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Theodoros Tsiligkaridis

Publications and source records attributed to Theodoros Tsiligkaridis.

At least 19 recordsLinked to original sources
arXiv2026

ToolUniverse: An open platform for democratizing AI scientists

AI scientists are emerging computational systems that serve as collaborative partners in discovery. These systems remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments that unify tools, data, and analyses into a common ecosystem. We present ToolUniverse, an open platform for building AI scientists from any language or reasoning model across open- and closed-weight models. ToolUniverse standardizes how AI scientists identify and call tools through an AI-tool interaction standard, in which every tool declares its purpose in natural language, a typed schema for its inputs and outputs, and a backend-agnostic invocation format, and applies that standard to more than 2,700 scientific tools and over 130 research skills spanning machine learning models, datasets, APIs, and scientific packages for data analysis, knowledge retrieval, and experimental design. It automatically refines tool interfaces for correct use by AI scientists, generates new tools from natural language descriptions, iteratively optimizes tool specifications, and composes tools into agentic workflows. In case studies, ToolUniverse was used to create AI scientists that carried out end-to-end analyses in target assessment, chemical strategy, and clinical-trial safety. The open-source ToolUniverse is available at https://aiscientist.tools.

cs.AI↗
arXiv2026

Adaptive Time Series Reasoning via Segment Selection

Time series reasoning tasks often start with a natural language question and require targeted analysis of a time series. Evidence may span the full series or appear in a few short intervals, so the model must decide what to inspect. Most existing approaches encode the entire time series into a fixed representation before inference, regardless of whether or not the entire sequence is relevant. We introduce ARTIST, which formulates time-series reasoning as a sequential decision problem. ARTIST interleaves reasoning with adaptive temporal segment selection. It adopts a controller-reasoner architecture and uses reinforcement learning to train the controller role to select informative segments and the reasoner role to generate segment-conditioned reasoning traces and final answers. During inference, the model actively acquires task-relevant information instead of relying on a static summary of the full sequence. We use a novel hierarchical policy optimization approach for post-training that allows the model to excel in both segment selection and question-answering behavior. We evaluate ARTIST on six time-series reasoning benchmarks and compare it with large language models, vision-language models, and prior time-series reasoning systems. ARTIST improves average accuracy by 6.46 absolute percentage points over the strongest baseline. The largest gains appear on rare event localization and multi-segment reasoning tasks. Supervised fine-tuning improves performance, and reinforcement learning provides additional gains by optimizing question-adaptive segment selection. These results show that selective data use drives effective time-series reasoning.

cs.LG↗
arXiv2026

When Sensors Fail: Temporal Sequence Models for Robust PPO under Sensor Drift

Real-world reinforcement learning systems must operate under distributional drift in their observation streams, yet most policy architectures implicitly assume fully observed and noise-free states. We study robustness of Proximal Policy Optimization (PPO) under temporally persistent sensor failures that induce partial observability and representation shift. To respond to this drift, we augment PPO with temporal sequence models, including Transformers and State Space Models (SSMs), to enable policies to infer missing information from history and maintain performance. Under a stochastic sensor failure process, we prove a high-probability bound on infinite-horizon reward degradation that quantifies how robustness depends on policy smoothness and failure persistence. Empirically, on MuJoCo continuous-control benchmarks with severe sensor dropout, we show Transformer-based sequence policies substantially outperform MLP, RNN, and SSM baselines in robustness, maintaining high returns even when large fractions of sensors are unavailable. These results demonstrate that temporal sequence reasoning provides a principled and practical mechanism for reliable operation under observation drift caused by sensor unreliability.

cs.LG↗
arXiv2025

The Inter-Intra Modal Measure: A Predictive Lens on Fine-Tuning Outcomes in Vision-Language Models

The fine-tuning of large vision-language foundation models remains an underexplored area, particularly regarding its impact on learning gains and catastrophic forgetting. Inspired by the significance of modality gaps in contrastive dual-encoders, we introduce the Inter-Intra Modal Measure (IIMM) - a predictive metric that quantifies the relationship between intra-modal image embedding similarity and inter-modal misalignment. Through extensive empirical analysis across four state-of-the-art vision-language models and five fine-tuning techniques, we establish a strong linear relationship: tasks with higher IIMM scores yield greater in-domain performance improvements but suffer from more pronounced out-of-domain degradation, with some parameter-efficient fine-tuning (PEFT) methods exhibiting severe forgetting. Compared to existing transferability measures, the IIMM demonstrates significantly stronger predictive power for accuracy changes post fine-tuning in dual-encoder models. Moreover, we provide a theoretical bound, proving that changes in IIMM are limited by the Wasserstein distance between pre- and post-fine-tuning embedding distributions, ensuring its stability and robustness as a predictive measure. With only a single forward pass of the target data, practitioners can leverage this key insight to evaluate the degree to which a model can be expected to improve following fine-tuning. When combined with prior knowledge of a model's performance across diverse tasks, the IIMM further enhances transferability predictions for novel tasks, offering a lightweight yet effective tool for guiding model adaptation strategies. Our code is provided at https://github.com/mit-ll/IIMM.

