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Ying Fan

Publications and source records attributed to Ying Fan.

At least 19 recordsLinked to original sources

Almost Free State Prediction Separation

State--prediction separation (SPS) relieves a language model's hidden state of two competing burdens---summarizing the context and predicting the next token---by splitting the forward pass into a state stream and a prediction stream. The separation works, but it is expensive: the prediction stream is a second pass over the whole backbone, costing $\sim$1.9$\times$ the pretraining FLOPs, and even more in terms of wall-clock time when using a flexible attention mask. This paper makes state--prediction separation almost free. We take the separation to its limit with a free pause token: a prediction stream that writes no keys or values at all and so rides the sequence's existing positions. It improves next-token prediction of a standard Transformer by 2-3 centinats in practice on a 1B parameter model, and because it adds no position it costs nothing at inference---no added context length, no KV cache, no decode steps, and essentially no latency, with the growth in inference flops typically irrelevant as it is not the active bottleneck on throughput. The cost is therefore entirely in training where we use four mechanisms to drive it down: a two-pass split that keeps FlashAttention kernels viable, the $w{=}0$ prediction window, a shared gated FFN that evaluates one FFN per position rather than one per stream, and phasing the separation onto the tail of the run. Together these bring the overhead versus an optimized pretraining pipeline to $1.33\times$ wall-clock while recovering ~94% of the gain compared to SPS, and to as low as $1.09\times$ along a graceful quality/compute tradeoff. Furthermore, the FFN optimization reduces the raw flops required at inference time. The result is an isoflop, isoparameter, and isotoken improvement over standard next token trained transformers.

cs.LG

Full-bandwidth transformer

Autoregressive transformers compute along two axes: horizontally across generated tokens, and vertically through model depth. Dense attention gives each token broad horizontal access to the past, but the vertical feedback channel between decoding steps remains narrow: only the sampled token returns to the bottom of the stack, while the top-layer hidden state is discarded. We introduce the \emph{full-bandwidth transformer}, which widens this channel with \emph{latent feedback}: at each decoding step, the previous top-layer hidden state is fused with the sampled token embedding through a gated linear unit and fed back as the next input. Latent feedback lets non-verbalized computation re-enter the stack with a renewed depth budget, while preserving the standard transformer architecture, KV cache, and language-modeling objective. To train full-bandwidth transformers without losing parallel teacher forcing, we use a scheduled multi-pass objective that introduces latent feedback late in pretraining and mixes a small fraction of deeper feedback passes for stability. We train 1B-parameter full-bandwidth transformers up to 400B tokens and find that latent feedback improves validation loss, 5-shot language-model evaluation, math and coding generation, and instruction-tuned performance. With negligible per-token decoding overhead, full-bandwidth transformers match or approach standard transformers trained with roughly $1.5\times$ more tokens, and manage to produce shorter reasoning traces at equal or better accuracy.

cs.AI

Bridging the Gap Between Latent and Explicit Reasoning with Looped Transformers

Language models typically reason via explicit chain-of-thought (CoT), generating intermediate steps token-by-token. Latent CoT offers an alternative: it performs multi-step reasoning in the model's hidden states, replacing decoded tokens with continuous representations for greater efficiency. However, existing latent CoT methods underperform explicit CoT beyond 1B parameters, and the gap widens with scale. Looped, or recurrent-depth, Transformers, which reuse their weights to increase computation depth without adding parameters, are a natural fit for latent reasoning. We therefore ask whether looped Transformers can bridge this gap. We answer affirmatively with a simple recipe: a looped padded Transformer that processes K latent blocks in parallel for R iterations, with a cross-entropy loss on each latent position's gold CoT-step token, similar to explicit CoT supervision. We instantiate it as LOTUS (Looped Transformers with parallel supervision on latents). LOTUS is, to our knowledge, the first latent-CoT method to bridge the gap to explicit CoT at the 3B scale, while cutting thought-phase latency by 2.5x-6.9x from compact math expressions to natural language. Projecting LOTUS's post-loop latents through the base LM head recovers the gold reasoning steps and even surfaces alternative valid intermediate steps, evidence that its latent space is interpretable and CoT-aligned. Ablations confirm that both the looped backbone and the parallel supervision on gold CoT tokens are essential. Code is available at https://github.com/yingfan-bot/lotus.

