of directly mixing image and text prototypes for few-shot classification and analyze this from a bias-variance perspective. We show that mixing prototypes acts like a shrinkage estimator. Although mixed prototypes improve classification performance, the image prototypes still add some noise in the form of instance-specific background or context information. In order to capture only information from the image space relevant to the given classification task, we propose projecting image prototypes onto the principal directions of the semantic text embedding space to obtain a text-aligned semantic image subspace. These text-aligned image prototypes, when mixed with text embeddings, further improve classification. However, for downstream datasets with poor cross-modal alignment in CLIP, semantic alignment might be suboptimal. We show that the image subspace can still be leveraged by modeling the anisotropy using class covariances. We demonstrate that combining a text-aligned mixed prototype classifier and an image-specific LDA classifier outperforms existing methods across few-shot classification benchmarks.

Semi-Supervised Learning with Balanced Deep Representation Distributions

Semi-Supervised Text Classification (SSTC) mainly works under the spirit of self-training. They initialize the deep classifier by training over labeled texts; and then alternatively predict unlabeled texts as their pseudo-labels and train the deep classifier over the mixture of labeled and pseudo-labeled texts. Naturally, their performance is largely affected by the accuracy of pseudo-labels for unlabeled texts. Unfortunately, they often suffer from low accuracy because of the margin bias problem caused by the large difference between representation distributions of labels in SSTC. To alleviate this problem, we apply the angular margin loss, and perform several Gaussian linear transformations to achieve balanced label angle variances, i.e., the variance of label angles of texts within the same label. More accuracy of predicted pseudo-labels can be achieved by constraining all label angle variances balanced, where they are estimated over both labeled and pseudo-labeled texts during self-training loops. With this insight, we propose a novel SSTC method, namely Semi-Supervised Text Classification with Balanced Deep representation Distributions (S2TC-BDD). We implement both multi-class classification and multi-label classification versions of S2TC-BDD by introducing some pseudo-labeling tricks and regularization terms. To evaluate S2 TC-BDD, we compare it against the state-of-the-art SSTC methods. Empirical results demonstrate the effectiveness of S2 TC-BDD, especially when the labeled texts are scarce.

InCTRLv2: Generalist Residual Models for Few-Shot Anomaly Detection and Segmentation

While recent anomaly detection (AD) methods have made substantial progress in recognizing abnormal patterns within specific domains, most of them are specialist models that are trained on large training samples from a specific target dataset, struggling to generalize to unseen datasets. To address this limitation, the paradigm of Generalist Anomaly Detection (GAD) has emerged in recent years, aiming to learn a single generalist model to detect anomalies across diverse domains without retraining. To this end, this work introduces InCTRLv2, a novel few-shot Generalist Anomaly Detection and Segmentation (GADS) framework that significantly extends our previously proposed GAD model, InCTRL. Building on the idea of learning in-context residuals with few-shot normal examples to detect anomalies as in InCTRL, InCTRLv2 introduces two new, complementary perspectives of anomaly perception under a dual-branch framework. This is accomplished by two novel modules upon InCTRL: i) Discriminative Anomaly Score Learning (DASL) with both normal and abnormal data in the main branch, which learns a semantic-guided abnormality and normality space that supports the classification of query samples from both the abnormality and normality perspectives; and ii) One-class Anomaly Score Learning (OASL) using only the normal data, which learns generalized normality patterns in a semantic space via an auxiliary branch, focusing on detecting anomalies through the lens of normality solely. Both branches are guided by rich visual-text semantic priors encoded by large-scale vision-language models. Together, they offer a dual semantic perspective for AD: one emphasizes normal-abnormal discriminations, while the other emphasizes normality-deviated semantics. Extensive experiments on ten AD datasets demonstrate that InCTRLv2 achieves SotA performance in both anomaly detection and segmentation tasks across various settings.

KUET at StanceNakba Shared Task: StanceMoE: Mixture-of-Experts Architecture for Stance Detection

Actor-level stance detection aims to determine an author expressed position toward specific geopolitical actors mentioned or implicated in a text. Although transformer-based models have achieved relatively good performance in stance classification, they typically rely on unified representations that may not sufficiently capture heterogeneous linguistic signals, such as contrastive discourse structures, framing cues, and salient lexical indicators. This motivates the need for adaptive architectures that explicitly model diverse stance-expressive patterns. In this paper, we propose StanceMoE, a context-enhanced Mixture-of-Experts (MoE) architecture built upon a fine-tuned BERT encoder for actor-level stance detection. Our model integrates six expert modules designed to capture complementary linguistic signals, including global semantic orientation, salient lexical cues, clause-level focus, phrase-level patterns, framing indicators, and contrast-driven discourse shifts. A context-aware gating mechanism dynamically weights expert contributions, enabling adaptive routing based on input characteristics. Experiments are conducted on the StanceNakba 2026 Subtask A dataset, comprising 1,401 annotated English texts where the target actor is implicit in the text. StanceMoE achieves a macro-F1 score of 94.26%, outperforming traditional baselines, and alternative BERT-based variants.

