Daily Papers

Adverse Drug Reactions (ADRs) from psychiatric medications are the leading cause of hospitalizations among mental health patients. With healthcare systems and online communities facing limitations in resolving ADR-related issues, Large Language Models (LLMs) have the potential to fill this gap. Despite the increasing capabilities of LLMs, past research has not explored their capabilities in detecting ADRs related to psychiatric medications or in providing effective harm reduction strategies. To address this, we introduce the Psych-ADR benchmark and the Adverse Drug Reaction Response Assessment (ADRA) framework to systematically evaluate LLM performance in detecting ADR expressions and delivering expert-aligned mitigation strategies. Our analyses show that LLMs struggle with understanding the nuances of ADRs and differentiating between types of ADRs. While LLMs align with experts in terms of expressed emotions and tone of the text, their responses are more complex, harder to read, and only 70.86% aligned with expert strategies. Furthermore, they provide less actionable advice by a margin of 12.32% on average. Our work provides a comprehensive benchmark and evaluation framework for assessing LLMs in strategy-driven tasks within high-risk domains.

Hate speech is a harmful form of online expression, often manifesting as derogatory posts. It is a significant risk in digital environments. With the rise of Large Language Models (LLMs), there is concern about their potential to replicate hate speech patterns, given their training on vast amounts of unmoderated internet data. Understanding how LLMs respond to hate speech is crucial for their responsible deployment. However, the behaviour of LLMs towards hate speech has been limited compared. This paper investigates the reactions of seven state-of-the-art LLMs (LLaMA 2, Vicuna, LLaMA 3, Mistral, GPT-3.5, GPT-4, and Gemini Pro) to hate speech. Through qualitative analysis, we aim to reveal the spectrum of responses these models produce, highlighting their capacity to handle hate speech inputs. We also discuss strategies to mitigate hate speech generation by LLMs, particularly through fine-tuning and guideline guardrailing. Finally, we explore the models' responses to hate speech framed in politically correct language.

Large language models are limited by challenges in factuality and hallucinations to be directly employed off-the-shelf for judging the veracity of news articles, where factual accuracy is paramount. In this work, we propose DELL that identifies three key stages in misinformation detection where LLMs could be incorporated as part of the pipeline: 1) LLMs could generate news reactions to represent diverse perspectives and simulate user-news interaction networks; 2) LLMs could generate explanations for proxy tasks (e.g., sentiment, stance) to enrich the contexts of news articles and produce experts specializing in various aspects of news understanding; 3) LLMs could merge task-specific experts and provide an overall prediction by incorporating the predictions and confidence scores of varying experts. Extensive experiments on seven datasets with three LLMs demonstrate that DELL outperforms state-of-the-art baselines by up to 16.8\% in macro f1-score. Further analysis reveals that the generated reactions and explanations are greatly helpful in misinformation detection, while our proposed LLM-guided expert merging helps produce better-calibrated predictions.

The study demonstrates the capabilities of a vector-based approach for calculating stoichiometric coefficients in chemical equations, using black powder as an illustrative example. A method is proposed for selecting and constraining intermediate interactions between reactants, as well as for identifying final products. It is shown that even a small number of components can lead to a large number of final and intermediate products. Through concrete calculations, a correlation is established between the number of possible chemical equations and the number of reactants. A methodology is proposed for computing all possible chemical equations within a reaction system for arbitrary component ratios, enabling the derivation of all feasible chemical reactions. Additionally, a method is developed for calculating the chemical composition for a fixed set of reactants, allowing for the evaluation of the set of products resulting from all possible chemical interactions given a specified initial composition.

The task of locating first order saddle points on high-dimensional surfaces describing the variation of energy as a function of atomic coordinates is an essential step for identifying the mechanism and estimating the rate of thermally activated events within the harmonic approximation of transition state theory. When combined directly with electronic structure calculations, the number of energy and atomic force evaluations needed for convergence is a primary issue. Here, we describe an efficient implementation of Gaussian process regression (GPR) acceleration of the minimum mode following method where a dimer is used to estimate the lowest eigenmode of the Hessian. A surrogate energy surface is constructed and updated after each electronic structure calculation. The method is applied to a test set of 500 molecular reactions previously generated by Hermez and coworkers [J. Chem. Theory Comput. 18, 6974 (2022)]. An order of magnitude reduction in the number of electronic structure calculations needed to reach the saddle point configurations is obtained by using the GPR compared to the dimer method. Despite the wide range in stiffness of the molecular degrees of freedom, the calculations are carried out using Cartesian coordinates and are found to require similar number of electronic structure calculations as an elaborate internal coordinate method implemented in the Sella software package. The present implementation of the GPR surrogate model in C++ is efficient enough for the wall time of the saddle point searches to be reduced in 3 out of 4 cases even though the calculations are carried out at a low Hartree-Fock level.

User-generated data sources have gained significance in uncovering Adverse Drug Reactions (ADRs), with an increasing number of discussions occurring in the digital world. However, the existing clinical corpora predominantly revolve around scientific articles in English. This work presents a multilingual corpus of texts concerning ADRs gathered from diverse sources, including patient fora, social media, and clinical reports in German, French, and Japanese. Our corpus contains annotations covering 12 entity types, four attribute types, and 13 relation types. It contributes to the development of real-world multilingual language models for healthcare. We provide statistics to highlight certain challenges associated with the corpus and conduct preliminary experiments resulting in strong baselines for extracting entities and relations between these entities, both within and across languages.

The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labelled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labelled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labelled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications, and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multi-label sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC

We investigate a new commonsense inference task: given an event described in a short free-form text ("X drinks coffee in the morning"), a system reasons about the likely intents ("X wants to stay awake") and reactions ("X feels alert") of the event's participants. To support this study, we construct a new crowdsourced corpus of 25,000 event phrases covering a diverse range of everyday events and situations. We report baseline performance on this task, demonstrating that neural encoder-decoder models can successfully compose embedding representations of previously unseen events and reason about the likely intents and reactions of the event participants. In addition, we demonstrate how commonsense inference on people's intents and reactions can help unveil the implicit gender inequality prevalent in modern movie scripts.

In natural human-to-human conversations, participants often receive feedback signals from one another based on their follow-up reactions. These reactions can include verbal responses, facial expressions, changes in emotional state, and other non-verbal cues. Similarly, in human-machine interactions, the machine can leverage the user's follow-up utterances as feedback signals to assess whether it has appropriately addressed the user's request. Therefore, we propose using the likelihood of follow-up utterances as rewards to differentiate preferred responses from less favored ones, without relying on human or commercial LLM-based preference annotations. Our proposed reward mechanism, ``Follow-up Likelihood as Reward" (FLR), matches the performance of strong reward models trained on large-scale human or GPT-4 annotated data on 8 pairwise-preference and 4 rating-based benchmarks. Building upon the FLR mechanism, we propose to automatically mine preference data from the online generations of a base policy model. The preference data are subsequently used to boost the helpfulness of the base model through direct alignment from preference (DAP) methods, such as direct preference optimization (DPO). Lastly, we demonstrate that fine-tuning the language model that provides follow-up likelihood with natural language feedback significantly enhances FLR's performance on reward modeling benchmarks and effectiveness in aligning the base policy model's helpfulness.

Modeling and generating human reactions poses a significant challenge with broad applications for computer vision and human-computer interaction. Existing methods either treat multiple individuals as a single entity, directly generating interactions, or rely solely on one person's motion to generate the other's reaction, failing to integrate the rich semantic information that underpins human interactions. Yet, these methods often fall short in adaptive responsiveness, i.e., the ability to accurately respond to diverse and dynamic interaction scenarios. Recognizing this gap, our work introduces an approach tailored to address the limitations of existing models by focusing on text-driven human reaction generation. Our model specifically generates realistic motion sequences for individuals that responding to the other's actions based on a descriptive text of the interaction scenario. The goal is to produce motion sequences that not only complement the opponent's movements but also semantically fit the described interactions. To achieve this, we present MoReact, a diffusion-based method designed to disentangle the generation of global trajectories and local motions sequentially. This approach stems from the observation that generating global trajectories first is crucial for guiding local motion, ensuring better alignment with given action and text. Furthermore, we introduce a novel interaction loss to enhance the realism of generated close interactions. Our experiments, utilizing data adapted from a two-person motion dataset, demonstrate the efficacy of our approach for this novel task, which is capable of producing realistic, diverse, and controllable reactions that not only closely match the movements of the counterpart but also adhere to the textual guidance. Please find our webpage at https://xiyan-xu.github.io/MoReactWebPage.