cs.CV↗
arXiv2025

Multimodal Unsupervised Domain Generalization by Retrieving Across the Modality Gap

Domain generalization (DG) is an important problem that learns a model which generalizes to unseen test domains leveraging one or more source domains, under the assumption of shared label spaces. However, most DG methods assume access to abundant source data in the target label space, a requirement that proves overly stringent for numerous real-world applications, where acquiring the same label space as the target task is prohibitively expensive. For this setting, we tackle the multimodal version of the unsupervised domain generalization (MUDG) problem, which uses a large task-agnostic unlabeled source dataset during finetuning. Our framework does not explicitly assume any relationship between the source dataset and target task. Instead, it relies only on the premise that the source dataset can be accurately and efficiently searched in a joint vision-language space. We make three contributions in the MUDG setting. Firstly, we show theoretically that cross-modal approximate nearest neighbor search suffers from low recall due to the large distance between text queries and the image centroids used for coarse quantization. Accordingly, we propose paired k-means, a simple clustering algorithm that improves nearest neighbor recall by storing centroids in query space instead of image space. Secondly, we propose an adaptive text augmentation scheme for target labels designed to improve zero-shot accuracy and diversify retrieved image data. Lastly, we present two simple but effective components to further improve downstream target accuracy. We compare against state-of-the-art name-only transfer, source-free DG and zero-shot (ZS) methods on their respective benchmarks and show consistent improvement in accuracy on 20 diverse datasets. Code is available: https://github.com/Chris210634/mudg

cs.CV↗
arXiv2025

Is Large-Scale Pretraining the Secret to Good Domain Generalization?

Multi-Source Domain Generalization (DG) is the task of training on multiple source domains and achieving high classification performance on unseen target domains. Recent methods combine robust features from web-scale pretrained backbones with new features learned from source data, and this has dramatically improved benchmark results. However, it remains unclear if DG finetuning methods are becoming better over time, or if improved benchmark performance is simply an artifact of stronger pre-training. Prior studies have shown that perceptual similarity to pre-training data correlates with zero-shot performance, but we find the effect limited in the DG setting. Instead, we posit that having perceptually similar data in pretraining is not enough; and that it is how well these data were learned that determines performance. This leads us to introduce the Alignment Hypothesis, which states that the final DG performance will be high if and only if alignment of image and class label text embeddings is high. Our experiments confirm the Alignment Hypothesis is true, and we use it as an analysis tool of existing DG methods evaluated on DomainBed datasets by splitting evaluation data into In-pretraining (IP) and Out-of-pretraining (OOP). We show that all evaluated DG methods struggle on DomainBed-OOP, while recent methods excel on DomainBed-IP. Put together, our findings highlight the need for DG methods which can generalize beyond pretraining alignment.

cs.CV↗
arXiv2025

TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools

Precision therapeutics require multimodal adaptive models that generate personalized treatment recommendations. We introduce TxAgent, an AI agent that leverages multi-step reasoning and real-time biomedical knowledge retrieval across a toolbox of 211 tools to analyze drug interactions, contraindications, and patient-specific treatment strategies. TxAgent evaluates how drugs interact at molecular, pharmacokinetic, and clinical levels, identifies contraindications based on patient comorbidities and concurrent medications, and tailors treatment strategies to individual patient characteristics. It retrieves and synthesizes evidence from multiple biomedical sources, assesses interactions between drugs and patient conditions, and refines treatment recommendations through iterative reasoning. It selects tools based on task objectives and executes structured function calls to solve therapeutic tasks that require clinical reasoning and cross-source validation. The ToolUniverse consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets. TxAgent outperforms leading LLMs, tool-use models, and reasoning agents across five new benchmarks: DrugPC, BrandPC, GenericPC, TreatmentPC, and DescriptionPC, covering 3,168 drug reasoning tasks and 456 personalized treatment scenarios. It achieves 92.1% accuracy in open-ended drug reasoning tasks, surpassing GPT-4o and outperforming DeepSeek-R1 (671B) in structured multi-step reasoning. TxAgent generalizes across drug name variants and descriptions. By integrating multi-step inference, real-time knowledge grounding, and tool-assisted decision-making, TxAgent ensures that treatment recommendations align with established clinical guidelines and real-world evidence, reducing the risk of adverse events and improving therapeutic decision-making.

