Zahra Shakeri

Song Jiang, Zahra Shakeri, Aaron Chan et al. · berkeley, meta-ai

Chain-of-thought (CoT) prompting, which offers step-by-step problem-solving rationales, has impressively unlocked the reasoning potential of large language models (LLMs). Yet, the standard CoT is less effective in problems demanding multiple reasoning steps. This limitation arises from the complex reasoning process in multi-step problems: later stages often depend on the results of several steps earlier, not just the results of the immediately preceding step. Such complexities suggest the reasoning process is naturally represented as a graph. The almost linear and straightforward structure of CoT prompting, however, struggles to capture this complex reasoning graph. To address this challenge, we propose Residual Connection Prompting (RESPROMPT), a new prompting strategy that advances multi-step reasoning in LLMs. Our key idea is to reconstruct the reasoning graph within prompts. We achieve this by integrating necessary connections-links present in the reasoning graph but missing in the linear CoT flow-into the prompts. Termed "residual connections", these links are pivotal in morphing the linear CoT structure into a graph representation, effectively capturing the complex reasoning graphs inherent in multi-step problems. We evaluate RESPROMPT on six benchmarks across three diverse domains: math, sequential, and commonsense reasoning. For the open-sourced LLaMA family of models, RESPROMPT yields a significant average reasoning accuracy improvement of 12.5% on LLaMA-65B and 6.8% on LLaMA2-70B. Breakdown analysis further highlights RESPROMPT particularly excels in complex multi-step reasoning: for questions demanding at least five reasoning steps, RESPROMPT outperforms the best CoT based benchmarks by a remarkable average improvement of 21.1% on LLaMA-65B and 14.3% on LLaMA2-70B. Through extensive ablation studies and analyses, we pinpoint how to most effectively build residual connections.

Xiaotian Han, Hanqing Zeng, Yu Chen et al.

This paper investigates the relationship between graph convolution and Mixup techniques. Graph convolution in a graph neural network involves aggregating features from neighboring samples to learn representative features for a specific node or sample. On the other hand, Mixup is a data augmentation technique that generates new examples by averaging features and one-hot labels from multiple samples. One commonality between these techniques is their utilization of information from multiple samples to derive feature representation. This study aims to explore whether a connection exists between these two approaches. Our investigation reveals that, under two mild conditions, graph convolution can be viewed as a specialized form of Mixup that is applied during both the training and testing phases. The two conditions are: 1) \textit{Homophily Relabel} - assigning the target node's label to all its neighbors, and 2) \textit{Test-Time Mixup} - Mixup the feature during the test time. We establish this equivalence mathematically by demonstrating that graph convolution networks (GCN) and simplified graph convolution (SGC) can be expressed as a form of Mixup. We also empirically verify the equivalence by training an MLP using the two conditions to achieve comparable performance.

Fang Sheng, Mohammad Noaeen, Zahra Shakeri

Antimicrobial resistance threatens healthcare sustainability and motivates low-cost computational discovery of antimicrobial peptides (AMPs). De novo peptide generation must optimize antimicrobial activity and safety through low predicted toxicity, but likelihood-trained generators do not enforce these goals explicitly. We introduce ProDCARL, a reinforcement-learning alignment framework that couples a diffusion-based protein generator (EvoDiff OA-DM 38M) with sequence property predictors for AMP activity and peptide toxicity. We fine-tune the diffusion prior on AMP sequences to obtain a domain-aware generator. Top-k policy-gradient updates use classifier-derived rewards plus entropy regularization and early stopping to preserve diversity and reduce reward hacking. In silico experiments show ProDCARL increases the mean predicted AMP score from 0.081 after fine-tuning to 0.178. The joint high-quality hit rate reaches 6.3\% with pAMP $>$0.7 and pTox $<$0.3. ProDCARL maintains high diversity, with $1-$mean pairwise identity equal to 0.929. Qualitative analyses with AlphaFold3 and ProtBERT embeddings suggest candidates show plausible AMP-like structural and semantic characteristics. ProDCARL serves as a candidate generator that narrows experimental search space, and experimental validation remains future work.