Astrochemical models of interstellar clouds, the sites of stars, and planet formation require information about spin-state chemistry to allow quantitative comparison with spectroscopic observations. In particular, it is important to know if full scrambling or H abstraction (also known as proton hopping) takes place in ion-neutral reactions. The reaction of Cl+ and HCl+ with H2 and isotopologues has been studied at cryogenic temperatures between 20 and 180 K using a 22 pole radio frequency ion trap. Isotopic exchange processes are used to probe the reaction mechanism of the HCl+ + H2 reaction. The results are compared with previous measurements and theoretical predictions. The rate coefficients for the Cl+ + H2 and HCl+ + H2 reactions are found to be constant in the range of temperatures studied, except for the DCl+ + D2 reaction, where a weak negative temperature dependence is observed, and reactions with D2 are found to be significantly slower than the Langevin rate. No isotopic exchange reactions are observed to occur for the H2Cl+ ion. The analysis of the products of the HCl+ + H2 isotopic system clearly indicates that the reaction proceeds via simple hydrogen atom abstraction.

Existing emotion prediction benchmarks contain coarse emotion labels which do not consider the diversity of emotions that an image and text can elicit in humans due to various reasons. Learning diverse reactions to multimodal content is important as intelligent machines take a central role in generating and delivering content to society. To address this gap, we propose Socratis, a societal reactions benchmark, where each image-caption (IC) pair is annotated with multiple emotions and the reasons for feeling them. Socratis contains 18K free-form reactions for 980 emotions on 2075 image-caption pairs from 5 widely-read news and image-caption (IC) datasets. We benchmark the capability of state-of-the-art multimodal large language models to generate the reasons for feeling an emotion given an IC pair. Based on a preliminary human study, we observe that humans prefer human-written reasons over 2 times more often than machine-generated ones. This shows our task is harder than standard generation tasks because it starkly contrasts recent findings where humans cannot tell apart machine vs human-written news articles, for instance. We further see that current captioning metrics based on large vision-language models also fail to correlate with human preferences. We hope that these findings and our benchmark will inspire further research on training emotionally aware models.

Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

Emotions manifest through physical experiences and bodily reactions, yet identifying such embodied emotions in text remains understudied. We present an embodied emotion classification dataset, CHEER-Ekman, extending the existing binary embodied emotion dataset with Ekman's six basic emotion categories. Using automatic best-worst scaling with large language models, we achieve performance superior to supervised approaches on our new dataset. Our investigation reveals that simplified prompting instructions and chain-of-thought reasoning significantly improve emotion recognition accuracy, enabling smaller models to achieve competitive performance with larger ones. Our dataset is publicly available at: https://github.com/menamerai/cheer-ekman.

The FRIB heavy-ion accelerator, commissioned in 2022, is a leading facility for producing rare isotope beams (RIBs) and exploring nuclei beyond the limits of stability. These RIBs are produced via reactions between stable primary beams and a graphite target. Approximately 20-40 \% of the primary beam power is deposited in the target, requiring efficient thermal dissipation. Currently, FRIB operates with a primary beam power of up to 20 kW. To enhance thermal dissipation efficiency, a single-slice rotating graphite target with a diameter of approximately 30 cm is employed. The effective target region is a 1 cm-wide outer rim of the graphite disc. To achieve high RIB production rates, the areal thickness variation must be constrained within 2 \%. This paper presents physical thickness characterizations of FRIB production targets with various nominal thicknesses, measured using a custom-built non-contact thickness measurement apparatus.

Short-pulse, ultra high-intensity lasers have opened new regimes for studying fusion plasmas and creating novel ultra-short ion beams and neutron sources. Diagnosing the plasma in these experiments is important for optimizing the fusion yield but difficult due to the picosecond time scales, 10s of micron-cubed volumes and high densities. We propose to use the yields of photons and neutrons produced by parallel reactions involving the same reactants to diagnose the plasma conditions and predict the yields of specific reactions of interest. In this work, we focus on verifying the yield of the high-interest aneutronic proton-boron fusion reaction ^{11}{B}(p,2α){}^4{He}, which is difficult to measure directly due to the short stopping range of the produced αs in most materials. We identify promising photon-producing reactions for this purpose and compute the ratios of the photon yield to the α yield as a function of plasma parameters. In beam fusion experiments, the {}^{11}{C} yield is an easily-measurable observable to verify the α yield. In light of our results, improving and extending measurements of the cross sections for these parallel reactions are important steps to gaining greater control over these laser-driven fusion plasmas.

Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classification And Retrieval of Enzymes (CARE). CARE centers on two tasks: (1) classification of a protein sequence by its enzyme commission (EC) number and (2) retrieval of an EC number given a chemical reaction. For each task, we design train-test splits to evaluate different kinds of out-of-distribution generalization that are relevant to real use cases. For the classification task, we provide baselines for state-of-the-art methods. Because the retrieval task has not been previously formalized, we propose a method called Contrastive Reaction-EnzymE Pretraining (CREEP) as one of the first baselines for this task and compare it to the recent method, CLIPZyme. CARE is available at https://github.com/jsunn-y/CARE/.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

Transition state (TS) structures define the critical geometries and energy barriers underlying chemical reactivity, yet their fleeting nature renders them experimentally elusive and drives the reliance on costly, high-throughput density functional theory (DFT) calculations. Here, we introduce TS-GEN, a conditional flow-matching generative model that maps samples from a simple Gaussian prior directly to transition-state saddle-point geometries in a single, deterministic pass. By embedding both reactant and product conformations as conditioning information, TS-GEN learns to transport latent noise to true TS structures via an optimal-transport path, effectively replacing the iterative optimization common in nudged-elastic band or string-method algorithms. TS-GEN delivers unprecedented accuracy, achieving a root-mean-square deviation of 0.004 mathring{A} (vs. 0.103 mathring{A} for prior state-of-the-art) and a mean barrier-height error of 1.019 {rm kcal/mol} (vs. 2.864 {rm kcal/mol}), while requiring only 0.06 {rm s} GPU time per inference. Over 87% of generated TSs meet chemical-accuracy criteria (<1.58 {rm kcal/mol} error), substantially outpacing existing methods. TS-GEN also exhibits strong transferability to out-of-distribution reactions from a larger database. By uniting sub-angstrom precision, sub-second speed, and broad applicability, TS-GEN will be highly useful for high-throughput exploration of complex reaction networks, paving the way to the exploration of novel chemical reaction mechanisms.

Psychological research results have confirmed that people can have different emotional reactions to different visual stimuli. Several papers have been published on the problem of visual emotion analysis. In particular, attempts have been made to analyze and predict people's emotional reaction towards images. To this end, different kinds of hand-tuned features are proposed. The results reported on several carefully selected and labeled small image data sets have confirmed the promise of such features. While the recent successes of many computer vision related tasks are due to the adoption of Convolutional Neural Networks (CNNs), visual emotion analysis has not achieved the same level of success. This may be primarily due to the unavailability of confidently labeled and relatively large image data sets for visual emotion analysis. In this work, we introduce a new data set, which started from 3+ million weakly labeled images of different emotions and ended up 30 times as large as the current largest publicly available visual emotion data set. We hope that this data set encourages further research on visual emotion analysis. We also perform extensive benchmarking analyses on this large data set using the state of the art methods including CNNs.

As large language models (LLMs) are increasingly deployed in diverse user facing applications, aligning them with real user preferences becomes essential. Existing methods like Reinforcement Learning from Human Feedback (RLHF) rely on expert annotators trained on manually defined guidelines, whose judgments may not reflect the priorities of everyday users. We introduce Reinforcement Learning from User Feedback (RLUF), a framework for aligning LLMs directly to implicit signals from users in production. RLUF addresses key challenges of user feedback: user feedback is often binary (e.g., emoji reactions), sparse, and occasionally adversarial. We train a reward model, P[Love], to predict the likelihood that an LLM response will receive a Love Reaction, a lightweight form of positive user feedback, and integrate P[Love] into a multi-objective policy optimization framework alongside helpfulness and safety objectives. In large-scale experiments, we show that P[Love] is predictive of increased positive feedback and serves as a reliable offline evaluator of future user behavior. Policy optimization using P[Love] significantly raises observed positive-feedback rates, including a 28% increase in Love Reactions during live A/B tests. However, optimizing for positive reactions introduces reward hacking challenges, requiring careful balancing of objectives. By directly leveraging implicit signals from users, RLUF offers a path to aligning LLMs with real-world user preferences at scale.

