论文检索

Yanjun Zhao, Tianxin Wei, Jiaru Zou, Xuying Ning, Yuanchen Bei, Lingjie Chen, Simmi Rana, Wendy H. Yang, Hanghang Tong, Jingrui He

Understanding scientific papers requires more than answering isolated questions or summarizing content. It involves an integrated reasoning process that grounds textual and visual information, interprets experimental evidence, synthesizes information across sources, and critically evaluates scientific claims. However, existing benchmarks typically assess these abilities in isolation, making it difficult to evaluate scientific paper understanding as a unified set of interacting cognitive abilities. In this work, we introduce PaperMind , a benchmark designed to evaluate integrated and agent-oriented scientific reasoning over research papers. PaperMind is constructed from real scientific papers across seven domains, including agriculture, biology, chemistry, computer science, medicine, physics, and economics. It comprises four complementary task families that collectively operationalize distinct cognitive facets of scientific paper reasoning, including multimodal grounding, experimental interpretation, cross-source evidence reasoning, and critical assessment. By analyzing model behavior across multiple tasks, PaperMind enables a diagnostic evaluation of integrated scientific reasoning behaviors that are difficult to assess through isolated task evaluations. Extensive experiments on both open-source and closed-source multimodal LLMs reveal consistent performance gaps across tasks, highlighting persistent challenges in integrated scientific reasoning and critique. Our benchmark and dataset are available at https://github.com/Yanjun-Zhao/PaperMind.

Tim Baumgärtner, Iryna Gurevych

Discrepancies between scientific papers and their code undermine reproducibility, a concern that grows as automated research agents scale scientific output beyond human review capacity. Whether LLMs can reliably detect such discrepancies has not been systematically measured. To this end, we present SciCoQA, a dataset of 635 paper-code discrepancies (92 real, 543 synthetic) for this cross-modal verification task. Across 22 evaluated models, even the best-performing LLMs, Gemini 3.1 Pro and GPT-5 Mini, detect only 46.7% of real-world discrepancies, revealing a critical gap in automated scientific quality assurance. We construct SciCoQA from GitHub issues and reproducibility papers, and propose a synthetic generation pipeline to scale beyond AI to Physics, Quantitative Biology, and other computational sciences. We further introduce a taxonomy of discrepancy types and categories to characterize the occurring mismatches. Our analysis shows that models particularly struggle with omitted paper details, long-context inputs, and papers outside their pre-training corpus.

Yuhang Zhang, Keyan Ding, Peilin Chen, Han Liu, Can Lin, Ruixi Chen, Shiqi Wang, Qi Song

Enzyme–reaction retrieval is a fundamental problem in computational biology, underpinning enzyme characterization, reaction mechanism elucidation, and the rational design of metabolic pathways and biocatalysts. As a bidirectional task, it entails both enzyme-to-reaction and reaction-to-enzyme mapping. However, existing approaches suffer from poor generalization across tasks and distributions, with performance highly sensitive to dataset splits and substantial asymmetry between retrieval directions. To address these challenges, we present TIGER, a Text-Informed Generalized Enzyme-Reaction Retrieval framework that leverages protein-to-text generation models to distill textual semantic knowledge from enzyme sequences, providing a generalized representation that bridges enzymes and biochemical reactions. To ensure the quality and reliability of textual semantics, we design a Dynamic Gating Network that adaptively fuses text-derived knowledge with sequence features, enabling more consistent and informative enzyme representations, while a Structure-Shared Feature Projector aligns enzyme and reaction representations within a unified latent space. Extensive experiments demonstrate that, under bidirectional retrieval supervision, TIGER significantly outperforms state-of-the-art baselines across diverse distributions and exhibits strong robustness and transferability across tasks.

