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Aug 13

A Survey of Neural Code Intelligence: Paradigms, Advances and Beyond

Neural Code Intelligence -- leveraging deep learning to understand, generate, and optimize code -- holds immense potential for transformative impacts on the whole society. Bridging the gap between Natural Language and Programming Language, this domain has drawn significant attention from researchers in both research communities over the past few years. This survey presents a systematic and chronological review of the advancements in code intelligence, encompassing over 50 representative models and their variants, more than 20 categories of tasks, and an extensive coverage of over 680 related works. We follow the historical progression to trace the paradigm shifts across different research phases (e.g., from modeling code with recurrent neural networks to the era of Large Language Models). Concurrently, we highlight the major technical transitions in models, tasks, and evaluations spanning through different stages. For applications, we also observe a co-evolving shift. It spans from initial endeavors to tackling specific scenarios, through exploring a diverse array of tasks during its rapid expansion, to currently focusing on tackling increasingly complex and varied real-world challenges. Building on our examination of the developmental trajectories, we further investigate the emerging synergies between code intelligence and broader machine intelligence, uncovering new cross-domain opportunities and illustrating the substantial influence of code intelligence across various domains. Finally, we delve into both the opportunities and challenges associated with this field, alongside elucidating our insights on the most promising research directions. An ongoing, dynamically updated project and resources associated with this survey have been released at https://github.com/QiushiSun/NCISurvey.

  • 18 authors
·
Mar 21, 2024

Enforcing temporal consistency in Deep Learning segmentation of brain MR images

Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on the similarity of images over time and the use of subject-specific priors to reduce random variation and improve the robustness and sensitivity of the overall longitudinal analysis. This is however slow and computationally intensive as subject-specific templates need to be rebuilt every time. The focus of this work to accelerate this analysis with the use of deep learning. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The state of art using 3D patches as inputs to modified Unet provides results around {0.91 pm 0.5} Dice and using multi-view atlas in CNNs provide around the same results. In this work, different models are explored, each offers better accuracy and fast results while increasing the segmentation quality. These methods are evaluated on 135 scans from the EADC-ADNI Harmonized Hippocampus Protocol. Proposed CNN based segmentation approaches demonstrate how 2D segmentation using prior slices can provide similar results to 3D segmentation while maintaining good continuity in the 3D dimension and improved speed. Just using 2D modified sagittal slices provide us a better Dice and longitudinal analysis for a given subject. For the ADNI dataset, using the simple UNet CNN technique gives us {0.84 pm 0.5} and while using modified CNN techniques on the same input yields {0.89 pm 0.5}. Rate of atrophy and RMS error are calculated for several test cases using various methods and analyzed.

  • 2 authors
·
Jun 13, 2019

What, How, Where, and How Well? A Survey on Test-Time Scaling in Large Language Models

As enthusiasm for scaling computation (data and parameters) in the pretraining era gradually diminished, test-time scaling (TTS), also referred to as ``test-time computing'' has emerged as a prominent research focus. Recent studies demonstrate that TTS can further elicit the problem-solving capabilities of large language models (LLMs), enabling significant breakthroughs not only in specialized reasoning tasks, such as mathematics and coding, but also in general tasks like open-ended Q&A. However, despite the explosion of recent efforts in this area, there remains an urgent need for a comprehensive survey offering a systemic understanding. To fill this gap, we propose a unified, multidimensional framework structured along four core dimensions of TTS research: what to scale, how to scale, where to scale, and how well to scale. Building upon this taxonomy, we conduct an extensive review of methods, application scenarios, and assessment aspects, and present an organized decomposition that highlights the unique functional roles of individual techniques within the broader TTS landscape. From this analysis, we distill the major developmental trajectories of TTS to date and offer hands-on guidelines for practical deployment. Furthermore, we identify several open challenges and offer insights into promising future directions, including further scaling, clarifying the functional essence of techniques, generalizing to more tasks, and more attributions.

  • 10 authors
·
Mar 31, 2025 2

Reasoning or Rhetoric? An Empirical Analysis of Moral Reasoning Explanations in Large Language Models

Do large language models reason morally, or do they merely sound like they do? We investigate whether LLM responses to moral dilemmas exhibit genuine developmental progression through Kohlberg's stages of moral development, or whether alignment training instead produces reasoning-like outputs that superficially resemble mature moral judgment without the underlying developmental trajectory. Using an LLM-as-judge scoring pipeline validated across three judge models, we classify more than 600 responses from 13 LLMs spanning a range of architectures, parameter scales, and training regimes across six classical moral dilemmas, and conduct ten complementary analyses to characterize the nature and internal coherence of the resulting patterns. Our results reveal a striking inversion: responses overwhelmingly correspond to post-conventional reasoning (Stages 5-6) regardless of model size, architecture, or prompting strategy, the effective inverse of human developmental norms, where Stage 4 dominates. Most strikingly, a subset of models exhibit moral decoupling: systematic inconsistency between stated moral justification and action choice, a form of logical incoherence that persists across scale and prompting strategy and represents a direct reasoning consistency failure independent of rhetorical sophistication. Model scale carries a statistically significant but practically small effect; training type has no significant independent main effect; and models exhibit near-robotic cross-dilemma consistency producing logically indistinguishable responses across semantically distinct moral problems. We posit that these patterns constitute evidence for moral ventriloquism: the acquisition, through alignment training, of the rhetorical conventions of mature moral reasoning without the underlying developmental trajectory those conventions are meant to represent.

  • 4 authors
·
Mar 23 2

How Far Are We From AGI

The evolution of artificial intelligence (AI) has profoundly impacted human society, driving significant advancements in multiple sectors. Yet, the escalating demands on AI have highlighted the limitations of AI's current offerings, catalyzing a movement towards Artificial General Intelligence (AGI). AGI, distinguished by its ability to execute diverse real-world tasks with efficiency and effectiveness comparable to human intelligence, reflects a paramount milestone in AI evolution. While existing works have summarized specific recent advancements of AI, they lack a comprehensive discussion of AGI's definitions, goals, and developmental trajectories. Different from existing survey papers, this paper delves into the pivotal questions of our proximity to AGI and the strategies necessary for its realization through extensive surveys, discussions, and original perspectives. We start by articulating the requisite capability frameworks for AGI, integrating the internal, interface, and system dimensions. As the realization of AGI requires more advanced capabilities and adherence to stringent constraints, we further discuss necessary AGI alignment technologies to harmonize these factors. Notably, we emphasize the importance of approaching AGI responsibly by first defining the key levels of AGI progression, followed by the evaluation framework that situates the status-quo, and finally giving our roadmap of how to reach the pinnacle of AGI. Moreover, to give tangible insights into the ubiquitous impact of the integration of AI, we outline existing challenges and potential pathways toward AGI in multiple domains. In sum, serving as a pioneering exploration into the current state and future trajectory of AGI, this paper aims to foster a collective comprehension and catalyze broader public discussions among researchers and practitioners on AGI.

  • 8 authors
·
May 16, 2024

The Grammar-Learning Trajectories of Neural Language Models

The learning trajectories of linguistic phenomena in humans provide insight into linguistic representation, beyond what can be gleaned from inspecting the behavior of an adult speaker. To apply a similar approach to analyze neural language models (NLM), it is first necessary to establish that different models are similar enough in the generalizations they make. In this paper, we show that NLMs with different initialization, architecture, and training data acquire linguistic phenomena in a similar order, despite their different end performance. These findings suggest that there is some mutual inductive bias that underlies these models' learning of linguistic phenomena. Taking inspiration from psycholinguistics, we argue that studying this inductive bias is an opportunity to study the linguistic representation implicit in NLMs. Leveraging these findings, we compare the relative performance on different phenomena at varying learning stages with simpler reference models. Results suggest that NLMs exhibit consistent "developmental" stages. Moreover, we find the learning trajectory to be approximately one-dimensional: given an NLM with a certain overall performance, it is possible to predict what linguistic generalizations it has already acquired. Initial analysis of these stages presents phenomena clusters (notably morphological ones), whose performance progresses in unison, suggesting a potential link between the generalizations behind them.

