Yujia Bao

Yujia Bao, Srinivasan Sivanandan, Theofanis Karaletsos

Vision Transformer (ViT) has emerged as a powerful architecture in the realm of modern computer vision. However, its application in certain imaging fields, such as microscopy and satellite imaging, presents unique challenges. In these domains, images often contain multiple channels, each carrying semantically distinct and independent information. Furthermore, the model must demonstrate robustness to sparsity in input channels, as they may not be densely available during training or testing. In this paper, we propose a modification to the ViT architecture that enhances reasoning across the input channels and introduce Hierarchical Channel Sampling (HCS) as an additional regularization technique to ensure robustness when only partial channels are presented during test time. Our proposed model, ChannelViT, constructs patch tokens independently from each input channel and utilizes a learnable channel embedding that is added to the patch tokens, similar to positional embeddings. We evaluate the performance of ChannelViT on ImageNet, JUMP-CP (microscopy cell imaging), and So2Sat (satellite imaging). Our results show that ChannelViT outperforms ViT on classification tasks and generalizes well, even when a subset of input channels is used during testing. Across our experiments, HCS proves to be a powerful regularizer, independent of the architecture employed, suggesting itself as a straightforward technique for robust ViT training. Lastly, we find that ChannelViT generalizes effectively even when there is limited access to all channels during training, highlighting its potential for multi-channel imaging under real-world conditions with sparse sensors. Our code is available at https://github.com/insitro/ChannelViT.

Yujia Bao, Regina Barzilay

Classifiers are biased when trained on biased datasets. As a remedy, we propose Learning to Split (ls), an algorithm for automatic bias detection. Given a dataset with input-label pairs, ls learns to split this dataset so that predictors trained on the training split cannot generalize to the testing split. This performance gap suggests that the testing split is under-represented in the dataset, which is a signal of potential bias. Identifying non-generalizable splits is challenging since we have no annotations about the bias. In this work, we show that the prediction correctness of each example in the testing split can be used as a source of weak supervision: generalization performance will drop if we move examples that are predicted correctly away from the testing split, leaving only those that are mis-predicted. ls is task-agnostic and can be applied to any supervised learning problem, ranging from natural language understanding and image classification to molecular property prediction. Empirical results show that ls is able to generate astonishingly challenging splits that correlate with human-identified biases. Moreover, we demonstrate that combining robust learning algorithms (such as group DRO) with splits identified by ls enables automatic de-biasing. Compared to previous state-of-the-art, we substantially improve the worst-group performance (23.4% on average) when the source of biases is unknown during training and validation.

Zhenting Wang, Qi Chang, Hemani Patel et al.

We introduce MCP-Bench, a benchmark for evaluating large language models (LLMs) on realistic, multi-step tasks that demand tool use, cross-tool coordination, precise parameter control, and planning/reasoning for solving tasks. Built on the Model Context Protocol (MCP), MCP-Bench connects LLMs to 28 representative live MCP servers spanning 250 tools across domains such as finance, traveling, scientific computing, and academic search. Unlike prior API-based benchmarks, each MCP server provides a set of complementary tools designed to work together, enabling the construction of authentic, multi-step tasks with rich input-output coupling. Tasks in MCP-Bench test agents' ability to retrieve relevant tools from fuzzy instructions without explicit tool names, plan multi-hop execution trajectories for complex objectives, ground responses in intermediate tool outputs, and orchestrate cross-domain workflows - capabilities not adequately evaluated by existing benchmarks that rely on explicit tool specifications, shallow few-step workflows, and isolated domain operations. We propose a multi-faceted evaluation framework covering tool-level schema understanding and usage, trajectory-level planning, and task completion. Experiments on 20 advanced LLMs reveal persistent challenges in MCP-Bench. Code and data: https://github.com/Accenture/mcp-bench.

Shafiuddin Rehan Ahmed, Ankit Parag Shah, Quan Hung Tran et al.