cs.AI↗
arXiv2024

ERM++: An Improved Baseline for Domain Generalization

Domain Generalization (DG) aims to develop classifiers that can generalize to new, unseen data distributions, a critical capability when collecting new domain-specific data is impractical. A common DG baseline minimizes the empirical risk on the source domains. Recent studies have shown that this approach, known as Empirical Risk Minimization (ERM), can outperform most more complex DG methods when properly tuned. However, these studies have primarily focused on a narrow set of hyperparameters, neglecting other factors that can enhance robustness and prevent overfitting and catastrophic forgetting, properties which are critical for strong DG performance. In our investigation of training data utilization (i.e., duration and setting validation splits), initialization, and additional regularizers, we find that tuning these previously overlooked factors significantly improves model generalization across diverse datasets without adding much complexity. We call this improved, yet simple baseline ERM++. Despite its ease of implementation, ERM++ improves DG performance by over 5\% compared to prior ERM baselines on a standard benchmark of 5 datasets with a ResNet-50 and over 15\% with a ViT-B/16. It also outperforms all state-of-the-art methods on DomainBed datasets with both architectures. Importantly, ERM++ is easy to integrate into existing frameworks like DomainBed, making it a practical and powerful tool for researchers and practitioners. Overall, ERM++ challenges the need for more complex DG methods by providing a stronger, more reliable baseline that maintains simplicity and ease of use. Code is available at \url{https://github.com/piotr-teterwak/erm_plusplus}

cs.LG↗
arXiv2024

UniTS: A Unified Multi-Task Time Series Model

Although pre-trained transformers and reprogrammed text-based LLMs have shown strong performance on time series tasks, the best-performing architectures vary widely across tasks, with most models narrowly focused on specific areas, such as time series forecasting. Unifying predictive and generative time series tasks within a single model remains challenging. We introduce UniTS, a unified multi-task time series model that utilizes task tokenization to integrate predictive and generative tasks into a single framework. UniTS employs a modified transformer block to capture universal time series representations, enabling transferability from a heterogeneous, multi-domain pre-training dataset-characterized by diverse dynamic patterns, sampling rates, and temporal scales-to a wide range of downstream datasets with varied task specifications and data domains. Tested on 38 datasets across human activity sensors, healthcare, engineering, and finance, UniTS achieves superior performance compared to 12 forecasting models, 20 classification models, 18 anomaly detection models, and 16 imputation models, including adapted text-based LLMs. UniTS also demonstrates strong few-shot and prompt capabilities when applied to new domains and tasks. In single-task settings, UniTS outperforms competitive task-specialized time series models. Code and datasets are available at https://github.com/mims-harvard/UniTS.

cs.LG↗
arXiv2024

Descriptor and Word Soups: Overcoming the Parameter Efficiency Accuracy Tradeoff for Out-of-Distribution Few-shot Learning

Over the past year, a large body of multimodal research has emerged around zero-shot evaluation using GPT descriptors. These studies boost the zero-shot accuracy of pretrained VL models with an ensemble of label-specific text generated by GPT. A recent study, WaffleCLIP, demonstrated that similar zero-shot accuracy can be achieved with an ensemble of random descriptors. However, both zero-shot methods are un-trainable and consequently sub-optimal when some few-shot out-of-distribution (OOD) training data is available. Inspired by these prior works, we present two more flexible methods called descriptor and word soups, which do not require an LLM at test time and can leverage training data to increase OOD target accuracy. Descriptor soup greedily selects a small set of textual descriptors using generic few-shot training data, then calculates robust class embeddings using the selected descriptors. Word soup greedily assembles a chain of words in a similar manner. Compared to existing few-shot soft prompt tuning methods, word soup requires fewer parameters by construction and less GPU memory, since it does not require backpropagation. Both soups outperform current published few-shot methods, even when combined with SoTA zero-shot methods, on cross-dataset and domain generalization benchmarks. Compared with SoTA prompt and descriptor ensembling methods, such as ProDA and WaffleCLIP, word soup achieves higher OOD accuracy with fewer ensemble members. Please checkout our code: github.com/Chris210634/word_soups

cs.CV↗
arXiv2024

Quantified Task Misalignment to Inform PEFT: An Exploration of Domain Generalization and Catastrophic Forgetting in CLIP

