Research

r0: 10f953633b3db3b4dc07e63a493e9b66

Contemporary AI lacks the imagination to diverge or negate in science

Bold projections that artificial intelligence will accelerate scientific discovery have raced ahead of evidence from working scientists, and the field still lacks large-scale, scientist-in-the-loop tests of these claims. Here we mount the largest such evaluation to date and map what AI cannot yet do for science. We invited authors of 121,640 recent preprints across biology, medicine, chemistry, and the social sciences to judge ideas that large language models (LLMs) generated from the context and puzzles of their own papers. 6,749 scientists returned 25,139 sets of ratings on novelty, empirical feasibility, probability of being true, and favorability of adoption. Three patterns emerge. First, non-reasoning LLMs collapse into a narrow «hivemind» of similar ideas; reasoning models roam a wider hypothesis space, yet no model class spontaneously proposes null hypotheses — a move humans make more freely. Second, scientists reward ideas that resemble their own and prize probability over novelty, though social scientists tolerate risk more readily than life scientists. Senior social scientists are the harshest critics, and their skepticism is well-earned: LLMs falter most in pluralistic fields like the social sciences that demand context-aware interpretation and evolving theories. Third, automated evaluators on which the community currently relies — LLM-as-a-judge, artificial metrics, and even state-of-the-art (SOTA) models — agree only weakly with expert judgment, and retrieval augmentation and scientist persona prompting yield only marginal gains. A Qwen3-14B reward model we post-trained on human ratings captures field taste nuances, beats SOTA models by up to 27%, and closes the gap to the inter-rater consistency of independent peer reviewers. For all the hype, today’s scientific AI still represents a collaborator whose imagination, outputs and judgment benefit from human grounding.

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r0:b621309bd8d28cda43682baaeb45707f

An Embarrassingly Simple Graph Heuristic Reveals Shortcut-Solvable Benchmarks for Sequential Recommendation

Sequential recommendation is a central task in recommender systems, and recent research has increasingly shifted toward generative recommenders that leverage both sequential patterns and semantic item information. However, these methods are often evaluated on a small set of widely used benchmarks. This raises a natural question: do these benchmarks actually require the advanced modeling capabilities of modern generative recommenders? We conduct a benchmark audit using an intentionally simple graph heuristic: starting from only the last one or two interacted items, it retrieves candidates from a few-hop item-transition graph and ranks them with item-feature similarity. Surprisingly, despite its simplicity, this heuristic matches or outperforms a broad set of modern baselines on a variety of popular sequential recommendation benchmarks. For example, it achieves relative NDCG@10 improvements of 38.10% and 44.18% over the best competing baseline on the widely used Amazon Review Sports and CDs datasets, respectively.

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r0:21222df107462b80fde54a74d060bc7e

When silence is safer: a review and decision-theoretic framework for LLM abstention in healthcare

Large language models (LLMs) are designed to generate answers to user prompts, which often drives them to respond even when uncertainty is high, information is incomplete, or a refusal would be more appropriate. In healthcare, this tendency can be dangerous: confidently stated but inaccurate medical advice can cause significant harm, making the ability to abstain especially important. In this paper, we review studies investigating LLM abstention behaviors in healthcare. The literature highlights two main motivations: (1) uncertainty-driven abstention, where the model withholds a response when confidence is low, and (2) safety-driven abstention, where the model declines to provide potentially harmful information. Most existing mechanisms are extrinsic and rely on auxiliary tools to determine when to abstain. We find that state-of-the-art LLMs still struggle to refuse inappropriate prompts, and that few benchmarks evaluate abstention in realistic medical scenarios, where performance lags behind other domains. Building on these findings, we introduce a decision-theoretic formalization of abstention that models the trade-off between answering and withholding responses under uncertainty and potential harm. Based on this formulation, we present MedSAFE, a framework for evaluating abstention in clinical dialogs, and demonstrate its operationalization through a proof-of-concept pilot across clinical scenarios derived from the review.

