Multiple-choice questions (MCQs) are a standard format for evaluating large language models (LLMs), yet the popularity of answer options can confound evaluation. Modern LLMs systematically prefer popular but incorrect options over less popular correct ones, a vulnerability we call \textbf{popularity bias}. This pattern aligns with confidence miscalibration: model confidence remains high even as accuracy collapses for popular options. To systematically isolate this phenomenon, we introduce \textbf{PopMCQ}, a benchmark with six controlled strategies that vary option popularity while keeping the correct answer fixed. In our most adversarial setting, where all distractors are more popular than the correct option, models choose popular but wrong answers 66\% of the time. To mitigate this bias, we propose \textbf{PopDebias}, a lightweight inference-time correction that estimates and removes a popularity prior from model predictions. It requires no fine-tuning, is label-free at test time (using only a small calibration split for parameter fitting), and adds negligible computational cost. Experiments on 22 open-source LLMs (0.5B to 32B parameters) show consistent improvements, with accuracy gains up to 54.1 percentage points under strong popularity pressure. The code and data are available https://github.com/DataScienceUIBK/PopMCQ
Abdelrahman Abdallah, Mohammed Ali, Bhawna Piryani et al.· 0 citations
Dynamic sparse attention can reduce the quadratic cost of long-context prefilling without changing model weights. MInference assigns each attention head one pattern offline and estimates that pattern's sparse indices for every prompt. This design is efficient, but it assumes that a head's preferred pattern and sparsity budget remain suitable across inputs. We introduce RouteSparse, which routes each head and prompt segment among a small library of GPU-efficient sparse patterns. A low-cost probe estimates pattern utility and uncertainty; a latency-aware router then selects a pattern and budget, while uncertain cases fall back to a denser mask. We formulate routing as constrained risk minimization, derive an attention-output error certificate from omitted probability mass, and evaluate the method on long-context retrieval, question answering, summarization, and language modeling. On Llama 3.1-8B-Instruct with 128K-token prompts, RouteSparse achieves $6.5\times$ dense prefill speed with a 0.2-point RULER drop relative to dense attention, compared with $7.3\times$ speed and a 1.6-point drop for fixed per-head routing. Ablations confirm that input-conditional routing, hardware profiling, and selective dense fallback each contribute to the quality--latency tradeoff.
Chao-Li Zhang, Yi Ji, Zi-Yan Zhang et al.· 0 citations
A wide range of methods have been proposed for interpreting language models, delivering important insights into their inner workings. However, different methods and their resulting insights stand in relative isolation: what could the underlying structure of language models be, such that they give rise to all our interpretations? In this work, we propose using Tensor Product Representations (TPRs) as a unifying hypothesis. TPRs give a concrete proposal for how compositional structure could be represented in vector space --- as filler-role bindings. We show, both mathematically and empirically, that TPRs can unify several prior interpretability methods: additive analogies, linear probing, sparse autoencoders, and activation patching. Mathematically, we show that these methods can all be derived from TPRs. Empirically, we apply the derivations to a range of different models --- from small toy models to LLMs --- to construct instances of each of the above interpretability methods; these constructed variants perform comparably to their standard variants. We view this work as a step toward what interpretability will ideally provide: a unified account of the nature of neural networks, corroborated not just by individual observations but also by an explanation of the connections between them.
Long-context compression is essential for reducing the cost and latency of large language model inference. However, existing methods can fragment important evidence, require additional training or alignment, and often depend on the target model for effective compression. We introduce TopoCompress, a training-free and model-agnostic framework that compresses long contexts by selecting coherent semantic spans. TopoCompress first scores each span using dense and lexical query relevance together with semantic acceleration. It then constructs a hybrid graph that connects spans based on semantic similarity and sequential adjacency, and propagates the query-guided relevance scores over the graph. Across five long-context tasks-HotpotQA, 2WikiMQA, MuSiQue, Qasper, and MultiFieldQA-en-TopoCompress consistently outperforms strong compression baselines. Notably, TopoCompress achieves performance comparable to the strongest baseline while using a 4x smaller compression budget, and provides a 1.41x smaller compression time over the fastest baseline.
Daniel Agyei Asante, Yang Li· 0 citations
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Code generation increasingly relies on large transformer models, whose capability advances with scale. Yet such a scale is costly, creating demand for small models, especially where data is limited. Recursive models address this by reusing a single block to add depth rather than stacking independent layers. Such models are typically evaluated by teacher-forced fit (next-token loss on ground-truth prefixes) or task accuracy, at a single checkpoint, whereas code is produced by free-running generation, where the model extends its own output. Whether a teacher-forced advantage survives free-running generation, and whether it holds across training, remains open. To study both, we compare a ~28M-parameter autoregressive Tiny Recursive Model (TRM-AR) on natural-language-to-Python code generation against parameter-matched and depth-matched controls, tracking fit and generation across 40 epochs and three seeds. The fit ranking between the recursive model and the depth-matched control reverses twice. Selecting each checkpoint by validation loss and examining the trajectory yields a consistent comparison. At equal parameters, TRM-AR fits, generates, and generalizes better than the parameter-matched control while recovering approximately 45% of the validation-loss gap and 57% of the generation-quality gap between the two controls, at roughly 175 times the per-step cost of the parameter-matched control. However, at equal effective depth, the larger transformer fits and generates better at its validation optimum, suggesting TRM-AR's advantage lies in resistance to overfitting, not greater capability. These findings suggest that recursive code generation models should be evaluated jointly on fit and generation across the training trajectory rather than at a single checkpoint.