Kamyar Kazari, Yong Chen, Zahra Shakeri

Public health researchers are increasingly interested in using social media data to study health-related behaviors, but manually labeling this data can be labor-intensive and costly. This study explores whether zero-shot labeling using large language models (LLMs) can match or surpass conventional crowd-sourced annotation for Twitter posts related to sleep disorders, physical activity, and sedentary behavior. Multiple annotation pipelines were designed to compare labels produced by domain experts, crowd workers, and LLM-driven approaches under varied prompt-engineering strategies. Our findings indicate that LLMs can rival human performance in straightforward classification tasks and significantly reduce labeling time, yet their accuracy diminishes for tasks requiring more nuanced domain knowledge. These results clarify the trade-offs between automated scalability and human expertise, demonstrating conditions under which LLM-based labeling can be efficiently integrated into public health research without undermining label quality.

Amirhossein Haji Mohammad Rezaei, Zahra Shakeri

Engineering sustainable and equitable healthcare requires medical language models that do not change clinically correct diagnoses when presented with non-decisive cultural information. We introduce a counterfactual benchmark that expands 150 MedQA test items into 1650 variants by inserting culture-related (i) identifier tokens, (ii) contextual cues, or (iii) their combination for three groups (Indigenous Canadian, Middle-Eastern Muslim, Southeast Asian), plus a length-matched neutral control, where a clinician verified that the gold answer remains invariant in all variants. We evaluate GPT-5.2, Llama-3.1-8B, DeepSeek-R1, and MedGemma (4B/27B) under option-only and brief-explanation prompting. Across models, cultural cues significantly affect accuracy (Cochran's Q, $p<10^-14$), with the largest degradation when identifier and context co-occur (up to 3-7 percentage points under option-only prompting), while neutral edits produce smaller, non-systematic changes. A human-validated rubric ($κ=0.76$) applied via an LLM-as-judge shows that more than half of culturally grounded explanations end in an incorrect answer, linking culture-referential reasoning to diagnostic failure. We release prompts and augmentations to support evaluation and mitigation of culturally induced diagnostic errors.

Javier Mencia-Ledo, Mohammad Noaeen, Zahra Shakeri

Metastatic castration-resistant prostate cancer (mCRPC) is a highly aggressive disease with poor prognosis and heterogeneous treatment response. In this work, we developed and externally validated a visit-level 180-day mortality risk model using longitudinal data from two Phase III cohorts (n=526 and n=640). Only visits with observable 180-day outcomes were labeled; right-censored cases were excluded from analysis. We compared five candidate architectures: Long Short-Term Memory, Gated Recurrent Unit (GRU), Cox Proportional Hazards, Random Survival Forest (RSF), and Logistic Regression. For each dataset, we selected the smallest risk-threshold that achieved an 85% sensitivity floor. The GRU and RSF models showed high discrimination capabilities initially (C-index: 87% for both). In external validation, the GRU obtained a higher calibration (slope: 0.93; intercept: 0.07) and achieved an PR-AUC of 0.87. Clinical impact analysis showed a median time-in-warning of 151.0 days for true positives (59.0 days for false positives) and 18.3 alerts per 100 patient-visits. Given late-stage frailty or cachexia and hemodynamic instability, permutation importance ranked BMI and systolic blood pressure as the strongest associations. These results suggest that longitudinal routine clinical markers can estimate short-horizon mortality risk in mCRPC and support proactive care planning over a multi-month window.

Juan Andres Medina Florez, Shaina Raza, Rashida Lynn et al.

Understanding the prevalence, disparities, and symptom variations of Post COVID-19 Condition (PCC) for vulnerable populations is crucial to improving care and addressing intersecting inequities. This study aims to develop a comprehensive framework for integrating social determinants of health (SDOH) into PCC research by leveraging NLP techniques to analyze disparities and variations in SDOH representation within PCC case reports. Following construction of a PCC Case Report Corpus, comprising over 7,000 case reports from the LitCOVID repository, a subset of 709 reports were annotated with 26 core SDOH-related entity types using pre-trained named entity recognition (NER) models, human review, and data augmentation to improve quality, diversity and representation of entity types. An NLP pipeline integrating NER, natural language inference (NLI), trigram and frequency analyses was developed to extract and analyze these entities. Both encoder-only transformer models and RNN-based models were assessed for the NER objective. Fine-tuned encoder-only BERT models outperformed traditional RNN-based models in generalizability to distinct sentence structures and greater class sparsity. Exploratory analysis revealed variability in entity richness, with prevalent entities like condition, age, and access to care, and underrepresentation of sensitive categories like race and housing status. Trigram analysis highlighted frequent co-occurrences among entities, including age, gender, and condition. The NLI objective (entailment and contradiction analysis) showed attributes like "Experienced violence or abuse" and "Has medical insurance" had high entailment rates (82.4%-80.3%), while attributes such as "Is female-identifying," "Is married," and "Has a terminal condition" exhibited high contradiction rates (70.8%-98.5%).