  • 4 authors
·
Apr 5, 2022

Regions are Who Walk Them: a Large Pre-trained Spatiotemporal Model Based on Human Mobility for Ubiquitous Urban Sensing

User profiling and region analysis are two tasks of significant commercial value. However, in practical applications, modeling different features typically involves four main steps: data preparation, data processing, model establishment, evaluation, and optimization. This process is time-consuming and labor-intensive. Repeating this workflow for each feature results in abundant development time for tasks and a reduced overall volume of task development. Indeed, human mobility data contains a wealth of information. Several successful cases suggest that conducting in-depth analysis of population movement data could potentially yield meaningful profiles about users and areas. Nonetheless, most related works have not thoroughly utilized the semantic information within human mobility data and trained on a fixed number of the regions. To tap into the rich information within population movement, based on the perspective that Regions Are Who walk them, we propose a large spatiotemporal model based on trajectories (RAW). It possesses the following characteristics: 1) Tailored for trajectory data, introducing a GPT-like structure with a parameter count of up to 1B; 2) Introducing a spatiotemporal fine-tuning module, interpreting trajectories as collection of users to derive arbitrary region embedding. This framework allows rapid task development based on the large spatiotemporal model. We conducted extensive experiments to validate the effectiveness of our proposed large spatiotemporal model. It's evident that our proposed method, relying solely on human mobility data without additional features, exhibits a certain level of relevance in user profiling and region analysis. Moreover, our model showcases promising predictive capabilities in trajectory generation tasks based on the current state, offering the potential for further innovative work utilizing this large spatiotemporal model.

  • 6 authors
·
Nov 17, 2023

Uncertainty-Aware Longitudinal Forecasting of Alzheimer's Disease Progression Using Deep Learning

Longitudinal modelling of Alzheimer's disease progression is clinically useful only if it can describe not just the most likely next diagnosis, but how a patient may evolve over time and how reliable that forecast is. Most deep learning approaches reduce this problem to single-step classification, treating cognitively normal, mild cognitive impairment, and dementia as flat categories while providing limited insight into how uncertainty accumulates across future visits. We propose a probabilistic framework that combines ordinal diagnosis prediction, multi-horizon trajectory generation, and decomposed uncertainty estimation. A Temporal Fusion Transformer encoder is adapted with a CORAL ordinal output layer, asymmetric loss weighting, and converter oversampling to respect disease-stage ordering and improve sensitivity to MCI-to-dementia transitions. Conditioned on the learned patient-context representation, an autoregressive Mixture Density Network generates five-year probabilistic trajectories for diagnosis state, CDR Sum of Boxes, MMSE orientation, and hippocampal volume. On ADNI, the model outperforms linear, recurrent, and transformer baselines for next-visit diagnosis prediction, with the strongest gains on MCI-versus-dementia discrimination. Generated trajectories achieve near-nominal 90% credible interval coverage, widening uncertainty across the forecast horizon, and biomarker dynamics consistent with expected Alzheimer's disease progression. We further separate aleatoric from epistemic uncertainty using analytic mixture variance and a five-member bootstrap ensemble, which provides the strongest encoder diversity and output-level epistemic signal. Epistemic uncertainty is higher for rare progression archetypes, MCI and dementia patients, and under external evaluation on OASIS-3, where it increases alongside prediction error.

  • 3 authors
·
Jun 22

Chreode: A Cell World Model for One-Step Temporal Dynamics and Perturbation Prediction

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

  • 7 authors
·
May 26

Using Sequences of Life-events to Predict Human Lives

Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.

  • 8 authors
·
Jun 5, 2023

MentraSuite: Post-Training Large Language Models for Mental Health Reasoning and Assessment

Mental health disorders affect hundreds of millions globally, and the Web now serves as a primary medium for accessing support, information, and assessment. Large language models (LLMs) offer scalable and accessible assistance, yet their deployment in mental-health settings remains risky when their reasoning is incomplete, inconsistent, or ungrounded. Existing psychological LLMs emphasize emotional understanding or knowledge recall but overlook the step-wise, clinically aligned reasoning required for appraisal, diagnosis, intervention planning, abstraction, and verification. To address these issues, we introduce MentraSuite, a unified framework for advancing reliable mental-health reasoning. We propose MentraBench, a comprehensive benchmark spanning five core reasoning aspects, six tasks, and 13 datasets, evaluating both task performance and reasoning quality across five dimensions: conciseness, coherence, hallucination avoidance, task understanding, and internal consistency. We further present Mindora, a post-trained model optimized through a hybrid SFT-RL framework with an inconsistency-detection reward to enforce faithful and coherent reasoning. To support training, we construct high-quality trajectories using a novel reasoning trajectory generation strategy, that strategically filters difficult samples and applies a structured, consistency-oriented rewriting process to produce concise, readable, and well-balanced trajectories. Across 20 evaluated LLMs, Mindora achieves the highest average performance on MentraBench and shows remarkable performances in reasoning reliability, demonstrating its effectiveness for complex mental-health scenarios.

NextGenWhu CLAIN-WHU
·
Dec 10, 2025 2

Which Reasoning Trajectories Teach Students to Reason Better? A Simple Metric of Informative Alignment

Long chain-of-thought (CoT) trajectories provide rich supervision signals for distilling reasoning from teacher to student LLMs. However, both prior work and our experiments show that trajectories from stronger teachers do not necessarily yield better students, highlighting the importance of data-student suitability in distillation. Existing methods assess suitability primarily through student likelihood, favoring trajectories that closely align with the model's current behavior but overlooking more informative ones. Addressing this, we propose Rank-Surprisal Ratio (RSR), a simple metric that captures both alignment and informativeness to assess the suitability of a reasoning trajectory. RSR is motivated by the observation that effective trajectories typically combine low absolute probability with relatively high-ranked tokens under the student model, balancing learning signal strength and behavioral alignment. Concretely, RSR is defined as the ratio of a trajectory's average token-wise rank to its average negative log-likelihood, and is straightforward to compute and interpret. Across five student models and reasoning trajectories from 11 diverse teachers, RSR strongly correlates with post-training performance (average Spearman 0.86), outperforming existing metrics. We further demonstrate its practical utility in both trajectory selection and teacher selection.

PFGM++: Unlocking the Potential of Physics-Inspired Generative Models

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

  • 6 authors
·
Feb 8, 2023

Multi-marginal Schrödinger Bridges with Iterative Reference Refinement

Practitioners frequently aim to infer an unobserved population trajectory using sample snapshots at multiple time points. For instance, in single-cell sequencing, scientists would like to learn how gene expression evolves over time. But sequencing any cell destroys that cell. So we cannot access any cell's full trajectory, but we can access snapshot samples from many cells. Stochastic differential equations are commonly used to analyze systems with full individual-trajectory access; since here we have only sample snapshots, these methods are inapplicable. The deep learning community has recently explored using Schr\"odinger bridges (SBs) and their extensions to estimate these dynamics. However, these methods either (1) interpolate between just two time points or (2) require a single fixed reference dynamic within the SB, which is often just set to be Brownian motion. But learning piecewise from adjacent time points can fail to capture long-term dependencies. And practitioners are typically able to specify a model class for the reference dynamic but not the exact values of the parameters within it. So we propose a new method that (1) learns the unobserved trajectories from sample snapshots across multiple time points and (2) requires specification only of a class of reference dynamics, not a single fixed one. In particular, we suggest an iterative projection method inspired by Schr\"odinger bridges; we alternate between learning a piecewise SB on the unobserved trajectories and using the learned SB to refine our best guess for the dynamics within the reference class. We demonstrate the advantages of our method via a well-known simulated parametric model from ecology, simulated and real data from systems biology, and real motion-capture data.

