Junhong Shen

Stephan Xie, Ben Cohen, Mononito Goswami et al. · cmu

Time series question-answering (TSQA), in which we ask natural language questions to infer and reason about properties of time series, is a promising yet underexplored capability of foundation models. In this work, we present ARFBench, a TSQA benchmark that evaluates the understanding of multimodal foundation models (FMs) on time series anomalies prevalent in software incident data. ARFBench consists of 750 questions across 142 time series and 5.38M data points from 63 production incidents sourced exclusively from internal telemetry at Datadog. We evaluate leading proprietary and open-source LLMs, VLMs, and time series FMs and observe that frontier VLMs perform markedly better than existing baselines; the leading model (GPT-5) achieves a 62.7% accuracy and 51.9% F1. We next demonstrate the promise of specialized multimodal approaches. We develop a novel TSFM + VLM hybrid prototype which we post-train on a small set of synthetic and real data that yields comparable overall F1 and accuracy with frontier models. Lastly, we find models and human domain experts exhibit complementary strengths. We define a model-expert oracle, a best-of-2 oracle selector over model and expert answers, yielding 82.8% F1 and 87.2% accuracy and establishing a new superhuman frontier for future TSQA models. The benchmark is available at https://huggingface.co/datasets/Datadog/ARFBench.

Junhong Shen, Liam Li, Lucio M. Dery et al.

Fine-tuning large-scale pretrained models has led to tremendous progress in well-studied modalities such as vision and NLP. However, similar gains have not been observed in many other modalities due to a lack of relevant pretrained models. In this work, we propose ORCA, a general cross-modal fine-tuning framework that extends the applicability of a single large-scale pretrained model to diverse modalities. ORCA adapts to a target task via an align-then-refine workflow: given the target input, ORCA first learns an embedding network that aligns the embedded feature distribution with the pretraining modality. The pretrained model is then fine-tuned on the embedded data to exploit the knowledge shared across modalities. Through extensive experiments, we show that ORCA obtains state-of-the-art results on 3 benchmarks containing over 60 datasets from 12 modalities, outperforming a wide range of hand-designed, AutoML, general-purpose, and task-specific methods. We highlight the importance of data alignment via a series of ablation studies and demonstrate ORCA's utility in data-limited regimes.

Junhong Shen, Mikhail Khodak, Ameet Talwalkar

While neural architecture search (NAS) has enabled automated machine learning (AutoML) for well-researched areas, its application to tasks beyond computer vision is still under-explored. As less-studied domains are precisely those where we expect AutoML to have the greatest impact, in this work we study NAS for efficiently solving diverse problems. Seeking an approach that is fast, simple, and broadly applicable, we fix a standard convolutional network (CNN) topology and propose to search for the right kernel sizes and dilations its operations should take on. This dramatically expands the model's capacity to extract features at multiple resolutions for different types of data while only requiring search over the operation space. To overcome the efficiency challenges of naive weight-sharing in this search space, we introduce DASH, a differentiable NAS algorithm that computes the mixture-of-operations using the Fourier diagonalization of convolution, achieving both a better asymptotic complexity and an up-to-10x search time speedup in practice. We evaluate DASH on ten tasks spanning a variety of application domains such as PDE solving, protein folding, and heart disease detection. DASH outperforms state-of-the-art AutoML methods in aggregate, attaining the best-known automated performance on seven tasks. Meanwhile, on six of the ten tasks, the combined search and retraining time is less than 2x slower than simply training a CNN backbone that is far less accurate.

Junhong Shen, Atishay Jain, Zedian Xiao et al.

Large Language Model (LLM) agents are rapidly improving to handle increasingly complex web-based tasks. Most of these agents rely on general-purpose, proprietary models like GPT-4 and focus on designing better prompts to improve their planning abilities. However, general-purpose LLMs are not specifically trained to understand specialized web contexts such as HTML, and they often struggle with long-horizon planning. We explore an alternative approach that fine-tunes open-source LLMs using production-scale workflow data collected from over 250 domains corresponding to 6 billion tokens. This simple yet effective approach shows substantial gains over prompting-based agents on existing benchmarks -- ScribeAgent achieves state-of-the-art direct generation performance on Mind2Web and improves the task success rate by 7.3% over the previous best text-only web agents on WebArena. We further perform detailed ablation studies on various fine-tuning design choices and provide insights into LLM selection, training recipes, context window optimization, and effect of dataset sizes.

