Supervised Fine-Tuning (SFT) has been a go-to and effective method for enhancing long chain-of-thought (CoT) reasoning in relatively small LLMs by fine-tuning them with long CoT responses from larger LLMs. To continually improve reasoning abilities, we can either collect new high-quality long CoT reasoning SFT data or repeatedly train on existing SFT datasets. However, acquiring new long CoT SFT data is costly and limited, while repeated training often results in a performance plateau or decline. To further boost the performance with the SFT data, we propose Thinking Preference Optimization (ThinkPO), a simple yet effective post-SFT method that enhances long CoT reasoning without requiring new long CoT responses. Instead, ThinkPO utilizes readily available or easily obtainable short CoT reasoning responses as rejected answers and long CoT responses as chosen answers for the same question. It then applies direct preference optimization to encourage the model to favor longer reasoning outputs. Experiments show that ThinkPO further improves the reasoning performance of SFT-ed models, e.g. it increases math reasoning accuracy of SFT-ed models by 8.6% and output length by 25.9%. Notably, ThinkPO is capable of continually boosting the performance of the publicly distilled SFT model, e.g., increasing the official DeepSeek-R1-Distill-Qwen-7B's performance on MATH500 from 87.4% to 91.2%.

In the pursuit of superior video-processing MLLMs, we have encountered a perplexing paradox: the "anti-scaling law", where more data and larger models lead to worse performance. This study unmasks the culprit: "temporal hacking", a phenomenon where models shortcut by fixating on select frames, missing the full video narrative. In this work, we systematically establish a comprehensive theory of temporal hacking, defining it from a reinforcement learning perspective, introducing the Temporal Perplexity (TPL) score to assess this misalignment, and proposing the Unhackable Temporal Rewarding (UTR) framework to mitigate the temporal hacking. Both theoretically and empirically, TPL proves to be a reliable indicator of temporal modeling quality, correlating strongly with frame activation patterns. Extensive experiments reveal that UTR not only counters temporal hacking but significantly elevates video comprehension capabilities. This work not only advances video-AI systems but also illuminates the critical importance of aligning proxy rewards with true objectives in MLLM development.

The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods [1-17]. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks (e.g. A motif-scaffolding method takes a motif as input and returns a set of putatively compatible scaffolds as output. This section details how motifs and scaffolds in MotifBench are specified, proposes metrics by which a scaffold set is evaluated, and describes how these metrics are computed. Appendix A describes considerations upon which these specifications and metrics were chosen. Motif specification (inputs): A motif is specified by the coordinates of the backbone atoms of several residues and (in some cases) the amino acid types of a subset of those residues.

Grammatical features across human languages show intriguing correlations often attributed to learning biases in humans. However, empirical evidence has been limited to experiments with highly simplified artificial languages, and whether these correlations arise from domain-general or language-specific biases remains a matter of debate. Language models (LMs) provide an opportunity to study artificial language learning at a large scale and with a high degree of naturalism. In this paper, we begin with an in-depth discussion of how LMs allow us to better determine the role of domain-general learning biases in language universals. We then assess learnability differences for LMs resulting from typologically plausible and implausible languages closely following the word-order universals identified by linguistic typologists. We conduct a symmetrical cross-lingual study training and testing LMs on an array of highly naturalistic but counterfactual versions of the English (head-initial) and Japanese (head-final) languages. Compared to similar work, our datasets are more naturalistic and fall closer to the boundary of plausibility. Our experiments show that these LMs are often slower to learn these subtly implausible languages, while ultimately achieving similar performance on some metrics regardless of typological plausibility. These findings lend credence to the conclusion that LMs do show some typologically-aligned learning preferences, and that the typological patterns may result from, at least to some degree, domain-general learning biases.

Automated Essay Scoring (AES) plays a crucial role in educational assessment by providing scalable and consistent evaluations of writing tasks. However, traditional AES systems face three major challenges: (1) reliance on handcrafted features that limit generalizability, (2) difficulty in capturing fine-grained traits like coherence and argumentation, and (3) inability to handle multimodal contexts. In the era of Multimodal Large Language Models (MLLMs), we propose EssayJudge, the first multimodal benchmark to evaluate AES capabilities across lexical-, sentence-, and discourse-level traits. By leveraging MLLMs' strengths in trait-specific scoring and multimodal context understanding, EssayJudge aims to offer precise, context-rich evaluations without manual feature engineering, addressing longstanding AES limitations. Our experiments with 18 representative MLLMs reveal gaps in AES performance compared to human evaluation, particularly in discourse-level traits, highlighting the need for further advancements in MLLM-based AES research. Our dataset and code will be available upon acceptance.