  • 3 authors
·
Aug 12, 2024

TrajPrism: A Multi-Task Benchmark for Language-Grounded Urban Trajectory Understanding

Urban mobility is naturally expressed both as trajectories in space and as natural-language descriptions of travel intent, constraints, and preferences. However, prior work rarely evaluates these two modalities together on the same real-world trajectories: trajectory modeling often stays geometry-centric, while language-centric mobility benchmarks frequently target route planning and tool use rather than fine-grained, verifiable alignment between text and the underlying route. We introduce TrajPrism, a multi-task benchmark for language-trajectory alignment that unifies (i) instruction-conditioned trajectory generation, (ii) language-driven semantic trajectory retrieval, and (iii) trajectory captioning, together with an evaluation protocol that measures trajectory fidelity, retrieval quality, and language groundedness. We construct TrajPrism by pairing real urban trajectories with judge-filtered language annotations generated under a four-dimensional travel-intent taxonomy. The benchmark contains 300K selected trajectories across Porto, San Francisco, and Beijing, yielding 2.1M task instances from three instruction variants, three retrieval queries, and one caption per trajectory. We further develop proof-of-concept models for each task: TrajAnchor for instruction-conditioned trajectory generation, TrajFuse for semantic trajectory retrieval, and TrajRap for trajectory captioning. These models instantiate the proposed tasks and show that geometry-only trajectory baselines leave a large gap on our protocol, especially where language is part of the input-output interface. We release TrajPrism with code and a reproducible annotation pipeline that is designed to be portable across cities, given compatible trajectory inputs and map resources.

  • 9 authors
·
May 10

Progress Reward Modeling for Robotic Learning: A Comprehensive Survey

Robotic learning takes place in dynamic environments with large behavior spaces. A terminal success signal only tells the robot whether the task is completed. It does not explain whether the current behavior is making progress, remaining unchanged, or undoing earlier progress. For this reason, recent studies have increasingly explored progress rewards that provide feedback during task execution. However, the current literature lacks a shared framework. Existing methods use different observations, goal specifications, output signals, supervision sources, and evaluation protocols. This makes it difficult to compare them and understand what their results actually validate. In this survey, we provide a unified view of progress reward modeling for robotic learning. We organize the field in three connected steps. We first study the interface of a progress model. This defines the problem from the outside by asking what information the model receives and what form of progress signal it produces. We then move inside the model and study the methods used to construct this signal. This reveals the different assumptions and mechanisms behind progress estimation and reward generation. Finally, we examine the data and benchmarks that support these methods. This shows how progress supervision is obtained and what different evaluations actually measure. Together, these three perspectives connect what a progress model is, how it is built, and how its quality is validated. We further summarize the main limitations of current approaches and discuss future research directions.

PIE: Simulating Disease Progression via Progressive Image Editing

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

  • 6 authors
·
Sep 20, 2023 1

A Vocabulary for Multi-Agent Automated Research Systems

We introduce a vocabulary for automated research systems built from one or more agents to make their design choices easier to describe and compare. The vocabulary specifies 1) who the agents are, 2) what operations are available in the system, 3) who may invoke them, 4) how agents communicate, 5) what information is visible within and across runs, 6) how the next action is chosen, 7) how a run begins, and 8) how outputs are evaluated. A trajectory records one run from the input task to the returned artifact. Because agents, operations, and initialization may be stochastic, repeated runs on the same task induce a distribution over trajectories rather than a single behavior. Our vocabulary turns structural design questions, such as when agents should communicate, gain or lose a capability, or carry information across runs, into testable choices. It also makes the evaluator a component of the system, since reported gains depend on how closely the proxy score matches true quality. That separation also splits the vague complaint that these systems lack taste into two failures with different solutions. Generative taste is the rate at which a system proposes novel trajectories before any score is observed, and evaluative taste is the gap between the proxy score and the quality it should match. We instantiate the vocabulary on recent autoresearch systems to illustrate that it covers designs that differ widely in structure.

  • 1 authors
·
Jul 12 2

Reasoning Models Don't Just Think Longer, They Move Differently

Reasoning-trained language models often spend more tokens on harder problems, but longer chains of thought do not show whether a model is merely computing for more steps or following a different internal trajectory. We study this distinction through hidden-state trajectories during chain-of-thought generation across competitive programming, mathematics, and Boolean satisfiability. Raw trajectory geometry is strongly shaped by generation length: longer generations mechanically alter path statistics, so difficulty-dependent comparisons are misleading without adjustment. After residualizing trajectory statistics on length, difficulty remains systematically coupled to corrected trajectory geometry across all domains studied. The clearest reasoning-specific separation appears in the code domain, where harder problems show more direct corrected trajectories and less heterogeneous local curvature in reasoning-trained models than in matched instruction-tuned baselines. Corrected difficulty-geometry coupling is weaker, but still present, in mathematics and Boolean satisfiability. Prompt-stage linear probes do not mirror the code-domain separation, and behavioral annotations show that stronger corrected coupling co-occurs with strategy shifts and uncertainty monitoring. Together, these findings establish length correction as a prerequisite for generation-time trajectory analysis and show that reasoning training can be associated with distinct corrected trajectory geometry, with the strength of the effect depending on the domain.

  • 3 authors
·
May 13

Student-in-the-Loop Chain-of-Thought Distillation via Generation-Time Selection

Large reasoning models achieve strong performance on complex tasks through long chain-of-thought (CoT) trajectories, but directly transferring such reasoning processes to smaller models remains challenging. A key difficulty is that not all teacher-generated reasoning trajectories are suitable for student learning. Existing approaches typically rely on post-hoc filtering, selecting trajectories after full generation based on heuristic criteria. However, such methods cannot control the generation process itself and may still produce reasoning paths that lie outside the student's learning capacity. To address this limitation, we propose Gen-SSD (Generation-time Self-Selection Distillation), a student-in-the-loop framework that performs generation-time selection. Instead of passively consuming complete trajectories, the student evaluates candidate continuations during the teacher's sampling process, guiding the expansion of only learnable reasoning paths and enabling early pruning of unhelpful branches. Experiments on mathematical reasoning benchmarks demonstrate that Gen-SSD consistently outperforms standard knowledge distillation and recent baselines, with improvements of around 5.9 points over Standard KD and up to 4.7 points over other baselines. Further analysis shows that Gen-SSD produces more stable and learnable reasoning trajectories, highlighting the importance of incorporating supervision during generation for effective distillation.

  • 5 authors
·
Apr 2

Progression as Latent Drift: Generative Forecasting of Slow-Evolving Pathologies

Forecasting the future anatomy of slow-evolving neurodegenerative diseases could enable earlier, more targeted intervention and improve clinical trial design, but it remains challenging because true progression signals are subtle in longitudinal MRI. In this low-signal regime, transferring modern generative sequence models directly is unreliable: training is dominated by stable baseline anatomy and confounded by dense, sample-specific nuisance variation. We first provide a theoretical analysis that explains these failures through two modes. Identity collapse occurs when optimization is driven toward reproducing the current anatomy, which prevents the model from learning faint temporal change. The continuous interpolation trap arises when standard smooth networks cannot separate localized biological drift from pervasive noise, which leads to spurious changes that diffuse across the volume. To address both issues, we propose Latent Drift, a progressive generative framework that learns change in a compressed semantic representation rather than synthesizing full-resolution anatomy. This design removes pixel-level identity from the prediction target and concentrates model capacity on progression-relevant dynamics. We further apply Finite Scalar Quantization to the learned change representation, which suppresses small, high-frequency nuisance fluctuations while preserving consistent structural drift. Experiments on longitudinal 3D brain MRI show that Latent Drift improves patient-specific neuro-forecasting over diffusion and autoregressive transformer baselines across generative fidelity and clinically relevant evaluation metrics. Project page: https://cutepkq.github.io/latent-drift{https://cutepkq.github.io/latent-drift}.

