Nonhuman Primate Brain Tissue Segmentation Using a Transfer Learning Approach

Non-human primates (NHPs) serve as critical models for understanding human brain function and neurological disorders due to their close evolutionary relationship with humans. Accurate brain tissue segmentation in NHPs is critical for understanding neurological disorders, but challenging due to the scarcity of annotated NHP brain MRI datasets, the small size of the NHP brain, the limited resolution of available imaging data and the anatomical differences between human and NHP brains. To address these challenges, we propose a novel approach utilizing STU-Net with transfer learning to leverage knowledge transferred from human brain MRI data to enhance segmentation accuracy in the NHP brain MRI, particularly when training data is limited. The combination of STU-Net and transfer learning effectively delineates complex tissue boundaries and captures fine anatomical details specific to NHP brains. Notably, our method demonstrated improvement in segmenting small subcortical structures such as putamen and thalamus that are challenging to resolve with limited spatial resolution and tissue contrast, and achieved DSC of over 0.88, IoU over 0.8 and HD95 under 7. This study introduces a robust method for multi-class brain tissue segmentation in NHPs, potentially accelerating research in evolutionary neuroscience and preclinical studies of neurological disorders relevant to human health.

Uncertainty Quantification and Confidence Calibration in Large Language Models: A Survey

Large Language Models (LLMs) excel in text generation, reasoning, and decision-making, enabling their adoption in high-stakes domains such as healthcare, law, and transportation. However, their reliability is a major concern, as they often produce plausible but incorrect responses. Uncertainty quantification (UQ) enhances trustworthiness by estimating confidence in outputs, enabling risk mitigation and selective prediction. However, traditional UQ methods struggle with LLMs due to computational constraints and decoding inconsistencies. Moreover, LLMs introduce unique uncertainty sources, such as input ambiguity, reasoning path divergence, and decoding stochasticity, that extend beyond classical aleatoric and epistemic uncertainty. To address this, we introduce a new taxonomy that categorizes UQ methods based on computational efficiency and uncertainty dimensions (input, reasoning, parameter, and prediction uncertainty). We evaluate existing techniques, assess their real-world applicability, and identify open challenges, emphasizing the need for scalable, interpretable, and robust UQ approaches to enhance LLM reliability.

MCQA-Eval: Efficient Confidence Evaluation in NLG with Gold-Standard Correctness Labels

Large Language Models (LLMs) require robust confidence estimation, particularly in critical domains like healthcare and law where unreliable outputs can lead to significant consequences. Despite much recent work in confidence estimation, current evaluation frameworks rely on correctness functions -- various heuristics that are often noisy, expensive, and possibly introduce systematic biases. These methodological weaknesses tend to distort evaluation metrics and thus the comparative ranking of confidence measures. We introduce MCQA-Eval, an evaluation framework for assessing confidence measures in Natural Language Generation (NLG) that eliminates dependence on an explicit correctness function by leveraging gold-standard correctness labels from multiple-choice datasets. MCQA-Eval enables systematic comparison of both internal state-based white-box (e.g. logit-based) and consistency-based black-box confidence measures, providing a unified evaluation methodology across different approaches. Through extensive experiments on multiple LLMs and widely used QA datasets, we report that MCQA-Eval provides efficient and more reliable assessments of confidence estimation methods than existing approaches.

Certifiably Byzantine-Robust Federated Conformal Prediction

Conformal prediction has shown impressive capacity in constructing statistically rigorous prediction sets for machine learning models with exchangeable data samples. The siloed datasets, coupled with the escalating privacy concerns related to local data sharing, have inspired recent innovations extending conformal prediction into federated environments with distributed data samples. However, this framework for distributed uncertainty quantification is susceptible to Byzantine failures. A minor subset of malicious clients can significantly compromise the practicality of coverage guarantees. To address this vulnerability, we introduce a novel framework Rob-FCP, which executes robust federated conformal prediction, effectively countering malicious clients capable of reporting arbitrary statistics with the conformal calibration process. We theoretically provide the conformal coverage bound of Rob-FCP in the Byzantine setting and show that the coverage of Rob-FCP is asymptotically close to the desired coverage level. We also propose a malicious client number estimator to tackle a more challenging setting where the number of malicious clients is unknown to the defender and theoretically shows its effectiveness. We empirically demonstrate the robustness of Rob-FCP against diverse proportions of malicious clients under a variety of Byzantine attacks on five standard benchmark and real-world healthcare datasets.

Contextualized Sequence Likelihood: Enhanced Confidence Scores for Natural Language Generation

The advent of large language models (LLMs) has dramatically advanced the state-of-the-art in numerous natural language generation tasks. For LLMs to be applied reliably, it is essential to have an accurate measure of their confidence. Currently, the most commonly used confidence score function is the likelihood of the generated sequence, which, however, conflates semantic and syntactic components. For instance, in question-answering (QA) tasks, an awkward phrasing of the correct answer might result in a lower probability prediction. Additionally, different tokens should be weighted differently depending on the context. In this work, we propose enhancing the predicted sequence probability by assigning different weights to various tokens using attention values elicited from the base LLM. By employing a validation set, we can identify the relevant attention heads, thereby significantly improving the reliability of the vanilla sequence probability confidence measure. We refer to this new score as the Contextualized Sequence Likelihood (CSL). CSL is easy to implement, fast to compute, and offers considerable potential for further improvement with task-specific prompts. Across several QA datasets and a diverse array of LLMs, CSL has demonstrated significantly higher reliability than state-of-the-art baselines in predicting generation quality, as measured by the AUROC or AUARC.

