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Mar 26

Toward Stable and Consistent Evaluation Results: A New Methodology for Base Model Evaluation

This paper poses two critical issues in evaluating base models (without post-training): (1) Unstable evaluation during training: in the early stages of pre-training, the models lack the capability to answer questions as required, leading to unstable evaluation results. This instability makes it difficult to provide solid conclusions to guide the training, especially for key experiments such as data ablation and scaling law. (2) Inconsistency between base and instruct models: base models generally exhibit poorer evaluation performance compared to corresponding instruct models. This gap poses a challenge for assessing whether a base model with better evaluation can truly lead to a better instruct model. To address these issues, we propose Base model Oriented Systematic Evaluation (BOSE), a method specifically designed to optimize the evaluation of base models. Specifically, BOSE introduces two key innovations: In-Context Light-instruction Prompt (ICLiP) for open-ended tasks and Blank-ppl for multi-choice tasks with candidate options, which transforms the standard perplexity (ppl) metric into a fill-in-the-blank format to mitigate early-stage evaluation fluctuations. Furthermore, we are the first to propose Kendall's rank correlation to quantitatively measure the evaluation stability and consistency. Experimental results demonstrate that BOSE significantly enhances both the stability of evaluations during pre-training and the consistency between base and instruct models, thereby providing more reliable guidance for the LLMs' training.

  • 7 authors
·
Mar 2, 2025

GEMA-Score: Granular Explainable Multi-Agent Score for Radiology Report Evaluation

Automatic medical report generation supports clinical diagnosis, reduces the workload of radiologists, and holds the promise of improving diagnosis consistency. However, existing evaluation metrics primarily assess the accuracy of key medical information coverage in generated reports compared to human-written reports, while overlooking crucial details such as the location and certainty of reported abnormalities. These limitations hinder the comprehensive assessment of the reliability of generated reports and pose risks in their selection for clinical use. Therefore, we propose a Granular Explainable Multi-Agent Score (GEMA-Score) in this paper, which conducts both objective quantification and subjective evaluation through a large language model-based multi-agent workflow. Our GEMA-Score parses structured reports and employs NER-F1 calculations through interactive exchanges of information among agents to assess disease diagnosis, location, severity, and uncertainty. Additionally, an LLM-based scoring agent evaluates completeness, readability, and clinical terminology while providing explanatory feedback. Extensive experiments validate that GEMA-Score achieves the highest correlation with human expert evaluations on a public dataset, demonstrating its effectiveness in clinical scoring (Kendall coefficient = 0.70 for Rexval dataset and Kendall coefficient = 0.54 for RadEvalX dataset). The anonymous project demo is available at: https://github.com/Zhenxuan-Zhang/GEMA_score.

  • 10 authors
·
Mar 7, 2025

PerSEval: Assessing Personalization in Text Summarizers

Personalized summarization models cater to individuals' subjective understanding of saliency, as represented by their reading history and current topics of attention. Existing personalized text summarizers are primarily evaluated based on accuracy measures such as BLEU, ROUGE, and METEOR. However, a recent study argued that accuracy measures are inadequate for evaluating the degree of personalization of these models and proposed EGISES, the first metric to evaluate personalized text summaries. It was suggested that accuracy is a separate aspect and should be evaluated standalone. In this paper, we challenge the necessity of an accuracy leaderboard, suggesting that relying on accuracy-based aggregated results might lead to misleading conclusions. To support this, we delve deeper into EGISES, demonstrating both theoretically and empirically that it measures the degree of responsiveness, a necessary but not sufficient condition for degree-of-personalization. We subsequently propose PerSEval, a novel measure that satisfies the required sufficiency condition. Based on the benchmarking of ten SOTA summarization models on the PENS dataset, we empirically establish that -- (i) PerSEval is reliable w.r.t human-judgment correlation (Pearson's r = 0.73; Spearman's rho = 0.62; Kendall's tau = 0.42), (ii) PerSEval has high rank-stability, (iii) PerSEval as a rank-measure is not entailed by EGISES-based ranking, and (iv) PerSEval can be a standalone rank-measure without the need of any aggregated ranking.

  • 5 authors
·
Jun 29, 2024

Geometric Attention: A Regime-Explicit Operator Semantics for Transformer Attention

Geometric Attention (GA) specifies an attention layer by four independent inputs: a finite carrier (what indices are addressable), an evidence-kernel rule (how masked proto-scores and a link induce nonnegative weights), a probe family (which observables are treated as admissible), and an anchor/update rule (which representative kernel is selected and how it is applied). Probe families induce an operational equivalence relation on kernels and therefore a gauge; anchors select representatives relative to that probe. Under a scalar relational-work representation and a multiplicative compositionality law for evidence, the admissible link family is exponential, yielding Gibbs weights; with row anchoring this includes the softmax kernel family as a subregime. After quotienting unary row/column score fields, the remaining interaction component admits a canonical rank-r normal form (Eckart-Young/SVD); dot-product score charts implement the corresponding low-rank interaction regime. Fixing the carrier and extensionalizing the update yields the standard fixed-token Transformer attention operator; allowing carrier updates yields adaptive-carrier and staged-depth regimes. The operator language also supports multihead/mixed kernels, plan-based anchors (e.g., entropic OT/Sinkhorn), and unary operators (e.g., FFN-style fields) as explicit regime choices. This separates invariant structure from modeling choice, enabling principled comparison and extension of attention mechanisms, and attention-based architectures.

