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Apr 17

Bioalignment: Measuring and Improving LLM Disposition Toward Biological Systems for AI Safety

Large language models (LLMs) trained on internet-scale corpora can exhibit systematic biases that increase the probability of unwanted behavior. In this study, we examined potential biases towards synthetic vs. biological technological solutions across four domains (materials, energy, manufacturing, and algorithms). A sample of 5 frontier and 5 open-weight models were measured using 50 curated Bioalignment prompts with a Kelly criterion-inspired evaluation framework. According to this metric, most models were not bioaligned in that they exhibit biases in favor of synthetic (non-biological) solutions. We next examined if fine-tuning could increase the preferences of two open-weight models, Llama 3.2-3B-Instruct and Qwen2.5-3B-Instruct, for biological-based approaches. A curated corpus of ~22M tokens from 6,636 PMC articles emphasizing biological problem-solving was used first to fine-tune Llama 3B with a mixed corpus of continued training and instruction-formatted. This was then extended to Qwen 3B using instruction-formatted only. We found that QLoRA fine-tuning significantly increased the scoring of biological solutions for both models without degrading general capabilities (Holm-Bonferroni-corrected p < 0.001 and p < 0.01, respectively). This suggests that even a small amount of fine-tuning can change how models weigh the relative value of biological and bioinspired vs. synthetic approaches. Although this work focused on small open-weight LLMs, it may be extensible to much larger models and could be used to develop models that favor bio-based approaches. We release the benchmark, corpus, code, and adapter weights.

  • 2 authors
·
Mar 9

AlignBot: Aligning VLM-powered Customized Task Planning with User Reminders Through Fine-Tuning for Household Robots

This paper presents AlignBot, a novel framework designed to optimize VLM-powered customized task planning for household robots by effectively aligning with user reminders. In domestic settings, aligning task planning with user reminders poses significant challenges due to the limited quantity, diversity, and multimodal nature of the reminders. To address these challenges, AlignBot employs a fine-tuned LLaVA-7B model, functioning as an adapter for GPT-4o. This adapter model internalizes diverse forms of user reminders-such as personalized preferences, corrective guidance, and contextual assistance-into structured instruction-formatted cues that prompt GPT-4o in generating customized task plans. Additionally, AlignBot integrates a dynamic retrieval mechanism that selects task-relevant historical successes as prompts for GPT-4o, further enhancing task planning accuracy. To validate the effectiveness of AlignBot, experiments are conducted in real-world household environments, which are constructed within the laboratory to replicate typical household settings. A multimodal dataset with over 1,500 entries derived from volunteer reminders is used for training and evaluation. The results demonstrate that AlignBot significantly improves customized task planning, outperforming existing LLM- and VLM-powered planners by interpreting and aligning with user reminders, achieving 86.8% success rate compared to the vanilla GPT-4o baseline at 21.6%, reflecting a 65% improvement and over four times greater effectiveness. Supplementary materials are available at: https://yding25.com/AlignBot/

  • 10 authors
·
Sep 18, 2024

Ferret-UI: Grounded Mobile UI Understanding with Multimodal LLMs

Recent advancements in multimodal large language models (MLLMs) have been noteworthy, yet, these general-domain MLLMs often fall short in their ability to comprehend and interact effectively with user interface (UI) screens. In this paper, we present Ferret-UI, a new MLLM tailored for enhanced understanding of mobile UI screens, equipped with referring, grounding, and reasoning capabilities. Given that UI screens typically exhibit a more elongated aspect ratio and contain smaller objects of interest (e.g., icons, texts) than natural images, we incorporate "any resolution" on top of Ferret to magnify details and leverage enhanced visual features. Specifically, each screen is divided into 2 sub-images based on the original aspect ratio (i.e., horizontal division for portrait screens and vertical division for landscape screens). Both sub-images are encoded separately before being sent to LLMs. We meticulously gather training samples from an extensive range of elementary UI tasks, such as icon recognition, find text, and widget listing. These samples are formatted for instruction-following with region annotations to facilitate precise referring and grounding. To augment the model's reasoning ability, we further compile a dataset for advanced tasks, including detailed description, perception/interaction conversations, and function inference. After training on the curated datasets, Ferret-UI exhibits outstanding comprehension of UI screens and the capability to execute open-ended instructions. For model evaluation, we establish a comprehensive benchmark encompassing all the aforementioned tasks. Ferret-UI excels not only beyond most open-source UI MLLMs, but also surpasses GPT-4V on all the elementary UI tasks.