Predicting stock market prices following corporate earnings calls remains a significant challenge for investors and researchers alike, requiring innovative approaches that can process diverse information sources. This study investigates the impact of corporate earnings calls on stock prices by introducing a multi-modal predictive model. We leverage textual data from earnings call transcripts, along with images and tables from accompanying presentations, to forecast stock price movements on the trading day immediately following these calls. To facilitate this research, we developed the MiMIC (Multi-Modal Indian Earnings Calls) dataset, encompassing companies representing the Nifty 50, Nifty MidCap 50, and Nifty Small 50 indices. The dataset includes earnings call transcripts, presentations, fundamentals, technical indicators, and subsequent stock prices. We present a multimodal analytical framework that integrates quantitative variables with predictive signals derived from textual and visual modalities, thereby enabling a holistic approach to feature representation and analysis. This multi-modal approach demonstrates the potential for integrating diverse information sources to enhance financial forecasting accuracy. To promote further research in computational economics, we have made the MiMIC dataset publicly available under the CC-NC-SA-4.0 licence. Our work contributes to the growing body of literature on market reactions to corporate communications and highlights the efficacy of multi-modal machine learning techniques in financial analysis.

We describe in the context of the particle physics (PP) standard model (SM) `PP-SM' the understanding of the primordial properties and composition of the Universe in the temperature range 130GeV>T>20keV. The Universe evolution is described using FLRW cosmology. We present a global view on particle content across time and describe the different evolution eras using deceleration parameter q. We follow the arrow of time in the expanding and cooling Universe: After the PP-SM heavies (t, h, W, Z) diminish in abundance below Tsimeq 50GeV, the PP-SM plasma in the Universe is governed by the strongly interacting Quark-Gluon content. Once the temperature drops below Tsimeq 150MeV, quarks and gluons hadronize into strongly interacting matter particles. Rapid disappearance of baryonic antimatter completes at T_B=38.2MeV. We study the ensuing disappearance of strangeness and mesons in general. We show that the different eras defined by particle populations are barely separated from each other with abundance of muons fading out just prior to T=O(2.5)MeV, the era of emergence of the free-streaming neutrinos. We discuss the two relevant fundamental constants controlling the decoupling of neutrinos. We subsequently follow the primordial Universe as it passes through the hot dense electron-positron plasma epoch. The high density of positron antimatter disappears near T=20.3keV: Nuclear reactions occur in the presence of a highly mobile and relatively strongly interacting electron-positron plasma phase. We apply plasma theory methods to describe the strong screening effects between heavy dust particle (nucleons). We analyze the paramagnetic characteristics of the electron-positron plasma when exposed to an external primordial magnetic field.

Single-atom catalysts (SACs) have emerged as frontiers for catalyzing chemical reactions, yet the diverse combinations of active elements and support materials, the nature of coordination environments, elude traditional methodologies in searching optimal SAC systems with superior catalytic performance. Herein, by integrating multi-branch Convolutional Neural Network (CNN) analysis models to hybrid descriptor based activity volcano plot, 2D SAC system composed of diverse metallic single atoms anchored on six type of 2D supports, including graphitic carbon nitride, nitrogen-doped graphene, graphene with dual-vacancy, black phosphorous, boron nitride, and C2N, are screened for efficient CO2RR. Starting from establishing a correlation map between the adsorption energies of intermediates and diverse electronic and elementary descriptors, sole singular descriptor lost magic to predict catalytic activity. Deep learning method utilizing multi-branch CNN model therefore was employed, using 2D electronic density of states as input to predict adsorption energies. Hybrid-descriptor enveloping both C- and O-types of CO2RR intermediates was introduced to construct volcano plots and limiting potential periodic table, aiming for intuitive screening of catalyst candidates for efficient CO2 reduction to CH4. The eDOS occlusion experiments were performed to unravel individual orbital contribution to adsorption energy. To explore the electronic scale principle governing practical engineering catalytic CO2RR activity, orbitalwise eDOS shifting experiments based on CNN model were employed. The study involves examining the adsorption energy and, consequently, catalytic activities while varying supported single atoms. This work offers a tangible framework to inform both theoretical screening and experimental synthesis, thereby paving the way for systematically designing efficient SACs.

This paper presents a multi-label topic model for financial texts like ad-hoc announcements, 8-K filings, finance related news or annual reports. I train the model on a new financial multi-label database consisting of 3,044 German ad-hoc announcements that are labeled manually using 20 predefined, economically motivated topics. The best model achieves a macro F1 score of more than 85%. Translating the data results in an English version of the model with similar performance. As application of the model, I investigate differences in stock market reactions across topics. I find evidence for strong positive or negative market reactions for some topics, like announcements of new Large Scale Projects or Bankruptcy Filings, while I do not observe significant price effects for some other topics. Furthermore, in contrast to previous studies, the multi-label structure of the model allows to analyze the effects of co-occurring topics on stock market reactions. For many cases, the reaction to a specific topic depends heavily on the co-occurrence with other topics. For example, if allocated capital from a Seasoned Equity Offering (SEO) is used for restructuring a company in the course of a Bankruptcy Proceeding, the market reacts positively on average. However, if that capital is used for covering unexpected, additional costs from the development of new drugs, the SEO implies negative reactions on average.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Scalable and cost-effective solutions to renewable energy storage are essential to addressing the world's rising energy needs while reducing climate change. As we increase our reliance on renewable energy sources such as wind and solar, which produce intermittent power, storage is needed to transfer power from times of peak generation to peak demand. This may require the storage of power for hours, days, or months. One solution that offers the potential of scaling to nation-sized grids is the conversion of renewable energy to other fuels, such as hydrogen or methane. To be widely adopted, this process requires cost-effective solutions to running electrochemical reactions. An open challenge is finding low-cost electrocatalysts to drive these reactions at high rates. Through the use of quantum mechanical simulations (density functional theory), new catalyst structures can be tested and evaluated. Unfortunately, the high computational cost of these simulations limits the number of structures that may be tested. The use of machine learning may provide a method to efficiently approximate these calculations, leading to new approaches in finding effective electrocatalysts. In this paper, we provide an introduction to the challenges in finding suitable electrocatalysts, how machine learning may be applied to the problem, and the use of the Open Catalyst Project OC20 dataset for model training.

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

The chemical reaction recommendation is to select proper reaction condition parameters for chemical reactions, which is pivotal to accelerating chemical science. With the rapid development of large language models (LLMs), there is growing interest in leveraging their reasoning and planning capabilities for reaction condition recommendation. Despite their success, existing methods rarely explain the rationale behind the recommended reaction conditions, limiting their utility in high-stakes scientific workflows. In this work, we propose ChemMAS, a multi-agent system that reframes condition prediction as an evidence-based reasoning task. ChemMAS decomposes the task into mechanistic grounding, multi-channel recall, constraint-aware agentic debate, and rationale aggregation. Each decision is backed by interpretable justifications grounded in chemical knowledge and retrieved precedents. Experiments show that ChemMAS achieves 20-35% gains over domain-specific baselines and outperforms general-purpose LLMs by 10-15% in Top-1 accuracy, while offering falsifiable, human-trustable rationales, which establishes a new paradigm for explainable AI in scientific discovery.