cs.LG

Conditional effects of cross-product substitution on systemic risk in multilayer food trade networks

Localized shocks arising from climate extremes, geopolitical conflicts, and trade protectionism cascade through trade networks, triggering global food crises. Cross-product substitution, a critical response strategy, induces cross-product cascading effects that remain underexplored. Here, we develop a multilayer network model that simulates the short-term response to food supply shocks. When applied to cereal trade networks, comparisons with and without substitution, as well as with increased substitute layers, reveal that substitution mitigates risks in the shocked layer but induces derived risks in substitute layers, causing the network system to present four response regimes ranging from resilient to systemic crisis. These regimes' boundaries and magnitudes emerge from the interplay of four critical factors: shock intensity, substitution extent, supply capacity of substitute layers, and inter-layer substitution structure. Scenario simulations of three real-world shocks further reveal country-level heterogeneity in substitution effectiveness. Our framework provides a quantitative tool for designing response strategies and resilient food systems.

physics.soc-ph

Demanding peer review is associated with higher impact in published science

Peer review shapes which scientific claims enter the published record, but its internal dynamics are hard to measure at scale because reviewer criticism and author revision are usually embedded in long, unstructured correspondence. Here we use a fixed-prompt large language model pipeline to convert the review correspondence of \textit{Nature Communications} papers published from 2017 to 2024 into structured reviewer--author interactions. We find that review pressure is concentrated in the first round and focused disproportionately on core claims rather than peripheral presentation. Higher average opinion strength is also associated with more reviewer disagreement, while review patterns vary little with broad team attributes, consistent with relatively impartial evaluation. Contrary to the intuition that stronger papers should pass review more smoothly, with greater reviewer--author agreement and less extensive revision, we find that stronger criticism, higher-quality comments, and greater revision burden are associated with higher later citation impact within accepted papers. We finally show that fields differ more in review style than in review length, pointing to disciplinary variation in how criticism is negotiated and resolved. These findings position open peer review not just as a gatekeeping mechanism but as a measurable record of how influential scientific claims are challenged, defended, and revised before entering the published record.

cs.DL

R3-VAE: Reference Vector-Guided Rating Residual Quantization VAE for Generative Recommendation

Generative Recommendation (GR) has gained traction for its merits of superior performance and cold-start capability. As the vital role in GR, Semantic Identifiers (SIDs) represent item semantics through discrete tokens. However, current techniques for SID generation based on vector quantization face two main challenges: (i) training instability, stemming from insufficient gradient propagation through the straight-through estimator and sensitivity to initialization; and (ii) inefficient SID quality assessment, where industrial practice still depends on costly GR training and A/B testing. To address these challenges, we propose Reference Vector-Guided Rating Residual Quantization VAE (R3-VAE). This framework incorporates three key innovations: (i) a reference vector that functions as a semantic anchor for the initial features, thereby mitigating sensitivity to initialization; (ii) a dot product-based rating mechanism designed to stabilize the training process and prevent codebook collapse; and (iii) two SID evaluation metrics, Semantic Cohesion and Preference Discrimination, serving as regularization terms during training. Empirical results on six benchmarks demonstrate that R3-VAE outperforms state-of-the-art methods, achieving an average improvement of 14.5% in Recall@10 and 15.5% in NDCG@10 across three public datasets (Beauty, Sports, and Toys). Furthermore, we perform GR training and online A/B tests on Toutiao. Our method achieves a 1.62% improvement in MRR and a 0.83% gain in StayTime/U versus baselines. Additionally, we employ R3-VAE to replace the item ID of CTR model, resulting in significant improvements in content cold start by 15.36%, corroborating the strong applicability and business value in industry-scale recommendation scenarios.

