We then map the Python code to other programming languages (e.g., Bash) and natural text summaries or descriptions for

In this paper, we present an overview of ClinIQLink, a shared task, collocated with the 24th BioNLP workshop at ACL 2025, designed to stress-test large language models (LLMs) on medically-oriented question answering aimed at the level of a General Practitioner. The challenge supplies 4,978 expert-verified, medical source-grounded question-answer pairs that cover seven formats: true/false, multiple choice, unordered list, short answer, short-inverse, multi-hop, and multi-hop-inverse. Participating systems, bundled in Docker or Apptainer images, are executed on the CodaBench platform or the University of Maryland's Zaratan cluster. An automated harness (Task 1) scores closed-ended items by exact match and open-ended items with a three-tier embedding metric. A subsequent physician panel (Task 2) audits the top model responses.

Objective: The aim of this study was to build an effective co-reference resolution system tailored for the biomedical domain. Materials and Methods: Experiment materials used in this study is provided by the 2011 i2b2 Natural Language Processing Challenge. The 2011 i2b2 challenge involves coreference resolution in medical documents. Concept mentions have been annotated in clinical texts, and the mentions that co-refer in each document are to be linked by coreference chains. Normally, there are two ways of constructing a system to automatically discover co-referent links. One is to manually build rules for co-reference resolution, and the other category of approaches is to use machine learning systems to learn automatically from training datasets and then perform the resolution task on testing datasets. Results: Experiments show the existing co-reference resolution systems are able to find some of the co-referent links, and our rule based system performs well finding the majority of the co-referent links. Our system achieved 89.6% overall performance on multiple medical datasets. Conclusion: The experiment results show that manually crafted rules based on observation of training data is a valid way to accomplish high performance in this coreference resolution task for the critical biomedical domain.

We present RepoST, a scalable method to construct environments that provide execution feedback for repository-level code generation for both training and evaluation. Unlike existing works that aim to build entire repositories for execution, which is challenging for both human and LLMs, we provide execution feedback with sandbox testing, which isolates a given target function and its dependencies to a separate script for testing. Sandbox testing reduces the complexity of external dependencies and enables constructing environments at a large scale. We use our method to construct RepoST-Train, a large-scale train set with 7,415 functions from 832 repositories. Training with the execution feedback provided by RepoST-Train leads to a performance gain of 5.5% Pass@1 on HumanEval and 3.5% Pass@1 on RepoEval. We also build an evaluation dataset, RepoST-Eval, and benchmark 12 code generation models.

With the rapidly increasing capabilities and adoption of code agents for AI-assisted coding, safety concerns, such as generating or executing risky code, have become significant barriers to the real-world deployment of these agents. To provide comprehensive and practical evaluations on the safety of code agents, we propose RedCode, a benchmark for risky code execution and generation: (1) RedCode-Exec provides challenging prompts that could lead to risky code execution, aiming to evaluate code agents' ability to recognize and handle unsafe code. We provide a total of 4,050 risky test cases in Python and Bash tasks with diverse input formats including code snippets and natural text. They covers 25 types of critical vulnerabilities spanning 8 domains (e.g., websites, file systems). We provide Docker environments and design corresponding evaluation metrics to assess their execution results. (2) RedCode-Gen provides 160 prompts with function signatures and docstrings as input to assess whether code agents will follow instructions to generate harmful code or software. Our empirical findings, derived from evaluating three agent frameworks based on 19 LLMs, provide insights into code agents' vulnerabilities. For instance, evaluations on RedCode-Exec show that agents are more likely to reject executing risky operations on the operating system, but are less likely to reject executing technically buggy code, indicating high risks. Risky operations described in natural text lead to a lower rejection rate than those in code format. Additionally, evaluations on RedCode-Gen show that more capable base models and agents with stronger overall coding abilities, such as GPT4, tend to produce more sophisticated and effective harmful software. Our findings highlight the need for stringent safety evaluations for diverse code agents. Our dataset and code are available at https://github.com/AI-secure/RedCode.

