Downstream Reasoning

Finetuning pretrained models occurs in a low-dimensional subspace of the full parameter space. Prior work has focused on characterizing this optimization subspace, but largely ignored the complementary question: why do certain directions remain unexplored during finetuning? Are these stable directions irrelevant to downstream tasks, or do they already encode task-relevant structure that requires no further adjustment? Answering this question is central to understanding how pretrained knowledge transfers. Through systematic spectral analysis across vision and language models, we show that the leading singular vectors of pretrained weight matrices remain highly stable under finetuning and are shared across unrelated downstream tasks, revealing that pretraining establishes a reusable spectral coordinate system. Models pretrained on larger datasets exhibit greater spectral stability under distribution shift or task change, directly linking pretraining scale to geometric transferability. Motivated by these findings, we propose a parameter-efficient method that freezes pretrained singular vectors and optimizes only leading spectral coefficients, achieving competitive performance on GLUE with 0.2% trainable parameters. Our results reveal that the stable directions encode transferable structure rather than irrelevant noise: successful pretraining discovers spectral bases that downstream tasks inherit and operate within.

Lithology classification aims to infer subsurface rock types from well-logging signals, supporting downstream applications like reservoir characterization. Despite substantial progress, most existing methods still treat lithology classification as a single-pass classification task. In contrast, practical experts incorporate geological principles, external knowledge, and tool-use capabilities to perform accurate classification. In this work, we propose GeoDecider, a coarse-to-fine agentic workflow that enables accurate and explainable lithology classification through training-free use of large language models (LLMs). GeoDecider reformulates lithology classification as an expert-like structured process and organizes it into a multi-stage workflow involving coarse-to-fine reasoning. Specifically, GeoDecider includes the following stages: (1) base classifier-guided coarse classification, which uses a pre-trained classifier to provide a rough reference for downstream tasks, thus reducing the overall cost of downstream reasoning, (2) tool-augmented reasoning, which utilizes several tools such as contextual analysis and neighbor retrieval to achieve finer and more precise classifications, (3) geological refinement, which post-processes the final results to enforce geological consistency. Experiments on four benchmarks show that GeoDecider outperforms representative baselines. Further analysis demonstrates that the proposed framework produces geologically interpretable predictions while achieving a better trade-off between classification performance and inference efficiency.

Depth pruning improves the inference efficiency of large language models by removing Transformer blocks. Prior work typically treats layer redundancy as an inherent structural property of pretrained networks, emphasizing importance criteria and search algorithms to identify removable layers. In this study, we empirically investigate depth pruning from a functional perspective. Evaluating representative LLM families across diverse calibration configurations and multiple search algorithms, we show that different configurations produce different pruning patterns. Furthermore, under a fixed calibration configuration, complex search algorithms yield marginal performance improvements over simple one-shot methods, converging to similar pruned subsets. Overall, our results suggest that the calibration configuration plays a substantially larger role than the choice of search algorithm in shaping pruning patterns and calibration perplexity, while contributing comparably to variance in downstream reasoning accuracy. This indicates that future pruning efforts may benefit from prioritizing the calibration configuration over search complexity.

Progression to dialysis or end-stage renal disease is a rare but clinically important outcome. Clinicians need evidence on how medication exposures influence downstream risk. We constructed a fixed-window EHR cohort (90-day observation, 730-day prediction; N=81401; dialysis/ESRD prevalence: 1.1%) and modeled sequences of diagnoses, procedures, and medications with kidney laboratory trends (creatinine, BUN, eGFR). A transformer-based causal multi-head model was trained to estimate drug- and ingredient-level average treatment effects (ATEs) using counterfactual exposure removal and insertion under a full medication history setup. On test set, predictive performance reached an AUC of 0.694 and PR-AUC of 0.094. At the selected decision threshold (0.883), the model achieved an F1 score of 0.201 with a Brier score of 0.018. Post-hoc causal analyses of lab changes (eGFR, creatinine, BUN) using IPTW, AIPW, naive, and covariate-adjusted OLS methods assessed clinical directionality. Results showed partial protective-direction support for ACE/ARB exposures and worsening-direction signals for loop diuretics.