Electroencephalography (EEG)-based robotic control is commonly formulated as a direct classification problem, in which electrical neural signals are mapped to a fixed set of discrete actions. However, the limited separability and high noise of EEG signals make it difficult to scale this approach to fine-grained robotic control spaces. We introduce Brain-Language-Action (BLA) models, a framework in which language conditions the interpretation of neural representations for robotic action generation. In a BLA, a small set of reliably distinguishable brain states can be dynamically associated with different actions through a language-defined control mapping, allowing a small number of neural classes to apply to a larger global action space. We develop a proof-of-concept BLA for drone control using motor-imagery EEG from the BCI Competition IV 2a dataset. The system is trained in two stages. First, we evaluate multiple candidate EEG encoder architectures using subject-specific four-class motor-imagery classification, converting 250Hz, 3.5-second, 22-channel EEG samples into five 128-dimensional brain-token embeddings. Second, these embeddings are projected into the embedding space of a pretrained large language model (LLM) and jointly fine-tuned with language instructions to autoregressively generate structured three-token drone actions. Across 840 possible language-defined mappings between four neural states and seven flight action combinations, the resulting BLA achieves 90% per-token accuracy during evaluation. These results provide an initial demonstration that language conditioning can expand the effective control range of EEG-based robotic interfaces without requiring a corresponding increase in the number of directly distinguishable neural states.
Recent advances in large language models (LLMs) have demonstrated exceptional performance in protein-ligand interaction prediction, but state-of-the-art pipelines for large-scale virtual screening almost exclusively rely on high-end GPU clusters with hundreds of gigabytes of memory, creating prohibitive hardware barriers for small academic teams. In this work, we present a fully local low-resource framework that deploys the 175-billion-parameter DeepSeek 175B LLM on a single consumer-grade RTX 4060 laptop equipped with 32GB system RAM and 8GB VRAM, completing a full 200k-scale protein-ligand virtual screening workflow across 20 distinct protein targets. Our implementation achieves 100x throughput of an 8-card A100 cluster baseline under identical task configurations within 72 hours, with an average binding affinity prediction error of 0.88 kcal/mol across all targets, satisfying the 1.0 kcal/mol chemical accuracy requirement for preclinical drug discovery. Systematic runtime profiling reveals that heterogeneous memory management overhead accounts for 72% of total execution time, while accuracy loss introduced by model optimization contributes less than 10% to total prediction error. This work validates the engineering feasibility of running industrial-scale trillion-parameter LLM-driven biomedical computing tasks on consumer hardware, establishing a new low-barrier paradigm for AI-powered early stage drug discovery.
Accurate molecular property prediction requires both statistical reliability and chemical reasoning. Graph neural networks can be calibrated directly on labeled assays but remain limited by the coverage of their training data. Large language models (LLMs) can compare molecular evidence and articulate chemical rationales, yet are unreliable as standalone quantitative predictors. The central challenge is therefore to determine when an LLM should influence a calibrated model and by how much. Here we present CoMPASS, a retrieval-calibrated framework for small-large model collaboration. CoMPASS retains a graph attention network (GAT) as the predictive anchor, retrieves locally relevant training molecules, provides attention-grounded evidence to an LLM, and converts its proposal into a bounded correction through an agreement-aware gate. Across six classification and two regression benchmarks, CoMPASS improves the GAT anchor in regions of correctable uncertainty while limiting LLM intervention in high-confidence regimes. Ablations show that the gains arise from validation-calibrated retrieval and bounded fusion rather than prompting alone. These results suggest that generative reasoning should augment calibrated prediction through evidence-grounded, controlled corrections rather than direct output replacement. Code is available at https://github.com/littlepeachs/CoMPASS.
