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.

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.

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.

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.

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.

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.