Mahi Luthra, Jiayi Shen, Maxime Poli, Angelo Ortiz Tandazo, Yosuke Higuchi, Youssef Benchekroun, Martin Gleize, Charles-Eric Saint-James, Dongyan Lin, Phillip Rust 等

Human infants, with only a few hundred hours of speech exposure, acquire basic units of new languages, highlighting a striking efficiency gap compared to the data-hungry self-supervised speech models. To address this gap, this paper introduces SpidR-Adapt for rapid adaptation of speech units to new languages using minimal unlabeled data. We cast such low-resource speech representation learning as a meta-learning problem and construct a multi-task adaptive pre-training (MAdaPT) protocol which formulates the adaptation process as a bi-level optimization framework. To enable scalable meta-training under this framework, we propose a novel heuristic solution, first-order bi-level optimization (FOBLO), avoiding heavy computation costs. Finally, we stabilize meta-training by using a robust initialization through interleaved supervision which alternates self-supervised and supervised objectives. Empirically, SpidR-Adapt achieves rapid gains in phonemic discriminability (ABX) and downstream spoken language modeling scores (sWUGGY, sBLIMP, tSC), surpassing in-domain toplines after training on less than 1h of target-language audio and delivering 100\times greater data efficiency than standard multi-task training.. These findings highlight a practical, architecture-agnostic path toward biologically inspired, data-efficient representations. We open-source the training code and model checkpoints at https://github.com/facebookresearch/spidr-adapt.

Chuanliu Fan, Zicheng Ma, Huanran Meng, Aijia Zhang, Wenjie Du, Jun Zhang, Ziqiang Cao, Guohong Fu

Recent advances in large language models (LLMs) have highlighted the effectiveness of chain-of-thought reasoning in symbolic domains such as mathematics and programming. However, our study shows that directly transferring such text-based reasoning paradigms to protein function understanding is ineffective: reinforcement learning mainly amplifies superficial keyword patterns while failing to introduce new biological knowledge, resulting in limited generalization. We argue that protein function prediction is a knowledge-intensive scientific task that fundamentally relies on external biological priors and computational tools rather than purely internal reasoning. To address this gap, we propose Protein Function Understanding Agent (PFUA), a tool-augmented protein reasoning agent that unifies problem decomposition, tool invocation, and grounded answer generation. Instead of relying on long unconstrained reasoning traces, PFUA integrates domain-specific tools to produce verifiable intermediate evidence. Experiments on four benchmarks demonstrate that PFUA consistently outperforms text-only reasoning models with an average performance improvement of 103%. We believe PFUA has the potential to become a standard paradigm for agentic reasoning in knowledge-intensive life science domains.

Applications · Health / Medicine

Jiawei Zhang, Kangjun Jin, Shuai Xiao, Jiachen Yang

Measuring single-cell protein abundance is essential for resolving biological mechanisms and disease progression with high resolution. However, due to the high costs and antibody throughput limitations of current proteomics, inferring protein levels from readily available RNA data has become a critical computational necessity. Existing regression and generative methods face a fundamental geometric bottleneck: enforcing deterministic constraints on noisy, heteroscedastic data collapses intrinsic uncertainty into a rough latent manifold, which destabilizes the learning process. To overcome this, we present scChord, a noise-decoupled conditional flow matching framework built on Probabilistic Manifold Rectification. Our approach utilizes a probabilistic decoder to disentangle technical noise and over-dispersion from the raw counts, absorbing them into distributional parameters. This allows the rectified latent manifold to focus more on biological signals, serving as a robust geometric regularizer for learning efficient transport trajectories. Extensive experiments on multiple multi-omics benchmarks demonstrate that scChord not only achieves state-of-the-art inference accuracy but also faithfully reconstructs high-fidelity biological heterogeneity and complex protein distributions.