  • 1 authors
·
Jan 10

Extending Mixture of Experts Model to Investigate Heterogeneity of Trajectories: When, Where and How to Add Which Covariates

Researchers are usually interested in examining the impact of covariates when separating heterogeneous samples into latent classes that are more homogeneous. The majority of theoretical and empirical studies with such aims have focused on identifying covariates as predictors of class membership in the structural equation modeling framework. In other words, the covariates only indirectly affect the sample heterogeneity. However, the covariates' influence on between-individual differences can also be direct. This article presents a mixture model that investigates covariates to explain within-cluster and between-cluster heterogeneity simultaneously, known as a mixture-of-experts (MoE) model. This study aims to extend the MoE framework to investigate heterogeneity in nonlinear trajectories: to identify latent classes, covariates as predictors to clusters, and covariates that explain within-cluster differences in change patterns over time. Our simulation studies demonstrate that the proposed model generally estimates the parameters unbiasedly, precisely and exhibits appropriate empirical coverage for a nominal 95% confidence interval. This study also proposes implementing structural equation model forests to shrink the covariate space of the proposed mixture model. We illustrate how to select covariates and construct the proposed model with longitudinal mathematics achievement data. Additionally, we demonstrate that the proposed mixture model can be further extended in the structural equation modeling framework by allowing the covariates that have direct effects to be time-varying.

  • 2 authors
·
Jul 5, 2020

A Zero-shot Explainable Doctor Ranking Framework with Large Language Models

Online medical service provides patients convenient access to doctors, but effectively ranking doctors based on specific medical needs remains challenging. Current ranking approaches typically lack the interpretability crucial for patient trust and informed decision-making. Additionally, the scarcity of standardized benchmarks and labeled data for supervised learning impedes progress in expertise-aware doctor ranking. To address these challenges, we propose an explainable ranking framework for doctor ranking powered by large language models in a zero-shot setting. Our framework dynamically generates disease-specific ranking criteria to guide the large language model in assessing doctor relevance with transparency and consistency. It further enhances interpretability by generating step-by-step rationales for its ranking decisions, improving the overall explainability of the information retrieval process. To support rigorous evaluation, we built and released DrRank, a novel expertise-driven dataset comprising 38 disease-treatment pairs and 4,325 doctor profiles. On this benchmark, our framework significantly outperforms the strongest baseline by +6.45 NDCG@10. Comprehensive analyses also show our framework is fair across disease types, patient gender, and geographic regions. Furthermore, verification by medical experts confirms the reliability and interpretability of our approach, reinforcing its potential for trustworthy, real-world doctor recommendation. To demonstrate its broader applicability, we validate our framework on two datasets from BEIR benchmark, where it again achieves superior performance. The code and associated data are available at: https://github.com/YangLab-BUPT/DrRank.

  • 3 authors
·
Mar 4, 2025

Partial Correlations in Compositional Data Analysis

Partial correlations quantify linear association between two variables adjusting for the influence of the remaining variables. They form the backbone for graphical models and are readily obtained from the inverse of the covariance matrix. For compositional data, the covariance structure is specified from log ratios of variables, so unless we try to "open" the data via a normalization, this implies changes in the definition and interpretation of partial correlations. In the present work, we elucidate how results derived by Aitchison (1986) lead to a natural definition of partial correlation that has a number of advantages over current measures of association. For this, we show that the residuals of log-ratios between a variable with a reference, when adjusting for all remaining variables including the reference, are reference-independent. Since the reference itself can be controlled for, correlations between residuals are defined for the variables directly without the necessity to recur to ratios except when specifying which variables are partialled out. Thus, perhaps surprisingly, partial correlations do not have the problems commonly found with measures of pairwise association on compositional data. They are well-defined between two variables, are properly scaled, and allow for negative association. By design, they are subcompositionally incoherent, but they share this property with conventional partial correlations (where results change when adjusting for the influence of fewer variables). We discuss the equivalence with normalization-based approaches whenever the normalizing variables are controlled for. We also discuss the partial variances and correlations we obtain from a previously studied data set of Roman glass cups.