  • 10 authors
·
Jul 8

Latent Traversals in Generative Models as Potential Flows

Despite the significant recent progress in deep generative models, the underlying structure of their latent spaces is still poorly understood, thereby making the task of performing semantically meaningful latent traversals an open research challenge. Most prior work has aimed to solve this challenge by modeling latent structures linearly, and finding corresponding linear directions which result in `disentangled' generations. In this work, we instead propose to model latent structures with a learned dynamic potential landscape, thereby performing latent traversals as the flow of samples down the landscape's gradient. Inspired by physics, optimal transport, and neuroscience, these potential landscapes are learned as physically realistic partial differential equations, thereby allowing them to flexibly vary over both space and time. To achieve disentanglement, multiple potentials are learned simultaneously, and are constrained by a classifier to be distinct and semantically self-consistent. Experimentally, we demonstrate that our method achieves both more qualitatively and quantitatively disentangled trajectories than state-of-the-art baselines. Further, we demonstrate that our method can be integrated as a regularization term during training, thereby acting as an inductive bias towards the learning of structured representations, ultimately improving model likelihood on similarly structured data.

  • 4 authors
·
Apr 25, 2023

Monitoring the Internal Monologue: Probe Trajectories Reveal Reasoning Dynamics

Large Reasoning Models (LRMs) introduce new opportunities for safety monitoring through their Chain of Thought (CoT) reasoning. However, CoT is not always faithful to the model's final output, undermining its reliability as a monitoring tool. To address this, we investigate the hidden representations of LRMs to determine whether future behavior can be predicted from prompt and CoT representations. By evaluating a probe at each generated token, we construct a probe trajectory, the continuous evolution of a concept's probability across the reasoning process. We find that future model behavior is more distinguishable when examined over the full trajectory than from a single static prediction. To characterize these temporal dynamics, we extract signal-processing features that capture volatility, trend, and steady-state behavior, significantly improving the separation of future model states. We also present two methodological insights. First, template-based training data achieves near-parity with dynamically generated model responses, eliminating the need for a costly initial inference and labeling. Second, the choice of pooling operation is critical: average-pooling and last-token methods collapse to near-random performance, while max-pooling achieves up to 95% AUROC and yields stable probe trajectories. Using four datasets and four reasoning models across the domains of safety and mathematics, we demonstrate that trajectory features encode task-specific dynamics that improve outcome separability. These findings establish probe trajectories as a complementary framework for monitoring LRM behavior. Warning: This article contains potentially harmful content.

  • 5 authors
·
May 17 1

SE-Agent: Self-Evolution Trajectory Optimization in Multi-Step Reasoning with LLM-Based Agents

Large Language Model (LLM)-based agents have recently shown impressive capabilities in complex reasoning and tool use via multi-step interactions with their environments. While these agents have the potential to tackle complicated tasks, their problem-solving process, i.e., agents' interaction trajectory leading to task completion, remains underexploited. These trajectories contain rich feedback that can navigate agents toward the right directions for solving problems correctly. Although prevailing approaches, such as Monte Carlo Tree Search (MCTS), can effectively balance exploration and exploitation, they ignore the interdependence among various trajectories and lack the diversity of search spaces, which leads to redundant reasoning and suboptimal outcomes. To address these challenges, we propose SE-Agent, a Self-Evolution framework that enables Agents to optimize their reasoning processes iteratively. Our approach revisits and enhances former pilot trajectories through three key operations: revision, recombination, and refinement. This evolutionary mechanism enables two critical advantages: (1) it expands the search space beyond local optima by intelligently exploring diverse solution paths guided by previous trajectories, and (2) it leverages cross-trajectory inspiration to efficiently enhance performance while mitigating the impact of suboptimal reasoning paths. Through these mechanisms, SE-Agent achieves continuous self-evolution that incrementally improves reasoning quality. We evaluate SE-Agent on SWE-bench Verified to resolve real-world GitHub issues. Experimental results across five strong LLMs show that integrating SE-Agent delivers up to 55% relative improvement, achieving state-of-the-art performance among all open-source agents on SWE-bench Verified. Our code and demonstration materials are publicly available at https://github.com/JARVIS-Xs/SE-Agent.

QuantaAlpha QuantaAlpha
·
Aug 4, 2025

An Interdisciplinary Comparison of Sequence Modeling Methods for Next-Element Prediction

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

  • 3 authors
·
Oct 31, 2018

TrajDLM: Topology-Aware Block Diffusion Language Model for Trajectory Generation

Generating high-fidelity synthetic GPS trajectories is increasingly important for applications in transportation, urban planning, and what-if scenario simulation, especially as privacy concerns limit access to real-world mobility data. Existing trajectory generation models face a trade-off between efficiency and faithfulness to road network topology: continuous-space methods enable fast generation but ignore the road network, while topology-aware approaches rely on search-based autoregressive decoding that limits generation speed. We propose TrajDLM, a topology-aware trajectory generation framework based on block diffusion language models that bridges this gap. TrajDLM models trajectories as sequences of discrete road segments, combining a block diffusion backbone for efficient denoising, topology-aware embeddings from a road network encoder, and topology-constrained sampling to ensure coherent and realistic trajectories. Across three city-scale datasets, TrajDLM achieves strong performance on fine-grained local similarity metrics while being up to 2.8times faster than prior work, and demonstrates strong zero-shot transfer across domains, including unseen transportation modes. These results highlight the effectiveness of block-wise discrete diffusion as a scalable approach to accurate and efficient trajectory generation. Our code is available at https://github.com/cruiseresearchgroup/TrajDLM/

Unlocking Implicit Experience: Synthesizing Tool-Use Trajectories from Text

Enabling Large Language Models (LLMs) to effectively utilize tools in multi-turn interactions is essential for building capable autonomous agents. However, acquiring diverse and realistic multi-turn tool-use data remains a significant challenge. In this work, we propose a novel text-based paradigm. We observe that textual corpora naturally contain rich, multi-step problem-solving experiences, which can serve as an untapped, scalable, and authentic data source for multi-turn tool-use tasks. Based on this insight, we introduce GEM, a data synthesis pipeline that enables the generation and extraction of multi-turn tool-use trajectories from text corpora through a four-stage process: relevance filtering, workflow & tool extraction, trajectory grounding, and complexity refinement. To reduce the computational cost, we further train a specialized Trajectory Synthesizer via supervised fine-tuning. This model distills the complex generation pipeline into an efficient, end-to-end trajectory generator. Experiments demonstrate that our GEM-32B achieve a 16.5% improvement on the BFCL V3 Multi-turn benchmark. Our models partially surpass the performance of models trained on τ - bench (Airline and Retail) in-domain data, highlighting the superior generalization capability derived from our text-based synthesis paradigm. Notably, our Trajectory Synthesizer matches the quality of the full pipeline while significantly reducing inference latency and costs.

meituan-longcat LongCat
·
Jan 15 4

Envisioning the Future, One Step at a Time

Accurately anticipating how complex, diverse scenes will evolve requires models that represent uncertainty, simulate along extended interaction chains, and efficiently explore many plausible futures. Yet most existing approaches rely on dense video or latent-space prediction, expending substantial capacity on dense appearance rather than on the underlying sparse trajectories of points in the scene. This makes large-scale exploration of future hypotheses costly and limits performance when long-horizon, multi-modal motion is essential. We address this by formulating the prediction of open-set future scene dynamics as step-wise inference over sparse point trajectories. Our autoregressive diffusion model advances these trajectories through short, locally predictable transitions, explicitly modeling the growth of uncertainty over time. This dynamics-centric representation enables fast rollout of thousands of diverse futures from a single image, optionally guided by initial constraints on motion, while maintaining physical plausibility and long-range coherence. We further introduce OWM, a benchmark for open-set motion prediction based on diverse in-the-wild videos, to evaluate accuracy and variability of predicted trajectory distributions under real-world uncertainty. Our method matches or surpasses dense simulators in predictive accuracy while achieving orders-of-magnitude higher sampling speed, making open-set future prediction both scalable and practical. Project page: http://compvis.github.io/myriad.