OASIC: Occlusion-Agnostic and Severity-Informed Classification

Severe occlusions of objects pose a major challenge for computer vision. We show that two root causes are (1) the loss of visible information and (2) the distracting patterns caused by the occluders. Our approach addresses both causes at the same time. First, the distracting patterns are removed at test-time, via masking of the occluding patterns. This masking is independent of the type of occlusion, by handling the occlusion through the lens of visual anomalies w.r.t. the object of interest. Second, to deal with less visual details, we follow standard practice by masking random parts of the object during training, for various degrees of occlusions. We discover that (a) it is possible to estimate the degree of the occlusion (i.e. severity) at test-time, and (b) that a model optimized for a specific degree of occlusion also performs best on a similar degree during test-time. Combining these two insights brings us to a severity-informed classification model called OASIC: Occlusion Agnostic Severity Informed Classification. We estimate the severity of occlusion for a test image, mask the occluder, and select the model that is optimized for the degree of occlusion. This strategy performs better than any single model optimized for any smaller or broader range of occlusion severities. Experiments show that combining gray masking with adaptive model selection improves $\text{AUC}_\text{occ}$ by +18.5 over standard training on occluded images and +23.7 over finetuning on unoccluded images.

Enhancing Hyperspace Analogue to Language (HAL) Representations via Attention-Based Pooling for Text Classification

The Hyperspace Analogue to Language (HAL) model relies on global word co-occurrence matrices to construct distributional semantic representations. While these representations capture lexical relationships effectively, aggregating them into sentence-level embeddings via standard mean pooling often results in information loss. Mean pooling assigns equal weight to all tokens, thereby diluting the impact of contextually salient words with uninformative structural tokens. In this paper, we address this limitation by integrating a learnable, temperature-scaled additive attention mechanism into the HAL representation pipeline. To mitigate the sparsity and high dimensionality of the raw co-occurrence matrices, we apply Truncated Singular Value Decomposition (SVD) to project the vectors into a dense latent space prior to the attention layer. We evaluate the proposed architecture on the IMDB sentiment analysis dataset. Empirical results demonstrate that the attention-based pooling approach achieves a test accuracy of 82.38%, yielding an absolute improvement of 6.74 percentage points over the traditional mean pooling baseline (75.64%). Furthermore, qualitative analysis of the attention weights indicates that the mechanism successfully suppresses stop-words and selectively attends to sentiment-bearing tokens, improving both classification performance and model interpretability.

MedGemma 1.5 Technical Report

We introduce MedGemma 1.5 4B, the latest model in the MedGemma collection. MedGemma 1.5 expands on MedGemma 1 by integrating additional capabilities: high-dimensional medical imaging (CT/MRI volumes and histopathology whole slide images), anatomical localization via bounding boxes, multi-timepoint chest X-ray analysis, and improved medical document understanding (lab reports, electronic health records). We detail the innovations required to enable these modalities within a single architecture, including new training data, long-context 3D volume slicing, and whole-slide pathology sampling. Compared to MedGemma 1 4B, MedGemma 1.5 4B demonstrates significant gains in these new areas, improving 3D MRI condition classification accuracy by 11% and 3D CT condition classification by 3% (absolute improvements). In whole slide pathology imaging, MedGemma 1.5 4B achieves a 47% macro F1 gain. Additionally, it improves anatomical localization with a 35% increase in Intersection over Union on chest X-rays and achieves a 4% macro accuracy for longitudinal (multi-timepoint) chest x-ray analysis. Beyond its improved multimodal performance over MedGemma 1, MedGemma 1.5 improves on text-based clinical knowledge and reasoning, improving by 5% on MedQA accuracy and 22% on EHRQA accuracy. It also achieves an average of 18% macro F1 on 4 different lab report information extraction datasets (EHR Datasets 2, 3, 4, and Mendeley Clinical Laboratory Test Reports). Taken together, MedGemma 1.5 serves as a robust, open resource for the community, designed as an improved foundation on which developers can create the next generation of medical AI systems. Resources and tutorials for building upon MedGemma 1.5 can be found at https://goo.gle/MedGemma.