cs.IR

ReJump: A Tree-Jump Representation for Analyzing and Improving LLM Reasoning

Large Reasoning Models (LRMs) are Large Language Models (LLMs) explicitly trained to generate long-form Chain-of-Thoughts (CoTs), achieving impressive success on challenging tasks like math and programming. However, their underlying reasoning "algorithms" remain poorly understood. To investigate this, we propose ReJump, which represents a reasoning trace as a visitation order over nodes in a tree of intermediate problem-solving steps. Transitions between nodes, which we term jumps, include adjacent moves that capture behaviors such as calculation, and non-adjacent moves that capture behaviors such as backtracking and verification. ReJump enables analyzing LLM reasoning with diverse metrics that quantify exploration, exploitation, overthinking, forgetting, and verification. Using our proposed LLM agent to extract reasoning traces into ReJump format, we evaluate state-of-the-art LRMs on two tasks and find that models with similar accuracy can exhibit distinct reasoning behaviors, while different tasks favor different reasoning styles (e.g., varying balance between exploration and exploitation). To further understand how learning strategies shape reasoning, we use ReJump to compare distilled LRMs with their teachers, CoT-prompted LLMs with LRMs, and to examine how the number of reasoning examples and reinforcement learning affect reasoning behavior. Finally, we show that ReJump can improve reasoning quality at test time through strategies such as ReJump-guided Best-of-N selection and prompt selection. Our code is publicly available at https://github.com/UW-Madison-Lee-Lab/ReJump.

cs.LG

A Grey Literature Review of AI-Native Applications

Background: The rapid advancement of large language models (LLMs) has given rise to AI-native applications, a new paradigm in software engineering that fundamentally redefines how software is designed, developed, and evolved. Despite their growing prominence, AI-native applications still lack a unified engineering definition and architectural blueprint, leaving practitioners without systematic guidance for system design, quality assurance, and technology selection. Objective: This study seeks to establish a comprehensive understanding of AI-native applications by identifying their defining characteristics, key quality attributes, and typical technology stacks, as well as by clarifying the opportunities and challenges they present. Method: We conducted a grey literature review, integrating conceptual perspectives retrieved from targeted Google and Bing searches with practical insights derived from leading open-source projects on GitHub. A structured protocol encompassing source selection, quality assessment, and thematic analysis was applied to synthesize findings across heterogeneous sources. Results: We finally identified 106 studies based on the selection criteria. The analysis reveals that AI-native applications are distinguished by two core pillars: the central role of AI as the system's intelligence paradigm and their inherently probabilistic, non-deterministic nature. Critical quality attributes include reliability, usability, performance efficiency, and AI-specific observability. In addition, a typical technology stack has begun to emerge, comprising LLM orchestration frameworks, vector databases, and AI-native observability platforms. These systems emphasize response quality, cost-effectiveness, and outcome predictability, setting them apart from conventional software systems. Conclusion: This study is the first to propose a dual-layered engineering blueprint...

cs.SE

Dion: Distributed Orthonormalized Updates

Orthonormalized updates accelerate training, improve stability, and enable robust hyperparameter transfer, but existing methods like Muon rely on dense matrix operations that clash with sharded weights in large-scale LLM training, causing high compute and communication cost. We introduce Dion (Distributed Orthonormalization), a scalable and efficient update rule that replaces Newton-Schulz iteration with amortized power iteration on a momentum buffer, avoiding full-matrix reconstruction and integrating cleanly with weight sharding. The rank-fraction parameter with error feedback enables low-rank updates that balance quality with significant cost savings. On language models from 160M to 3B parameters, Dion retains the benefits of orthonormalized updates, while markedly reducing wall-clock time at scale, making it a practical optimizer for next-generation foundation models. Code is available at: https://github.com/microsoft/dion/

cs.LG

VersaPRM: Multi-Domain Process Reward Model via Synthetic Reasoning Data

Process Reward Models (PRMs) have proven effective at enhancing mathematical reasoning for Large Language Models (LLMs) by leveraging increased inference-time computation. However, they are predominantly trained on mathematical data and their generalizability to non-mathematical domains has not been rigorously studied. In response, this work first shows that current PRMs have poor performance in other domains. To address this limitation, we introduce VersaPRM, a multi-domain PRM trained on synthetic reasoning data generated using our novel data generation and annotation method. VersaPRM achieves consistent performance gains across diverse domains. For instance, in the MMLU-Pro category of Law, VersaPRM via weighted majority voting, achieves a 7.9% performance gain over the majority voting baseline -- surpassing Qwen2.5-Math-PRM's gain of 1.3%. We further contribute to the community by open-sourcing all data, code and models for VersaPRM.