CompVis CompVis
·
Apr 9 2

ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images

Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains challenging due to high dimensionality, irregular sampling, and data sparsity. To address these issues, we propose ImageFlowNet, a novel model designed to forecast disease trajectories from initial images while preserving spatial details. ImageFlowNet first learns multiscale joint representation spaces across patients and time points, then optimizes deterministic or stochastic flow fields within these spaces using a position-parameterized neural ODE/SDE framework. The model leverages a UNet architecture to create robust multiscale representations and mitigates data scarcity by combining knowledge from all patients. We provide theoretical insights that support our formulation of ODEs, and motivate our regularizations involving high-level visual features, latent space organization, and trajectory smoothness. We validate ImageFlowNet on three longitudinal medical image datasets depicting progression in geographic atrophy, multiple sclerosis, and glioblastoma, demonstrating its ability to effectively forecast disease progression and outperform existing methods. Our contributions include the development of ImageFlowNet, its theoretical underpinnings, and empirical validation on real-world datasets. The official implementation is available at https://github.com/KrishnaswamyLab/ImageFlowNet.

  • 11 authors
·
Jun 20, 2024

Progressive Pretext Task Learning for Human Trajectory Prediction

Human trajectory prediction is a practical task of predicting the future positions of pedestrians on the road, which typically covers all temporal ranges from short-term to long-term within a trajectory. However, existing works attempt to address the entire trajectory prediction with a singular, uniform training paradigm, neglecting the distinction between short-term and long-term dynamics in human trajectories. To overcome this limitation, we introduce a novel Progressive Pretext Task learning (PPT) framework, which progressively enhances the model's capacity of capturing short-term dynamics and long-term dependencies for the final entire trajectory prediction. Specifically, we elaborately design three stages of training tasks in the PPT framework. In the first stage, the model learns to comprehend the short-term dynamics through a stepwise next-position prediction task. In the second stage, the model is further enhanced to understand long-term dependencies through a destination prediction task. In the final stage, the model aims to address the entire future trajectory task by taking full advantage of the knowledge from previous stages. To alleviate the knowledge forgetting, we further apply a cross-task knowledge distillation. Additionally, we design a Transformer-based trajectory predictor, which is able to achieve highly efficient two-step reasoning by integrating a destination-driven prediction strategy and a group of learnable prompt embeddings. Extensive experiments on popular benchmarks have demonstrated that our proposed approach achieves state-of-the-art performance with high efficiency. Code is available at https://github.com/iSEE-Laboratory/PPT.

  • 4 authors
·
Jul 16, 2024

Towards Early Prediction of Human iPSC Reprogramming Success

This paper presents advancements in automated early-stage prediction of the success of reprogramming human induced pluripotent stem cells (iPSCs) as a potential source for regenerative cell therapies.The minuscule success rate of iPSC-reprogramming of around 0.01% to 0.1% makes it labor-intensive, time-consuming, and exorbitantly expensive to generate a stable iPSC line. Since that requires culturing of millions of cells and intense biological scrutiny of multiple clones to identify a single optimal clone. The ability to reliably predict which cells are likely to establish as an optimal iPSC line at an early stage of pluripotency would therefore be ground-breaking in rendering this a practical and cost-effective approach to personalized medicine. Temporal information about changes in cellular appearance over time is crucial for predicting its future growth outcomes. In order to generate this data, we first performed continuous time-lapse imaging of iPSCs in culture using an ultra-high resolution microscope. We then annotated the locations and identities of cells in late-stage images where reliable manual identification is possible. Next, we propagated these labels backwards in time using a semi-automated tracking system to obtain labels for early stages of growth. Finally, we used this data to train deep neural networks to perform automatic cell segmentation and classification. Our code and data are available at https://github.com/abhineet123/ipsc_prediction.

  • 6 authors
·
May 23, 2023

Disentangling the Factors of Convergence between Brains and Computer Vision Models

Many AI models trained on natural images develop representations that resemble those of the human brain. However, the factors that drive this brain-model similarity remain poorly understood. To disentangle how the model, training and data independently lead a neural network to develop brain-like representations, we trained a family of self-supervised vision transformers (DINOv3) that systematically varied these different factors. We compare their representations of images to those of the human brain recorded with both fMRI and MEG, providing high resolution in spatial and temporal analyses. We assess the brain-model similarity with three complementary metrics focusing on overall representational similarity, topographical organization, and temporal dynamics. We show that all three factors - model size, training amount, and image type - independently and interactively impact each of these brain similarity metrics. In particular, the largest DINOv3 models trained with the most human-centric images reach the highest brain-similarity. This emergence of brain-like representations in AI models follows a specific chronology during training: models first align with the early representations of the sensory cortices, and only align with the late and prefrontal representations of the brain with considerably more training. Finally, this developmental trajectory is indexed by both structural and functional properties of the human cortex: the representations that are acquired last by the models specifically align with the cortical areas with the largest developmental expansion, thickness, least myelination, and slowest timescales. Overall, these findings disentangle the interplay between architecture and experience in shaping how artificial neural networks come to see the world as humans do, thus offering a promising framework to understand how the human brain comes to represent its visual world.

  • 8 authors
·
Aug 25, 2025

ProcVLM: Learning Procedure-Grounded Progress Rewards for Robotic Manipulation

Long-horizon robotic manipulation requires dense feedback that reflects how a task advances through its procedural stages, not merely whether the final outcome is successful. Existing reward models often rely on trajectory-level success labels or time-based interpolation, which can conflate elapsed time with true task progress and therefore fail to capture unfinished steps, stagnation, and failure states. We present ProcVLM, a progress-aware vision-language model that learns procedure-grounded progress as a dense reward signal for manipulation. Rather than deriving progress from terminal outcomes or temporal proxies, ProcVLM grounds progress estimation in procedural structure and intra-stage visual change, and further adopts a reasoning-before-estimation paradigm that infers the remaining atomic actions before estimating task progress. Specifically, we construct this supervision by synthesizing frame-level subtask-semantic annotations, assigning progress budgets according to subtask structure, and distributing each budget based on intra-subtask visual change. To train ProcVLM at scale, we build a standardized procedural supervision synthesis pipeline and construct ProcCorpus-60M from 30 embodied datasets with 60M annotated frames, from which we derive ProcVQA for procedure-aware pretraining, with progress estimation as the central task alongside action segmentation and future planning. Experiments on ProcVQA and reward-model benchmarks show that ProcVLM improves embodied procedural reasoning and yields more discriminative trajectory-internal progress estimates than representative baselines, supporting its use as a dense reward model for downstream reward-guided policy optimization. Project page: https://procvlm.github.io/

  • 10 authors
·
May 8

OS-Genesis: Automating GUI Agent Trajectory Construction via Reverse Task Synthesis

Graphical User Interface (GUI) agents powered by Vision-Language Models (VLMs) have demonstrated human-like computer control capability. Despite their utility in advancing digital automation, a critical bottleneck persists: collecting high-quality trajectory data for training. Common practices for collecting such data rely on human supervision or synthetic data generation through executing pre-defined tasks, which are either resource-intensive or unable to guarantee data quality. Moreover, these methods suffer from limited data diversity and significant gaps between synthetic data and real-world environments. To address these challenges, we propose OS-Genesis, a novel GUI data synthesis pipeline that reverses the conventional trajectory collection process. Instead of relying on pre-defined tasks, OS-Genesis enables agents first to perceive environments and perform step-wise interactions, then retrospectively derive high-quality tasks to enable trajectory-level exploration. A trajectory reward model is then employed to ensure the quality of the generated trajectories. We demonstrate that training GUI agents with OS-Genesis significantly improves their performance on highly challenging online benchmarks. In-depth analysis further validates OS-Genesis's efficiency and its superior data quality and diversity compared to existing synthesis methods. Our codes, data, and checkpoints are available at https://qiushisun.github.io/OS-Genesis-Home/{OS-Genesis Homepage}.