Siddharth Gururani, Kilol Gupta, Dhaval Shah et al.

This paper presents a simple yet effective method to achieve prosody transfer from a reference speech signal to synthesized speech. The main idea is to incorporate well-known acoustic correlates of prosody such as pitch and loudness contours of the reference speech into a modern neural text-to-speech (TTS) synthesizer such as Tacotron2 (TC2). More specifically, a small set of acoustic features are extracted from reference audio and then used to condition a TC2 synthesizer. The trained model is evaluated using subjective listening tests and a novel objective evaluation of prosody transfer is proposed. Listening tests show that the synthesized speech is rated as highly natural and that prosody is successfully transferred from the reference speech signal to the synthesized signal.

Mohsen Ghassemi, Zahra Shakeri, Anand D. Sarwate et al.

This work addresses the problem of learning sparse representations of tensor data using structured dictionary learning. It proposes learning a mixture of separable dictionaries to better capture the structure of tensor data by generalizing the separable dictionary learning model. Two different approaches for learning mixture of separable dictionaries are explored and sufficient conditions for local identifiability of the underlying dictionary are derived in each case. Moreover, computational algorithms are developed to solve the problem of learning mixture of separable dictionaries in both batch and online settings. Numerical experiments are used to show the usefulness of the proposed model and the efficacy of the developed algorithms.

Zahra Shakeri, Anand D. Sarwate, Waheed U. Bajwa

This paper derives sufficient conditions for local recovery of coordinate dictionaries comprising a Kronecker-structured dictionary that is used for representing $K$th-order tensor data. Tensor observations are assumed to be generated from a Kronecker-structured dictionary multiplied by sparse coefficient tensors that follow the separable sparsity model. This work provides sufficient conditions on the underlying coordinate dictionaries, coefficient and noise distributions, and number of samples that guarantee recovery of the individual coordinate dictionaries up to a specified error, as a local minimum of the objective function, with high probability. In particular, the sample complexity to recover $K$ coordinate dictionaries with dimensions $m_k \times p_k$ up to estimation error $\varepsilon_k$ is shown to be $\max_{k \in [K]}\mathcal{O}(m_kp_k^3\varepsilon_k^{-2})$.

Mohsen Ghassemi, Zahra Shakeri, Anand D. Sarwate et al.

In recent years, a class of dictionaries have been proposed for multidimensional (tensor) data representation that exploit the structure of tensor data by imposing a Kronecker structure on the dictionary underlying the data. In this work, a novel algorithm called "STARK" is provided to learn Kronecker structured dictionaries that can represent tensors of any order. By establishing that the Kronecker product of any number of matrices can be rearranged to form a rank-1 tensor, we show that Kronecker structure can be enforced on the dictionary by solving a rank-1 tensor recovery problem. Because rank-1 tensor recovery is a challenging nonconvex problem, we resort to solving a convex relaxation of this problem. Empirical experiments on synthetic and real data show promising results for our proposed algorithm.

Zahra Shakeri, Waheed U. Bajwa, Anand D. Sarwate

Dictionary learning is the problem of estimating the collection of atomic elements that provide a sparse representation of measured/collected signals or data. This paper finds fundamental limits on the sample complexity of estimating dictionaries for tensor data by proving a lower bound on the minimax risk. This lower bound depends on the dimensions of the tensor and parameters of the generative model. The focus of this paper is on second-order tensor data, with the underlying dictionaries constructed by taking the Kronecker product of two smaller dictionaries and the observed data generated by sparse linear combinations of dictionary atoms observed through white Gaussian noise. In this regard, the paper provides a general lower bound on the minimax risk and also adapts the proof techniques for equivalent results using sparse and Gaussian coefficient models. The reported results suggest that the sample complexity of dictionary learning for tensor data can be significantly lower than that for unstructured data.