Chanakya Ekbote

Moksh Jain, Emmanuel Bengio, Alex-Hernandez Garcia et al. · mila

Design of de novo biological sequences with desired properties, like protein and DNA sequences, often involves an active loop with several rounds of molecule ideation and expensive wet-lab evaluations. These experiments can consist of multiple stages, with increasing levels of precision and cost of evaluation, where candidates are filtered. This makes the diversity of proposed candidates a key consideration in the ideation phase. In this work, we propose an active learning algorithm leveraging epistemic uncertainty estimation and the recently proposed GFlowNets as a generator of diverse candidate solutions, with the objective to obtain a diverse batch of useful (as defined by some utility function, for example, the predicted anti-microbial activity of a peptide) and informative candidates after each round. We also propose a scheme to incorporate existing labeled datasets of candidates, in addition to a reward function, to speed up learning in GFlowNets. We present empirical results on several biological sequence design tasks, and we find that our method generates more diverse and novel batches with high scoring candidates compared to existing approaches.

Chanakya Ekbote, Moksh Jain, Payel Das et al. · mila

Generative Flow Networks (GFlowNets) have demonstrated significant performance improvements for generating diverse discrete objects $x$ given a reward function $R(x)$, indicating the utility of the object and trained independently from the GFlowNet by supervised learning to predict a desirable property $y$ given $x$. We hypothesize that this can lead to incompatibility between the inductive optimization biases in training $R$ and in training the GFlowNet, potentially leading to worse samples and slow adaptation to changes in the distribution. In this work, we build upon recent work on jointly learning energy-based models with GFlowNets and extend it to learn the joint over multiple variables, which we call Joint Energy-Based GFlowNets (JEBGFNs), such as peptide sequences and their antimicrobial activity. Joint learning of the energy-based model, used as a reward for the GFlowNet, can resolve the issues of incompatibility since both the reward function $R$ and the GFlowNet sampler are trained jointly. We find that this joint training or joint energy-based formulation leads to significant improvements in generating anti-microbial peptides. As the training sequences arose out of evolutionary or artificial selection for high antibiotic activity, there is presumably some structure in the distribution of sequences that reveals information about the antibiotic activity. This results in an advantage to modeling their joint generatively vs. pure discriminative modeling. We also evaluate JEBGFN in an active learning setting for discovering anti-microbial peptides.

Sai Surya Duvvuri, Chanakya Ekbote, Rachit Bansal et al. · berkeley

Multi-Head Attention (MHA) is the core computational primitive underlying modern Large Language Models (LLMs). However, MHA suffers from a fundamental linear scaling limitation: $H$ attention heads produce exactly $H$ independent attention matrices, with no communication between heads during attention computation. This becomes problematic for multi-step reasoning, where correct answers depend on aggregating evidence from multiple parts of the context and composing latent token-to-token relations over a chain of intermediate inferences. To address this, we propose Interleaved Head Attention (IHA), which enables cross-head mixing by constructing $P$ pseudo-heads per head (typically $P=H$), where each pseudo query/key/value is a learned linear combination of all $H$ original queries, keys and values respectively. Interactions between pseudo-query and pseudo-key heads induce up to $P^2$ attention patterns per head with modest parameter overhead $\mathcal{O}(H^2P)$. We provide theory showing improved efficiency in terms of number of parameters on the synthetic Polynomial task (IHA uses $Θ(\sqrt{k}n^2)$ parameters vs. $Θ(kn^2)$ for MHA) and on the synthetic order-sensitive CPM-3 task (IHA uses $\lceil\sqrt{N_{\max}}\rceil$ heads vs. $N_{\max}$ for MHA). On real-world benchmarks, IHA improves Multi-Key retrieval on RULER by 10-20% (4k-16k) and, after fine-tuning for reasoning on OpenThoughts, improves GSM8K by 5.8% and MATH-500 by 2.8% (Majority Vote) over full attention.

Chanakya Ekbote, Ajinkya Pankaj Deshpande, Arun Iyer et al.

Unsupervised node representations learnt using contrastive learning-based methods have shown good performance on downstream tasks. However, these methods rely on augmentations that mimic low-pass filters, limiting their performance on tasks requiring different eigen-spectrum parts. This paper presents a simple filter-based augmentation method to capture different parts of the eigen-spectrum. We show significant improvements using these augmentations. Further, we show that sharing the same weights across these different filter augmentations is possible, reducing the computational load. In addition, previous works have shown that good performance on downstream tasks requires high dimensional representations. Working with high dimensions increases the computations, especially when multiple augmentations are involved. We mitigate this problem and recover good performance through lower dimensional embeddings using simple random Fourier feature projections. Our method, FiGURe achieves an average gain of up to 4.4%, compared to the state-of-the-art unsupervised models, across all datasets in consideration, both homophilic and heterophilic. Our code can be found at: https://github.com/microsoft/figure.