Cross-Table Pretraining towards a Universal Function Space for Heterogeneous Tabular Data

Tabular data from different tables exhibit significant diversity due to varied definitions and types of features, as well as complex inter-feature and feature-target relationships. Cross-dataset pretraining, which learns reusable patterns from upstream data to support downstream tasks, have shown notable success in various fields. Yet, when applied to tabular data prediction, this paradigm faces challenges due to the limited reusable patterns among diverse tabular datasets (tables) and the general scarcity of tabular data available for fine-tuning. In this study, we fill this gap by introducing a cross-table pretrained Transformer, XTFormer, for versatile downstream tabular prediction tasks. Our methodology insight is pretraining XTFormer to establish a "meta-function" space that encompasses all potential feature-target mappings. In pre-training, a variety of potential mappings are extracted from pre-training tabular datasets and are embedded into the "meta-function" space, and suited mappings are extracted from the "meta-function" space for downstream tasks by a specified coordinate positioning approach. Experiments show that, in 190 downstream tabular prediction tasks, our cross-table pretrained XTFormer wins both XGBoost and Catboost on 137 (72%) tasks, and surpasses representative deep learning models FT-Transformer and the tabular pre-training approach XTab on 144 (76%) and 162 (85%) tasks.

Conformal Drug Property Prediction with Density Estimation under Covariate Shift

In drug discovery, it is vital to confirm the predictions of pharmaceutical properties from computational models using costly wet-lab experiments. Hence, obtaining reliable uncertainty estimates is crucial for prioritizing drug molecules for subsequent experimental validation. Conformal Prediction (CP) is a promising tool for creating such prediction sets for molecular properties with a coverage guarantee. However, the exchangeability assumption of CP is often challenged with covariate shift in drug discovery tasks: Most datasets contain limited labeled data, which may not be representative of the vast chemical space from which molecules are drawn. To address this limitation, we propose a method called CoDrug that employs an energy-based model leveraging both training data and unlabelled data, and Kernel Density Estimation (KDE) to assess the densities of a molecule set. The estimated densities are then used to weigh the molecule samples while building prediction sets and rectifying for distribution shift. In extensive experiments involving realistic distribution drifts in various small-molecule drug discovery tasks, we demonstrate the ability of CoDrug to provide valid prediction sets and its utility in addressing the distribution shift arising from de novo drug design models. On average, using CoDrug can reduce the coverage gap by over 35% when compared to conformal prediction sets not adjusted for covariate shift.

Generating with Confidence: Uncertainty Quantification for Black-box Large Language Models

Large language models (LLMs) specializing in natural language generation (NLG) have recently started exhibiting promising capabilities across a variety of domains. However, gauging the trustworthiness of responses generated by LLMs remains an open challenge, with limited research on uncertainty quantification for NLG. Furthermore, existing literature typically assumes white-box access to language models, which is becoming unrealistic either due to the closed-source nature of the latest LLMs or due to computational constraints. In this work, we investigate uncertainty quantification in NLG for $\textit{black-box}$ LLMs. We first differentiate two closely-related notions: $\textit{uncertainty}$, which depends only on the input, and $\textit{confidence}$, which additionally depends on the generated response. We then propose and compare several confidence/uncertainty metrics, applying them to $\textit{selective NLG}$, where unreliable results could either be ignored or yielded for further assessment. Our findings on several popular LLMs and datasets reveal that a simple yet effective metric for the average semantic dispersion can be a reliable predictor of the quality of LLM responses. This study can provide valuable insights for practitioners on uncertainty management when adopting LLMs. The code to replicate all our experiments is available at https://github.com/zlin7/UQ-NLG.

Fast Online Value-Maximizing Prediction Sets with Conformal Cost Control

Many real-world multi-label prediction problems involve set-valued predictions that must satisfy specific requirements dictated by downstream usage. We focus on a typical scenario where such requirements, separately encoding \textit{value} and \textit{cost}, compete with each other. For instance, a hospital might expect a smart diagnosis system to capture as many severe, often co-morbid, diseases as possible (the value), while maintaining strict control over incorrect predictions (the cost). We present a general pipeline, dubbed as FavMac, to maximize the value while controlling the cost in such scenarios. FavMac can be combined with almost any multi-label classifier, affording distribution-free theoretical guarantees on cost control. Moreover, unlike prior works, FavMac can handle real-world large-scale applications via a carefully designed online update mechanism, which is of independent interest. Our methodological and theoretical contributions are supported by experiments on several healthcare tasks and synthetic datasets - FavMac furnishes higher value compared with several variants and baselines while maintaining strict cost control.

Conformal Prediction Intervals with Temporal Dependence

Cross-sectional prediction is common in many domains such as healthcare, including forecasting tasks using electronic health records, where different patients form a cross-section. We focus on the task of constructing valid prediction intervals (PIs) in time-series regression with a cross-section. A prediction interval is considered valid if it covers the true response with (a pre-specified) high probability. We first distinguish between two notions of validity in such a setting: cross-sectional and longitudinal. Cross-sectional validity is concerned with validity across the cross-section of the time series data, while longitudinal validity accounts for the temporal dimension. Coverage guarantees along both these dimensions are ideally desirable; however, we show that distribution-free longitudinal validity is theoretically impossible. Despite this limitation, we propose Conformal Prediction with Temporal Dependence (CPTD), a procedure which is able to maintain strict cross-sectional validity while improving longitudinal coverage. CPTD is post-hoc and light-weight, and can easily be used in conjunction with any prediction model as long as a calibration set is available. We focus on neural networks due to their ability to model complicated data such as diagnosis codes for time-series regression, and perform extensive experimental validation to verify the efficacy of our approach. We find that CPTD outperforms baselines on a variety of datasets by improving longitudinal coverage and often providing more efficient (narrower) PIs.