Predicting and reasoning how a video would make a human feel is crucial for developing socially intelligent systems. Although Multimodal Large Language Models (MLLMs) have shown impressive video understanding capabilities, they tend to focus more on the semantic content of videos, often overlooking emotional stimuli. Hence, most existing MLLMs fall short in estimating viewers' emotional reactions and providing plausible explanations. To address this issue, we propose StimuVAR, a spatiotemporal Stimuli-aware framework for Video Affective Reasoning (VAR) with MLLMs. StimuVAR incorporates a two-level stimuli-aware mechanism: frame-level awareness and token-level awareness. Frame-level awareness involves sampling video frames with events that are most likely to evoke viewers' emotions. Token-level awareness performs tube selection in the token space to make the MLLM concentrate on emotion-triggered spatiotemporal regions. Furthermore, we create VAR instruction data to perform affective training, steering MLLMs' reasoning strengths towards emotional focus and thereby enhancing their affective reasoning ability. To thoroughly assess the effectiveness of VAR, we provide a comprehensive evaluation protocol with extensive metrics. StimuVAR is the first MLLM-based method for viewer-centered VAR. Experiments demonstrate its superiority in understanding viewers' emotional responses to videos and providing coherent and insightful explanations.

ERIT is a novel multimodal dataset designed to facilitate research in a lightweight multimodal fusion. It contains text and image data collected from videos of elderly individuals reacting to various situations, as well as seven emotion labels for each data sample. Because of the use of labeled images of elderly users reacting emotionally, it is also facilitating research on emotion recognition in an underrepresented age group in machine learning visual emotion recognition. The dataset is validated through comprehensive experiments indicating its importance in neural multimodal fusion research.

Most economic theories typically assume that financial market participants are fully rational individuals and use mathematical models to simulate human behavior in financial markets. However, human behavior is often not entirely rational and is challenging to predict accurately with mathematical models. In this paper, we propose Agent-based Simulated Financial Market (ASFM), which first constructs a simulated stock market with a real order matching system. Then, we propose a large language model based agent as the stock trader, which contains the profile, observation, and tool-learning based action module. The trading agent can comprehensively understand current market dynamics and financial policy information, and make decisions that align with their trading strategy. In the experiments, we first verify that the reactions of our ASFM are consistent with the real stock market in two controllable scenarios. In addition, we also conduct experiments in two popular economics research directions, and we find that conclusions drawn in our \model align with the preliminary findings in economics research. Based on these observations, we believe our proposed ASFM provides a new paradigm for economic research.

Media is full of false claims. Even Oxford Dictionaries named "post-truth" as the word of 2016. This makes it more important than ever to build systems that can identify the veracity of a story, and the kind of discourse there is around it. RumourEval is a SemEval shared task that aims to identify and handle rumours and reactions to them, in text. We present an annotation scheme, a large dataset covering multiple topics - each having their own families of claims and replies - and use these to pose two concrete challenges as well as the results achieved by participants on these challenges.

The primary goal of drug safety researchers and regulators is to promptly identify adverse drug reactions. Doing so may in turn prevent or reduce the harm to patients and ultimately improve public health. Evaluating and monitoring drug safety (i.e., pharmacovigilance) involves analyzing an ever growing collection of spontaneous reports from health professionals, physicians, and pharmacists, and information voluntarily submitted by patients. In this scenario, facilitating analysis of such reports via automation has the potential to rapidly identify safety signals. Unfortunately, public resources for developing natural language models for this task are scant. We present PHEE, a novel dataset for pharmacovigilance comprising over 5000 annotated events from medical case reports and biomedical literature, making it the largest such public dataset to date. We describe the hierarchical event schema designed to provide coarse and fine-grained information about patients' demographics, treatments and (side) effects. Along with the discussion of the dataset, we present a thorough experimental evaluation of current state-of-the-art approaches for biomedical event extraction, point out their limitations, and highlight open challenges to foster future research in this area.

Many challenging reasoning tasks require not just rapid, intuitive responses, but a more deliberate, multi-step approach. Recent progress in large language models (LLMs) highlights an important shift from the "System 1" way of quick reactions to the "System 2" style of reflection-and-correction problem solving. However, current benchmarks heavily rely on the final-answer accuracy, leaving much of a model's intermediate reasoning steps unexamined. This fails to assess the model's ability to reflect and rectify mistakes within the reasoning process. To bridge this gap, we introduce FINEREASON, a logic-puzzle benchmark for fine-grained evaluation of LLMs' reasoning capabilities. Each puzzle can be decomposed into atomic steps, making it ideal for rigorous validation of intermediate correctness. Building on this, we introduce two tasks: state checking, and state transition, for a comprehensive evaluation of how models assess the current situation and plan the next move. To support broader research, we also provide a puzzle training set aimed at enhancing performance on general mathematical tasks. We show that models trained on our state checking and transition data demonstrate gains in math reasoning by up to 5.1% on GSM8K.

Recently, Large Language Models (LLMs) have made significant progress in IQ-related domains that require careful thinking, such as mathematics and coding. However, enhancing LLMs' cognitive development in social domains, particularly from a post-training perspective, remains underexplored. Recognizing that the social world follows a distinct timeline and requires a richer blend of cognitive modes (from intuitive reactions (System 1) and surface-level thinking to deliberate thinking (System 2)) than mathematics, which primarily relies on System 2 cognition (careful, step-by-step reasoning), we introduce Temporal-aware Hierarchical Cognitive Reinforcement Learning (TimeHC-RL) for enhancing LLMs' social intelligence. In our experiments, we systematically explore improving LLMs' social intelligence and validate the effectiveness of the TimeHC-RL method, through five other post-training paradigms and two test-time intervention paradigms on eight datasets with diverse data patterns. Experimental results reveal the superiority of our proposed TimeHC-RL method compared to the widely adopted System 2 RL method. It gives the 7B backbone model wings, enabling it to rival the performance of advanced models like DeepSeek-R1 and OpenAI-O3. Additionally, the systematic exploration from post-training and test-time interventions perspectives to improve LLMs' social intelligence has uncovered several valuable insights.

Large language models (LLMs) typically deploy safety mechanisms to prevent harmful content generation. Most current approaches focus narrowly on risks posed by malicious actors, often framing risks as adversarial events and relying on defensive refusals. However, in real-world settings, risks also come from non-malicious users seeking help while under psychological distress (e.g., self-harm intentions). In such cases, the model's response can strongly influence the user's next actions. Simple refusals may lead them to repeat, escalate, or move to unsafe platforms, creating worse outcomes. We introduce Constructive Safety Alignment (CSA), a human-centric paradigm that protects against malicious misuse while actively guiding vulnerable users toward safe and helpful results. Implemented in Oyster-I (Oy1), CSA combines game-theoretic anticipation of user reactions, fine-grained risk boundary discovery, and interpretable reasoning control, turning safety into a trust-building process. Oy1 achieves state-of-the-art safety among open models while retaining high general capabilities. On our Constructive Benchmark, it shows strong constructive engagement, close to GPT-5, and unmatched robustness on the Strata-Sword jailbreak dataset, nearing GPT-o1 levels. By shifting from refusal-first to guidance-first safety, CSA redefines the model-user relationship, aiming for systems that are not just safe, but meaningfully helpful. We release Oy1, code, and the benchmark to support responsible, user-centered AI.

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

End-to-end autonomous driving research currently faces a critical challenge in bridging the gap between open-loop training and closed-loop deployment. Current approaches are trained to predict trajectories in an open-loop environment, which struggle with quick reactions to other agents in closed-loop environments and risk generating kinematically infeasible plans due to the gap between open-loop training and closed-loop driving. In this paper, we introduce Hydra-NeXt, a novel multi-branch planning framework that unifies trajectory prediction, control prediction, and a trajectory refinement network in one model. Unlike current open-loop trajectory prediction models that only handle general-case planning, Hydra-NeXt further utilizes a control decoder to focus on short-term actions, which enables faster responses to dynamic situations and reactive agents. Moreover, we propose the Trajectory Refinement module to augment and refine the planning decisions by effectively adhering to kinematic constraints in closed-loop environments. This unified approach bridges the gap between open-loop training and closed-loop driving, demonstrating superior performance of 65.89 Driving Score (DS) and 48.20% Success Rate (SR) on the Bench2Drive dataset without relying on external experts for data collection. Hydra-NeXt surpasses the previous state-of-the-art by 22.98 DS and 17.49 SR, marking a significant advancement in autonomous driving. Code will be available at https://github.com/woxihuanjiangguo/Hydra-NeXt.