  • 8 authors
·
Apr 8, 2024 3

SEFE: Superficial and Essential Forgetting Eliminator for Multimodal Continual Instruction Tuning

Multimodal Continual Instruction Tuning (MCIT) aims to enable Multimodal Large Language Models (MLLMs) to incrementally learn new tasks without catastrophic forgetting. In this paper, we explore forgetting in this context, categorizing it into superficial forgetting and essential forgetting. Superficial forgetting refers to cases where the model's knowledge may not be genuinely lost, but its responses to previous tasks deviate from expected formats due to the influence of subsequent tasks' answer styles, making the results unusable. By contrast, essential forgetting refers to situations where the model provides correctly formatted but factually inaccurate answers, indicating a true loss of knowledge. Assessing essential forgetting necessitates addressing superficial forgetting first, as severe superficial forgetting can obscure the model's knowledge state. Hence, we first introduce the Answer Style Diversification (ASD) paradigm, which defines a standardized process for transforming data styles across different tasks, unifying their training sets into similarly diversified styles to prevent superficial forgetting caused by style shifts. Building on this, we propose RegLoRA to mitigate essential forgetting. RegLoRA stabilizes key parameters where prior knowledge is primarily stored by applying regularization, enabling the model to retain existing competencies. Experimental results demonstrate that our overall method, SEFE, achieves state-of-the-art performance.

  • 7 authors
·
May 5, 2025

Decoupling Task-Solving and Output Formatting in LLM Generation

Large language models (LLMs) are increasingly adept at following instructions containing task descriptions to solve complex problems, such as mathematical reasoning and automatic evaluation (LLM-as-a-Judge). However, as prompts grow more complex, models often struggle to adhere to all instructions. This difficulty is especially common when instructive prompts intertwine reasoning directives -- specifying what the model should solve -- with rigid formatting requirements that dictate how the solution must be presented. The entanglement creates competing goals for the model, suggesting that more explicit separation of these two aspects could lead to improved performance. To this front, we introduce Deco-G, a decoding framework that explicitly decouples format adherence from task solving. Deco-G handles format compliance with a separate tractable probabilistic model (TPM), while prompts LLMs with only task instructions. At each decoding step, Deco-G combines next token probabilities from the LLM with the TPM calculated format compliance likelihood to form the output probability. To make this approach both practical and scalable for modern instruction-tuned LLMs, we introduce three key innovations: instruction-aware distillation, a flexible trie-building algorithm, and HMM state pruning for computational efficiency. We demonstrate the effectiveness of Deco-G across a wide range of tasks with diverse format requirements, including mathematical reasoning, LLM-as-a-judge, and event argument extraction. Overall, our approach yields 1.0% to 6.0% relative gain over regular prompting practice with guaranteed format compliance.

  • 3 authors
·
Oct 3, 2025

Layout and Task Aware Instruction Prompt for Zero-shot Document Image Question Answering

Layout-aware pre-trained models has achieved significant progress on document image question answering. They introduce extra learnable modules into existing language models to capture layout information within document images from text bounding box coordinates obtained by OCR tools. However, extra modules necessitate pre-training on extensive document images. This prevents these methods from directly utilizing off-the-shelf instruction-tuning language foundation models, which have recently shown promising potential in zero-shot learning. Instead, in this paper, we find that instruction-tuning language models like Claude and ChatGPT can understand layout by spaces and line breaks. Based on this observation, we propose the LAyout and Task aware Instruction Prompt (LATIN-Prompt), which consists of layout-aware document content and task-aware instruction. Specifically, the former uses appropriate spaces and line breaks to recover the layout information among text segments obtained by OCR tools, and the latter ensures that generated answers adhere to formatting requirements. Moreover, we propose the LAyout and Task aware Instruction Tuning (LATIN-Tuning) to improve the performance of small instruction-tuning models like Alpaca. Experimental results show that LATIN-Prompt enables zero-shot performance of Claude and ChatGPT to be comparable to the fine-tuning performance of SOTAs on document image question answering, and LATIN-Tuning enhances the zero-shot performance of Alpaca significantly. For example, LATIN-Prompt improves the performance of Claude and ChatGPT on DocVQA by 263% and 20% respectively. LATIN-Tuning improves the performance of Alpaca on DocVQA by 87.7%. Quantitative and qualitative analyses demonstrate the effectiveness of LATIN-Prompt and LATIN-Tuning. We provide the code in supplementary and will release it to facilitate future research.