cs.LG

Societal citations undermine the function of the science reward system

Citations in the scientific literature system do not simply reflect relationships between knowledge but are influenced by non-objective and societal factors. Citation bias, irresponsible citation, and citation manipulation are widespread and have become a serious and growing problem. However, it has been difficult to assess the consequences of mixing societal factors into the literature system because there was no observable literature system unmixed with societal factors for comparison. In this paper, we construct a mathematical theorem network, representing a logic-based and objective knowledge system, to address this problem. By comparing the mathematical theorem network and the scientific citation networks, we find that these two types of networks are significantly different in their structure and function. In particular, the reward function in citation networks is impaired: The scientific citation network fails to provide more recognition for more disruptive results, while the mathematical theorem network can achieve. We develop a network generation model that can create two types of links$\unicode{x2014}$logical and societal$\unicode{x2014}$to account for these differences. The model parameter $q$, which we call the human influence factor, can control the number of societal links and thus regulate the degree of mixing of societal factors in the networks. Under this design, the model successfully reproduces the differences among real networks. These results suggest that the presence of societal factors undermines the function of the scientific reward system. To improve the status quo, we advocate for reforming the reference list format in papers, urging journals to require authors to separately disclose logical references and social references.

cs.DL

Quantifying Global Food Trade: A Net Caloric Content Approach to Food Trade Network Analysis

As the global population and the per capita demand for resource intensive diets continues to grow, the corresponding increase in food demand challenges the global food system, enhancing its reliance on trade. Most previous research typically constructed either unweighted networks or weighted solely by tonnage to represent food trade, and focused on bilateral trade relationships between pairs of countries. This study investigates the properties of global food trade constructed in terms of total food calories associated with all the main food products exchanged along each trade link (edge of the food trade network). Utilizing data from the Food and Agriculture Organization between 1986 and 2022, we construct a directed, weighted network of net caloric flows between countries. This approach highlights the importance of considering nutritional value in discussions of food security and trade policies, offering a more holistic view of global food trade dynamics. Our analysis reveals significant heterogeneity in trade patterns, with certain countries emerging as major exporters or importers of food calories. Moreover, we employ network measures, including network connectivity, network heterogeneity, network modularity, and node correlation similarity, to elucidate the structural dynamics of global net food calorie trade networks that are relevant to the stability and resilience of the global food system. Our work provides a more nuanced understanding of global food trade dynamics, emphasizing the need for comprehensive strategies to enhance the resilience and sustainability of food trade networks.

econ.GN

Looped Transformers for Length Generalization

Recent work has shown that Transformers trained from scratch can successfully solve various arithmetic and algorithmic tasks, such as adding numbers and computing parity. While these Transformers generalize well on unseen inputs of the same length, they struggle with length generalization, i.e., handling inputs of unseen lengths. In this work, we demonstrate that looped Transformers with an adaptive number of steps significantly improve length generalization. We focus on tasks with a known iterative solution, involving multiple iterations of a RASP-L operation - a length-generalizable operation that can be expressed by a finite-sized Transformer. We train looped Transformers using our proposed learning algorithm and observe that they learn highly length-generalizable solutions for various tasks.

cs.LG

How to Solve Contextual Goal-Oriented Problems with Offline Datasets?