  • 15 authors
·
Dec 27, 2024 4

Trajectory Forcing: Structure-First Generation with Controllable Semantic Trajectories

Diffusion and flow-based generative models produce strong images, yet their controllability remains largely endpoint-centric: users specify conditions and receive final outputs, while the intermediate generative dynamics remain hidden. Recent methods have begun to exploit generation order and process decomposition to improve sample quality, but still treat intermediate states as internal computation rather than objects for interaction. We propose Trajectory Forcing (TF), a trajectory-centric framework that makes the generation path explicit, semantic, and editable. TF organizes synthesis as a sequence of semantically structured stages, progressing from global layout to object-, part-, and detail-level representations. Each stage produces a decodable latent state that can be inspected, evaluated, and locally edited before the next stage begins. To instantiate this path, we derive coarse-to-fine teacher hierarchies by clustering pretrained visual representations such as DINOv2, and train a hierarchy-conditioned one-step flow-matching model at each level. We further introduce trajectory-aware metrics that measure structural consistency and local controllability beyond endpoint quality metrics such as FID. Experiments show that TF achieves competitive sample quality while exposing coherent intermediate states and supporting localized edits across semantic levels. By shifting the focus from final images to the generative path itself, TF opens a route toward controllable, trajectory-aware image synthesis.

  • 4 authors
·
Jun 20

TrajBooster: Boosting Humanoid Whole-Body Manipulation via Trajectory-Centric Learning

Recent Vision-Language-Action models show potential to generalize across embodiments but struggle to quickly align with a new robot's action space when high-quality demonstrations are scarce, especially for bipedal humanoids. We present TrajBooster, a cross-embodiment framework that leverages abundant wheeled-humanoid data to boost bipedal VLA. Our key idea is to use end-effector trajectories as a morphology-agnostic interface. TrajBooster (i) extracts 6D dual-arm end-effector trajectories from real-world wheeled humanoids, (ii) retargets them in simulation to Unitree G1 with a whole-body controller trained via a heuristic-enhanced harmonized online DAgger to lift low-dimensional trajectory references into feasible high-dimensional whole-body actions, and (iii) forms heterogeneous triplets that couple source vision/language with target humanoid-compatible actions to post-pre-train a VLA, followed by only 10 minutes of teleoperation data collection on the target humanoid domain. Deployed on Unitree G1, our policy achieves beyond-tabletop household tasks, enabling squatting, cross-height manipulation, and coordinated whole-body motion with markedly improved robustness and generalization. Results show that TrajBooster allows existing wheeled-humanoid data to efficiently strengthen bipedal humanoid VLA performance, reducing reliance on costly same-embodiment data while enhancing action space understanding and zero-shot skill transfer capabilities. For more details, For more details, please refer to our https://jiachengliu3.github.io/TrajBooster/.

  • 11 authors
·
Sep 15, 2025

Trajectory Geometry of Transformer Representations Across Layers

Understanding how transformer representations evolve across layers, not merely what they encode, remains an open problem in mechanistic interpretability. We recast the transformer forward pass as a discrete population trajectory through a high-dimensional representation manifold, drawing on geometric tools from computational neuroscience. Rather than probing for pre-specified features, we characterize trajectory geometry using five metrics computed directly in the ambient space: trajectory length, curvature, a semantic convergence index, layerwise cosine similarity, and representational stability. Across three model families (GPT-2, TinyLlama, Qwen2.5) and five controlled prompt families, we report four findings. First, semantically related prompts converge significantly in middle-to-late layers (peak CI 0.41--0.58, p<0.001, Mann-Whitney U), consistent with attractor-like dynamics. Second, reasoning tasks produce trajectories of greater curvature than lexical variations (0.71--0.83 rad vs. 0.27--0.31 rad), suggesting curvature encodes computational complexity. Third, ambiguous tokens exhibit trajectory bifurcation with up to 5.6x representational separation by the final layer, absent in unambiguous controls. Fourth, layerwise cosine similarity reveals a universal three-phase structure: encoding, elaboration, and output preparation, consistent across all three architectures. All four effects vanish under shuffled-layer and random-embedding controls. We release a fully open-source, model-agnostic pipeline and argue that trajectory geometry constitutes a principled, probe-free lens for mechanistic interpretability.

  • 3 authors
·
Jun 9

TraceVision: Trajectory-Aware Vision-Language Model for Human-Like Spatial Understanding

Recent Large Vision-Language Models (LVLMs) demonstrate remarkable capabilities in image understanding and natural language generation. However, current approaches focus predominantly on global image understanding, struggling to simulate human visual attention trajectories and explain associations between descriptions and specific regions. We propose TraceVision, a unified vision-language model integrating trajectory-aware spatial understanding in an end-to-end framework. TraceVision employs a Trajectory-aware Visual Perception (TVP) module for bidirectional fusion of visual features and trajectory information. We design geometric simplification to extract semantic keypoints from raw trajectories and propose a three-stage training pipeline where trajectories guide description generation and region localization. We extend TraceVision to trajectory-guided segmentation and video scene understanding, enabling cross-frame tracking and temporal attention analysis. We construct the Reasoning-based Interactive Localized Narratives (RILN) dataset to enhance logical reasoning and interpretability. Extensive experiments on trajectory-guided captioning, text-guided trajectory prediction, understanding, and segmentation demonstrate that TraceVision achieves state-of-the-art performance, establishing a foundation for intuitive spatial interaction and interpretable visual understanding.

  • 8 authors
·
Feb 23

EigenTrajectory: Low-Rank Descriptors for Multi-Modal Trajectory Forecasting

Capturing high-dimensional social interactions and feasible futures is essential for predicting trajectories. To address this complex nature, several attempts have been devoted to reducing the dimensionality of the output variables via parametric curve fitting such as the B\'ezier curve and B-spline function. However, these functions, which originate in computer graphics fields, are not suitable to account for socially acceptable human dynamics. In this paper, we present EigenTrajectory (ET), a trajectory prediction approach that uses a novel trajectory descriptor to form a compact space, known here as ET space, in place of Euclidean space, for representing pedestrian movements. We first reduce the complexity of the trajectory descriptor via a low-rank approximation. We transform the pedestrians' history paths into our ET space represented by spatio-temporal principle components, and feed them into off-the-shelf trajectory forecasting models. The inputs and outputs of the models as well as social interactions are all gathered and aggregated in the corresponding ET space. Lastly, we propose a trajectory anchor-based refinement method to cover all possible futures in the proposed ET space. Extensive experiments demonstrate that our EigenTrajectory predictor can significantly improve both the prediction accuracy and reliability of existing trajectory forecasting models on public benchmarks, indicating that the proposed descriptor is suited to represent pedestrian behaviors. Code is publicly available at https://github.com/inhwanbae/EigenTrajectory .