Climate change has intensified the need for transparency and accountability in organizational practices, making Environmental, Social, and Governance (ESG) reporting increasingly crucial. Frameworks like the Global Reporting Initiative (GRI) and the new European Sustainability Reporting Standards (ESRS) aim to standardize ESG reporting, yet generating comprehensive reports remains challenging due to the considerable length of ESG documents and variability in company reporting styles. To facilitate ESG report automation, Retrieval-Augmented Generation (RAG) systems can be employed, but their development is hindered by a lack of labeled data suitable for training retrieval models. In this paper, we leverage an underutilized source of weak supervision -- the disclosure content index found in past ESG reports -- to create a comprehensive dataset, ESG-CID, for both GRI and ESRS standards. By extracting mappings between specific disclosure requirements and corresponding report sections, and refining them using a Large Language Model as a judge, we generate a robust training and evaluation set. We benchmark popular embedding models on this dataset and show that fine-tuning BERT-based models can outperform commercial embeddings and leading public models, even under temporal data splits for cross-report style transfer from GRI to ESRS. Data: https://huggingface.co/datasets/airefinery/esg_cid_retrieval

Yaxuan Wang, Zhongteng Cai, Yujia Bao et al.

The rapid advancement of large language models (LLMs) has led to growing interest in using synthetic data to train future models. However, this creates a self-consuming retraining loop, where models are trained on their own outputs and may cause performance drops and induce emerging biases. In real-world applications, previously deployed LLMs may influence the data they generate, leading to a dynamic system driven by user feedback. For example, if a model continues to underserve users from a group, less query data will be collected from this particular demographic of users. In this study, we introduce the concept of \textbf{S}elf-\textbf{C}onsuming \textbf{P}erformative \textbf{L}oop (\textbf{SCPL}) and investigate the role of synthetic data in shaping bias during these dynamic iterative training processes under controlled performative feedback. This controlled setting is motivated by the inaccessibility of real-world user preference data from dynamic production systems, and enables us to isolate and analyze feedback-driven bias evolution in a principled manner. We focus on two types of loops, including the typical retraining setting and the incremental fine-tuning setting, which is largely underexplored. Through experiments on three real-world tasks, we find that the performative loop increases preference bias and decreases disparate bias. We design a reward-based rejection sampling strategy to mitigate the bias, moving towards more trustworthy self-improving systems.

Yujia Bao, Shiyu Chang, Regina Barzilay

While unbiased machine learning models are essential for many applications, bias is a human-defined concept that can vary across tasks. Given only input-label pairs, algorithms may lack sufficient information to distinguish stable (causal) features from unstable (spurious) features. However, related tasks often share similar biases -- an observation we may leverage to develop stable classifiers in the transfer setting. In this work, we explicitly inform the target classifier about unstable features in the source tasks. Specifically, we derive a representation that encodes the unstable features by contrasting different data environments in the source task. We achieve robustness by clustering data of the target task according to this representation and minimizing the worst-case risk across these clusters. We evaluate our method on both text and image classifications. Empirical results demonstrate that our algorithm is able to maintain robustness on the target task for both synthetically generated environments and real-world environments. Our code is available at https://github.com/YujiaBao/Tofu.

Yujia Bao, Shiyu Chang, Regina Barzilay

We propose Predict then Interpolate (PI), a simple algorithm for learning correlations that are stable across environments. The algorithm follows from the intuition that when using a classifier trained on one environment to make predictions on examples from another environment, its mistakes are informative as to which correlations are unstable. In this work, we prove that by interpolating the distributions of the correct predictions and the wrong predictions, we can uncover an oracle distribution where the unstable correlation vanishes. Since the oracle interpolation coefficients are not accessible, we use group distributionally robust optimization to minimize the worst-case risk across all such interpolations. We evaluate our method on both text classification and image classification. Empirical results demonstrate that our algorithm is able to learn robust classifiers (outperforms IRM by 23.85% on synthetic environments and 12.41% on natural environments). Our code and data are available at https://github.com/YujiaBao/Predict-then-Interpolate.

