arXiv:2603.22364v1 Announce Type: cross Abstract: Diffusion models have achieved state-of-the-art performance in generative modeling, but their success often relies heavily on classifier-free guidance (CFG), an inference-time heuristic that modifies the sampling trajectory. From a theoretical perspective, diffusion models trained with standard denoising score matching (DSM) are expected to recover the target data distribution, raising the question of why inference-time guidance is necessary in practice. In this work, we ask whether the DSM training objective can be modified in a principled manner such that standard reverse-time sampling, without inference-time guidance, yields effects comparable to CFG. We identify insufficient inter-class separation as a key limitation of standard diffusion models. To address this, we propose MCLR, a principled alignment objective that explicitly maximizes inter-class likelihood-ratios during training. Models fine-tuned with MCLR exhibit CFG-like improvements under standard sampling, achieving comparable qualitative and quantitative gains without requiring inference-time guidance. Beyond empirical benefits, we provide a theoretical result showing that the CFG-guided score is exactly the optimal solution to a weighted MCLR objective. This establishes a formal equivalence between classifier-free guidance and alignment-based objectives, offering a mechanistic interpretation of CFG.

arXiv:2511.05919v3 Announce Type: replace-cross Abstract: LLMs are now an integral part of information retrieval. As such, their role as question answering chatbots raises significant concerns due to their shown vulnerability to adversarial man-in-the-middle (MitM) attacks. Here, we propose the first principled attack evaluation on LLM factual memory under prompt injection via Xmera, our novel, theory-grounded MitM framework. By perturbing the input given to "victim" LLMs in three closed-book and fact-based QA settings, we undermine the correctness of the responses and assess the uncertainty of their generation process. Surprisingly, trivial instruction-based attacks report the highest success rate (up to ~85.3%) while simultaneously having a high uncertainty for incorrectly answered questions. To provide a simple defense mechanism against Xmera, we train Random Forest classifiers on the response uncertainty levels to distinguish between attacked and unattacked queries (average AUC of up to ~94.8%). We believe that signaling users to be cautious about the answers they receive from black-box and potentially corrupt LLMs is a first checkpoint toward user cyberspace safety.

arXiv:2601.13719v2 Announce Type: replace-cross Abstract: Long video understanding presents significant challenges for vision-language models due to extremely long context windows. Existing solutions relying on naive chunking strategies with retrieval-augmented generation, typically suffer from information fragmentation and a loss of global coherence. We present HAVEN, a unified framework for long-video understanding that enables coherent and comprehensive reasoning by integrating audiovisual entity cohesion and hierarchical video indexing with agentic search. First, we preserve semantic consistency by integrating entity-level representations across visual and auditory streams, while organizing content into a structured hierarchy spanning global summary, scene, segment, and entity levels. Then we employ an agentic search mechanism to enable dynamic retrieval and reasoning across these layers, facilitating coherent narrative reconstruction and fine-grained entity tracking. Extensive experiments demonstrate that our method achieves good temporal coherence, entity consistency, and retrieval efficiency, establishing a new state-of-the-art with an overall accuracy of 84.1% on LVBench. Notably, it achieves outstanding performance in the challenging reasoning category, reaching 80.1%. These results highlight the effectiveness of structured, multimodal reasoning for comprehensive and context-consistent understanding of long-form videos.

arXiv:2603.12634v1 Announce Type: cross Abstract: Test-time scaling has become a dominant paradigm for improving LLM agent reliability, yet current approaches treat compute as an abundant resource, allowing agents to exhaust token and tool budgets on redundant steps or dead-end trajectories. Existing budget-aware methods either require expensive fine-tuning or rely on coarse, trajectory-level heuristics that cannot intervene mid-execution. We propose the Budget-Aware Value Tree (BAVT), a training-free inference-time framework that models multi-hop reasoning as a dynamic search tree guided by step-level value estimation within a single LLM backbone. Another key innovation is a budget-conditioned node selection mechanism that uses the remaining resource ratio as a natural scaling exponent over node values, providing a principled, parameter-free transition from broad exploration to greedy exploitation as the budget depletes. To combat the well-known overconfidence of LLM self-evaluation, BAVT employs a residual value predictor that scores relative progress rather than absolute state quality, enabling reliable pruning of uninformative or redundant tool calls. We further provide a theoretical convergence guarantee, proving that BAVT reaches a terminal answer with probability at least $1-\epsilon$ under an explicit finite budget bound. Extensive evaluations on four multi-hop QA benchmarks across two model families demonstrate that BAVT consistently outperforms parallel sampling baselines. Most notably, BAVT under strict low-budget constraints surpasses baseline performance at $4\times$ the resource allocation, establishing that intelligent budget management fundamentally outperforms brute-force compute scaling.

arXiv:2502.08942v3 Announce Type: replace-cross Abstract: While many advances in time series models focus exclusively on numerical data, research on multimodal time series, particularly those involving contextual textual information, remains in its infancy. With recent progress in large language models and time series learning, we revisit the integration of paired texts with time series through the Platonic Representation Hypothesis, which posits that representations of different modalities converge to shared spaces. In this context, we identify that time-series-paired texts may naturally exhibit periodic properties that closely mirror those of the original time series. Building on this insight, we propose a novel framework, Texts as Time Series (TaTS), which considers the time-series-paired texts to be auxiliary variables of the time series. TaTS can be plugged into any existing numerical-only time series models and effectively enable them to handle time series data with paired texts. Through extensive experiments on both multimodal time series forecasting and imputation tasks across benchmark datasets with various existing time series models, we demonstrate that TaTS can enhance multimodal predictive performance without modifying model architectures. Our Code is available at https://github.com/iDEA-iSAIL-Lab-UIUC/TaTS.