  • 4 authors
·
Jun 1, 2023

When Thinking Fails: The Pitfalls of Reasoning for Instruction-Following in LLMs

Reasoning-enhanced large language models (RLLMs), whether explicitly trained for reasoning or prompted via chain-of-thought (CoT), have achieved state-of-the-art performance on many complex reasoning tasks. However, we uncover a surprising and previously overlooked phenomenon: explicit CoT reasoning can significantly degrade instruction-following accuracy. Evaluating 15 models on two benchmarks: IFEval (with simple, rule-verifiable constraints) and ComplexBench (with complex, compositional constraints), we consistently observe performance drops when CoT prompting is applied. Through large-scale case studies and an attention-based analysis, we identify common patterns where reasoning either helps (e.g., with formatting or lexical precision) or hurts (e.g., by neglecting simple constraints or introducing unnecessary content). We propose a metric, constraint attention, to quantify model focus during generation and show that CoT reasoning often diverts attention away from instruction-relevant tokens. To mitigate these effects, we introduce and evaluate four strategies: in-context learning, self-reflection, self-selective reasoning, and classifier-selective reasoning. Our results demonstrate that selective reasoning strategies, particularly classifier-selective reasoning, can substantially recover lost performance. To our knowledge, this is the first work to systematically expose reasoning-induced failures in instruction-following and offer practical mitigation strategies.

  • 8 authors
·
May 16, 2025

Quantifying Language Models' Sensitivity to Spurious Features in Prompt Design or: How I learned to start worrying about prompt formatting

As large language models (LLMs) are adopted as a fundamental component of language technologies, it is crucial to accurately characterize their performance. Because choices in prompt design can strongly influence model behavior, this design process is critical in effectively using any modern pre-trained generative language model. In this work, we focus on LLM sensitivity to a quintessential class of meaning-preserving design choices: prompt formatting. We find that several widely used open-source LLMs are extremely sensitive to subtle changes in prompt formatting in few-shot settings, with performance differences of up to 76 accuracy points when evaluated using LLaMA-2-13B. Sensitivity remains even when increasing model size, the number of few-shot examples, or performing instruction tuning. Our analysis suggests that work evaluating LLMs with prompting-based methods would benefit from reporting a range of performance across plausible prompt formats, instead of the currently-standard practice of reporting performance on a single format. We also show that format performance only weakly correlates between models, which puts into question the methodological validity of comparing models with an arbitrarily chosen, fixed prompt format. To facilitate systematic analysis we propose FormatSpread, an algorithm that rapidly evaluates a sampled set of plausible prompt formats for a given task, and reports the interval of expected performance without accessing model weights. Furthermore, we present a suite of analyses that characterize the nature of this sensitivity, including exploring the influence of particular atomic perturbations and the internal representation of particular formats.

  • 4 authors
·
Oct 17, 2023

ReasonIF: Large Reasoning Models Fail to Follow Instructions During Reasoning

The ability of large language models (LLMs) to follow user instructions is central to their reliability, safety, and usefulness. While prior studies assess instruction adherence in the model's main responses, we argue that it is also critical for large reasoning models (LRMs) to follow user instructions throughout their reasoning process. Reasoning instruction following makes LRMs more controllable and transparent, while reducing risks of undesirable shortcuts, hallucinations, or reward hacking within reasoning traces. To evaluate this dimension, we introduce ReasonIF, a systematic benchmark for assessing reasoning instruction following. ReasonIF includes six categories of instruction prompts, spanning multilingual reasoning, formatting and length control. Across many open-source LRMs including GPT-OSS, Qwen3, and DeepSeek-R1, we find substantial failures in reasoning instruction adherence: the highest instruction following score (IFS) remains below 0.25, meaning that fewer than 25% of reasoning traces comply with the given instructions. Notably, as task difficulty increases, reasoning instruction following degrades further. We also explore two strategies to enhance reasoning instruction fidelity. (1) multi-turn reasoning and (2) Reasoning Instruction Finetuning (RIF) using synthetic data. RIF improves the IFS of GPT-OSS-20B from 0.11 to 0.27, indicating measurable progress but leaving ample room for improvement.

  • 5 authors
·
Oct 16, 2025

Saudi-Dialect-ALLaM: LoRA Fine-Tuning for Dialectal Arabic Generation

Large language models (LLMs) for Arabic are still dominated by Modern Standard Arabic (MSA), with limited support for Saudi dialects such as Najdi and Hijazi. This underrepresentation hinders their ability to capture authentic dialectal variation. Using a privately curated Saudi Dialect Instruction dataset (Hijazi and Najdi; 5,466 synthetic instruction-response pairs; 50/50 split), we LoRA-tune ALLaM-7B-Instruct-preview, the first foundation model developed in Saudi Arabia, for Saudi dialect generation. We investigate two variants: (i) Dialect-Token training, which prepends an explicit dialect tag to the instruction, and (ii) No-Token training, which omits the tag at formatting time. Evaluation on a held-out test set combines an external dialect classifier with text fidelity metrics (chrF++ and BERTScore) and diversity measures. The Dialect-Token model achieves the best control, raising the Saudi rate from 47.97% to 84.21% and reducing MSA leakage from 32.63% to 6.21%; fidelity also improves (chrF++ +3.53, BERTScore +0.059). Both LoRA variants outperform strong generic instruction models (Falcon-7B-Instruct, Llama-3.1-8B-Instruct, Qwen-2.5-7B-Instruct, AceGPT-v2-8B-Chat, JAIS-13B-Chat) in dialect control and fidelity, while avoiding metadata-tag echoing that these baselines frequently exhibit. We do not release the dataset or any model weights/adapters; instead, we release training/evaluation/inference code and a detailed datasheet (schema and aggregate statistics) to support independent verification.