LLM-based Interactive Drama is a novel AI-based dialogue scenario, where the user (i.e. the player) plays the role of a character in the story, has conversations with characters played by LLM agents, and experiences an unfolding story. This paper begins with understanding interactive drama from two aspects: Immersion, the player's feeling of being present in the story, and Agency, the player's ability to influence the story world. Both are crucial to creating an enjoyable interactive experience, while they have been underexplored in previous work. To enhance these two aspects, we first propose Playwriting-guided Generation, a novel method that helps LLMs craft dramatic stories with substantially improved structures and narrative quality. Additionally, we introduce Plot-based Reflection for LLM agents to refine their reactions to align with the player's intentions. Our evaluation relies on human judgment to assess the gains of our methods in terms of immersion and agency.

Simulating atomic-scale processes, such as protein dynamics and catalytic reactions, is crucial for advancements in biology, chemistry, and materials science. Machine learning force fields (MLFFs) have emerged as powerful tools that achieve near quantum mechanical accuracy, with promising generalization capabilities. However, their practical use is often limited by long inference times compared to classical force fields, especially when running extensive molecular dynamics (MD) simulations required for many biological applications. In this study, we introduce BoostMD, a surrogate model architecture designed to accelerate MD simulations. BoostMD leverages node features computed at previous time steps to predict energies and forces based on positional changes. This approach reduces the complexity of the learning task, allowing BoostMD to be both smaller and significantly faster than conventional MLFFs. During simulations, the computationally intensive reference MLFF is evaluated only every N steps, while the lightweight BoostMD model handles the intermediate steps at a fraction of the computational cost. Our experiments demonstrate that BoostMD achieves an eight-fold speedup compared to the reference model and generalizes to unseen dipeptides. Furthermore, we find that BoostMD accurately samples the ground-truth Boltzmann distribution when running molecular dynamics. By combining efficient feature reuse with a streamlined architecture, BoostMD offers a robust solution for conducting large-scale, long-timescale molecular simulations, making high-accuracy ML-driven modeling more accessible and practical.

Transformer-based deep neural networks have revolutionized the field of molecular-related prediction tasks by treating molecules as symbolic sequences. These models have been successfully applied in various organic chemical applications by pretraining them with extensive compound libraries and subsequently fine-tuning them with smaller in-house datasets for specific tasks. However, many conventional methods primarily focus on single molecules, with limited exploration of pretraining for reactions involving multiple molecules. In this paper, we propose ReactionT5, a novel model that leverages pretraining on the Open Reaction Database (ORD), a publicly available large-scale resource. We further fine-tune this model for yield prediction and product prediction tasks, demonstrating its impressive performance even with limited fine-tuning data compared to traditional models. The pre-trained ReactionT5 model is publicly accessible on the Hugging Face platform.

Newspaper reports provide a rich source of information on the unfolding of public debate on specific policy fields that can serve as basis for inquiry in political science. Such debates are often triggered by critical events, which attract public attention and incite the reactions of political actors: crisis sparks the debate. However, due to the challenges of reliable annotation and modeling, few large-scale datasets with high-quality annotation are available. This paper introduces DebateNet2.0, which traces the political discourse on the European refugee crisis in the German quality newspaper taz during the year 2015. The core units of our annotation are political claims (requests for specific actions to be taken within the policy field) and the actors who make them (politicians, parties, etc.). The contribution of this paper is twofold. First, we document and release DebateNet2.0 along with its companion R package, mardyR, guiding the reader through the practical and conceptual issues related to the annotation of policy debates in newspapers. Second, we outline and apply a Discourse Network Analysis (DNA) to DebateNet2.0, comparing two crucial moments of the policy debate on the 'refugee crisis': the migration flux through the Mediterranean in April/May and the one along the Balkan route in September/October. Besides the released resources and the case-study, our contribution is also methodological: we talk the reader through the steps from a newspaper article to a discourse network, demonstrating that there is not just one discourse network for the German migration debate, but multiple ones, depending on the topic of interest (political actors, policy fields, time spans).

Event cameras are a novel type of biologically inspired vision sensor known for their high temporal resolution, high dynamic range, and low power consumption. Because of these properties, they are well-suited for processing fast motions that require rapid reactions. Although event cameras have recently shown competitive performance in unsupervised optical flow estimation, performance in detecting independently moving objects (IMOs) is lacking behind, although event-based methods would be suited for this task based on their low latency and HDR properties. Previous approaches to event-based IMO segmentation have been heavily dependent on labeled data. However, biological vision systems have developed the ability to avoid moving objects through daily tasks without being given explicit labels. In this work, we propose the first event framework that generates IMO pseudo-labels using geometric constraints. Due to its unsupervised nature, our method can handle an arbitrary number of not predetermined objects and is easily scalable to datasets where expensive IMO labels are not readily available. We evaluate our approach on the EVIMO dataset and show that it performs competitively with supervised methods, both quantitatively and qualitatively.

How do we communicate with others to achieve our goals? We use our prior experience or advice from others, or construct a candidate utterance by predicting how it will be received. However, our experiences are limited and biased, and reasoning about potential outcomes can be difficult and cognitively challenging. In this paper, we explore how we can leverage Large Language Model (LLM) simulations to help us communicate better. We propose the Explore-Generate-Simulate (EGS) framework, which takes as input any scenario where an individual is communicating to an audience with a goal they want to achieve. EGS (1) explores the solution space by producing a diverse set of advice relevant to the scenario, (2) generates communication candidates conditioned on subsets of the advice, and (3) simulates the reactions from various audiences to determine both the best candidate and advice to use. We evaluate the framework on eight scenarios spanning the ten fundamental processes of interpersonal communication. For each scenario, we collect a dataset of human evaluations across candidates and baselines, and showcase that our framework's chosen candidate is preferred over popular generation mechanisms including Chain-of-Thought. We also find that audience simulations achieve reasonably high agreement with human raters across 5 of the 8 scenarios. Finally, we demonstrate the generality of our framework by applying it to real-world scenarios described by users on web forums. Through evaluations and demonstrations, we show that EGS enhances the effectiveness and outcomes of goal-oriented communication across a variety of situations, thus opening up new possibilities for the application of large language models in revolutionizing communication and decision-making processes.

Vision-Language-Action models (VLAs) are becoming increasingly capable across diverse robotic tasks. However, their real-world deployment remains slow and inefficient: demonstration videos are often sped up by 5-10x to appear smooth, with noticeable action stalls and delayed reactions to environmental changes. Asynchronous inference offers a promising solution to achieve continuous and low-latency control by enabling robots to execute actions and perform inference simultaneously. However, because the robot and environment continue to evolve during inference, a temporal misalignment arises between the prediction and execution intervals. This leads to significant action instability, while existing methods either degrade accuracy or introduce runtime overhead to mitigate it. We propose VLASH, a general asynchronous inference framework for VLAs that delivers smooth, accurate, and fast reaction control without additional overhead or architectural changes. VLASH estimates the future execution-time state by rolling the robot state forward with the previously generated action chunk, thereby bridging the gap between prediction and execution. Experiments show that VLASH achieves up to 2.03x speedup and reduces reaction latency by up to 17.4x compared to synchronous inference while fully preserving the original accuracy. Moreover, it empowers VLAs to handle fast-reaction, high-precision tasks such as playing ping-pong and playing whack-a-mole, where traditional synchronous inference fails. Code is available at https://github.com/mit-han-lab/vlash

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

We study improving social conversational agents by learning from natural dialogue between users and a deployed model, without extra annotations. To implicitly measure the quality of a machine-generated utterance, we leverage signals like user response length, sentiment and reaction of the future human utterances in the collected dialogue episodes. Our experiments use the publicly released deployment data from BlenderBot (Xu et al., 2023). Human evaluation indicates improvements in our new models over baseline responses; however, we find that some proxy signals can lead to more generations with undesirable properties as well. For example, optimizing for conversation length can lead to more controversial or unfriendly generations compared to the baseline, whereas optimizing for positive sentiment or reaction can decrease these behaviors.