arXiv:2502.17262v4 Announce Type: replace-cross Abstract: The escalating scale and cost of Large Language Models (LLMs) training necessitate accurate pre-training prediction of downstream task performance for comprehensive understanding of scaling properties. This is challenged by: 1) the emergence phenomenon, where unpredictable capabilities appearing suddenly at critical model scales; and 2) uneven task difficulty and inconsistent performance scaling patterns, leading to high metric variability. Current prediction methods lack accuracy and reliability. We propose a Clustering-On-Difficulty (COD) framework for downstream performance prediction. The COD framework clusters tasks by their difficulty scaling features, thereby constructing a more stable and predictable task subset that exhibits well-behaved scaling characteristics with the increase of compute budget. We adopt a performance scaling law to predict cluster-wise performance with theoretical support. Predictable subset performance acts as an intermediate predictor for the full evaluation set. We further derive a mapping function to accurately extrapolate the performance of the subset to the full set. Applied to an LLM with 70B parameters, COD achieved a 1.55\% average prediction error across eight key LLM benchmarks, thus providing actionable insights for scaling properties and training monitoring during LLM pre-training.

arXiv:2507.17731v2 Announce Type: replace-cross Abstract: Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.

Oncogene, Published online: 05 March 2026; doi:10.1038/s41388-026-03713-z

KRAS-extrachromosomal DNA drives intratumoral heterogeneity in gastric cancer

arXiv:2603.03752v1 Announce Type: cross Abstract: Large language models (LLMs) demonstrate superior reasoning capabilities compared to small language models (SLMs), but incur substantially higher costs. We propose COllaborative REAsoner (COREA), a system that cascades an SLM with an LLM to achieve a balance between accuracy and cost in complex reasoning tasks. COREA first attempts to answer questions using the SLM, which outputs both an answer and a verbalized confidence score. Questions with confidence below a predefined threshold are deferred to the LLM for more accurate resolution. We introduce a reinforcement learning-based training algorithm that aligns the SLM's confidence through an additional confidence calibration reward. Extensive experiments demonstrate that our method jointly improves the SLM's reasoning ability and confidence calibration across diverse datasets and model backbones. Compared to using the LLM alone, COREA reduces cost by 21.5% and 16.8% on out-of-domain math and non-math datasets, respectively, with only an absolute pass@1 drop within 2%.

arXiv:2211.12817v3 Announce Type: replace-cross Abstract: Humans rarely perceive objects in isolation but interpret scenes through relationships among co-occurring elements. How such contextual knowledge is acquired without explicit supervision remains unclear. Here we combine human psychophysics experiments with computational modelling to study the emergence of contextual reasoning. Participants were exposed to novel objects embedded in naturalistic scenes that followed predefined contextual rules capturing global context, local context and crowding. After viewing short training videos, participants completed a "lift-the-flap" task in which a hidden object had to be inferred from the surrounding context under variations in size, resolution and spatial arrangement. Humans rapidly learned these contextual associations without labels or feedback and generalised robustly across contextual changes. We then introduce SeCo (Self-supervised learning for Context Reasoning), a biologically inspired model that learns contextual relationships from complex scenes. SeCo encodes targets and context with separate vision encoders and stores latent contextual priors in a learnable external memory module. Given contextual cues, the model retrieves likely object representations to infer hidden targets. SeCo outperforms state-of-the-art self-supervised learning approaches and predicts object placements most consistent with human behaviour, highlighting the central role of contextual associations in scene understanding.

arXiv:2506.17337v3 Announce Type: replace-cross Abstract: Vision Language Models (VLMs) have shown promise in automating image diagnosis and interpretation in clinical settings. However, developing specialist medical VLMs requires substantial computational resources and carefully curated datasets, and it remains unclear under which conditions generalist and specialist medical VLMs each perform best. This study highlights the complementary strengths of specialist medical and generalist VLMs. Specialists remain valuable in modality-aligned use cases, but we find that efficiently fine-tuned generalist VLMs can achieve comparable or even superior performance in most tasks, particularly when transferring to unseen or rare OOD medical modalities. These results suggest that generalist VLMs, rather than being constrained by their lack of specialist medical pretraining, may offer a scalable and cost-effective pathway for advancing clinical AI development.

arXiv:2506.15715v2 Announce Type: replace-cross Abstract: Drawing inspiration from our human brain that designs different neurons for different tasks, recent advances in deep learning have explored modifying a network's neurons to develop so-called task-driven neurons. Prototyping task-driven neurons (referred to as NeuronSeek) employs symbolic regression (SR) to discover the optimal neuron formulation and construct a network from these optimized neurons. Along this direction, this work replaces symbolic regression with tensor decomposition (TD) to discover optimal neuronal formulations, offering enhanced stability and faster convergence. Furthermore, we establish theoretical guarantees that modifying the aggregation functions with common activation functions can empower a network with a fixed number of parameters to approximate any continuous function with an arbitrarily small error, providing a rigorous mathematical foundation for the NeuronSeek framework. Extensive empirical evaluations demonstrate that our NeuronSeek-TD framework not only achieves superior stability, but also is competitive relative to the state-of-the-art models across diverse benchmarks. The code is available at https://github.com/HanyuPei22/NeuronSeek.