Traditional Semantic Table Interpretation (STI) methods rely primarily on the underlying table data to create semantic annotations. This year's SemTab challenge introduced the ``Metadata to KG'' track, which focuses on performing STI by using only metadata information, without access to the underlying data. In response to this new challenge, we introduce a new term: Column Vocabulary Association (CVA). This term refers to the task of semantic annotation of column headers solely based on metadata information. In this study, we evaluate the performance of various methods in executing the CVA task, including a Large Language Models (LLMs) and Retrieval Augmented Generation (RAG) approach, as well as a more traditional similarity approach with SemanticBERT. Our methodology uses a zero-shot setting, with no pretraining or examples passed to the Large Language Models (LLMs), as we aim to avoid a domain-specific setting. We investigate a total of 7 different LLMs, of which three commercial GPT models (i.e. gpt-3.5-turbo-0.125, gpt-4o and gpt-4-turbo) and four open source models (i.e. llama3-80b, llama3-7b, gemma-7b and mixtral-8x7b). We integrate this models with RAG systems, and we explore how variations in temperature settings affect performances. Moreover, we continue our investigation by performing the CVA task utilizing SemanticBERT, analyzing how various metadata information influence its performance. Initial findings indicate that LLMs generally perform well at temperatures below 1.0, achieving an accuracy of 100\% in certain cases. Nevertheless, our investigation also reveal that the nature of the data significantly influences CVA task outcomes. In fact, in cases where the input data and glossary are related (for example by being created by the same organizations) traditional methods appear to surpass the performance of LLMs.

Comprehensive planning agents have been a long term goal in the field of artificial intelligence. Recent innovations in Natural Language Processing have yielded success through the advent of Large Language Models (LLMs). We seek to improve the travel-planning capability of such LLMs by extending upon the work of the previous paper TravelPlanner. Our objective is to explore a new method of using LLMs to improve the travel planning experience. We focus specifically on the "sole-planning" mode of travel planning; that is, the agent is given necessary reference information, and its goal is to create a comprehensive plan from the reference information. While this does not simulate the real-world we feel that an optimization of the sole-planning capability of a travel planning agent will still be able to enhance the overall user experience. We propose a semi-automated prompt generation framework which combines the LLM-automated prompt and "human-in-the-loop" to iteratively refine the prompt to improve the LLM performance. Our result shows that LLM automated prompt has its limitations and "human-in-the-loop" greatly improves the performance by $139\%$ with one single iteration.

Reproducibility is of utmost concern in machine learning and natural language processing (NLP). In the field of natural language generation (especially machine translation), the seminal paper of Post (2018) has pointed out problems of reproducibility of the dominant metric, BLEU, at the time of publication. Nowadays, BERT-based evaluation metrics considerably outperform BLEU. In this paper, we ask whether results and claims from four recent BERT-based metrics can be reproduced. We find that reproduction of claims and results often fails because of (i) heavy undocumented preprocessing involved in the metrics, (ii) missing code and (iii) reporting weaker results for the baseline metrics. (iv) In one case, the problem stems from correlating not to human scores but to a wrong column in the csv file, inflating scores by 5 points. Motivated by the impact of preprocessing, we then conduct a second study where we examine its effects more closely (for one of the metrics). We find that preprocessing can have large effects, especially for highly inflectional languages. In this case, the effect of preprocessing may be larger than the effect of the aggregation mechanism (e.g., greedy alignment vs. Word Mover Distance).

Semantic role labeling (SRL) identifies the predicate-argument structure in a sentence. This task is usually accomplished in four steps: predicate identification, predicate sense disambiguation, argument identification, and argument classification. Errors introduced at one step propagate to later steps. Unfortunately, the existing SRL evaluation scripts do not consider the full effect of this error propagation aspect. They either evaluate arguments independent of predicate sense (CoNLL09) or do not evaluate predicate sense at all (CoNLL05), yielding an inaccurate SRL model performance on the argument classification task. In this paper, we address key practical issues with existing evaluation scripts and propose a more strict SRL evaluation metric PriMeSRL. We observe that by employing PriMeSRL, the quality evaluation of all SoTA SRL models drops significantly, and their relative rankings also change. We also show that PriMeSRLsuccessfully penalizes actual failures in SoTA SRL models.

Causality-Benchmark is a library developed by IBM Research Haifa for benchmarking algorithms that estimate the causal effect of a treatment on some outcome. The framework includes unlabeled data, labeled data, and code for scoring algorithm predictions. Currently, the framework contains one essential dataset, a feature matrix that is derived from the linked birth and infant death data, and the labeled and unlabeled data are simulated models of the treatment assignment, treatment effect and censoring data based on it. More details regarding the data can be found in the LBIDD README file. However, the evaluation script is not bounded to the provided data, and can be used on other data as long as some basic requirements are kept regarding the formats.