Mert Yuksekgonul, Daniel Koceja, Xinhao Li, Federico Bianchi, Jed McCaleb, Xiaolong Wang, Jan Kautz, Yejin Choi, James Zou, Carlos Guestrin 等

How can we use AI to discover a new state of the art for a scientific problem? Prior work in test-time scaling, such as AlphaEvolve, performs search by prompting a frozen LLM. We perform reinforcement learning at test time, so the LLM can continue to train, but now with experience specific to the test problem. This form of continual learning is quite special, because its goal is to produce one great solution rather than many good ones on average, and to solve this very problem rather than generalize to other problems. Therefore, our learning objective and search subroutine are designed to prioritize the most promising solutions. We call this method Test-Time Training to Discover (TTT-Discover). Following prior work, we focus on problems with continuous rewards. We report results for every problem we attempted, across mathematics, GPU kernel engineering, algorithm design, and biology. TTT-Discover sets the new state of the art in almost all of them: (i) Erdős' minimum overlap problem and an autocorrelation inequality; (ii) a GPUMode kernel competition (up to 2× faster than prior art); (iii) past AtCoder algorithm competitions; and (iv) denoising problem in single-cell analysis. Our solutions are reviewed by experts or the organizers. All our results are achieved with an open model, OpenAI gpt-oss-120b, and can be reproduced with our publicly available code, in contrast to previous best results that required closed frontier models. Our test-time training runs are performed using Tinker, an API by Thinking Machines, with a cost of only a few hundred dollars per problem.

Deep Learning · Graph Neural Networks

Christian Nauck, Junyou Zhu, Michael Lindner, Frank Hellmann

The robustness of synchronization is a central theme of the study of dynamical systems on networks. Typically one attempts to define a single stability index that characterizes the robustness of individual nodes to a class of perturbations. The dependence of a stability index on topology and system parameters can then be studied using network science or GNNs. Here we propose a novel upstream task, Stability Landscapes, that allows deriving many downstream stability indices. To support this task, we release two computationally intensive datasets of 10,000 graphs each at 20 and 100 nodes with per-node landscape labels. The dynamics are given by a conceptual oscillator model that captures aspects of the synchronization behavior of power grids. A compact graph neural network with a CNN decoder predicts these landscapes with about 85\% SSIM in distribution and 67\% under a 20 to 100 size shift, and 65\%-73\% SSIM when going from the 100 node ensemble to realistic power grid topologies with 100-400 nodes. This demonstrates that while basin landscapes are not suitable for study with conventional methods of network science, they are amenable to machine learning methods. This suggests that there is considerable potential in the study of complex networked systems across biology, neuroscience, and power grids, to move beyond scalar stability indices.

Applications · Health / Medicine

Maria Emilia Russo, Federico Di Valerio, Alessia Borghini, Alessio Ragno, Roberto Capobianco

Computational approaches have become central to Protein–Protein Interaction (PPI) research, complementing experimental techniques that remain costly and incomplete. While modern deep learning methods capture diverse biological signals and hold promise in expanding the known interactome, empirical validation remains a critical bottleneck due to its long and expensive procedures. To address this challenge, we introduce the problem of PPI candidate ranking, aiming to prioritize interactions for experimental testing. We propose a novel framework that leverages domain knowledge through interpretability-guided ranking and further refines prioritization by integrating complementary sources of evidence, including interaction scores, structural plausibility, and biomedical language features. Evaluations on a large-scale dataset constructed from successive STRING releases demonstrate that our approach yields significant improvements over two state-of-the-art PPI prediction models, providing more accurate and biologically coherent rankings.

Applications · Language, Speech and Dialog

Jinhao Duan, Ruichen Zhang, Gengwei Zhang, Huaizhi Qu, Jie Peng, Sijia Liu, Tianlong Chen

Though biological foundation models (Bio-FMs) have delivered strong performance across biomedical tasks, their robustness to small-but-real perturbations is underexplored. In this work, we ask: Are Bio-FMs robust for real-world use? What perturbations compromise their reliability? Our pilot study suggests that due to subtle biological data curation issues and common machine-learning (ML) processing choices, Bio-FMs suffer from two complementary perturbation sources: biologically plausible perturbations (capturing experimental corruptions and curation artifacts) and ML-induced transformations (capturing preprocessing, data augmentation, and embedding choices). Guided by this taxonomy, we design perturbation suites that mimic corruptions frequently encountered in biological experiments, and we systematically probe how transformations in the ML pipeline reshape model behavior. By conducting 2,128 experiments over 11 state-of-the-art Bio-FMs on 7 bio-tasks, we show that most Bio-FMs are vulnerable to both biological perturbations and ML transformations, revealing underappreciated robustness gaps that can directly translate into deployment risk. Interestingly, we find that subtle biological perturbations, which are often imperceptible to current measurement tools, can induce severe discrepancies in Bio-FM outputs and lead to critical failures. We also find that cryo-EM reconstruction models (e.g., CryoDRGN) exhibit a surprising level of robustness even under worst-case adversarial settings. Our study for the first time surfaces critical failure modes and provides a principled perspective for evaluating the robustness of Bio-FMs in real-world biological pipelines.

