Reconstruction: A Blind Benchmark for Recovering Research Ideas from Pre-Publication Bibliographies

Can a language model recover the true research idea of a published paper when given only that paper's pre-publication bibliography? We introduce Reconstruction, a blind idea-recovery benchmark that withholds the seed paper and all contemporaneous or future literature, and asks models to propose hypotheses that an independent large language model judge matches against the held-out ground-truth idea. A strict anti-leakage protocol-temporal citation cutoff, anonymous reference IDs, and frozen per-paper bibliographies, which prevents prompt-time leakage of the seed idea. Across six scientific domains and 643 evaluated papers, seven frontier models achieve only modest Match rates (approx. 3-15%). We then evaluate a reference-only multi-agent (top 4) pipeline that combines cross-model review with a Swiss tournament over aligned hypothesis slots, without external web search. Cross-model review plus tournament selection raises Match rates to approx. 23-42% across all six domains, which is an observed approx. 2.4x lift over the best single-model baseline. This draft reports the protocol, anti-leakage design, and current results as an arXiv timestamp.

How Do Agents Fail on AutoResearch: End-to-End Diagnostic Evaluation on 100 Real-World Frontier Research Tasks

AI has long assisted scientific research, but the rapid advance of LLMs and agentic scaffolds is reshaping the landscape; a single system can now carry whole-stage research from an initial hypothesis all the way to final published paper, which is a paradigm now referred to as AutoResearch. Existing evaluations reveal little about how these agents operate or where they break down. Tasks are narrowly-scoped, evaluation measures performance but not process, and failure diagnoses lack systematic coverage or artifact-level visibility. To address this gap, we introduce AutoResearchEval, featuring 100 tasks grounded in published frontier science across 7 scientific domains and the full research lifecycle, including ideation, retrieval, execution, analysis, writing, and review. Evaluating 8 harness-model combinations yields 800 autoresearch agent trajectories, with process-level annotation. We organize these insights into AutoResearch Failure Taxonomy or ARFT, a framework of 45 empirically-grounded failure patterns. To enable scalable fine-grained attribution, we leverage a human-calibrated agent-as-a-judge pipeline to inspect complete trajectories and intermediate artifacts. Failure patterns converge on a single overarching limitation, namely that current agents lack a metacognitive loop, which entails the ability to check what they produced against what they found, revise when it does not hold up, and question whether the path they took was sound. The same patterns recur across all 8 harness-model combinations, including the strongest models tested, locating the deficit at the model level rather than in any particular scaffold; whether orchestration-level interventions can close it is an open question this work does not test. We publicly release AutoResearchEval and ARFT to facilitate continued research and development in autonomous scientific discovery.

Interpretability-Guided Layer Selection over Subspace Projection: SAEs as Stethoscopes, Not Scalpels, for Raw Task Vector Model Editing

LLMs increasingly require surgical model editing to enhance domain-specific capabilities without incurring the computational cost or catastrophic forgetting associated with full fine-tuning. Sparse Autoencoders (SAEs) have emerged as a promising tool in this setting, in principle allowing for feature-level identification of where to intervene. In this work, we rigorously evaluate an SAE-guided editing pipeline for mathematical reasoning on Gemma-3-4B-IT and uncover a fundamental failure mode: the intuitively appealing approach of projecting task vectors onto SAE feature subspaces acts as an information bottleneck that discards approximately 97% of the modification energy, yielding no statistically significant improvements across seven math subjects. We show that this failure stems from a geometric misalignment between activation-space SAE directions and weight-space task vectors. We then propose a shift in perspective: SAE as a Stethoscope, Not a Scalpel, where SAEs are used for layer-level diagnosis rather than intervention-level filtering. By injecting unfiltered raw task vectors only into layers identified by an SAE-derived specificity score, we improve Number Theory accuracy from 29.6% to 39.4% (z=+3.41, p=0.0007) on the Minerva Math benchmark; 5 of 7 math subjects significantly improved and none significantly degraded. Our method is fully deterministic, requires no additional inference cost, and provides a principled framework for interpretability-guided model editing.

AdaDPO: Self-Adaptive Direct Preference Optimization with Balanced Gradient Updates

DPO has become a widely adopted alternative to RLHF for aligning LLMs with human preferences, eliminating the need for a separate reward model or RL loop. Recent theoretical analysis uncovers an asymmetric gradient behavior in DPO: the loss suppresses dispreferred responses substantially faster than it promotes preferred ones, causing the model to learn to avoid bad answers rather than to generate good ones. We propose AdaDPO, a Self-Adaptive variant of the DPO algorithm that introduces per-preference-pair, stop-gradient-based coefficients derived directly from the policy model's generation probabilities, with the reference model's probabilities as an optional component. AdaDPO is constructed to enforce equality of gradient magnitudes between preferred and dispreferred probabilities; the practical implementation balances per-token gradients and applies a numerical clipping bound for stability, while retaining DPO's original hyperparameter structure. On Llama-3-8B-Instruct trained on UltraFeedback under a SimPO similar setup, AdaDPO consistently outperforms DPO on AlpacaEval 2: it achieves higher length-controlled win rates (LC) in 81% of hyperparameter combinations, attains the global best LC (48.3%) and raw win rate (46.1%), and enlarges the LC-over-WR margin in 88% of combinations, indicating effective mitigation of length bias. Additional analyses on KL divergence, reward margin, and reward accuracy confirm that AdaDPO rectifies the gradient imbalance and yields more efficient optimization. Because it operates purely at the loss level, AdaDPO can be dropped into existing preference-based alignment pipelines without changing data collection or model architectures. The method requires only a few lines of code, and the same self-adaptive principle generalizes to a broad family of pairwise contrastive preference losses including SimPO, R-DPO, IPO, CPO, and ORPO.