Foundations models are presented as generalists that often perform well over a myriad of tasks. Fine-tuning these models, even on limited data, provides an additional boost in task-specific performance but often at the cost of their wider generalization, an effect termed catastrophic forgetting. In this paper, we analyze the relation between task difficulty in the CLIP model and the performance of several simple parameter-efficient fine-tuning methods through the lens of domain generalization and catastrophic forgetting. We provide evidence that the silhouette score of the zero-shot image and text embeddings is a better measure of task difficulty than the average cosine similarity of correct image/label embeddings, and discuss observable relationships between task difficulty, fine-tuning method, domain generalization, and catastrophic forgetting. Additionally, the averaged results across tasks and performance measures demonstrate that a simplified method that trains only a subset of attention weights, which we call A-CLIP, yields a balance between domain generalization and catastrophic forgetting.

cs.CV↗
arXiv2024

Image-Caption Encoding for Improving Zero-Shot Generalization

Recent advances in vision-language models have combined contrastive approaches with generative methods to achieve state-of-the-art (SOTA) on downstream inference tasks like zero-shot image classification. However, a persistent issue of these models for image classification is their out-of-distribution (OOD) generalization capabilities. We first show that when an OOD data point is misclassified, the correct class can be typically found in the Top-K predicted classes. In order to steer the model prediction toward the correct class within the top predicted classes, we propose the Image-Caption Encoding (ICE) method, a straightforward approach that directly enforces consistency between the image-conditioned and caption-conditioned predictions at evaluation time only. Intuitively, we take advantage of unique properties of the generated captions to guide our local search for the correct class label within the Top-K predicted classes. We show that our method can be easily combined with other SOTA methods to enhance Top-1 OOD accuracies by 0.5% on average and up to 3% on challenging datasets. Our code: https://github.com/Chris210634/ice

cs.CV↗
arXiv2023

Robust Fine-Tuning of Vision-Language Models for Domain Generalization

Transfer learning enables the sharing of common knowledge among models for a variety of downstream tasks, but traditional methods suffer in limited training data settings and produce narrow models incapable of effectively generalizing under distribution shifts. Foundation models have recently demonstrated impressive zero-shot inference capabilities and robustness under distribution shifts. However, zero-shot evaluation for these models has been predominantly confined to benchmarks with simple distribution shifts, limiting our understanding of their effectiveness under the more realistic shifts found in practice. Moreover, common fine-tuning methods for these models have yet to be evaluated against vision models in few-shot scenarios where training data is limited. To address these gaps, we present a new recipe for few-shot fine-tuning of the popular vision-language foundation model CLIP and evaluate its performance on challenging benchmark datasets with realistic distribution shifts from the WILDS collection. Our experimentation demonstrates that, while zero-shot CLIP fails to match performance of trained vision models on more complex benchmarks, few-shot CLIP fine-tuning outperforms its vision-only counterparts in terms of in-distribution and out-of-distribution accuracy at all levels of training data availability. This provides a strong incentive for adoption of foundation models within few-shot learning applications operating with real-world data. Code is available at https://github.com/mit-ll/robust-vision-language-finetuning

cs.CV↗
arXiv2023

Encoding Time-Series Explanations through Self-Supervised Model Behavior Consistency

Interpreting time series models is uniquely challenging because it requires identifying both the location of time series signals that drive model predictions and their matching to an interpretable temporal pattern. While explainers from other modalities can be applied to time series, their inductive biases do not transfer well to the inherently challenging interpretation of time series. We present TimeX, a time series consistency model for training explainers. TimeX trains an interpretable surrogate to mimic the behavior of a pretrained time series model. It addresses the issue of model faithfulness by introducing model behavior consistency, a novel formulation that preserves relations in the latent space induced by the pretrained model with relations in the latent space induced by TimeX. TimeX provides discrete attribution maps and, unlike existing interpretability methods, it learns a latent space of explanations that can be used in various ways, such as to provide landmarks to visually aggregate similar explanations and easily recognize temporal patterns. We evaluate TimeX on eight synthetic and real-world datasets and compare its performance against state-of-the-art interpretability methods. We also conduct case studies using physiological time series. Quantitative evaluations demonstrate that TimeX achieves the highest or second-highest performance in every metric compared to baselines across all datasets. Through case studies, we show that the novel components of TimeX show potential for training faithful, interpretable models that capture the behavior of pretrained time series models.