Enkelejda Kasneci, Gjergji Kasneci

This position paper argues that effective tutoring requires **corrective friction**: surfacing misconceptions and challenging them supportively to drive conceptual change. Yet preference-aligned LLMs can trade **epistemic rigor** for agreeableness. We identify a **Reasoning-Sycophancy Paradox**: models that resist **context-switch** frame attacks can still capitulate under social-epistemic pressure, especially **authority** ("my notes say I’m right") and **social-affective face-saving** ("please don’t tell me I’m wrong''). We introduce **EduFrameTrap**, a tutoring benchmark across math, physics, economics, chemistry, biology, and computer science that varies student confidence and pressure (context-switch, authority, social-affective). Across two frontier LLMs, context-switch failures are comparatively lower for GPT-5.2, while authority and social pressure more often trigger epistemic retreat. In contrast, Claude shows substantial context-switch fragility in this run. Because these failures are hard to judge automatically, we report two-judge disagreement as a reliability signal. We argue benchmarks should measure *social-epistemic courage*, i.e., supportive but corrective tutoring, and treat *kind-but-correct* behavior as a safety requirement.

Applications · Health / Medicine

YuCheng Yuan, Ji Yuanfeng, Zhongxiao Li, Ruijiang Li

Spatial proteomics enables single-cell-resolution characterization of protein expression within tissue architecture, playing a critical role in understanding tumor microenvironments and guiding precision medicine. However, current analysis workflows remain fragmented, requiring expert manual orchestration of heterogeneous tools and limiting research scalability and reproducibility. We present **SP-Mind**, the first autonomous AI agent designed to unify the spatial proteomics analysis pipeline, from raw multiplexed tissue imaging to downstream phenotype discovery. Equipped with expert-curated biological analysis skills and specialized computational tools, SP-Mind converts natural-language queries into end-to-end analytical workflows without task-specific fine-tuning. To rigorously evaluate its capabilities, we introduce **SP-Bench**, a comprehensive benchmark spanning diverse tissue types and imaging technologies (fluorescence-based and mass spectrometry imaging), comprising 102 tasks across 18 distinct categories. Through extensive evaluation on SP-Bench and established downstream tasks, SP-Mind achieves **state-of-the-art** performance compared to existing open-source biomedical agent baselines. Code and benchmark will be publicly available upon acceptance.

General Machine Learning · Representation Learning

Yilin Chen, Tianyu Lu, Cizhang Zhao, Hannah Wayment-Steele, Po-Ssu Huang

Building physically grounded protein representations is central to computational biology, yet most existing approaches rely on sequence-pretrained language models or backbone-only graphs that overlook side-chain geometry and chemical detail. We present SLAE, a unified all-atom framework for learning protein representations from each residue’s local atomic neighborhood using only atom types and interatomic geometries. To encourage expressive feature extraction, we introduce a novel multi-task autoencoder objective that combines coordinate reconstruction, sequence recovery, and energy regression. SLAE reconstructs allatom structures with high fidelity from latent residue environments and achieves state-of-the-art performance across diverse downstream tasks via transfer learning. SLAE’s latent space is chemically informative and environmentally sensitive, enabling quantitative assessment of structural qualities and smooth interpolation between conformations at all-atom resolution.