  • 1 authors
·
Aug 19, 2025

OctoThinker: Mid-training Incentivizes Reinforcement Learning Scaling

Different base language model families, such as Llama and Qwen, exhibit divergent behaviors during post-training with reinforcement learning (RL), especially on reasoning-intensive tasks. What makes a base language model suitable for reinforcement learning? Gaining deeper insight into this question is essential for developing RL-scalable foundation models of the next generation. In this work, we investigate how mid-training strategies shape RL dynamics, focusing on two representative model families: Qwen and Llama. Our study reveals that (1) high-quality mathematical corpora, such as MegaMath-Web-Pro, significantly improve both base model and RL performance, while existing alternatives (e.g., FineMath-4plus) fail to do so; (2) further adding QA-style data, particularly long chain-of-thought (CoT) reasoning examples, enhances RL outcomes, and instruction data further unlocks this effect; (3) while long-CoT improves reasoning depth, it can also induce verbosity of model responses and unstability of RL training, underscoring the importance of data formatting; (4) scaling mid-training consistently leads to stronger downstream RL performance. Building on these insights, we introduce a two-stage mid-training strategy, Stable-then-Decay, in which base models are first trained on 200B tokens with a constant learning rate, followed by 20B tokens across three CoT-focused branches with learning rate decay. This yields OctoThinker, a family of models demonstrating strong RL compatibility and closing the performance gap with more RL-friendly model families, i.e., Qwen. We hope our work will help shape pre-training strategies for foundation models in the RL era. To support further research, we release our open-source models along with a curated math reasoning-intensive corpus of over 70 billion tokens (i.e., MegaMath-Web-Pro-Max).

  • 4 authors
·
Jun 25, 2025 1

Struc-Bench: Are Large Language Models Really Good at Generating Complex Structured Data?

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

  • 5 authors
·
Sep 16, 2023 1

Can Large Language Models Be an Alternative to Human Evaluations?

Human evaluation is indispensable and inevitable for assessing the quality of texts generated by machine learning models or written by humans. However, human evaluation is very difficult to reproduce and its quality is notoriously unstable, hindering fair comparisons among different natural language processing (NLP) models and algorithms. Recently, large language models (LLMs) have demonstrated exceptional performance on unseen tasks when only the task instructions are provided. In this paper, we explore if such an ability of the LLMs can be used as an alternative to human evaluation. We present the LLMs with the exact same instructions, samples to be evaluated, and questions used to conduct human evaluation, and then ask the LLMs to generate responses to those questions; we dub this LLM evaluation. We use human evaluation and LLM evaluation to evaluate the texts in two NLP tasks: open-ended story generation and adversarial attacks. We show that the result of LLM evaluation is consistent with the results obtained by expert human evaluation: the texts rated higher by human experts are also rated higher by the LLMs. We also find that the results of LLM evaluation are stable over different formatting of the task instructions and the sampling algorithm used to generate the answer. We are the first to show the potential of using LLMs to assess the quality of texts and discuss the limitations and ethical considerations of LLM evaluation.

  • 2 authors
·
May 3, 2023

CCR-Bench: A Comprehensive Benchmark for Evaluating LLMs on Complex Constraints, Control Flows, and Real-World Cases

Enhancing the ability of large language models (LLMs) to follow complex instructions is critical for their deployment in real-world applications. However, existing evaluation methods often oversimplify instruction complexity as a mere additive combination of atomic constraints, failing to adequately capture the high-dimensional complexity arising from the intricate interplay of content and format, logical workflow control, and real-world applications. This leads to a significant gap between current evaluation practices and practical demands. To bridge this gap, we introduce CCR-Bench, a novel benchmark designed to assess LLMs' adherence to complex instructions. CCR-Bench is characterized by: (1) deep entanglement of content and formatting requirements in task specifications; (2) instructions that involve intricate task decomposition, conditional reasoning, and procedural planning; and (3) evaluation samples derived entirely from real-world industrial scenarios. Extensive experiments on CCR-Bench demonstrate that even state-of-the-art models exhibit substantial performance deficiencies, clearly quantifying the gap between current LLM capabilities and the demands of realworld instruction understanding. We believe that CCR-Bench offers a more rigorous and realistic evaluation framework, advancing the development of LLMs toward the next generation of models capable of understanding and executing complex tasks in industrial applications.

  • 12 authors
·
Mar 8