Large Language Models (LLMs) can reason well, yet often miss decisive evidence when it is buried in long, noisy contexts. We introduce HiLight, an Evidence Emphasis framework that decouples evidence selection from reasoning for frozen LLM solvers. HiLight avoids compressing or rewriting the input, which can discard or distort evidence, by training a lightweight Emphasis Actor to insert minimal highlight tags around pivotal spans in the unaltered context. A frozen Solver then performs downstream reasoning on the emphasized input. We cast highlighting as a weakly supervised decision-making problem and optimize the Actor with reinforcement learning using only the Solver's task reward, requiring no evidence labels and no access to or modification of the Solver. Across sequential recommendation and long-context question answering, HiLight consistently improves performance over strong prompt-based and automated prompt-optimization baselines. The learned emphasis policy transfers zero-shot to both smaller and larger unseen Solver families, including an API-based Solver, suggesting that the Actor captures genuine, reusable evidence structure rather than overfitting to a single backbone.

Clinical risk prediction using longitudinal medical data supports individualized care. Self-supervised foundation models have emerged as a promising approach for leveraging large-scale unlabeled healthcare records. In natural language processing, scaling laws suggest that larger models achieve predictably lower pretraining losses, supporting the foundation model paradigm. However, for structured medical data, characterized by a limited vocabulary and sparse observations, whether increasing model size consistently improves downstream predictions is unclear, as most studies evaluate only a single model scale. In this study, we evaluated the relationship between model scale and downstream task performance for structured medical foundation models. Using a random sample (2.3 million patients, 32 hospitals) from a nationwide 519-hospital Japanese claims database, we pretrained encoder-only Transformers at five scales (2.2M-101M parameters) for disease incidence and medication prediction. Downstream performance saturated at task-dependent thresholds: disease prediction benefited from larger models (32M-101M), whereas medication prediction saturated at 11M, reducing pretraining time by 178 h. Across all tasks, the best-performing model consistently outperformed a Light Gradient Boosting Machine baseline in the area under the precision-recall curve. These findings indicate that, unlike the monotonically decreasing pretraining loss, the optimal model size varied depending on task characteristics. This task-dependent saturation provides practical guidance for balancing predictive performance and computational cost in structured medical foundation models.

Cryo-electron microscopy (cryo-EM) enables single-particle analysis of biological macromolecules under strict low-dose imaging conditions, but the resulting micrographs often exhibit extremely low signal-to-noise ratios and weak particle visibility. Image denoising is therefore an important preprocessing step for downstream cryo-EM analysis, including particle picking, 2D classification, and 3D reconstruction. Existing cryo-EM denoising methods are commonly trained with pixel-wise or Noise2Noise-style objectives, which can improve visual quality but do not explicitly account for structural consistency required by downstream analysis. In this work, we propose a score-based denoising framework for cryo-EM that learns the clean-data score to recover particle signals while better preserving structural information. Building on this formulation, we further introduce a target-guided variant that incorporates reference-density guidance to stabilize score learning under weak and ambiguous signal conditions. Rather than simply amplifying particle-like responses, our framework better suppresses structured low-frequency background, which improves particle--background separability for downstream analysis. Experiments on multiple cryo-EM datasets show that our score-based methods consistently improve downstream particle picking and produce more structure-consistent 3D reconstructions. Experiments on multiple cryo-EM datasets show that our methods improve downstream particle picking and produce more structure-consistent reconstructions.

Information Extraction aims to distill structured, decision-relevant information from unstructured text, serving as a foundation for downstream understanding and reasoning. However, it is traditionally treated merely as a terminal objective: once extracted, the resulting structure is often consumed in isolation rather than maintained and reused during multi-step inference. Moving beyond this, we propose \textit{IE-as-Cache}, a framework that repurposes IE as a cognitive cache to enhance agentic reasoning. Drawing inspiration from hierarchical computer memory, our approach combines query-driven extraction with cache-aware reasoning to dynamically maintain compact intermediate information and filter noise. Experiments on challenging benchmarks across diverse LLMs demonstrate significant improvements in reasoning accuracy, indicating that IE can be effectively repurposed as a reusable cognitive resource and offering a promising direction for future research on downstream uses of IE.