  • 3 authors
·
Jul 18, 2023

'Explaining RL Decisions with Trajectories': A Reproducibility Study

This work investigates the reproducibility of the paper 'Explaining RL decisions with trajectories'. The original paper introduces a novel approach in explainable reinforcement learning based on the attribution decisions of an agent to specific clusters of trajectories encountered during training. We verify the main claims from the paper, which state that (i) training on less trajectories induces a lower initial state value, (ii) trajectories in a cluster present similar high-level patterns, (iii) distant trajectories influence the decision of an agent, and (iv) humans correctly identify the attributed trajectories to the decision of the agent. We recover the environments used by the authors based on the partial original code they provided for one of the environments (Grid-World), and implemented the remaining from scratch (Seaquest, HalfCheetah, Breakout and Q*Bert). While we confirm that (i), (ii), and (iii) partially hold, we extend on the largely qualitative experiments from the authors by introducing a quantitative metric to further support (iii), and new experiments and visual results for (i). Moreover, we investigate the use of different clustering algorithms and encoder architectures to further support (ii). We could not support (iv), given the limited extent of the original experiments. We conclude that, while some of the claims can be supported, further investigations and experiments could be of interest. We recognise the novelty of the work from the authors and hope that our work paves the way for clearer and more transparent approaches.

  • 4 authors
·
Nov 11, 2024

DoTime: A Synthetic Benchmark Generator for Interventional and Counterfactual Time Series

Most benchmarks for causal inference over time series are observational, small, or domain-specific, leaving interventional and counterfactual estimation under-served exactly where it matters most, such as in healthcare, policy evaluation, and climate science. We introduce DoTime, an open, scalable, and theoretically grounded generator of multivariate temporal structural causal models (TSCMs) with interventions, released as the dotime PyPI package together with four frozen evaluation suites. Beyond existing work, it adds capabilities absent from prior generators: continuous-time intervention windows, counterfactual sampling modes with a positivity guard, regime-switching SCMs as a strict generalization of interrupted time series, non-stationary dynamics by construction with switching SCM parameters, and deterministic ramp and sinusoidal intervention profiles that place trends and structural breaks inside the evaluation window. Moreover, it demonstrates the suitability of the generator as a prior for a causal foundation model reference implementation. The released suites span a training-scale snapshot of 100{,}000 trajectories and eight named identification structures, each with exact ground truth: paired interventional trajectories from the same SCM throughout, and shared-noise counterfactuals in the continuous-time suite. We ship reference baseline implementations with an evaluation harness, and pose a falsifiable claim: interventional training buys a measurable direction-accuracy advantage over an observational model of identical capacity. It is tested across three training seeds per arm. Under structure-matched evaluation on held-out episodes, the interventional prior-fitted network's (PFN) gap is positive in every structure, trajectory length, and seed tested.

  • 3 authors
·
Jul 28

Toward Physically Consistent Driving Video World Models under Challenging Trajectories

Video generation models have shown strong potential as world models for autonomous driving simulation. However, existing approaches are primarily trained on real-world driving datasets, which mostly contain natural and safe driving scenarios. As a result, current models often fail when conditioned on challenging or counterfactual trajectories-such as imperfect trajectories generated by simulators or planning systems-producing videos with severe physical inconsistencies and artifacts. To address this limitation, we propose PhyGenesis, a world model designed to generate driving videos with high visual fidelity and strong physical consistency. Our framework consists of two key components: (1) a physical condition generator that transforms potentially invalid trajectory inputs into physically plausible conditions, and (2) a physics-enhanced video generator that produces high-fidelity multi-view driving videos under these conditions. To effectively train these components, we construct a large-scale, physics-rich heterogeneous dataset. Specifically, in addition to real-world driving videos, we generate diverse challenging driving scenarios using the CARLA simulator, from which we derive supervision signals that guide the model to learn physically grounded dynamics under extreme conditions. This challenging-trajectory learning strategy enables trajectory correction and promotes physically consistent video generation. Extensive experiments demonstrate that PhyGenesis consistently outperforms state-of-the-art methods, especially on challenging trajectories. Our project page is available at: https://wm-research.github.io/PhyGenesis/.

  • 13 authors
·
Mar 25 2

Generating the Traces You Need: A Conditional Generative Model for Process Mining Data

In recent years, trace generation has emerged as a significant challenge within the Process Mining community. Deep Learning (DL) models have demonstrated accuracy in reproducing the features of the selected processes. However, current DL generative models are limited in their ability to adapt the learned distributions to generate data samples based on specific conditions or attributes. This limitation is particularly significant because the ability to control the type of generated data can be beneficial in various contexts, enabling a focus on specific behaviours, exploration of infrequent patterns, or simulation of alternative 'what-if' scenarios. In this work, we address this challenge by introducing a conditional model for process data generation based on a conditional variational autoencoder (CVAE). Conditional models offer control over the generation process by tuning input conditional variables, enabling more targeted and controlled data generation. Unlike other domains, CVAE for process mining faces specific challenges due to the multiperspective nature of the data and the need to adhere to control-flow rules while ensuring data variability. Specifically, we focus on generating process executions conditioned on control flow and temporal features of the trace, allowing us to produce traces for specific, identified sub-processes. The generated traces are then evaluated using common metrics for generative model assessment, along with additional metrics to evaluate the quality of the conditional generation

  • 8 authors
·
Nov 4, 2024

Enhancing Spatiotemporal Disease Progression Models via Latent Diffusion and Prior Knowledge

In this work, we introduce Brain Latent Progression (BrLP), a novel spatiotemporal disease progression model based on latent diffusion. BrLP is designed to predict the evolution of diseases at the individual level on 3D brain MRIs. Existing deep generative models developed for this task are primarily data-driven and face challenges in learning disease progressions. BrLP addresses these challenges by incorporating prior knowledge from disease models to enhance the accuracy of predictions. To implement this, we propose to integrate an auxiliary model that infers volumetric changes in various brain regions. Additionally, we introduce Latent Average Stabilization (LAS), a novel technique to improve spatiotemporal consistency of the predicted progression. BrLP is trained and evaluated on a large dataset comprising 11,730 T1-weighted brain MRIs from 2,805 subjects, collected from three publicly available, longitudinal Alzheimer's Disease (AD) studies. In our experiments, we compare the MRI scans generated by BrLP with the actual follow-up MRIs available from the subjects, in both cross-sectional and longitudinal settings. BrLP demonstrates significant improvements over existing methods, with an increase of 22% in volumetric accuracy across AD-related brain regions and 43% in image similarity to the ground-truth scans. The ability of BrLP to generate conditioned 3D scans at the subject level, along with the novelty of integrating prior knowledge to enhance accuracy, represents a significant advancement in disease progression modeling, opening new avenues for precision medicine. The code of BrLP is available at the following link: https://github.com/LemuelPuglisi/BrLP.

  • 3 authors
·
May 6, 2024

Geometric Trajectory Diffusion Models

Generative models have shown great promise in generating 3D geometric systems, which is a fundamental problem in many natural science domains such as molecule and protein design. However, existing approaches only operate on static structures, neglecting the fact that physical systems are always dynamic in nature. In this work, we propose geometric trajectory diffusion models (GeoTDM), the first diffusion model for modeling the temporal distribution of 3D geometric trajectories. Modeling such distribution is challenging as it requires capturing both the complex spatial interactions with physical symmetries and temporal correspondence encapsulated in the dynamics. We theoretically justify that diffusion models with equivariant temporal kernels can lead to density with desired symmetry, and develop a novel transition kernel leveraging SE(3)-equivariant spatial convolution and temporal attention. Furthermore, to induce an expressive trajectory distribution for conditional generation, we introduce a generalized learnable geometric prior into the forward diffusion process to enhance temporal conditioning. We conduct extensive experiments on both unconditional and conditional generation in various scenarios, including physical simulation, molecular dynamics, and pedestrian motion. Empirical results on a wide suite of metrics demonstrate that GeoTDM can generate realistic geometric trajectories with significantly higher quality.