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r0:e8a2060e33594781594577f87d876bb1

Advancing regulatory variant effect prediction with AlphaGenome

Deep learning models that predict functional genomic measurements from DNA sequences are powerful tools for deciphering the genetic regulatory code. Existing methods involve a trade-off between input sequence length and prediction resolution, thereby limiting their modality scope and performance1,2,3,4,5. We present AlphaGenome, a unified DNA sequence model, which takes as input 1 Mb of DNA sequence and predicts thousands of functional genomic tracks up to single-base-pair resolution across diverse modalities. The modalities include gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding, chromatin contact maps, splice site usage and splice junction coordinates and strength. Trained on human and mouse genomes, AlphaGenome matches or exceeds the strongest available external models in 25 of 26 evaluations of variant effect prediction. The ability of AlphaGenome to simultaneously score variant effects across all modalities accurately recapitulates the mechanisms of clinically relevant variants near the TAL1 oncogene6. To facilitate broader use, we provide tools for making genome track and variant effect predictions from sequence.

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ro:035d2ee6677504e68a7eb8820884a335

Sequence Feature Extraction for Malware Family Analysis via Graph Neural Network

Malicious software (malware) causes much harm to our devices and life. We are eager to understand the malware behavior and the threat it made. Most of the record files of malware are variable length and text-based files with time stamps, such as event log data and dynamic analysis profiles. Using the time stamps, we can sort such data into sequence-based data for the following analysis. However, dealing with the text-based sequences with variable lengths is difficult. In addition, unlike natural language text data, most sequential data in information security have specific properties and structure, such as loop, repeated call, noise, etc. To deeply analyze the API call sequences with their structure, we use graphs to represent the sequences, which can further investigate the information and structure, such as the Markov model. Therefore, we design and implement an Attention Aware Graph Neural Network (AWGCN) to analyze the API call sequences. Through AWGCN, we can obtain the sequence embeddings to analyze the behavior of the malware. Moreover, the classification experiment result shows that AWGCN outperforms other classifiers in the call-like datasets, and the embedding can further improve the classic model’s performance.

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r0:e605066113bd05bcb2ad6161c651d958- Auto Quantum Circuits

Auto Quantum Circuits

«AutoQML, self-assembling circuits, hyper-parameterized Quantum ML platform, using cirq, tensorflow and tfq. Trillions of possible qubit registries, gate combinations and moment sequences, ready to be adapted into your ML flow. Here I demonstrate climatechange, jameswebbspacetelescope and microbiology vision applications… [Thus far, a circuit with 16-Qubits and a gate sequence of [ YY ] – [ XX ] – [CNOT] has performed the best, per my blend of metrics…].

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R0:507c2e7fe07ef9a317eb4c7a51869fdc-Federated Learning: Issues in Medical Application

Federated Learning: Issues in Medical Application

In this presentation, the current issues to make federated learning flawlessly useful in the real world will be briefly overviewed. They are related to data/system heterogeneity, client management, traceability, and security. Also, we introduce the modularized federated learning framework, we currently develop, to experiment various techniques and protocols to find solutions for aforementioned issues. The framework will be open to public after development completes.

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R0:884a5f6297216a3c5e883ae639b13721-Between words and characters: A Brief History of Open-Vocabulary Modeling and Tokenization in NLP

Between words and characters: A Brief History of Open-Vocabulary Modeling and Tokenization in NLP

In this survey, we connect several lines of work from the pre-neural and neural era, by showing how hybrid approaches of words and characters as well as subword-based approaches based on learned segmentation have been proposed and evaluated. We conclude that there is and likely will never be a silver bullet singular solution for all applications and that thinking seriously about tokenization remains important for many applications

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R0:7194c033807f71949262faf563aef58e-Scientific Visualization: Python + Matplotlib

Scientific Visualization: Python + Matplotlib

The Python scientific visualisation landscape is huge. It is composed of a myriad of tools, ranging from the most versatile and widely used down to the more specialised and confidential. Some of these tools are community based while others are developed by companies. Some are made specifically for the web, others are for the desktop only, some deal with 3D and large data, while others target flawless 2D rendering.

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R0:62a6aa3b4882ad9b194a4ae5c97b4d58-Ethics-based auditing of automated decision-making systems: intervention points and policy implications

Ethics-based auditing of automated decision-making systems: intervention points and policy implications

Organisations increasingly use automated decision-making systems (ADMS) to inform decisions that affect humans and their environment. While the use of ADMS can improve the accuracy and efficiency of decision-making processes, it is also coupled with ethical challenges. Unfortunately, the governance mechanisms currently used to oversee human decision-making often fail when applied to ADMS.

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