Tabular deep-learning methods require embedding numerical and categorical input features into high-dimensional spaces before processing them. Existing methods deal with this heterogeneous nature of tabular data by employing separate type-specific encoding approaches. This limits the cross-table transfer potential and the exploitation of pre-trained knowledge. We propose a novel approach that first transforms tabular data into text, and then leverages pre-trained representations from LLMs to encode this data, resulting in a plug-and-play solution to improv ing deep-learning tabular methods. We demonstrate that our approach improves accuracy over competitive models, such as MLP, ResNet and FT-Transformer, by validating on seven classification datasets.

Masked Image Modeling (MIM) offers a promising approach to self-supervised representation learning, however existing MIM models still lag behind the state-of-the-art. In this paper, we systematically analyze target representations, loss functions, and architectures, to introduce CAPI - a novel pure-MIM framework that relies on the prediction of latent clusterings. Our approach leverages a clustering-based loss, which is stable to train, and exhibits promising scaling properties. Our ViT-L backbone, CAPI, achieves 83.8% accuracy on ImageNet and 32.1% mIoU on ADE20K with simple linear probes, substantially outperforming previous MIM methods and approaching the performance of the current state-of-the-art, DINOv2. We release all our code and models.

We propose a novel paradigm for automatic fact-checking that leverages frame semantics to enhance the structured understanding of claims and guide the process of fact-checking them. To support this, we introduce a pilot dataset of real-world claims extracted from PolitiFact, specifically annotated for large-scale structured data. This dataset underpins two case studies: the first investigates voting-related claims using the Vote semantic frame, while the second explores various semantic frames based on data sources from the Organisation for Economic Co-operation and Development (OECD). Our findings demonstrate the effectiveness of frame semantics in improving evidence retrieval and explainability for fact-checking. Finally, we conducted a survey of frames evoked in fact-checked claims, identifying high-impact frames to guide future work in this direction.

Various benchmarks have been proposed to assess the performance of large language models (LLMs) in different coding scenarios. We refer to them as code-related benchmarks. However, there are no systematic guidelines by which such a benchmark should be developed to ensure its quality, reliability, and reproducibility. We propose How2Bench, which is comprised of a 55-criteria checklist as a set of guidelines to govern the development of code-related benchmarks comprehensively. Using HOW2BENCH, we profiled 274 benchmarks released within the past decade and found concerning issues. Nearly 70% of the benchmarks did not take measures for data quality assurance; over 10% did not even open source or only partially open source. Many highly cited benchmarks have loopholes, including duplicated samples, incorrect reference codes/tests/prompts, and unremoved sensitive/confidential information. Finally, we conducted a human study involving 49 participants, which revealed significant gaps in awareness of the importance of data quality, reproducibility, and transparency.

Medical language models (MLMs) have become pivotal in advancing medical natural language processing. However, prior models that rely on pre-training or supervised fine-tuning often exhibit low data efficiency and limited practicality in real-world clinical applications. While OpenAI's o1 highlights test-time scaling in mathematics, attempts to replicate this approach in medicine typically distill responses from GPT-series models to open-source models, focusing primarily on multiple-choice tasks. This strategy, though straightforward, neglects critical concerns like data privacy and realistic deployment in clinical settings. In this work, we present a deployable, small-scale medical reasoning system, MedS3, designed for long-chain reasoning in clinical tasks using a self-evolution paradigm. Starting with a seed dataset of around 8,000 instances spanning five domains and 16 datasets, we prompt a base policy model to perform Monte Carlo Tree Search (MCTS) to construct rule-verifiable reasoning chains. Each reasoning step is assigned an evolution rollout value, allowing verified trajectories to train the policy model and the process reward model (PRM). During inference, the policy model generates multiple responses, and the reward model selects the one with a newly proposed PRM-guided Vote-Sum (P-VS) strategy. Experiments on eleven evaluation datasets demonstrate that MedS3 outperforms not only the prior strongest medical model by 6.59, but also 32B-level general reasoning models by 8.71 points. Code and data are available at https://github.com/pixas/MedSSS.