cs.LG↗
arXiv2023

Domain Adaptation for Time Series Under Feature and Label Shifts

Unsupervised domain adaptation (UDA) enables the transfer of models trained on source domains to unlabeled target domains. However, transferring complex time series models presents challenges due to the dynamic temporal structure variations across domains. This leads to feature shifts in the time and frequency representations. Additionally, the label distributions of tasks in the source and target domains can differ significantly, posing difficulties in addressing label shifts and recognizing labels unique to the target domain. Effectively transferring complex time series models remains a formidable problem. We present Raincoat, the first model for both closed-set and universal domain adaptation on complex time series. Raincoat addresses feature and label shifts by considering both temporal and frequency features, aligning them across domains, and correcting for misalignments to facilitate the detection of private labels. Additionally, Raincoat improves transferability by identifying label shifts in target domains. Our experiments with 5 datasets and 13 state-of-the-art UDA methods demonstrate that Raincoat can improve transfer learning performance by up to 16.33% and can handle both closed-set and universal domain adaptation.

cs.LG↗
arXiv2023

Supervised Metric Learning to Rank for Retrieval via Contextual Similarity Optimization

There is extensive interest in metric learning methods for image retrieval. Many metric learning loss functions focus on learning a correct ranking of training samples, but strongly overfit semantically inconsistent labels and require a large amount of data. To address these shortcomings, we propose a new metric learning method, called contextual loss, which optimizes contextual similarity in addition to cosine similarity. Our contextual loss implicitly enforces semantic consistency among neighbors while converging to the correct ranking. We empirically show that the proposed loss is more robust to label noise, and is less prone to overfitting even when a large portion of train data is withheld. Extensive experiments demonstrate that our method achieves a new state-of-the-art across four image retrieval benchmarks and multiple different evaluation settings. Code is available at: https://github.com/Chris210634/metric-learning-using-contextual-similarity

cs.LG↗
arXiv2023

Diverse Gaussian Noise Consistency Regularization for Robustness and Uncertainty Calibration

Deep neural networks achieve high prediction accuracy when the train and test distributions coincide. In practice though, various types of corruptions occur which deviate from this setup and cause severe performance degradations. Few methods have been proposed to address generalization in the presence of unforeseen domain shifts. In particular, digital noise corruptions arise commonly in practice during the image acquisition stage and present a significant challenge for current methods. In this paper, we propose a diverse Gaussian noise consistency regularization method for improving robustness of image classifiers under a variety of corruptions while still maintaining high clean accuracy. We derive bounds to motivate and understand the behavior of our Gaussian noise consistency regularization using a local loss landscape analysis. Our approach improves robustness against unforeseen noise corruptions by 4.2-18.4% over adversarial training and other strong diverse data augmentation baselines across several benchmarks. Furthermore, it improves robustness and uncertainty calibration by 3.7% and 5.5%, respectively, against all common corruptions (weather, digital, blur, noise) when combined with state-of-the-art diverse data augmentations.

cs.LG↗
arXiv2022

Self-Supervised Contrastive Pre-Training For Time Series via Time-Frequency Consistency

Pre-training on time series poses a unique challenge due to the potential mismatch between pre-training and target domains, such as shifts in temporal dynamics, fast-evolving trends, and long-range and short-cyclic effects, which can lead to poor downstream performance. While domain adaptation methods can mitigate these shifts, most methods need examples directly from the target domain, making them suboptimal for pre-training. To address this challenge, methods need to accommodate target domains with different temporal dynamics and be capable of doing so without seeing any target examples during pre-training. Relative to other modalities, in time series, we expect that time-based and frequency-based representations of the same example are located close together in the time-frequency space. To this end, we posit that time-frequency consistency (TF-C) -- embedding a time-based neighborhood of an example close to its frequency-based neighborhood -- is desirable for pre-training. Motivated by TF-C, we define a decomposable pre-training model, where the self-supervised signal is provided by the distance between time and frequency components, each individually trained by contrastive estimation. We evaluate the new method on eight datasets, including electrodiagnostic testing, human activity recognition, mechanical fault detection, and physical status monitoring. Experiments against eight state-of-the-art methods show that TF-C outperforms baselines by 15.4% (F1 score) on average in one-to-one settings (e.g., fine-tuning an EEG-pretrained model on EMG data) and by 8.4% (precision) in challenging one-to-many settings (e.g., fine-tuning an EEG-pretrained model for either hand-gesture recognition or mechanical fault prediction), reflecting the breadth of scenarios that arise in real-world applications. Code and datasets: https://github.com/mims-harvard/TFC-pretraining.

cs.LG↗