Jingbo Yang, Bairu Hou, Wei Wei et al.

We describe KVLink, an approach for efficient key-value (KV) cache reuse in large language models (LLMs). In many LLM applications, different inputs can share overlapping context, such as the same retrieved document appearing in multiple queries. However, the LLMs still need to encode the entire context for each query, leading to redundant computation. In this paper, we investigate a new strategy to eliminate such inefficiency, where the KV cache of each document is precomputed independently. During inference, the KV caches of retrieved documents are concatenated, allowing the model to reuse cached representations instead of recomputing them. To mitigate the performance degradation when using KV caches computed independently for each document, KVLink introduces two key techniques: adjusting positional embeddings of the KV cache at inference to match the global position after concatenation, and using trainable special tokens to restore self-attention across independently encoded documents. Experiments across 7 datasets demonstrate that KVLink improves question answering accuracy by an average of 4% over state-of-the-art methods. Furthermore, by leveraging precomputed KV caches, our approach reduces time-to-first-token by up to 96% compared to standard LLM inference, making it a scalable and efficient solution for context reuse. Additionally, KVLink can be combined with KV cache compression to further save cache loading and storage overhead while outperforming the baselines.

Alireza Rezazadeh, Zichao Li, Wei Wei et al.

Recent advancements in large language models have significantly improved their context windows, yet challenges in effective long-term memory management remain. We introduce MemTree, an algorithm that leverages a dynamic, tree-structured memory representation to optimize the organization, retrieval, and integration of information, akin to human cognitive schemas. MemTree organizes memory hierarchically, with each node encapsulating aggregated textual content, corresponding semantic embeddings, and varying abstraction levels across the tree's depths. Our algorithm dynamically adapts this memory structure by computing and comparing semantic embeddings of new and existing information to enrich the model's context-awareness. This approach allows MemTree to handle complex reasoning and extended interactions more effectively than traditional memory augmentation methods, which often rely on flat lookup tables. Evaluations on benchmarks for multi-turn dialogue understanding and document question answering show that MemTree significantly enhances performance in scenarios that demand structured memory management.

Menghua Wu, Yujia Bao, Regina Barzilay et al.

Causal discovery, the task of inferring causal structure from data, has the potential to uncover mechanistic insights from biological experiments, especially those involving perturbations. However, causal discovery algorithms over larger sets of variables tend to be brittle against misspecification or when data are limited. For example, single-cell transcriptomics measures thousands of genes, but the nature of their relationships is not known, and there may be as few as tens of cells per intervention setting. To mitigate these challenges, we propose a foundation model-inspired approach: a supervised model trained on large-scale, synthetic data to predict causal graphs from summary statistics -- like the outputs of classical causal discovery algorithms run over subsets of variables and other statistical hints like inverse covariance. Our approach is enabled by the observation that typical errors in the outputs of a discovery algorithm remain comparable across datasets. Theoretically, we show that the model architecture is well-specified, in the sense that it can recover a causal graph consistent with graphs over subsets. Empirically, we train the model to be robust to misspecification and distribution shift using diverse datasets. Experiments on biological and synthetic data confirm that this model generalizes well beyond its training set, runs on graphs with hundreds of variables in seconds, and can be easily adapted to different underlying data assumptions.

Alireza Rezazadeh, Zichao Li, Ange Lou et al.