  • 5 authors
·
Oct 16, 2024

SADM: Sequence-Aware Diffusion Model for Longitudinal Medical Image Generation

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

  • 5 authors
·
Dec 15, 2022

Measuring What the Crawler Sees: Discovery Curves, Core Persistence, and Shell Dynamics in Longitudinal Web Crawls

A longitudinal web crawl is a sequence of partial samples of an evolving URL population. Pairwise containment between two crawls is the standard probe; under a simple urn model of the crawl -- each round samples a fraction of the URLs and replaces a fraction -- it recovers two interpretable rates, per-round survival α and coverage c, but treats the population as uniform and consumes one pair at a time. In this work, we define a formal language for talking about a crawl. We extend this analysis with the discovery curve U(s, T), the cumulative URL footprint over a sliding window of T crawls starting at s, which under the same urn model is also a closed-form function of (α, c). Containment and the discovery curve are then two projections of one process: independent fits agree on (α, c) when the urn is homogeneous, so any disagreement is itself a measurement. Applied to Common Crawl (2020--2025, domain granularity) and to the German Academic Web (GAW, URL granularity), the two projections disagree on both archives, and a two-component urn with a persistent core fraction κ alongside shell parameters (α_partial, c_partial) reconciles the disagreement. A residual on c_partial remains, signaling that the shell itself is not homogeneous; κ is recorded as the scalar entry point to a rank-resolved generalization, which is left to follow-up work. web archive \and crawl coverage \and discovery curve \and urn model \and two-component model \and URL lifetime

  • 3 authors
·
Jul 14

QDTraj: Exploration of Diverse Trajectory Primitives for Articulated Objects Robotic Manipulation

Thanks to the latest advances in learning and robotics, domestic robots are beginning to enter homes, aiming to execute household chores autonomously. However, robots still struggle to perform autonomous manipulation tasks in open-ended environments. In this context, this paper presents a method that enables a robot to manipulate a wide spectrum of articulated objects. In this paper, we automatically generate different robot low-level trajectory primitives to manipulate given object articulations. A very important point when it comes to generating expert trajectories is to consider the diversity of solutions to achieve the same goal. Indeed, knowing diverse low-level primitives to accomplish the same task enables the robot to choose the optimal solution in its real-world environment, with live constraints and unexpected changes. To do so, we propose a method based on Quality-Diversity algorithms that leverages sparse reward exploration in order to generate a set of diverse and high-performing trajectory primitives for a given manipulation task. We validated our method, QDTraj, by generating diverse trajectories in simulation and deploying them in the real world. QDTraj generates at least 5 times more diverse trajectories for both hinge and slider activation tasks, outperforming the other methods we compared against. We assessed the generalization of our method over 30 articulations of the PartNetMobility articulated object dataset, with an average of 704 different trajectories by task. Code is publicly available at: https://kappel.web.isir.upmc.fr/trajectory_primitive_website

  • 5 authors
·
Apr 23

Antagonising explanation and revealing bias directly through sequencing and multimodal inference

Deep generative models produce data according to a learned representation, e.g. diffusion models, through a process of approximation computing possible samples. Approximation can be understood as reconstruction and the large datasets used to train models as sets of records in which we represent the physical world with some data structure (photographs, audio recordings, manuscripts). During the process of reconstruction, e.g., image frames develop each timestep towards a textual input description. While moving forward in time, frame sets are shaped according to learned bias and their production, we argue here, can be considered as going back in time; not by inspiration on the backward diffusion process but acknowledging culture is specifically marked in the records. Futures of generative modelling, namely in film and audiovisual arts, can benefit by dealing with diffusion systems as a process to compute the future by inevitably being tied to the past, if acknowledging the records as to capture fields of view at a specific time, and to correlate with our own finite memory ideals. Models generating new data distributions can target video production as signal processors and by developing sequences through timelines we ourselves also go back to decade-old algorithmic and multi-track methodologies revealing the actual predictive failure of contemporary approaches to synthesis in moving image, both as relevant to composition and not explanatory.

  • 3 authors
·
Aug 25, 2023

Enfold: Folding World Model Imagination into Predictive Representations for Ultra-Efficient Embodied Control

World generative models are typically used through what they produce: a rendered future, a video-conditioned action, or latent context computed by a costly generative branch. We argue that their more reusable asset is the computation that constructs a future. As a generator transforms a corrupted future into a coherent trajectory, its intermediate states organize appearance, spatial layout, and interaction across levels of abstraction. Can this future-generative computation be internalized in a representation inferred from the present alone? We present Enfold, which transfers this computation into a representation predicted from the current visual context and language instruction. During training, multi-level states exposed as the generator processes the observed future supervise a current-only encoder. The learned representation is fed back to condition future generation and is read by task heads without allowing task gradients to reshape the encoder. At deployment, action prediction no longer executes the generator. Across LIBERO, RoboTwin2.0, and real-robot tasks, Enfold supports strong control while reducing action latency by 3.7times relative to Fast--WAM, Enfold-Flash reaches 10.1times. Representation analyses show that it suppresses nuisance variation and preferentially captures changes that emerge over longer horizons. When the current scene is altered by human intervention, both the generated continuation and the executed actions adapt, which is inconsistent with fixed trajectory replay. These results recast a world generator as a source of predictive control representations: its future need not be materialized at every step if its internal structure can be enfolded into the present.

  • 13 authors
·
Aug 5 3

STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics

The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.

  • 9 authors
·
Jul 15, 2025

Multicell-Fold: geometric learning in folding multicellular life

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how every single cell decides to position itself relative to its neighboring cells. Despite its importance, it remains a major challenge to understand and predict the behavior of every cell within the living tissue over time during such intricate processes. To tackle this question, we propose a geometric deep learning model that can predict multicellular folding and embryogenesis, accurately capturing the highly convoluted spatial interactions among cells. We demonstrate that multicellular data can be represented with both granular and foam-like physical pictures through a unified graph data structure, considering both cellular interactions and cell junction networks. We successfully use our model to achieve two important tasks, interpretable 4-D morphological sequence alignment, and predicting local cell rearrangements before they occur at single-cell resolution. Furthermore, using an activation map and ablation studies, we demonstrate that cell geometries and cell junction networks together regulate local cell rearrangement which is critical for embryo morphogenesis. This approach provides a novel paradigm to study morphogenesis, highlighting a unified data structure and harnessing the power of geometric deep learning to accurately model the mechanisms and behaviors of cells during development. It offers a pathway toward creating a unified dynamic morphological atlas for a variety of developmental processes such as embryogenesis.

  • 5 authors
·
Jul 9, 2024

LoMeVQA: A Comprehensive Benchmark for Longitudinal Medical VQA

In clinical practice, patients often undergo multiple imaging examinations over successive visits, yielding longitudinal data. Modeling such temporal information is crucial for reliable assessment of disease progression and treatment response. However, despite the rapid advancement of multimodal large language models (MLLMs), longitudinal medical visual reasoning remains largely underexplored. To fill this gap, we propose LoMeVQA, a comprehensive benchmark consisting of 206K longitudinal visual question answering (VQA) pairs for temporal medical image analysis. LoMeVQA covers five tasks: progress classification, progress description, progress report generation, differential region grounding, and differential region description. To construct the dataset, we develop an automated pipeline that (1) organizes patient records chronologically, (2) extracts clinically meaningful entities via a medical knowledge graph, and (3) models their temporal evolution to guide large language models in generating high-quality longitudinal VQA pairs. Extensive evaluations demonstrate that both general-purpose and medical-domain MLLMs perform poorly on LoMeVQA, revealing substantial limitations in temporal reasoning. To address these limitations, we introduce MedLong-8B, which achieves state-of-the-art performance across all tasks. Beyond benchmarking, we conduct detailed analyses that uncover key failure modes and shed light on how to improve longitudinal medical visual reasoning. Our data is available at: https://github.com/pepperbubble/LoMeVQA

  • 7 authors
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Jul 29