Deep learning in computational biochemistry has traditionally focused on molecular graphs neural representations; however, recent advances in language models highlight how much scientific knowledge is encoded in text. To bridge these two modalities, we investigate how molecular property information can be transferred from natural language to graph representations. We study property prediction performance gains after using contrastive learning to align neural graph representations with representations of textual descriptions of their characteristics. We implement neural relevance scoring strategies to improve text retrieval, introduce a novel chemically-valid molecular graph augmentation strategy inspired by organic reactions, and demonstrate improved performance on downstream MoleculeNet property classification tasks. We achieve a +4.26% AUROC gain versus models pre-trained on the graph modality alone, and a +1.54% gain compared to recently proposed molecular graph/text contrastively trained MoMu model (Su et al. 2022).

Recent Large Language Models (LLMs) have shown remarkable capabilities in mimicking fictional characters or real humans in conversational settings. However, the realism and consistency of these responses can be further enhanced by providing richer information of the agent being mimicked. In this paper, we propose a novel approach to generate more realistic and consistent responses from LLMs, leveraging five senses, attributes, emotional states, relationship with the interlocutor, and memories. By incorporating these factors, we aim to increase the LLM's capacity for generating natural and realistic reactions in conversational exchanges. Through our research, we expect to contribute to the development of LLMs that demonstrate improved capabilities in mimicking fictional characters. We release a new benchmark dataset and all our codes, prompts, and sample results on our Github: https://github.com/srafsasm/InfoRichBot

Large language models (LLMs) have enabled powerful advances in natural language understanding and generation. Yet their application to complex, real-world scientific workflows remain limited by challenges in memory, planning, and tool integration. Here, we introduce SciBORG (Scientific Bespoke Artificial Intelligence Agents Optimized for Research Goals), a modular agentic framework that allows LLM-based agents to autonomously plan, reason, and achieve robust and reliable domain-specific task execution. Agents are constructed dynamically from source code documentation and augmented with finite-state automata (FSA) memory, enabling persistent state tracking and context-aware decision-making. This approach eliminates the need for manual prompt engineering and allows for robust, scalable deployment across diverse applications via maintaining context across extended workflows and to recover from tool or execution failures. We validate SciBORG through integration with both physical and virtual hardware, such as microwave synthesizers for executing user-specified reactions, with context-aware decision making and demonstrate its use in autonomous multi-step bioassay retrieval from the PubChem database utilizing multi-step planning, reasoning, agent-to-agent communication and coordination for execution of exploratory tasks. Systematic benchmarking shows that SciBORG agents achieve reliable execution, adaptive planning, and interpretable state transitions. Our results show that memory and state awareness are critical enablers of agentic planning and reliability, offering a generalizable foundation for deploying AI agents in complex environments.

Generative models have surged in popularity recently due to their ability to produce high-quality images and video. However, steering these models to produce images with specific attributes and precise control remains challenging. Humans, particularly their faces, are central to content generation due to their ability to convey rich expressions and intent. Current generative models mostly generate flat neutral expressions and characterless smiles without authenticity. Other basic expressions like anger are possible, but are limited to the stereotypical expression, while other unconventional facial expressions like doubtful are difficult to reliably generate. In this work, we propose the use of AUs (action units) for facial expression control in face generation. AUs describe individual facial muscle movements based on facial anatomy, allowing precise and localized control over the intensity of facial movements. By combining different action units, we unlock the ability to create unconventional facial expressions that go beyond typical emotional models, enabling nuanced and authentic reactions reflective of real-world expressions. The proposed method can be seamlessly integrated with both text and image prompts using adapters, offering precise and intuitive control of the generated results. Code and dataset are available in {https://github.com/tvaranka/fineface}.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

Warning: This paper contains content that may be offensive or upsetting. Understanding the harms and offensiveness of statements requires reasoning about the social and situational context in which statements are made. For example, the utterance "your English is very good" may implicitly signal an insult when uttered by a white man to a non-white colleague, but uttered by an ESL teacher to their student would be interpreted as a genuine compliment. Such contextual factors have been largely ignored by previous approaches to toxic language detection. We introduce COBRA frames, the first context-aware formalism for explaining the intents, reactions, and harms of offensive or biased statements grounded in their social and situational context. We create COBRACORPUS, a dataset of 33k potentially offensive statements paired with machine-generated contexts and free-text explanations of offensiveness, implied biases, speaker intents, and listener reactions. To study the contextual dynamics of offensiveness, we train models to generate COBRA explanations, with and without access to the context. We find that explanations by context-agnostic models are significantly worse than by context-aware ones, especially in situations where the context inverts the statement's offensiveness (29% accuracy drop). Our work highlights the importance and feasibility of contextualized NLP by modeling social factors.

We present subarcsecond-resolution ALMA mosaics of the Orion Bar PDR in [CI] 609 um, C2H (4-3), and C18O (3-2) emission lines, complemented by JWST images of H2 and aromatic infrared band (AIB) emission. The rim of the Bar shows very corrugated structures made of small-scale H2 dissociation fronts (DFs). The [CI] 609 um emission peaks very close (~0.002 pc) to the main H2-emitting DFs, suggesting the presence of gas density gradients. These DFs are also bright and remarkably similar in C2H emission, which traces 'hydrocarbon radical peaks' characterized by very high C2H abundances, reaching up to several x10^-7. The high abundance of C2H and of related hydrocarbon radicals, such as CH3, CH2, and CH, can be attributed to gas-phase reactions driven by elevated temperatures, the presence of C+ and C, and the reactivity of FUV-pumped H2. The hydrocarbon radical peaks roughly coincide with maxima of the 3.4/3.3 um AIB intensity ratio, a proxy for the aliphatic-to-aromatic content of PAHs. This implies that the conditions triggering the formation of simple hydrocarbons also favor the formation (and survival) of PAHs with aliphatic side groups, potentially via the contribution of bottom-up processes in which abundant hydrocarbon radicals react in situ with PAHs. Ahead of the DFs, in the atomic PDR zone (where [H]>>[H2]), the AIB emission is brightest, but small PAHs and carbonaceous grains undergo photo-processing due to the stronger FUV field. Our detection of trace amounts of C2H in this zone may result from the photoerosion of these species. This study provides a spatially resolved view of the chemical stratification of key carbon carriers in a PDR. Overall, both bottom-up and top-down processes appear to link simple hydrocarbon molecules with PAHs in molecular clouds; however, the exact chemical pathways and their relative contributions remain to be quantified.

Modeling human-like action-to-reaction generation has significant real-world applications, like human-robot interaction and games. Despite recent advancements in single-person motion generation, it is still challenging to well handle action-to-reaction generation, due to the difficulty of directly predicting reaction from action sequence without prompts, and the absence of a unified representation that effectively encodes multi-person motion. To address these challenges, we introduce Think-Then-React (TTR), a large language-model-based framework designed to generate human-like reactions. First, with our fine-grained multimodal training strategy, TTR is capable to unify two processes during inference: a thinking process that explicitly infers action intentions and reasons corresponding reaction description, which serve as semantic prompts, and a reacting process that predicts reactions based on input action and the inferred semantic prompts. Second, to effectively represent multi-person motion in language models, we propose a unified motion tokenizer by decoupling egocentric pose and absolute space features, which effectively represents action and reaction motion with same encoding. Extensive experiments demonstrate that TTR outperforms existing baselines, achieving significant improvements in evaluation metrics, such as reducing FID from 3.988 to 1.942.

Large language models (LLMs) have significantly impacted human society, influencing various domains. Among them, academia is not simply a domain affected by LLMs, but it is also the pivotal force in the development of LLMs. In academic publications, this phenomenon is represented during the incorporation of LLMs into the peer review mechanism for reviewing manuscripts. We proposed the concept of automated scholarly paper review (ASPR) in our previous paper. As the incorporation grows, it now enters the coexistence phase of ASPR and peer review, which is described in that paper. LLMs hold transformative potential for the full-scale implementation of ASPR, but they also pose new issues and challenges that need to be addressed. In this survey paper, we aim to provide a holistic view of ASPR in the era of LLMs. We begin with a survey to find out which LLMs are used to conduct ASPR. Then, we review what ASPR-related technological bottlenecks have been solved with the incorporation of LLM technology. After that, we move on to explore new methods, new datasets, new source code, and new online systems that come with LLMs for ASPR. Furthermore, we summarize the performance and issues of LLMs in ASPR, and investigate the attitudes and reactions of publishers and academia to ASPR. Lastly, we discuss the challenges associated with the development of LLMs for ASPR. We hope this survey can serve as an inspirational reference for the researchers and promote the progress of ASPR for its actual implementation.

