YaleNLP @ PerAnsSumm 2025: Multi-Perspective Integration via Mixture-of-Agents for Enhanced Healthcare QA Summarization

Automated summarization of healthcare community question-answering forums is challenging due to diverse perspectives presented across multiple user responses to each question. The PerAnsSumm Shared Task was therefore proposed to tackle this challenge by identifying perspectives from different answers and then generating a comprehensive answer to the question. In this study, we address the PerAnsSumm Shared Task using two complementary paradigms: (i) a training-based approach through QLoRA fine-tuning of LLaMA-3.3-70B-Instruct, and (ii) agentic approaches including zero- and few-shot prompting with frontier LLMs (LLaMA-3.3-70B-Instruct and GPT-4o) and a Mixture-of-Agents (MoA) framework that leverages a diverse set of LLMs by combining outputs from multi-layer feedback aggregation. For perspective span identification/classification, GPT-4o zero-shot achieves an overall score of 0.57, substantially outperforming the 0.40 score of the LLaMA baseline. With a 2-layer MoA configuration, we were able to improve LLaMA performance up by 28 percent to 0.51. For perspective-based summarization, GPT-4o zero-shot attains an overall score of 0.42 compared to 0.28 for the best LLaMA zero-shot, and our 2-layer MoA approach boosts LLaMA performance by 32 percent to 0.37. Furthermore, in few-shot setting, our results show that the sentence-transformer embedding-based exemplar selection provides more gain than manually selected exemplars on LLaMA models, although the few-shot prompting is not always helpful for GPT-4o. The YaleNLP team's approach ranked the overall second place in the shared task.

Z1: Efficient Test-time Scaling with Code

Large Language Models (LLMs) can achieve enhanced complex problem-solving through test-time computing scaling, yet this often entails longer contexts and numerous reasoning token costs. In this paper, we propose an efficient test-time scaling method that trains LLMs on code-related reasoning trajectories, facilitating their reduction of excess thinking tokens while maintaining performance. First, we create Z1-Code-Reasoning-107K, a curated dataset of simple and complex coding problems paired with their short and long solution trajectories. Second, we present a novel Shifted Thinking Window to mitigate overthinking overhead by removing context-delimiting tags (e.g., <think>. . . </think>) and capping reasoning tokens. Trained with long and short trajectory data and equipped with Shifted Thinking Window, our model, Z1-7B, demonstrates the ability to adjust its reasoning level as the complexity of problems and exhibits efficient test-time scaling across different reasoning tasks that matches R1-Distill-Qwen-7B performance with about 30% of its average thinking tokens. Notably, fine-tuned with only code trajectories, Z1-7B demonstrates generalization to broader reasoning tasks (47.5% on GPQA Diamond). Our analysis of efficient reasoning elicitation also provides valuable insights for future research.

MCTS-RAG: Enhancing Retrieval-Augmented Generation with Monte Carlo Tree Search

We introduce MCTS-RAG, a novel approach that enhances the reasoning capabilities of small language models on knowledge-intensive tasks by leveraging retrieval-augmented generation (RAG) to provide relevant context and Monte Carlo Tree Search (MCTS) to refine reasoning paths. MCTS-RAG dynamically integrates retrieval and reasoning through an iterative decision-making process. Unlike standard RAG methods, which typically retrieve information independently from reasoning and thus integrate knowledge suboptimally, or conventional MCTS reasoning, which depends solely on internal model knowledge without external facts, MCTS-RAG combines structured reasoning with adaptive retrieval. This integrated approach enhances decision-making, reduces hallucinations, and ensures improved factual accuracy and response consistency. The experimental results on multiple reasoning and knowledge-intensive datasets datasets (i.e., ComplexWebQA, GPQA, and FoolMeTwice) show that our method enables small-scale LMs to achieve performance comparable to frontier LLMs like GPT-4o by effectively scaling inference-time compute, setting a new standard for reasoning in small-scale models.

Survey on Evaluation of LLM-based Agents

The emergence of LLM-based agents represents a paradigm shift in AI, enabling autonomous systems to plan, reason, use tools, and maintain memory while interacting with dynamic environments. This paper provides the first comprehensive survey of evaluation methodologies for these increasingly capable agents. We systematically analyze evaluation benchmarks and frameworks across four critical dimensions: (1) fundamental agent capabilities, including planning, tool use, self-reflection, and memory; (2) application-specific benchmarks for web, software engineering, scientific, and conversational agents; (3) benchmarks for generalist agents; and (4) frameworks for evaluating agents. Our analysis reveals emerging trends, including a shift toward more realistic, challenging evaluations with continuously updated benchmarks. We also identify critical gaps that future research must address-particularly in assessing cost-efficiency, safety, and robustness, and in developing fine-grained, and scalable evaluation methods. This survey maps the rapidly evolving landscape of agent evaluation, reveals the emerging trends in the field, identifies current limitations, and proposes directions for future research.

LocAgent: Graph-Guided LLM Agents for Code Localization

Code localization--identifying precisely where in a codebase changes need to be made--is a fundamental yet challenging task in software maintenance. Existing approaches struggle to efficiently navigate complex codebases when identifying relevant code sections. The challenge lies in bridging natural language problem descriptions with the appropriate code elements, often requiring reasoning across hierarchical structures and multiple dependencies. We introduce LocAgent, a framework that addresses code localization through graph-based representation. By parsing codebases into directed heterogeneous graphs, LocAgent creates a lightweight representation that captures code structures (files, classes, functions) and their dependencies (imports, invocations, inheritance), enabling LLM agents to effectively search and locate relevant entities through powerful multi-hop reasoning. Experimental results on real-world benchmarks demonstrate that our approach significantly enhances accuracy in code localization. Notably, our method with the fine-tuned Qwen-2.5-Coder-Instruct-32B model achieves comparable results to SOTA proprietary models at greatly reduced cost (approximately 86% reduction), reaching up to 92.7% accuracy on file-level localization while improving downstream GitHub issue resolution success rates by 12% for multiple attempts (Pass@10). Our code is available at https://github.com/gersteinlab/LocAgent.

MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning

Large Language Models (LLMs) have shown impressive performance on existing medical question-answering benchmarks. This high performance makes it increasingly difficult to meaningfully evaluate and differentiate advanced methods. We present MedAgentsBench, a benchmark that focuses on challenging medical questions requiring multi-step clinical reasoning, diagnosis formulation, and treatment planning-scenarios where current models still struggle despite their strong performance on standard tests. Drawing from seven established medical datasets, our benchmark addresses three key limitations in existing evaluations: (1) the prevalence of straightforward questions where even base models achieve high performance, (2) inconsistent sampling and evaluation protocols across studies, and (3) lack of systematic analysis of the interplay between performance, cost, and inference time. Through experiments with various base models and reasoning methods, we demonstrate that the latest thinking models, DeepSeek R1 and OpenAI o3, exhibit exceptional performance in complex medical reasoning tasks. Additionally, advanced search-based agent methods offer promising performance-to-cost ratios compared to traditional approaches. Our analysis reveals substantial performance gaps between model families on complex questions and identifies optimal model selections for different computational constraints. Our benchmark and evaluation framework are publicly available at https://github.com/gersteinlab/medagents-benchmark.

Investigating Generalization of One-shot LLM Steering Vectors

Steering vectors have emerged as a promising approach for interpreting and controlling LLMs, but current methods typically require large contrastive datasets that are often impractical to construct and may capture spurious correlations. We propose directly optimizing steering vectors through gradient descent on a single training example, and systematically investigate how these vectors generalize. We consider several steering optimization techniques, including multiple novel ones, and find that the resulting vectors effectively mediate safety-relevant behaviors in multiple models. Indeed, in experiments on an alignment-faking model, we are able to optimize one-shot steering vectors that induce harmful behavior on benign examples and whose negations suppress harmful behavior on malign examples. And in experiments on refusal suppression, we demonstrate that one-shot optimized steering vectors can transfer across inputs, yielding a Harmbench attack success rate of 96.9%. Furthermore, to quantitatively assess steering effectiveness in instruction-tuned models, we develop a novel evaluation framework using sequence probabilities from the corresponding base model. With this framework, we analyze how steering vectors modulate an instruction-tuned LLM's ability to recover from outputting false information, and find that this ability derives from the base model. Overall, our findings suggest that optimizing steering vectors on a single example can mediate misaligned behavior in LLMs, and provide a path toward better understanding the relationship between LLM behavior and activation space structure.

ATEB: Evaluating and Improving Advanced NLP Tasks for Text Embedding Models

Traditional text embedding benchmarks primarily evaluate embedding models' capabilities to capture semantic similarity. However, more advanced NLP tasks require a deeper understanding of text, such as safety and factuality. These tasks demand an ability to comprehend and process complex information, often involving the handling of sensitive content, or the verification of factual statements against reliable sources. We introduce a new benchmark designed to assess and highlight the limitations of embedding models trained on existing information retrieval data mixtures on advanced capabilities, which include factuality, safety, instruction following, reasoning and document-level understanding. This benchmark includes a diverse set of tasks that simulate real-world scenarios where these capabilities are critical and leads to identification of the gaps of the currently advanced embedding models. Furthermore, we propose a novel method that reformulates these various tasks as retrieval tasks. By framing tasks like safety or factuality classification as retrieval problems, we leverage the strengths of retrieval models in capturing semantic relationships while also pushing them to develop a deeper understanding of context and content. Using this approach with single-task fine-tuning, we achieved performance gains of 8\% on factuality classification and 13\% on safety classification. Our code and data will be publicly available.

TESS 2: A Large-Scale Generalist Diffusion Language Model

We introduce TESS 2, a general instruction-following diffusion language model that outperforms contemporary instruction-tuned diffusion models, as well as matches and sometimes exceeds strong autoregressive (AR) models. We train TESS 2 by first adapting a strong AR model via continued pretraining with the usual cross-entropy as diffusion loss, and then performing further instruction tuning. We find that adaptation training as well as the choice of the base model is crucial for training good instruction-following diffusion models. We further propose reward guidance, a novel and modular inference-time guidance procedure to align model outputs without needing to train the underlying model. Finally, we show that TESS 2 further improves with increased inference-time compute, highlighting the utility of diffusion LMs in having fine-grained controllability over the amount of compute used at inference time. Code and models are available at https://github.com/hamishivi/tess-2.

mFollowIR: a Multilingual Benchmark for Instruction Following in Retrieval

Retrieval systems generally focus on web-style queries that are short and underspecified. However, advances in language models have facilitated the nascent rise of retrieval models that can understand more complex queries with diverse intents. However, these efforts have focused exclusively on English; therefore, we do not yet understand how they work across languages. We introduce mFollowIR, a multilingual benchmark for measuring instruction-following ability in retrieval models. mFollowIR builds upon the TREC NeuCLIR narratives (or instructions) that span three diverse languages (Russian, Chinese, Persian) giving both query and instruction to the retrieval models. We make small changes to the narratives and isolate how well retrieval models can follow these nuanced changes. We present results for both multilingual (XX-XX) and cross-lingual (En-XX) performance. We see strong cross-lingual performance with English-based retrievers that trained using instructions, but find a notable drop in performance in the multilingual setting, indicating that more work is needed in developing data for instruction-based multilingual retrievers.