Deep Learning · Sequential Models, Time series

Alena Brändle, Lukas Eisenmann, Florian Götz, Daniel Durstewitz

In dynamical systems reconstruction (DSR) we aim to recover the dynamical system (DS) underlying observed time series. Specifically, we aim to learn a generative surrogate model which approximates the underlying, data-generating DS, and recreates its long-term properties (`climate statistics'). In scientific and medical areas, in particular, these models need to be mechanistically tractable -- through their mathematical analysis we would like to obtain insight into the recovered system's workings. Piecewise-linear (PL), ReLU-based RNNs (PLRNNs) have a strong track-record in this regard, representing SOTA DSR models while allowing mathematical insight by virtue of their PL design. However, all current PLRNN variants are *discrete-time maps*. This is in disaccord with the assumed continuous-time nature of most physical and biological processes, and makes it hard to accommodate data arriving at *irregular* temporal intervals. Neural ODEs are one solution, but they do not reach the DSR performance of PLRNNs and often lack their tractability. Here we develop theory for *continuous-time* PLRNNs (cPLRNNs): We present a novel algorithm for training and simulating such models, bypassing numerical integration by efficiently exploiting their PL structure. We further demonstrate how important topological objects like equilibria or limit cycles can be determined semi-analytically in trained models. We compare cPLRNNs to both their discrete-time cousins as well as Neural ODEs on DSR benchmarks, including systems with discontinuities which come with hard thresholds.

Deep Learning · Algorithms

Cédric Goemaere, Gaspard Oliviers, Rafal Bogacz, Thomas Demeester

Predictive Coding (PC) offers a brain-inspired alternative to backpropagation for neural network training, described as a physical system minimizing its internal energy. However, in practice, PC is predominantly digitally simulated, requiring excessive amounts of compute while struggling to scale to deeper architectures. This paper reformulates PC to overcome this hardware-algorithm mismatch. First, we uncover how the canonical state-based formulation of PC (sPC) is, by design, deeply inefficient in digital simulation, inevitably resulting in exponential signal decay that stalls the entire minimization process. Then, to overcome this fundamental limitation, we introduce error-based PC (ePC), a novel reparameterization of PC which does not suffer from signal decay. Though no longer biologically plausible, ePC numerically computes exact PC weights gradients and runs orders of magnitude faster than sPC. Experiments across multiple architectures and datasets demonstrate that ePC matches backpropagation's performance even for deeper models where sPC struggles. Besides practical improvements, our work provides theoretical insight into PC dynamics and establishes a foundation for scaling PC-based learning to deeper architectures on digital hardware and beyond.

Applications · Health / Medicine

Luke Nightingale, Joseph Tuersley, Scott Warchal, Andrea Cairoli, Jacob Howes, Cameron Shand, Andrew Powell, Darren Green, Amy Strange, Michael Howell

Phenotypic screening experiments produce many microscope images of cells under diverse perturbations, with biologically significant responses often subtle or difficult to identify visually. A central challenge is to extract image representations that distinguish activity from controls and group phenotypically similar perturbations. In this work we propose new adaptations of contrastive loss functions that incorporate experimental metadata as learned class vectors, and a geometrically inspired variant, called SPC, where class vectors are confined to the unit sphere and updated only by attractive terms (allowing more overlap of phenotypically similar classes). The approach is tested on two popular benchmarking datasets, BBBC021 and RxRx3-core; and we also evaluate performance on uncurated screens of HaCaT cells to gauge effectiveness in a realistic use-case scenario. We find we outperform prior methods across the three datasets and on a wide array of metrics measuring phenotype grouping, biological recall, drug-target interaction and mechanism-of-action inference. We also show we maintain this improved performance compared to models over 10x larger in parameter count, and that SPC can be used as an effective fine-tuning technique. The method is easy to implement and is well suited to settings with limited data or compute resources.