Zongzhe Xu, Ritvik Gupta, Wenduo Cheng et al.

Following its success for vision and text, the "foundation model" (FM) paradigm -- pretraining large models on massive data, then fine-tuning on target tasks -- has rapidly expanded to domains in the sciences, engineering, healthcare, and beyond. Has this achieved what the original FMs accomplished, i.e. the supplanting of traditional supervised learning in their domains? To answer we look at three modalities -- genomics, satellite imaging, and time series -- with multiple recent FMs and compare them to a standard supervised learning workflow: model development, hyperparameter tuning, and training, all using only data from the target task. Across these three specialized domains, we find that it is consistently possible to train simple supervised models -- no more complicated than a lightly modified wide ResNet or UNet -- that match or even outperform the latest foundation models. Our work demonstrates that the benefits of large-scale pretraining have yet to be realized in many specialized areas, reinforces the need to compare new FMs to strong, well-tuned baselines, and introduces two new, easy-to-use, open-source, and automated workflows for doing so.

Junhong Shen, Hao Bai, Lunjun Zhang et al. · cmu

The current paradigm of test-time scaling relies on generating long reasoning traces ("thinking" more) before producing a response. In agent problems that require interaction, this can be done by generating thinking traces before acting in the world. However, this process does not allow agents to acquire new information from the environment or adapt their behavior over time. In this work, we propose to scale test-time interaction, an untapped dimension of test-time scaling that increases the agent's interaction horizon to enable running rich behaviors such as exploration, backtracking, and dynamic re-planning within a single rollout. To demonstrate the promise of this scaling dimension, we study the domain of web agents. We first show that even prompting-based interaction scaling without any training can improve task success on web benchmarks non-trivially. Building on this, we introduce TTI (Test-Time Interaction), a curriculum-based online reinforcement learning (RL) approach that trains agents by adaptively adjusting their rollout lengths. Using a Gemma 3 12B model, TTI produces state-of-the-art open-source, open-data web agents on WebVoyager and WebArena benchmarks. We further show that TTI enables agents to balance exploration and exploitation adaptively. Our results establish interaction scaling as a powerful, complementary axis to scaling per-step compute, offering new avenues for training adaptive agents.

Shanda Li, Tanya Marwah, Junhong Shen et al.

Partial differential equations (PDEs) are fundamental to modeling physical systems, yet solving them remains a complex challenge. Traditional numerical solvers rely on expert knowledge to implement and are computationally expensive, while neural-network-based solvers require large training datasets and often lack interpretability. In this work, we frame PDE solving as a code generation task and introduce CodePDE, the first inference framework for generating PDE solvers using large language models (LLMs). Leveraging advanced inference-time algorithms and scaling strategies, CodePDE unlocks critical capacities of LLM for PDE solving: reasoning, debugging, selfrefinement, and test-time scaling -- all without task-specific tuning. CodePDE achieves superhuman performance across a range of representative PDE problems. We also present a systematic empirical analysis of LLM generated solvers, analyzing their accuracy, efficiency, and numerical scheme choices. Our findings highlight the promise and the current limitations of LLMs in PDE solving, offering a new perspective on solver design and opportunities for future model development. Our code is available at https://github.com/LithiumDA/CodePDE.