State-of-the-Art Arabic Language Modeling with Sparse MoE Fine-Tuning and Chain-of-Thought Distillation

This paper introduces Arabic-DeepSeek-R1, an application-driven open-source Arabic LLM that leverages a sparse MoE backbone to address the digital equity gap for under-represented languages, and establishes a new SOTA across the entire Open Arabic LLM Leaderboard (OALL). Our four-phase CoT distillation scheme integrates Arabic-specific linguistic verification and regional ethical norms into a 372M-token, contamination-controlled 80/20 Arabic-English training mixture. Arabic-DeepSeek-R1 achieves the highest average score across the seven-benchmark OALL suite while establishing SOTA or near-SOTA, including dominant results on grammar-focused MadinahQA (surpassing both GPT-5.1 and the OALL leader by substantial margins), safety-oriented AraTrust, multi-ability AlGhafa, and retrieval-augmented ALRAGE. Our results indicate that the combination of sparse MoE architecture, culturally-informed CoT distillation with explicit Arabic linguistic checks, and strategic bilingual data curation enables an open-source adapted model to systematically outperform the proprietary frontier system GPT-5.1 on the majority of benchmarks evaluating comprehensive language-specific tasks: the first such demonstration for Arabic LLMs. These findings indicate that much of Arabic's performance deficit in current LLM ecosystems stems from under-specialization rather than architectural limitations, and that parameter-efficient adaptation of open reasoning models can yield breakthrough SOTA performance without industrial-scale pretraining costs. Arabic-DeepSeek-R1 establishes a validated and replicable framework for sovereign and domain-specific language technologies, demonstrating that strategic, culturally-grounded adaptation of sparse MoE backbones offers a viable and cost-effective pathway to achieving record-breaking performance across standardized benchmarks for low-resource languages.

Application-Driven Pedagogical Knowledge Optimization of Open-Source LLMs via Reinforcement Learning and Supervised Fine-Tuning

We present an innovative multi-stage optimization strategy combining reinforcement learning (RL) and supervised fine-tuning (SFT) to enhance the pedagogical knowledge of large language models (LLMs), as illustrated by EduQwen 32B-RL1, EduQwen 32B-SFT, and an optional third-stage model EduQwen 32B-SFT-RL2: (1) RL optimization that implements progressive difficulty training, focuses on challenging examples, and employs extended reasoning rollouts; (2) a subsequent SFT phase that leverages the RL-trained model to synthesize high-quality training data with difficulty-weighted sampling; and (3) an optional second round of RL optimization. EduQwen 32B-RL1, EduQwen 32B-SFT, and EduQwen 32B-SFT-RL2 are an application-driven family of open-source pedagogical LLMs built on a dense Qwen3-32B backbone. These models remarkably achieve high enough accuracy on the Cross-Domain Pedagogical Knowledge (CDPK) Benchmark to establish new state-of-the-art (SOTA) results across the interactive Pedagogy Benchmark Leaderboard and surpass significantly larger proprietary systems such as the previous benchmark leader Gemini-3 Pro. These dense 32-billion-parameter models demonstrate that domain-specialized optimization can transform mid-sized open-source LLMs into true pedagogical domain experts that outperform much larger general-purpose systems, while preserving the transparency, customizability, and cost-efficiency required for responsible educational AI deployment.

OpenMedLM: Prompt engineering can out-perform fine-tuning in medical question-answering with open-source large language models

LLMs have become increasingly capable at accomplishing a range of specialized-tasks and can be utilized to expand equitable access to medical knowledge. Most medical LLMs have involved extensive fine-tuning, leveraging specialized medical data and significant, thus costly, amounts of computational power. Many of the top performing LLMs are proprietary and their access is limited to very few research groups. However, open-source (OS) models represent a key area of growth for medical LLMs due to significant improvements in performance and an inherent ability to provide the transparency and compliance required in healthcare. We present OpenMedLM, a prompting platform which delivers state-of-the-art (SOTA) performance for OS LLMs on medical benchmarks. We evaluated a range of OS foundation LLMs (7B-70B) on four medical benchmarks (MedQA, MedMCQA, PubMedQA, MMLU medical-subset). We employed a series of prompting strategies, including zero-shot, few-shot, chain-of-thought (random selection and kNN selection), and ensemble/self-consistency voting. We found that OpenMedLM delivers OS SOTA results on three common medical LLM benchmarks, surpassing the previous best performing OS models that leveraged computationally costly extensive fine-tuning. The model delivers a 72.6% accuracy on the MedQA benchmark, outperforming the previous SOTA by 2.4%, and achieves 81.7% accuracy on the MMLU medical-subset, establishing itself as the first OS LLM to surpass 80% accuracy on this benchmark. Our results highlight medical-specific emergent properties in OS LLMs which have not yet been documented to date elsewhere, and showcase the benefits of further leveraging prompt engineering to improve the performance of accessible LLMs for medical applications.

Perspective: Energy Landscapes for Machine Learning

Machine learning techniques are being increasingly used as flexible non-linear fitting and prediction tools in the physical sciences. Fitting functions that exhibit multiple solutions as local minima can be analysed in terms of the corresponding machine learning landscape. Methods to explore and visualise molecular potential energy landscapes can be applied to these machine learning landscapes to gain new insight into the solution space involved in training and the nature of the corresponding predictions. In particular, we can define quantities analogous to molecular structure, thermodynamics, and kinetics, and relate these emergent properties to the structure of the underlying landscape. This Perspective aims to describe these analogies with examples from recent applications, and suggest avenues for new interdisciplinary research.