Complex tasks are increasingly delegated to ensembles of specialized LLM-based agents that reason, communicate, and coordinate actions-both among themselves and through interactions with external tools, APIs, and databases. While persistent memory has been shown to enhance single-agent performance, most approaches assume a monolithic, single-user context-overlooking the benefits and challenges of knowledge transfer across users under dynamic, asymmetric permissions. We introduce Collaborative Memory, a framework for multi-user, multi-agent environments with asymmetric, time-evolving access controls encoded as bipartite graphs linking users, agents, and resources. Our system maintains two memory tiers: (1) private memory-private fragments visible only to their originating user; and (2) shared memory-selectively shared fragments. Each fragment carries immutable provenance attributes (contributing agents, accessed resources, and timestamps) to support retrospective permission checks. Granular read policies enforce current user-agent-resource constraints and project existing memory fragments into filtered transformed views. Write policies determine fragment retention and sharing, applying context-aware transformations to update the memory. Both policies may be designed conditioned on system, agent, and user-level information. Our framework enables safe, efficient, and interpretable cross-user knowledge sharing, with provable adherence to asymmetric, time-varying policies and full auditability of memory operations.

Jingbo Yang, Bairu Hou, Wei Wei et al.

Large language model (LLM) agents are becoming competent at straightforward web tasks, such as opening an item page or submitting a form, but still struggle with objectives that require long horizon navigation, large scale information extraction, and reasoning under constraints. We present WebDART, a general framework that enables a single LLM to handle such complex chores. WebDART (i) dynamically decomposes each objective into three focused subtasks: navigation, information extraction, and execution, so the model concentrates on one skill at a time, and (ii) continuously replans the decomposition as new webpages are revealed, taking advantage of newly discovered filters or shortcuts and avoiding redundant exploration. Evaluated on WebChoreArena, WebDART lifts success rates by up to 13.7 percentage points over previous SOTA agents, while matching their performance on the easier WebArena suite and completing tasks with up to 14.7 fewer navigation steps.

Gyuhak Kim, Sumiran Singh Thakur, Su Min Park et al.

Supervised fine-tuning (SFT) has become an essential step in tailoring large language models (LLMs) to align with human expectations and specific downstream tasks. However, existing SFT methods typically treat each training instance as a uniform sequence, giving equal importance to all tokens regardless of their relevance. This overlooks the fact that only a subset of tokens often contains critical, task-specific information. To address this limitation, we introduce Supervised Fine-Tuning with Group Optimization (SFT-GO), a novel approach that treats groups of tokens differently based on their importance.SFT-GO groups tokens in each sample based on their importance values and optimizes the LLM using a weighted combination of the worst-group loss and the standard cross-entropy loss. This mechanism adaptively emphasizes the most challenging token groups and guides the model to better handle different group distributions, thereby improving overall learning dynamics. We provide a theoretical analysis of SFT-GO's convergence rate, demonstrating its efficiency. Empirically, we apply SFT-GO with three different token grouping strategies and show that models trained with SFT-GO consistently outperform baseline approaches across popular LLM benchmarks. These improvements hold across various datasets and base models, demonstrating the robustness and the effectiveness of our method.

Yujia Bao, Ankit Parag Shah, Neeru Narang et al.

This paper introduces Fortune Analytics Language Model (FALM). FALM empowers users with direct access to comprehensive business analysis, including market trends, company performance metrics, and expert insights. Unlike generic LLMs, FALM leverages a curated knowledge base built from professional journalism, enabling it to deliver precise and in-depth answers to intricate business questions. Users can further leverage natural language queries to directly visualize financial data, generating insightful charts and graphs to understand trends across diverse business sectors clearly. FALM fosters user trust and ensures output accuracy through three novel methods: 1) Time-aware reasoning guarantees accurate event registration and prioritizes recent updates. 2) Thematic trend analysis explicitly examines topic evolution over time, providing insights into emerging business landscapes. 3) Content referencing and task decomposition enhance answer fidelity and data visualization accuracy. We conduct both automated and human evaluations, demonstrating FALM's significant performance improvements over baseline methods while prioritizing responsible AI practices. These benchmarks establish FALM as a cutting-edge LLM in the business and media domains, with exceptional accuracy and trustworthiness.