Weixin Liang, Junhong Shen, Genghan Zhang et al. · stanford

State Space Models (SSMs) have emerged as efficient alternatives to Transformers for sequential modeling, but their inability to leverage modality-specific features limits their performance in multi-modal pretraining. Here, we propose Mixture-of-Mamba, a novel SSM architecture that introduces modality-aware sparsity through modality-specific parameterization of the Mamba block. Building on Mixture-of-Transformers (W. Liang et al. arXiv:2411.04996; 2024), we extend the benefits of modality-aware sparsity to SSMs while preserving their computational efficiency. We evaluate Mixture-of-Mamba across three multi-modal pretraining settings: Transfusion (interleaved text and continuous image tokens with diffusion loss), Chameleon (interleaved text and discrete image tokens), and an extended three-modality framework incorporating speech. Mixture-of-Mamba consistently reaches the same loss values at earlier training steps with significantly reduced computational costs. In the Transfusion setting, Mixture-of-Mamba achieves equivalent image loss using only 34.76% of the training FLOPs at the 1.4B scale. In the Chameleon setting, Mixture-of-Mamba reaches similar image loss with just 42.50% of the FLOPs at the 1.4B scale, and similar text loss with just 65.40% of the FLOPs. In the three-modality setting, MoM matches speech loss at 24.80% of the FLOPs at the 1.4B scale. Our ablation study highlights the synergistic effects of decoupling projection components, where joint decoupling yields greater gains than individual modifications. These results establish modality-aware sparsity as a versatile and effective design principle, extending its impact from Transformers to SSMs and setting new benchmarks in multi-modal pretraining. Our code can be accessed at https://github.com/Weixin-Liang/Mixture-of-Mamba

Junhong Shen, Neil Tenenholtz, James Brian Hall et al. · harvard, microsoft-research

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM's embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM's performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

Junhong Shen, Tanya Marwah, Ameet Talwalkar

We present Unified PDE Solvers (UPS), a data- and compute-efficient approach to developing unified neural operators for diverse families of spatiotemporal PDEs from various domains, dimensions, and resolutions. UPS embeds different PDEs into a shared representation space and processes them using a FNO-transformer architecture. Rather than training the network from scratch, which is data-demanding and computationally expensive, we warm-start the transformer from pretrained LLMs and perform explicit alignment to reduce the modality gap while improving data and compute efficiency. The cross-modal UPS achieves state-of-the-art results on a wide range of 1D and 2D PDE families from PDEBench, outperforming existing unified models using 4 times less data and 26 times less compute. Meanwhile, it is capable of few-shot transfer to unseen PDE families and coefficients.

Junhong Shen, Kushal Tirumala, Michihiro Yasunaga et al.

Most existing image tokenizers encode images into a fixed number of tokens or patches, overlooking the inherent variability in image complexity. To address this, we introduce Content-Adaptive Tokenizer (CAT), which dynamically adjusts representation capacity based on the image content and encodes simpler images into fewer tokens. We design a caption-based evaluation system that leverages large language models (LLMs) to predict content complexity and determine the optimal compression ratio for a given image, taking into account factors critical to human perception. Trained on images with diverse compression ratios, CAT demonstrates robust performance in image reconstruction. We also utilize its variable-length latent representations to train Diffusion Transformers (DiTs) for ImageNet generation. By optimizing token allocation, CAT improves the FID score over fixed-ratio baselines trained with the same flops and boosts the inference throughput by 18.5%.

Junhong Shen, Mu Cai, Bo Hu et al.

Multimodal Large Language Models (MLLMs) struggle with precise reasoning for structured visuals like charts and diagrams, as pixel-based perception lacks a mechanism for verification. To address this, we propose to leverage derendering -- the process of reverse-engineering visuals into executable code -- as a new modality for verifiable visual reasoning. Specifically, we propose RECODE, an agentic framework that first generates multiple candidate programs to reproduce the input image. It then uses a critic to select the most faithful reconstruction and iteratively refines the code. This process not only transforms an ambiguous perceptual task into a verifiable, symbolic problem, but also enables precise calculations and logical inferences later on. On various visual reasoning benchmarks such as CharXiv, ChartQA, and Geometry3K, RECODE significantly outperforms methods that do not leverage code or only use code for drawing auxiliary lines or cropping. Our work demonstrates that grounding visual perception in executable code provides a new path toward more accurate and verifiable multimodal reasoning.

Renbo Tu, Nicholas Roberts, Mikhail Khodak et al.