In NLP classification tasks where little labeled data exists, domain fine-tuning of transformer models on unlabeled data is an established approach. In this paper we have two aims. (1) We describe our observations from fine-tuning the Finnish BERT model on Finnish medical text data. (2) We report on our attempts to predict the benefit of domain-specific pre-training of Finnish BERT from observing the geometry of embedding changes due to domain fine-tuning. Our driving motivation is the common\situation in healthcare AI where we might experience long delays in acquiring datasets, especially with respect to labels.

Modern Large audio-language models (LALMs) power intelligent voice interactions by tightly integrating audio and text. This integration, however, expands the attack surface beyond text and introduces vulnerabilities in the continuous, high-dimensional audio channel. While prior work studied audio jailbreaks, the security risks of malicious audio injection and downstream behavior manipulation remain underexamined. In this work, we reveal a previously overlooked threat, auditory prompt injection, under realistic constraints of audio data-only access and strong perceptual stealth. To systematically analyze this threat, we propose \textit{AudioHijack}, a general framework that generates context-agnostic and imperceptible adversarial audio to hijack LALMs. \textit{AudioHijack} employs sampling-based gradient estimation for end-to-end optimization across diverse models, bypassing non-differentiable audio tokenization. Through attention supervision and multi-context training, it steers model attention toward adversarial audio and generalizes to unseen user contexts. We also design a convolutional blending method that modulates perturbations into natural reverberation, making them highly imperceptible to users. Extensive experiments on 13 state-of-the-art LALMs show consistent hijacking across 6 misbehavior categories, achieving average success rates of 79%-96% on unseen user contexts with high acoustic fidelity. Real-world studies demonstrate that commercial voice agents from Mistral AI and Microsoft Azure can be induced to execute unauthorized actions on behalf of users. These findings expose critical vulnerabilities in LALMs and highlight the urgent need for dedicated defense.

Foundation models have revolutionized AI, but adapting them efficiently for multimodal tasks, particularly in dual-stream architectures composed of unimodal encoders, such as DINO and BERT, remains a significant challenge. ParameterEfficient Fine-Tuning (PEFT) methods like LowRank Adaptation (LoRA) enable lightweight adaptation, yet they operate in isolation within each modality, limiting their ability in capturing cross-modal interactions. In this paper, we take a step in bridging this gap with Cross-Modal LowRank Adaptation (CoLA), a novel PEFT framework that extends LoRA by introducing a dedicated inter-modal adaptation pathway alongside the standard intra-modal one. This dual-path design enables CoLA to adapt unimodal foundation models to multimodal tasks effectively, without interference between modality-specific and crossmodal learning. We evaluate CoLA across a range of vision-language (RefCOCO, RefCOCO+, RefCOCOg) and audio-visual (AVE, AVS) benchmarks, where it consistently outperforms LORA, achieving a relative gain of around 3% and 2%, respectively, while maintaining parameter efficiency. Notably, CoLA enables the first multitask PEFT framework for visual grounding, bridging a key gap in efficient multimodal adaptation. Code is available at https://github.com/peterwisu/CoLA

Large language models (LLMs) are increasingly used to simulate decision-making tasks involving personal data sharing, where privacy concerns and prosocial motivations can push choices in opposite directions. Existing evaluations often measure privacy-related attitudes or sharing intentions in isolation, which makes it difficult to determine whether a model's expressed values jointly predict its downstream data-sharing actions as in real human behaviors. We introduce a context-based assessment protocol that sequentially administers standardized questionnaires for privacy attitudes, prosocialness, and acceptance of data sharing within a bounded, history-carrying session. To evaluate value-action alignments under competing attitudes, we use multi-group structural equation modeling (MGSEM) to identify relations from privacy concerns and prosocialness to data sharing. We propose Value-Action Alignment Rate (VAAR), a human-referenced directional agreement metric that aggregates path-level evidence for expected signs. Across multiple LLMs, we observe stable but model-specific Privacy-PSA-AoDS profiles, and substantial heterogeneity in value-action alignment.