Hengzhi Li, Justin Zhang, Brendon Jiang et al.

Puzzlehunts are a genre of complex, multi-step puzzles lacking well-defined problem definitions. In contrast to conventional reasoning benchmarks consisting of tasks with clear instructions and constrained environments, puzzlehunts requires discovering the underlying problem structure from multimodal evidence and iterative reasoning, mirroring real-world domains such as scientific discovery, exploratory data analysis, or investigative problem-solving. Despite progress in foundation models, their performance on open-ended settings remains largely untested. We introduce PuzzleWorld, a comprehensive benchmark of 667 puzzlehunt-style problems designed to assess step-by-step, open-ended, and creative multimodal reasoning. Each puzzle is annotated with the final solution, detailed reasoning traces, and cognitive skill labels, enabling holistic benchmarking and fine-grained diagnostic analysis. Most state-of-the-art models achieve only 1-4% final answer accuracy. On PuzzleWorld, the best model solves only 18% of puzzles and reaches 40% stepwise accuracy, matching human puzzle novices but falling significantly behind puzzle enthusiasts. To demonstrate the value of our reasoning annotations, we show that fine-tuning a small model on reasoning traces boosts stepwise accuracy from 4% to 11%, which translates to improvements in downstream visual reasoning tasks. Our detailed error analysis reveals that current models exhibit myopic reasoning, are bottlenecked by the limitations of language-based inference, and lack sketching capabilities crucial for visual and spatial reasoning. We release PuzzleWorld at https://github.com/MIT-MI/PuzzleWorld to support future work on building more general, open-ended, and creative reasoning systems.

Keane Ong, Sabri Boughorbel, Luwei Xiao et al.

To develop socially intelligent AI, existing approaches typically model human behavioral dimensions (e.g., affective, cognitive, or social attributes) in isolation. Although useful, task-specific modeling often increases training costs and limits generalization across behavioral settings. Recent reasoning RL methods facilitate training a single unified model across multiple behavioral tasks, but do not explicitly address learning across different heterogeneous behavioral data. To address this gap, we introduce Heterogeneity-Aware Relative Policy Optimization (HARPO), an RL method that balances leaning across heterogeneous tasks and samples. This is achieved by modulating advantages to ensure that no single task or sample carries disproportionate influence during policy optimization. Using HARPO, we develop and release Omnisapiens-7B 2.0, a foundation model for social behavior processing. Relative to existing behavioral foundation models, Omnisapiens-7B 2.0 achieves the strongest performance across behavioral tasks, with gains of up to +16.85% and +9.37% on multitask and held-out settings respectively, while producing more explicit and robust reasoning traces. We also validate HARPO against recent RL methods, where it achieves the most consistently strong performance across behavioral tasks.

Chanakya Ekbote, Vijay Lingam, Behrooz Omidvar-Tehrani et al.

Reinforcement Learning with Verifiable Rewards (RLVR) has emerged as a powerful framework for enhancing the reasoning capabilities of large language models (LLMs). However, existing approaches such as Group Relative Policy Optimization (GRPO) and its variants, while effective on reasoning benchmarks, struggle with agentic tasks that require iterative decision-making. We introduce Murphy, a multi-turn reflective optimization framework that extends GRPO by incorporating iterative self-correction during training. By leveraging both quantitative and qualitative execution feedback, Murphy enables models to progressively refine their reasoning across multiple turns. Evaluations on code generation benchmarks with model families such as Qwen and OLMo show that Murphy consistently improves performance, achieving up to a 8% relative gain in pass@1 over GRPO, on similar compute budgets.

Megan Tjandrasuwita, Chanakya Ekbote, Liu Ziyin et al.

Multimodal representation learning is fundamentally about transforming incomparable modalities into comparable representations. While prior research primarily focused on explicitly aligning these representations through targeted learning objectives and model architectures, a recent line of work has found that independently trained unimodal models of increasing scale and performance can become implicitly aligned with each other. These findings raise fundamental questions regarding the emergence of aligned representations in multimodal learning. Specifically: (1) when and why does alignment emerge implicitly? and (2) is alignment a reliable indicator of performance? Through a comprehensive empirical investigation, we demonstrate that both the emergence of alignment and its relationship with task performance depend on several critical data characteristics. These include, but are not necessarily limited to, the degree of similarity between the modalities and the balance between redundant and unique information they provide for the task. Our findings suggest that alignment may not be universally beneficial; rather, its impact on performance varies depending on the dataset and task. These insights can help practitioners determine whether increasing alignment between modalities is advantageous or, in some cases, detrimental to achieving optimal performance. Code is released at https://github.com/MeganTj/multimodal_alignment.