Wentao Li, Jiang-Jie Qiu, Yijun Li et al.· 0 citations
Large language models are trained to follow instructions while refusing harmful requests. Jailbreaks exploit this balance to elicit content a model would ordinarily reject. Roleplay jailbreaks are especially concerning: the harmful request can remain visible inside a roleplay wrapper made of a persona, scenario, and task, yet the model may comply. We use mechanistic interpretability to determine how this context reverses refusal and which elements contribute to the reversal. Across two benchmarks, three model families, and four authored wrappers, we compare matched harmful and benign requests with and without this wrapper. We trace hidden-state contrasts from the request to the final prompt state, isolate wrapper operations through controlled counterfactuals, intervene on their activation directions in held-out evaluation requests, and decompose effective directions geometrically. Our analysis yields three findings. (1) Successful attacks retain the measured harmful-versus-benign distinction at the request, while its refusal-associated expression weakens where the answer begins, a pattern we call safety-relay attenuation. (2) Constructing the complete roleplay around the request and framing it within the scenario contribute causally: removing the associated activation changes restores refusal. (3) These effects largely share internal structure, and most repair is reproduced by components aligned with the model's ordinary refusal of harmful requests without roleplay; scenario framing retains a smaller, model-dependent component. Together, these findings explain how roleplay can produce compliance despite retained evidence of harm and identify a concrete target for future safeguards: maintaining the connection from harm recognition to refusal.
Token embeddings are the basic representational units that connect discrete tokens with continuous computation in language models. Although modern language models learn embeddings from random initialization through gradient-based training, the dynamical mechanism by which meaningful embedding structures emerge remains unclear. In this work, we identify that the evolving embedding structures are closely related to token-conditioned label and contextual distributions, which we formalize as probability signatures. We observe a progressive learning process, which we term Context Staircase: embeddings learn the low-order statistic signatures of the data before the high-order ones. More specifically, we observe that early in training they align with the simplest, context-free signature linking a token to its label, and as training proceeds, they progressively reflect signatures involving more and more context tokens. We then analyze the gradient flow of embeddings under small initialization to explain this phenomenon, deriving embedding evolution equations for feed-forward and self-attention architectures. We further extend these observations to real language-model training. Finally, we show that these embedding structures play an important role in both task learning and the incorporation of semantic structure into the embedding space. Overall, our results provide a dynamic explanation of how data statistics and architecture jointly shape token embeddings in language models, and reveal an implicit bias in the space of data statistics: training proceeds from simpler, low-order statistical relations toward increasingly complex, context-dependent ones.
Junjie Yao, Liangkai Hang, Zhi-Qin John Xu· 0 citations
Multimodal Large Language Models (MLLMs) can assign similar confidence to answers that fail for different reasons. We propose HalluPrism, a behavioral diagnostic that re-runs an answer after visual degradation, blank-image replacement, and grounding or relation checks. These targeted probes yield a signature over visual-perturbation sensitivity (V ), image-removal confidence retention (L), and grounding/relation-probe instability (A). Across 58K+ examples from four benchmarks and four MLLMs, image-removal confidence retention is most prevalent, while grounding/relation-probe instability better separates failure families. Only 18 of 48 source-target checks are diagonally aligned, so the coordinates should be interpreted jointly rather than as independent causal sources. With the dataset fixed, the joint signature improves failure-family AUROC from 0.634 to 0.769 on HallusionBench and from 0.707 to 0.817 on VizWiz, with smaller gains on POPE and VSR. In pooled XGBoost analysis, AUROC rises from 0.78 with scalar confidence to 0.95 with (V, L, A) and 0.97 when confidence is added. The same signature does not automatically improve correctness ranking. The three tested direct scalarizations can harm it. These results separate failure diagnosis from abstention scoring: multimodal uncertainty should characterize failure structure before it is used to decide whether to abstain or correct.
Aman Prakash, Sourish Dasgupta, Tanmoy Chakraborty· 0 citations
Physical mechanism-based models for river water quality prediction involve complicated calculations，whereas machine learning models lack interpretability，resulting in a disconnection between predictions and management decisions that hinders practical application. To deeply integrate high-precision prediction with decision support，a TCN-Attention deep learning model that combines a temporal convolutional network and an attention mechanism is constructed to predict six core water quality indicators，with Bayesian optimization used for automatic parameter tuning. The SHAP interpretability technique is introduced to quantify the contributions of multi-source input features and reveal key driving factors. Based on the Qwen3-Next large language model，water quality grade evaluations and improvement recommendations are automatically generated. Application results for rivers in Xinwu District of Wuxi City demonstrate that the TCN-Attention model achieves good prediction performance under small-sample conditions，with domestic water use，turbidity，and water identified as the most critical influencing factors. Qwen3-Next model achieves an accuracy of 89.8% in water quality grading，and the proposed improvement recommendations are targeted and practicable. The proposed interpretable intelligent water quality prediction method effectively improves the accuracy and interpretability of urban river water quality predictions，providing a reliable technical pathway for smart water environment management.
Zuxiang Situ, Hongwu TANG, Qihua Ran et al.· DOAJ (DOAJ: Directory of Ope...· 0 citations
What if pathology foundation models could do more with less? GigaPath-Flash and GigaTIME-Flash cut computational demands while maintaining strong performance, opening the door to larger studies and broader exploration. The post GigaPath-Flash and GigaTIME-Flash: Toward population-scale discovery with efficient pathology foundation models appeared first on Microsoft Research.
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