Applications · Everything Else

Arnav Shah, Junzhe Li, Parsa Idehpour, Adibvafa Fallahpour, Brandon Wang, Sukjun Hwang, BO WANG, Patrick Hsu, Hani Goodarzi, Albert Gu

Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff. Standard subword tokenizers fragment biologically meaningful motifs such as codons and regulatory elements, while nucleotide-level models preserve biological coherence but incur prohibitive computational costs for long contexts. We introduce dnaHNet, a state-of-the-art tokenizer-free autoregressive model that segments and models genomic sequences end to end. Using a differentiable dynamic chunking mechanism, dnaHNet compresses raw nucleotides into latent tokens adaptively, balancing compression with predictive accuracy. Pretrained on prokaryotic genomes, dnaHNet outperforms leading architectures including StripedHyena2 in scaling and efficiency. This recursive chunking yields quadratic FLOP reductions, enabling $>3 \times$ inference speedup over Transformers. On zero-shot tasks, dnaHNet achieves superior performance in predicting protein variant fitness and gene essentiality, while automatically discovering hierarchical biological structures without supervision. These results establish dnaHNet as a scalable, interpretable framework for next-generation genomic modeling.

Applications · Everything Else

Arnav Shah, Junzhe Li, Parsa Idehpour, Adibvafa Fallahpour, Brandon Wang, Sukjun Hwang, BO WANG, Patrick Hsu, Hani Goodarzi, Albert Gu

Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff. Standard subword tokenizers fragment biologically meaningful motifs such as codons and regulatory elements, while nucleotide-level models preserve biological coherence but incur prohibitive computational costs for long contexts. We introduce dnaHNet, a state-of-the-art tokenizer-free autoregressive model that segments and models genomic sequences end to end. Using a differentiable dynamic chunking mechanism, dnaHNet compresses raw nucleotides into latent tokens adaptively, balancing compression with predictive accuracy. Pretrained on prokaryotic genomes, dnaHNet outperforms leading architectures including StripedHyena2 in scaling and efficiency. This recursive chunking yields quadratic FLOP reductions, enabling $>3 \times$ inference speedup over Transformers. On zero-shot tasks, dnaHNet achieves superior performance in predicting protein variant fitness and gene essentiality, while automatically discovering hierarchical biological structures without supervision. These results establish dnaHNet as a scalable, interpretable framework for next-generation genomic modeling.

Applications · Neuroscience, Cognitive Science

Nicholas Blauch, George Alvarez, Talia Konkle

Human vision is foveated, with variable resolution peaking at the center of a large field of view; this reflects an efficient trade-off for active sensing, allowing eye-movements to bring different parts of the world into focus with other parts of the world in context. In contrast, most computer vision systems encode the visual world at a uniform resolution, raising challenges for processing full-field high-resolution images efficiently. We propose a foveated vision interface (FOVI) based on the human retina and primary visual cortex, that reformats a variable-resolution retina-like sensor array into a uniformly dense, V1-like sensor manifold. Receptive fields are defined as k-nearest-neighborhoods (kNNs) on the sensor manifold, enabling kNN-convolution via a novel kernel mapping technique. We demonstrate two use cases: (1) an end-to-end kNN-convolutional architecture, and (2) a foveated adaptation of the foundational DINOv3 ViT model, leveraging low-rank adaptation (LoRA). These models provide competitive performance at a fraction of the computational cost of non-foveated baselines, opening pathways for efficient and scalable active sensing for high-resolution egocentric vision.

Social Aspects · Everything Else

Erik Bekkers, Anna Ciaunica

Imagine an Artificial Intelligence (AI) that perfectly mimics human emotion and begs for its continued existence. Is it morally permissible to unplug it? What if limited resources force a choice between unplugging such a pleading AI or a silent pre-term infant? We term this the unplugging paradox. This position paper critically examines the deeply ingrained physicalist assumptions—specifically computational functionalism—that keep this dilemma afloat. We introduce Biological Idealism, a framework that—unlike physicalism—remains logically coherent and empirically consistent. In this view, conscious experiences are fundamental and autopoietic life its necessary physical signature. This yields a definitive conclusion: AI is at best a functional mimic, not a conscious experiencing subject. We discuss how current AI consciousness theories erode moral standing criteria, and urge a shift from speculative machine rights to protecting human conscious life. The real moral issue lies not in making AI conscious and afraid of death, but in avoiding transforming humans into zombies.