Most existing neural architecture search (NAS) benchmarks and algorithms prioritize well-studied tasks, e.g. image classification on CIFAR or ImageNet. This makes the performance of NAS approaches in more diverse areas poorly understood. In this paper, we present NAS-Bench-360, a benchmark suite to evaluate methods on domains beyond those traditionally studied in architecture search, and use it to address the following question: do state-of-the-art NAS methods perform well on diverse tasks? To construct the benchmark, we curate ten tasks spanning a diverse array of application domains, dataset sizes, problem dimensionalities, and learning objectives. Each task is carefully chosen to interoperate with modern CNN-based search methods while possibly being far-afield from its original development domain. To speed up and reduce the cost of NAS research, for two of the tasks we release the precomputed performance of 15,625 architectures comprising a standard CNN search space. Experimentally, we show the need for more robust NAS evaluation of the kind NAS-Bench-360 enables by showing that several modern NAS procedures perform inconsistently across the ten tasks, with many catastrophically poor results. We also demonstrate how NAS-Bench-360 and its associated precomputed results will enable future scientific discoveries by testing whether several recent hypotheses promoted in the NAS literature hold on diverse tasks. NAS-Bench-360 is hosted at https://nb360.ml.cmu.edu.

Junhong Shen, Lin F. Yang

Recently, deep reinforcement learning (RL) has achieved remarkable empirical success by integrating deep neural networks into RL frameworks. However, these algorithms often require a large number of training samples and admit little theoretical understanding. To mitigate these issues, we propose a theoretically principled nearest neighbor (NN) function approximator that can improve the value networks in deep RL methods. Inspired by human similarity judgments, the NN approximator estimates the action values using rollouts on past observations and can provably obtain a small regret bound that depends only on the intrinsic complexity of the environment. We present (1) Nearest Neighbor Actor-Critic (NNAC), an online policy gradient algorithm that demonstrates the practicality of combining function approximation with deep RL, and (2) a plug-and-play NN update module that aids the training of existing deep RL methods. Experiments on classical control and MuJoCo locomotion tasks show that the NN-accelerated agents achieve higher sample efficiency and stability than the baseline agents. Based on its theoretical benefits, we believe that the NN approximator can be further applied to other complex domains to speed-up learning.

Luyao Yuan, Dongruo Zhou, Junhong Shen et al.

In human pedagogy, teachers and students can interact adaptively to maximize communication efficiency. The teacher adjusts her teaching method for different students, and the student, after getting familiar with the teacher's instruction mechanism, can infer the teacher's intention to learn faster. Recently, the benefits of integrating this cooperative pedagogy into machine concept learning in discrete spaces have been proved by multiple works. However, how cooperative pedagogy can facilitate machine parameter learning hasn't been thoroughly studied. In this paper, we propose a gradient optimization based teacher-aware learner who can incorporate teacher's cooperative intention into the likelihood function and learn provably faster compared with the naive learning algorithms used in previous machine teaching works. We give theoretical proof that the iterative teacher-aware learning (ITAL) process leads to local and global improvements. We then validate our algorithms with extensive experiments on various tasks including regression, classification, and inverse reinforcement learning using synthetic and real data. We also show the advantage of modeling teacher-awareness when agents are learning from human teachers.

Luyao Yuan, Zipeng Fu, Jingyue Shen et al.

Pragmatics studies how context can contribute to language meanings. In human communication, language is never interpreted out of context, and sentences can usually convey more information than their literal meanings. However, this mechanism is missing in most multi-agent systems, restricting the communication efficiency and the capability of human-agent interaction. In this paper, we propose an algorithm, using which agents can spontaneously learn the ability to "read between lines" without any explicit hand-designed rules. We integrate the theory of mind (ToM) in a cooperative multi-agent pedagogical situation and propose an adaptive reinforcement learning (RL) algorithm to develop a communication protocol. ToM is a profound cognitive science concept, claiming that people regularly reason about other's mental states, including beliefs, goals, and intentions, to obtain performance advantage in competition, cooperation or coalition. With this ability, agents consider language as not only messages but also rational acts reflecting others' hidden states. Our experiments demonstrate the advantage of pragmatic protocols over non-pragmatic protocols. We also show the teaching complexity following the pragmatic protocol empirically approximates to recursive teaching dimension (RTD).