Yujia Bao, Theofanis Karaletsos

We introduce Contextual Vision Transformers (ContextViT), a method designed to generate robust image representations for datasets experiencing shifts in latent factors across various groups. Derived from the concept of in-context learning, ContextViT incorporates an additional context token to encapsulate group-specific information. This integration allows the model to adjust the image representation in accordance with the group-specific context. Specifically, for a given input image, ContextViT maps images with identical group membership into this context token, which is appended to the input image tokens. Additionally, we introduce a context inference network to predict such tokens on-the-fly, given a batch of samples from the group. This enables ContextViT to adapt to new testing distributions during inference time. We demonstrate the efficacy of ContextViT across a wide range of applications. In supervised fine-tuning, we show that augmenting pre-trained ViTs with our proposed context conditioning mechanism results in consistent improvements in out-of-distribution generalization on iWildCam and FMoW. We also investigate self-supervised representation learning with ContextViT. Our experiments on the Camelyon17 pathology imaging benchmark and the JUMP-CP microscopy imaging benchmark demonstrate that ContextViT excels in learning stable image featurizations amidst distribution shift, consistently outperforming its ViT counterpart.

Yujia Bao, Menghua Wu, Shiyu Chang et al.

In this paper, we explore meta-learning for few-shot text classification. Meta-learning has shown strong performance in computer vision, where low-level patterns are transferable across learning tasks. However, directly applying this approach to text is challenging--lexical features highly informative for one task may be insignificant for another. Thus, rather than learning solely from words, our model also leverages their distributional signatures, which encode pertinent word occurrence patterns. Our model is trained within a meta-learning framework to map these signatures into attention scores, which are then used to weight the lexical representations of words. We demonstrate that our model consistently outperforms prototypical networks learned on lexical knowledge (Snell et al., 2017) in both few-shot text classification and relation classification by a significant margin across six benchmark datasets (20.0% on average in 1-shot classification).

Yujia Bao, Zhengyi Deng, Yan Wang et al.

PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We developed and evaluated two machine learning models to classify abstracts as relevant to the penetrance (risk of cancer for germline mutation carriers) or prevalence of germline genetic mutations. METHODS: We conducted literature searches in PubMed and retrieved paper titles and abstracts to create an annotated dataset for training and evaluating the two machine learning classification models. Our first model is a support vector machine (SVM) which learns a linear decision rule based on the bag-of-ngrams representation of each title and abstract. Our second model is a convolutional neural network (CNN) which learns a complex nonlinear decision rule based on the raw title and abstract. We evaluated the performance of the two models on the classification of papers as relevant to penetrance or prevalence. RESULTS: For penetrance classification, we annotated 3740 paper titles and abstracts and used 60% for training the model, 20% for tuning the model, and 20% for evaluating the model. The SVM model achieves 89.53% accuracy (percentage of papers that were correctly classified) while the CNN model achieves 88.95 % accuracy. For prevalence classification, we annotated 3753 paper titles and abstracts. The SVM model achieves 89.14% accuracy while the CNN model achieves 89.13 % accuracy. CONCLUSION: Our models achieve high accuracy in classifying abstracts as relevant to penetrance or prevalence. By facilitating literature review, this tool could help clinicians and researchers keep abreast of the burgeoning knowledge of gene-cancer associations and keep the knowledge bases for clinical decision support tools up to date.

Yujia Bao, Shiyu Chang, Mo Yu et al.

Attention-based models are successful when trained on large amounts of data. In this paper, we demonstrate that even in the low-resource scenario, attention can be learned effectively. To this end, we start with discrete human-annotated rationales and map them into continuous attention. Our central hypothesis is that this mapping is general across domains, and thus can be transferred from resource-rich domains to low-resource ones. Our model jointly learns a domain-invariant representation and induces the desired mapping between rationales and attention. Our empirical results validate this hypothesis and show that our approach delivers significant gains over state-of-the-art baselines, yielding over 15% average error reduction on benchmark datasets.