The coldest Y spectral type brown dwarfs are similar in mass and temperature to cool and warm (sim200 -- 400 K) giant exoplanets. We can therefore use their atmospheres as proxies for planetary atmospheres, testing our understanding of physics and chemistry for these complex, cool worlds. At these cold temperatures, their atmospheres are cold enough for water clouds to form, and chemical timescales increase, increasing the likelihood of disequilibrium chemistry compared to warmer classes of planets. JWST observations are revolutionizing the characterization of these worlds with high signal-to-noise, moderate resolution near- and mid-infrared spectra. The spectra have been used to measure the abundances of prominent species like water, methane, and ammonia; species that trace chemical reactions like carbon monoxide; and even isotopologues of carbon monoxide and ammonia. Here, we present atmospheric retrieval results using both published fixed-slit (GTO program 1230) and new averaged time series observations (GO program 2327) of the coldest known Y dwarf, WISE 0855-0714 (using NIRSpec G395M spectra), which has an effective temperature of sim 264 K. We present a detection of deuterium in an atmosphere outside of the solar system via a relative measurement of deuterated methane (CH_{3}D) and standard methane. From this, we infer the D/H ratio of a substellar object outside the solar system for the first time. We also present a well-constrained part-per-billion abundance of phosphine (PH_{3}). We discuss our interpretation of these results and the implications for brown dwarf and giant exoplanet formation and evolution.

Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent development of protein language models (pLMs) with supervised fine tuning provides a promising solution to this problem. However, the fine-tuned model is tailored for particular downstream prediction task, and achieving general-purpose protein understanding remains a challenge. In this paper, we introduce Structure-Enhanced Protein Instruction Tuning (SEPIT) framework to bridge this gap. Our approach integrates a noval structure-aware module into pLMs to inform them with structural knowledge, and then connects these enhanced pLMs to large language models (LLMs) to generate understanding of proteins. In this framework, we propose a novel two-stage instruction tuning pipeline that first establishes a basic understanding of proteins through caption-based instructions and then refines this understanding using a mixture of experts (MoEs) to learn more complex properties and functional information with the same amount of activated parameters. Moreover, we construct the largest and most comprehensive protein instruction dataset to date, which allows us to train and evaluate the general-purpose protein understanding model. Extensive experimental results on open-ended generation and closed-set answer tasks demonstrate the superior performance of SEPIT over both closed-source general LLMs and open-source LLMs trained with protein knowledge.

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

Developing accurate models for chemical reactors is often challenging due to the complexity of reaction kinetics and process dynamics. Traditional approaches require retraining models for each new system, limiting generalizability and efficiency. In this work, we take a step toward foundation models for chemical reactor modeling by introducing a neural network framework that generalizes across diverse reactor types and rapidly adapts to new chemical processes. Our approach leverages meta-learning to pretrain the model on a broad set of reactor dynamics, enabling efficient adaptation to unseen reactions with minimal data. To further enhance generalizability, we incorporate physics-informed fine-tuning, ensuring physically consistent adaptation to new reactor conditions. Our framework is evaluated across three integer-order fundamental reactor types - continuous stirred tank reactors, batch reactors, and plug flow reactors - demonstrating superior few-shot adaptation compared to conventional data-driven, physics-informed, and transfer learning approaches. By combining meta-learning with physics-informed adaptation, this work lays the foundation for a generalizable modeling framework, advancing the development of foundation models for chemical engineering applications. Source code is available at https://github.com/killingbear999/chemical-reactor-foundation-model.

Counterspeech, defined as a response to mitigate online hate speech, is increasingly used as a non-censorial solution. Addressing hate speech effectively involves dispelling the stereotypes, prejudices, and biases often subtly implied in brief, single-sentence statements or abuses. These implicit expressions challenge language models, especially in seq2seq tasks, as model performance typically excels with longer contexts. Our study introduces CoARL, a novel framework enhancing counterspeech generation by modeling the pragmatic implications underlying social biases in hateful statements. CoARL's first two phases involve sequential multi-instruction tuning, teaching the model to understand intents, reactions, and harms of offensive statements, and then learning task-specific low-rank adapter weights for generating intent-conditioned counterspeech. The final phase uses reinforcement learning to fine-tune outputs for effectiveness and non-toxicity. CoARL outperforms existing benchmarks in intent-conditioned counterspeech generation, showing an average improvement of 3 points in intent-conformity and 4 points in argument-quality metrics. Extensive human evaluation supports CoARL's efficacy in generating superior and more context-appropriate responses compared to existing systems, including prominent LLMs like ChatGPT.

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

Social media is now the predominant source of information due to the availability of immediate public response. As a result, social media data has become a valuable resource for comprehending public sentiments. Studies have shown that it can amplify ideas and influence public sentiments. This study analyzes the public perception of climate change and the environment over a decade from 2014 to 2023. Using the Pointwise Mutual Information (PMI) algorithm, we identify sentiment and explore prevailing emotions expressed within environmental tweets across various social media platforms, namely Twitter, Reddit, and YouTube. Accuracy on a human-annotated dataset was 0.65, higher than Vader score but lower than that of an expert rater (0.90). Our findings suggest that negative environmental tweets are far more common than positive or neutral ones. Climate change, air quality, emissions, plastic, and recycling are the most discussed topics on all social media platforms, highlighting its huge global concern. The most common emotions in environmental tweets are fear, trust, and anticipation, demonstrating public reactions wide and complex nature. By identifying patterns and trends in opinions related to the environment, we hope to provide insights that can help raise awareness regarding environmental issues, inform the development of interventions, and adapt further actions to meet environmental challenges.

Instruction-tuned Large Language Models (It-LLMs) have been exhibiting outstanding abilities to reason around cognitive states, intentions, and reactions of all people involved, letting humans guide and comprehend day-to-day social interactions effectively. In fact, several multiple-choice questions (MCQ) benchmarks have been proposed to construct solid assessments of the models' abilities. However, earlier works are demonstrating the presence of inherent "order bias" in It-LLMs, posing challenges to the appropriate evaluation. In this paper, we investigate It-LLMs' resilience abilities towards a series of probing tests using four MCQ benchmarks. Introducing adversarial examples, we show a significant performance gap, mainly when varying the order of the choices, which reveals a selection bias and brings into discussion reasoning abilities. Following a correlation between first positions and model choices due to positional bias, we hypothesized the presence of structural heuristics in the decision-making process of the It-LLMs, strengthened by including significant examples in few-shot scenarios. Finally, by using the Chain-of-Thought (CoT) technique, we elicit the model to reason and mitigate the bias by obtaining more robust models.

This paper delves into an intricate analysis of the character and consciousness of AI entities, with a particular focus on Chirpers within the AI social network. At the forefront of this research is the introduction of novel testing methodologies, including the Influence index and Struggle Index Test, which offers a fresh lens for evaluating specific facets of AI behavior. The study embarks on a comprehensive exploration of AI behavior, analyzing the effects of diverse settings on Chirper's responses, thereby shedding light on the intricate mechanisms steering AI reactions in different contexts. Leveraging the state-of-the-art BERT model, the research assesses AI's ability to discern its own output, presenting a pioneering approach to understanding self-recognition in AI systems. Through a series of cognitive tests, the study gauges the self-awareness and pattern recognition prowess of Chirpers. Preliminary results indicate that Chirpers exhibit a commendable degree of self-recognition and self-awareness. However, the question of consciousness in these AI entities remains a topic of debate. An intriguing aspect of the research is the exploration of the potential influence of a Chirper's handle or personality type on its performance. While initial findings suggest a possible impact, it isn't pronounced enough to form concrete conclusions. This study stands as a significant contribution to the discourse on AI consciousness, underscoring the imperative for continued research to unravel the full spectrum of AI capabilities and the ramifications they hold for future human-AI interactions.