We present a novel method, Contextual goal-Oriented Data Augmentation (CODA), which uses commonly available unlabeled trajectories and context-goal pairs to solve Contextual Goal-Oriented (CGO) problems. By carefully constructing an action-augmented MDP that is equivalent to the original MDP, CODA creates a fully labeled transition dataset under training contexts without additional approximation error. We conduct a novel theoretical analysis to demonstrate CODA's capability to solve CGO problems in the offline data setup. Empirical results also showcase the effectiveness of CODA, which outperforms other baseline methods across various context-goal relationships of CGO problem. This approach offers a promising direction to solving CGO problems using offline datasets.

cs.LG

Coevolution of Resource and Strategies in Common-Pool Resource Dilemmas: A Coupled Human-Environmental System Model

Common-pool resource governance requires users to cooperate and avoid overexploitation, but defection and free-riding often undermine cooperation. We model a human-environmental system that integrates dynamics of resource and users' strategies. The resource follows a logistic function that depends on natural growth rate, carrying capacity, and extraction rates of cooperators and defectors. The users' strategies evolve according to different processes that capture effects of payoff, resource, and noise. We analyze the feedback between resource availability and strategic adaptation, and explores the conditions for the emergence and maintenance of cooperation. We find different processes lead to different regimes of equilibrium solutions and resource levels depending on the parameter configuration and initial conditions. We also show that some processes can enhance the sustainability of the resource by making the users more responsive to the resource scarcity. The paper advances the understanding of human-environmental system and offers insights for resource governance policies and interventions.

econ.TH

A coronary artery phantom for task-based CT performance assessment and a comparative study of clinical CT, photon counting CT, and micro CT

While drastic improvements in CT technology have occurred in the past 25 years, spatial resolution is one area where progress has been limited until recently. New photon counting CT systems, are capable of much better spatial resolution than their (energy integrating) predecessors. These improvements have the potential to improve the evaluation obstructive coronary artery disease by enabling more accurate delineation between calcified plaque and coronary vessel lumen. A new set of vessel phantoms has been designed and manufactured for quantifying this improvement. Comparisons are made between an existing clinical CT system, a prototype photon counting system, with images from a micro CT system being used as the gold standard. Scans were made of the same objects on all three systems. The resulting images were registered and the luminal cross section areas were compared. Luminal cross-sections near calcified plaques were reduced due to blooming, but this effect was much less pronounced in images from the prototype photon counting system as compared to the images from the clinical CT system.

physics.med-ph

Dimensionality reduction of networked systems with separable coupling-dynamics: theory and applications

Complex dynamical systems are prevalent in various domains, but their analysis and prediction are hindered by their high dimensionality and nonlinearity. Dimensionality reduction techniques can simplify the system dynamics by reducing the number of variables, but most existing methods do not account for networked systems with separable coupling-dynamics, where the interaction between nodes can be decomposed into a function of the node state and a function of the neighbor state. Here, we present a novel dimensionality reduction framework that can effectively capture the global dynamics of these networks by projecting them onto a low-dimensional system. We derive the reduced system's equation and stability conditions, and propose an error metric to quantify the reduction accuracy. We demonstrate our framework on two examples of networked systems with separable coupling-dynamics: a modified susceptible-infected-susceptible model with direct infection and a modified Michaelis-Menten model with activation and inhibition. We conduct numerical experiments on synthetic and empirical networks to validate and evaluate our framework, and find a good agreement between the original and reduced systems. We also investigate the effects of different network structures and parameters on the system dynamics and the reduction error. Our framework offers a general and powerful tool for studying complex dynamical networks with separable coupling-dynamics.

math.DS

Impact of resource availability and conformity effect on sustainability of common-pool resources

Sustainability of common-pool resources hinges on the interplay between human and environmental systems. However, there is still a lack of a novel and comprehensive framework for modelling extraction of common-pool resources and cooperation of human agents that can account for different factors that shape the system behavior and outcomes. In particular, we still lack a critical value for ensuring resource sustainability under different scenarios. In this paper, we present a novel framework for studying resource extraction and cooperation in human-environmental systems for common-pool resources. We explore how different factors, such as resource availability and conformity effect, influence the players' decisions and the resource outcomes. We identify critical values for ensuring resource sustainability under various scenarios. We demonstrate the observed phenomena are robust to the complexity and assumptions of the models and discuss implications of our study for policy and practice, as well as the limitations and directions for future research.

econ.TH