  • 1 authors
·
Apr 20, 2019

Automatic Personalized Impression Generation for PET Reports Using Large Language Models

In this study, we aimed to determine if fine-tuned large language models (LLMs) can generate accurate, personalized impressions for whole-body PET reports. Twelve language models were trained on a corpus of PET reports using the teacher-forcing algorithm, with the report findings as input and the clinical impressions as reference. An extra input token encodes the reading physician's identity, allowing models to learn physician-specific reporting styles. Our corpus comprised 37,370 retrospective PET reports collected from our institution between 2010 and 2022. To identify the best LLM, 30 evaluation metrics were benchmarked against quality scores from two nuclear medicine (NM) physicians, with the most aligned metrics selecting the model for expert evaluation. In a subset of data, model-generated impressions and original clinical impressions were assessed by three NM physicians according to 6 quality dimensions (3-point scale) and an overall utility score (5-point scale). Each physician reviewed 12 of their own reports and 12 reports from other physicians. Bootstrap resampling was used for statistical analysis. Of all evaluation metrics, domain-adapted BARTScore and PEGASUSScore showed the highest Spearman's rank correlations (0.568 and 0.563) with physician preferences. Based on these metrics, the fine-tuned PEGASUS model was selected as the top LLM. When physicians reviewed PEGASUS-generated impressions in their own style, 89% were considered clinically acceptable, with a mean utility score of 4.08 out of 5. Physicians rated these personalized impressions as comparable in overall utility to the impressions dictated by other physicians (4.03, P=0.41). In conclusion, personalized impressions generated by PEGASUS were clinically useful, highlighting its potential to expedite PET reporting.

  • 11 authors
·
Sep 18, 2023

Learning from the Best, Differently: A Diversity-Driven Rethinking on Data Selection

High-quality pre-training data is crutial for large language models, where quality captures factual reliability and semantic value, and diversity ensures broad coverage and distributional heterogeneity. Existing approaches typically rely on single or multiple-dimensional score-based selection. However, directly selecting top-scored data often degrades performance, and sampling from a broader range is required to recover results. The above non-monotonicity between dataset scores and downstream benchmark results reveals a fundamental bias: score-based methods collapse correlated dimensions, causing top-scored data to appear high-quality while systematically overlooking diversity. We argue that ensuring diversity requires decomposing correlated metrics into orthogonal feature dimensions, from which the top-scored data can be directly selected. Therefore, we proposed the Orthogonal Diversity-Aware Selection (ODiS) algorithm, which preserves both quality and diversity during data selection. First, ODiS evaluates data from multiple dimensions, covering language quality, knowledge quality, and comprehension difficulty. The multi-dimensional scores are then decorrelated via Principal Component Analysis (PCA), yielding orthogonal evaluation dimensions. For each dimension, a Roberta-based scorer is trained to regress the data onto PCA-projected scores, enabling scalable inference on large corpora. Finally, ODiS constructs the training dataset by selecting top-scored data within each orthogonal dimension, thereby ensuring both quality and diversity. Empirical results show that ODiS-selected data exhibit less than 2\% inter-dimension overlap, confirming orthogonality between dimensions. More importantly, models trained with ODiS-selected data significantly outperform other baselines on downstream benchmarks, highlighting the necessity of orthogonal, diversity-aware data selection for LLMs.

  • 9 authors
·
Oct 20, 2025 3

Duplicate Question Retrieval and Confirmation Time Prediction in Software Communities

Community Question Answering (CQA) in different domains is growing at a large scale because of the availability of several platforms and huge shareable information among users. With the rapid growth of such online platforms, a massive amount of archived data makes it difficult for moderators to retrieve possible duplicates for a new question and identify and confirm existing question pairs as duplicates at the right time. This problem is even more critical in CQAs corresponding to large software systems like askubuntu where moderators need to be experts to comprehend something as a duplicate. Note that the prime challenge in such CQA platforms is that the moderators are themselves experts and are therefore usually extremely busy with their time being extraordinarily expensive. To facilitate the task of the moderators, in this work, we have tackled two significant issues for the askubuntu CQA platform: (1) retrieval of duplicate questions given a new question and (2) duplicate question confirmation time prediction. In the first task, we focus on retrieving duplicate questions from a question pool for a particular newly posted question. In the second task, we solve a regression problem to rank a pair of questions that could potentially take a long time to get confirmed as duplicates. For duplicate question retrieval, we propose a Siamese neural network based approach by exploiting both text and network-based features, which outperforms several state-of-the-art baseline techniques. Our method outperforms DupPredictor and DUPE by 5% and 7% respectively. For duplicate confirmation time prediction, we have used both the standard machine learning models and neural network along with the text and graph-based features. We obtain Spearman's rank correlation of 0.20 and 0.213 (statistically significant) for text and graph based features respectively.

  • 5 authors
·
Sep 10, 2023