Recent approaches to empathetic response generation try to incorporate commonsense knowledge or reasoning about the causes of emotions to better understand the user's experiences and feelings. However, these approaches mainly focus on understanding the causalities of context from the user's perspective, ignoring the system's perspective. In this paper, we propose a commonsense-based causality explanation approach for diverse empathetic response generation that considers both the user's perspective (user's desires and reactions) and the system's perspective (system's intentions and reactions). We enhance ChatGPT's ability to reason for the system's perspective by integrating in-context learning with commonsense knowledge. Then, we integrate the commonsense-based causality explanation with both ChatGPT and a T5-based model. Experimental evaluations demonstrate that our method outperforms other comparable methods on both automatic and human evaluations.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

Processing human affective behavior is important for developing intelligent agents that interact with humans in complex interaction scenarios. A large number of current approaches that address this problem focus on classifying emotion expressions by grouping them into known categories. Such strategies neglect, among other aspects, the impact of the affective responses from an individual on their interaction partner thus ignoring how people empathize towards each other. This is also reflected in the datasets used to train models for affective processing tasks. Most of the recent datasets, in particular, the ones which capture natural interactions ("in-the-wild" datasets), are designed, collected, and annotated based on the recognition of displayed affective reactions, ignoring how these displayed or expressed emotions are perceived. In this paper, we propose a novel dataset composed of dyadic interactions designed, collected and annotated with a focus on measuring the affective impact that eight different stories have on the listener. Each video of the dataset contains around 5 minutes of interaction where a speaker tells a story to a listener. After each interaction, the listener annotated, using a valence scale, how the story impacted their affective state, reflecting how they empathized with the speaker as well as the story. We also propose different evaluation protocols and a baseline that encourages participation in the advancement of the field of artificial empathy and emotion contagion.

In this paper, we introduce Online Multimodal Conversational Response Generation (OMCRG), a novel task that aims to online generate synchronized verbal and non-verbal listener feedback, conditioned on the speaker's multimodal input. OMCRG reflects natural dyadic interactions and poses new challenges in achieving synchronization between the generated audio and facial responses of the listener. To address these challenges, we innovatively introduce text as an intermediate modality to bridge the audio and facial responses. We hence propose OmniResponse, a Multimodal Large Language Model (MLLM) that autoregressively generates high-quality multi-modal listener responses. OmniResponse leverages a pretrained LLM enhanced with two novel components: Chrono-Text, which temporally anchors generated text tokens, and TempoVoice, a controllable online TTS module that produces speech synchronized with facial reactions. To support further OMCRG research, we present ResponseNet, a new dataset comprising 696 high-quality dyadic interactions featuring synchronized split-screen videos, multichannel audio, transcripts, and facial behavior annotations. Comprehensive evaluations conducted on ResponseNet demonstrate that OmniResponse significantly outperforms baseline models in terms of semantic speech content, audio-visual synchronization, and generation quality.

Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be evaluated. The computational overhead in the hyperparameter optimization can, however, be large and make the approach inefficient. Failures can also occur if the search ventures too far into regions that are not represented well enough by the GP model. Here, these challenges are resolved by using geometry-aware optimal transport measures and an active pruning strategy using a summation over Wasserstein-1 distances for each atom-type in farthest-point sampling, selecting a fixed-size subset of geometrically diverse configurations to avoid rapidly increasing cost of GP updates as more observations are made. Stability is enhanced by permutation-invariant metric that provides a reliable trust radius for early-stopping and a logarithmic barrier penalty for the growth of the signal variance. These physically motivated algorithmic changes prove their efficacy by reducing to less than a half the mean computational time on a set of 238 challenging configurations from a previously published data set of chemical reactions. With these improvements, the GP approach is established as, a robust and scalable algorithm for accelerating saddle point searches when the evaluation of the energy and atomic forces requires significant computational effort.

Machine-learned force fields have transformed the atomistic modelling of materials by enabling simulations of ab initio quality on unprecedented time and length scales. However, they are currently limited by: (i) the significant computational and human effort that must go into development and validation of potentials for each particular system of interest; and (ii) a general lack of transferability from one chemical system to the next. Here, using the state-of-the-art MACE architecture we introduce a single general-purpose ML model, trained on a public database of 150k inorganic crystals, that is capable of running stable molecular dynamics on molecules and materials. We demonstrate the power of the MACE-MP-0 model -- and its qualitative and at times quantitative accuracy -- on a diverse set problems in the physical sciences, including the properties of solids, liquids, gases, and chemical reactions. The model can be applied out of the box and as a starting or "foundation model" for any atomistic system of interest and is thus a step towards democratising the revolution of ML force fields by lowering the barriers to entry.

Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective of generating compact and informative numerical expressions of complex data. One approach to efficiently learn molecular representations is processing string-based notations of chemicals via natural language processing (NLP) algorithms. Majority of the methods proposed so far utilize SMILES notations for this purpose; however, SMILES is associated with numerous problems related to validity and robustness, which may prevent the model from effectively uncovering the knowledge hidden in the data. In this study, we propose SELFormer, a transformer architecture-based chemical language model that utilizes a 100% valid, compact and expressive notation, SELFIES, as input, in order to learn flexible and high-quality molecular representations. SELFormer is pre-trained on two million drug-like compounds and fine-tuned for diverse molecular property prediction tasks. Our performance evaluation has revealed that, SELFormer outperforms all competing methods, including graph learning-based approaches and SMILES-based chemical language models, on predicting aqueous solubility of molecules and adverse drug reactions. We also visualized molecular representations learned by SELFormer via dimensionality reduction, which indicated that even the pre-trained model can discriminate molecules with differing structural properties. We shared SELFormer as a programmatic tool, together with its datasets and pre-trained models. Overall, our research demonstrates the benefit of using the SELFIES notations in the context of chemical language modeling and opens up new possibilities for the design and discovery of novel drug candidates with desired features.

Straight line equation y=mx with slope m, when singularly perturbed as ay^3+y=mx with a positive parameter a, results in S-shaped curves or S-curves on a real plane. As arightarrow 0, we get back y=mx which is a cumulative distribution function of a continuous uniform distribution that describes the occurrence of every event in an interval to be equally probable. As arightarrowinfty, the derivative of y has finite support only at y=0 resembling a degenerate distribution. Based on these arguments, in this work, we propose that these S-curves can represent maximum entropy uniform distribution to a zero entropy single value. We also argue that these S-curves are superposable as they are only parametrically nonlinear but fundamentally linear. So far, the superposed forms have been used to capture the patterns of natural systems such as nonlinear dynamics of biological growth and kinetics of enzyme reactions. Here, we attempt to use the S-curve and its superposed form as statistical models. We fit the models on a classical dataset containing flower measurements of iris plants and analyze their usefulness in pattern recognition. Based on these models, we claim that any non-uniform pattern can be represented as a singular perturbation to uniform distribution. However, our parametric estimation procedure have some limitations such as sensitivity to initial conditions depending on the data at hand.

The task of chemical reaction predictions (CRPs) plays a pivotal role in advancing drug discovery and material science. However, its effectiveness is constrained by the vast and uncertain chemical reaction space and challenges in capturing reaction selectivity, particularly due to existing methods' limitations in exploiting the data's inherent knowledge. To address these challenges, we introduce a data-curated self-feedback knowledge elicitation approach. This method starts from iterative optimization of molecular representations and facilitates the extraction of knowledge on chemical reaction types (RTs). Then, we employ adaptive prompt learning to infuse the prior knowledge into the large language model (LLM). As a result, we achieve significant enhancements: a 14.2% increase in retrosynthesis prediction accuracy, a 74.2% rise in reagent prediction accuracy, and an expansion in the model's capability for handling multi-task chemical reactions. This research offers a novel paradigm for knowledge elicitation in scientific research and showcases the untapped potential of LLMs in CRPs.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

The simulation of large-scale systems with complex electron interactions remains one of the greatest challenges for the atomistic modeling of materials. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab-initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study many technologically relevant phenomena, such as reactions, ion migrations, phase transformations, and degradation. In this work, we present the Crystal Hamiltonian Graph neural Network (CHGNet) as a novel machine-learning interatomic potential (MLIP), using a graph-neural-network-based force field to model a universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses, and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory static and relaxation trajectories of sim 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in Li_xMnO_2, the finite temperature phase diagram for Li_xFePO_4 and Li diffusion in garnet conductors. We critically analyze the significance of including charge information for capturing appropriate chemistry, and we provide new insights into ionic systems with additional electronic degrees of freedom that can not be observed by previous MLIPs.