Divya Shyamal, Marta Knežević, Lan Tran et al.

Test-time scaling (TTS) improves large language models (LLMs) by allocating additional compute at inference time. In practice, TTS is often achieved through parallel scaling: generating multiple candidate responses and selecting the best via a Best-of-N (BoN) strategy. Its effectiveness therefore hinges on the scoring function. Learned scorers such as process reward models (PRMs) can be strong, but they are expensive to train and run. Lightweight confidence heuristics based on token log-probabilities are much cheaper, yet we find that they often perform substantially worse. To improve on lightweight confidence heuristics without incurring the full cost of stronger learned scorers, we introduce SCATR, a simple and efficient BoN ranking method that learns a lightweight scorer from a small calibration set using hidden representations from the base model. Across coding and mathematical reasoning benchmarks, SCATR improves over prior confidence-based baselines by up to 9%. Relative to LoRA fine-tuning on the same calibration data, it achieves comparable accuracy with up to 8000x fewer trainable parameters and much lower compute, reducing training and inference latency by up to 150x and 1000x, respectively. SCATR is also competitive with strong PRM baselines, and in several settings improves accuracy by up to 7.8% on math and 4.2% on coding while enabling up to 1000x faster inference. Overall, SCATR offers a strong accuracy-efficiency trade-off for scalable test-time selection.

Wei Dai, Peilin Chen, Chanakya Ekbote et al.

Clinical decision-making routinely demands reasoning over heterogeneous data, yet existing multimodal language models (MLLMs) remain largely vision-centric and fail to generalize across clinical specialties. To bridge this gap, we introduce QoQ-Med-7B/32B, the first open generalist clinical foundation model that jointly reasons across medical images, time-series signals, and text reports. QoQ-Med is trained with Domain-aware Relative Policy Optimization (DRPO), a novel reinforcement-learning objective that hierarchically scales normalized rewards according to domain rarity and modality difficulty, mitigating performance imbalance caused by skewed clinical data distributions. Trained on 2.61 million instruction tuning pairs spanning 9 clinical domains, we show that DRPO training boosts diagnostic performance by 43% in macro-F1 on average across all visual domains as compared to other critic-free training methods like GRPO. Furthermore, with QoQ-Med trained on intensive segmentation data, it is able to highlight salient regions related to the diagnosis, with an IoU 10x higher than open models while reaching the performance of OpenAI o4-mini. To foster reproducibility and downstream research, we release (i) the full model weights, (ii) the modular training pipeline, and (iii) all intermediate reasoning traces at https://github.com/DDVD233/QoQ_Med.

Konstantinos Kontras, Trui Osselaer, Stylianos G. Mouslech et al.

Foundation models (FMs) promise to extract unified representations that generalize across downstream tasks. They have emerged across fields, including electroencephalography (EEG), but it is less clear how effective they are in this particular field. Published evaluations differ in datasets, in the EEG-specific preprocessing that might influence reported results, and in the reported metrics, frequently obscuring the clinical relevance in EEG. We introduce NeuroAtlas, the largest EEG benchmark to date: 42 datasets and 260k hours covering clinical EEG (epilepsy, sleep medicine, brain age estimation) and brain-computer interfaces, and include multiple datasets per task along with bespoke clinical evaluation metrics. Besides evaluating EEG-FMs with respect to supervised baselines, we present results from generic time-series FMs. We report three findings. First, EEG-specific FMs do not consistently outperform time-series FMs, which have neither EEG-focused architectures nor been pretrained on EEG. Second, standard machine learning metrics are insufficient to assess clinical utility: thus, we thoroughly evaluate more appropriate measures such as the quality of event-level decision-making, hypnogram-derived features, and the brain-age gap in the domains of epilepsy, sleep, and brain age, respectively. Third, model rankings and performance can vary substantially within domains. We conclude that pretrained models perform largely on par, with only narrow advantages for a few, and that current models do not yet deliver on the promise of an out-of-the-box unified EEG model. NeuroAtlas exposes this gap and provides the datasets and metrics for the next generation of unified EEG FMs.

Ashok Vardhan Makkuva, Marco Bondaschi, Chanakya Ekbote et al.

In recent years, transformer-based models have revolutionized deep learning, particularly in sequence modeling. To better understand this phenomenon, there is a growing interest in using Markov input processes to study transformers. However, our current understanding in this regard remains limited with many fundamental questions about how transformers learn Markov chains still unanswered. In this paper, we address this by focusing on first-order Markov chains and single-layer transformers, providing a comprehensive characterization of the learning dynamics in this context. Specifically, we prove that transformer parameters trained on next-token prediction loss can either converge to global or local minima, contingent on the initialization and the Markovian data properties, and we characterize the precise conditions under which this occurs. To the best of our knowledge, this is the first result of its kind highlighting the role of initialization. We further demonstrate that our theoretical findings are corroborated by empirical evidence. Based on these insights, we provide guidelines for the initialization of transformer parameters and demonstrate their effectiveness. Finally, we outline several open problems in this arena. Code is available at: https://github.com/Bond1995/Markov.

Jaewoo Lee, Keyang Xuan, Chanakya Ekbote et al.

Multimodal Large Language Models (MLLMs) have shown remarkable versatility in understanding diverse multimodal data and tasks. However, these capabilities come with an increased model scale. While post-training pruning reduces model size in unimodal models, its application to MLLMs often yields limited success. Our analysis discovers that conventional methods fail to account for the unique token attributes across layers and modalities inherent to MLLMs. Inspired by this observation, we propose TAMP, a simple yet effective pruning framework tailored for MLLMs, featuring two key components: (1) Diversity-Aware Sparsity, which adjusts sparsity ratio per layer based on diversities among multimodal output tokens, preserving more parameters in high-diversity layers; and (2) Adaptive Multimodal Input Activation, which identifies representative multimodal input tokens using attention scores to guide unstructured weight pruning. We validate our method on two state-of-the-art MLLMs: LLaVA-NeXT, designed for vision-language tasks, and VideoLLaMA2, capable of processing audio, visual, and language modalities. Empirical experiments across various multimodal evaluation benchmarks demonstrate that each component of our approach substantially outperforms existing pruning techniques.

Chanakya Ekbote, Marco Bondaschi, Nived Rajaraman et al.

In-context learning (ICL) is a hallmark capability of transformers, through which trained models learn to adapt to new tasks by leveraging information from the input context. Prior work has shown that ICL emerges in transformers due to the presence of special circuits called induction heads. Given the equivalence between induction heads and conditional k-grams, a recent line of work modeling sequential inputs as Markov processes has revealed the fundamental impact of model depth on its ICL capabilities: while a two-layer transformer can efficiently represent a conditional 1-gram model, its single-layer counterpart cannot solve the task unless it is exponentially large. However, for higher order Markov sources, the best known constructions require at least three layers (each with a single attention head) - leaving open the question: can a two-layer single-head transformer represent any kth-order Markov process? In this paper, we precisely address this and theoretically show that a two-layer transformer with one head per layer can indeed represent any conditional k-gram. Thus, our result provides the tightest known characterization of the interplay between transformer depth and Markov order for ICL. Building on this, we further analyze the learning dynamics of our two-layer construction, focusing on a simplified variant for first-order Markov chains, illustrating how effective in-context representations emerge during training. Together, these results deepen our current understanding of transformer-based ICL and illustrate how even shallow architectures can surprisingly exhibit strong ICL capabilities on structured sequence modeling tasks.

Vijay Lingam, Chanakya Ekbote, Manan Sharma et al.

Graph Neural Networks (GNNs) exploit signals from node features and the input graph topology to improve node classification task performance. However, these models tend to perform poorly on heterophilic graphs, where connected nodes have different labels. Recently proposed GNNs work across graphs having varying levels of homophily. Among these, models relying on polynomial graph filters have shown promise. We observe that solutions to these polynomial graph filter models are also solutions to an overdetermined system of equations. It suggests that in some instances, the model needs to learn a reasonably high order polynomial. On investigation, we find the proposed models ineffective at learning such polynomials due to their designs. To mitigate this issue, we perform an eigendecomposition of the graph and propose to learn multiple adaptive polynomial filters acting on different subsets of the spectrum. We theoretically and empirically show that our proposed model learns a better filter, thereby improving classification accuracy. We study various aspects of our proposed model including, dependency on the number of eigencomponents utilized, latent polynomial filters learned, and performance of the individual polynomials on the node classification task. We further show that our model is scalable by evaluating over large graphs. Our model achieves performance gains of up to 5% over the state-of-the-art models and outperforms existing polynomial filter-based approaches in general.