This exception only happened when Tweet Class was used. I cannot find the reason why I should use Serializable. I did the mapping myself in GeneticMessage.hbm.xml. All the types (long & Date) in Tweet Class are basic type in Hibernate (I think so). 
Actually, the problem can be solved by just implementing Serializable for Tweet as mentioned in the Exception. But I still want to know the reason.
Method
Domain domain = (Domain) objects[0];
Query q = session.createQuery("FROM PreprocessedMessage WHERE domain = ?");
q.setEntity(0, domain);
return q.list(); // this line
Exception:
java.lang.ClassCastException: idv.petrie.prtm.model.Tweet cannot be cast to java.io.Serializable
    org.hibernate.type.CollectionType.getKeyOfOwner(CollectionType.java:381)
    org.hibernate.type.CollectionType.resolve(CollectionType.java:425)
    org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:139)
    org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:982)
    org.hibernate.loader.Loader.doQuery(Loader.java:857)
    org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:274)
    org.hibernate.loader.Loader.doList(Loader.java:2533)
    org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2276)
    org.hibernate.loader.Loader.list(Loader.java:2271)
    org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:452)
    org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363)
    org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196)
    org.hibernate.impl.SessionImpl.list(SessionImpl.java:1268)
    org.hibernate.impl.QueryImpl.list(QueryImpl.java:102)
    idv.petrie.prtm.model.helper.PreprocessedMessageHelper$3.execute(PreprocessedMessageHelper.java:66)
    idv.petrie.prtm.util.ModelHelper.execute(ModelHelper.java:36)
    idv.petrie.prtm.model.helper.PreprocessedMessageHelper.findMessageByDomain(PreprocessedMessageHelper.java:69)
    idv.petrie.prtm.servlet.MessageEvaluationServlet.doGet(MessageEvaluationServlet.java:44)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
PreprocessedMessage.java
package idv.petrie.prtm.model;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
public class PreprocessedMessage extends GeneticMessage {
    private GeneticMessage message;
    private Set dependencies;
    private Set tokens;
    public PreprocessedMessage() {
        super();
    }
    public PreprocessedMessage(GeneticMessage message, String content) {
        this();
        this.setMessage(message);
        this.setContent(content);
        this.setDomain(message.getDomain());
    }
    public PreprocessedMessage(GeneticMessage message) {
        this(message, message.getContent());
    }
    public PreprocessedMessage(GeneticMessage message,
            Set dependencies) {
        this(message);
        this.dependencies = dependencies;
    }
    public static Collection convertToCollection(
            Collection messages) {
        Collection result = new HashSet();
        for (GeneticMessage message : messages) {
            result.add(new PreprocessedMessage(message));
        }
        return result;
    }
    public void setMessage(GeneticMessage message) {
        this.message = message;
    }
    public GeneticMessage getMessage() {
        return message;
    }
    public Set getDependencies() {
        return dependencies;
    }
    public void setDependencies(Set dependencies) {
        for (Dependency d : dependencies) {
            d.setMessage(this);
        }
        this.dependencies = dependencies;
    }
    public Collection getTokens() {
        return tokens;
    }
    public void setTokens(Set tokens) {
        for (Token t : tokens) {
            t.setMessage(this);
        }
        this.tokens = tokens;
    }
}
Tweet.java
package idv.petrie.prtm.model;
import java.util.Date;
public class Tweet extends GeneticMessage {
    private long tweetId;
    private Date createdAt;
    private long fromUserId;
    public Tweet() {
        super();
    }
    public Tweet(String content) {
        this();
        setContent(content);
    }
    public Date getCreatedAt() {
        return createdAt;
    }
    public void setCreatedAt(Date createdAt) {
        this.createdAt = createdAt;
    }
    public long getFromUserId() {
        return fromUserId;
    }
    public void setFromUserId(long fromUserId) {
        this.fromUserId = fromUserId;
    }
    public void setTweetId(long tweetId) {
        this.tweetId = tweetId;
    }
    public long getTweetId() {
        return tweetId;
    }
}
GeneticMessage.java
package idv.petrie.prtm.model;
import java.util.Date;
public class GeneticMessage implements Comparable {
    public enum Status {
        NEW(0), PREPROCESSED(1);
        private int id;
        private Status(int id) {
            this.id = id;
        }
        public int getId() {
            return id;
        }
    }
    private long id;
    private Date modifiedAt;
    private String content;
    private Status status;
    private Domain domain;
    public GeneticMessage() {
        setModifiedAt();
        setStatus(Status.NEW);
    }
    public long getId() {
        return id;
    }
    public void setId(long id) {
        this.id = id;
    }
    public String getContent() {
        return content;
    }
    public void setContent(String content) {
        this.content = content;
    }
    public void setModifiedAt() {
        this.modifiedAt = new Date();
    }
    public Date getModifiedAt() {
        return modifiedAt;
    }
    public void setStatus(Status status) {
        this.status = status;
    }
    public Status getStatus() {
        return status;
    }
    public void setDomain(Domain domain) {
        this.domain = domain;
    }
    public Domain getDomain() {
        return domain;
    }
    public int compareTo(GeneticMessage o) {
        String content = this.getContent();
        String anotherContent = o.getContent();
        return content.compareTo(anotherContent);
    }
    public void setModifiedAt(Date modifiedAt) {
        this.modifiedAt = modifiedAt;
    }
}
GeneticMessage.hbm.xml
<code>
<?xml version="1.0" encoding="utf-8"?> 
<!DOCTYPE hibernate-mapping 
 PUBLIC "-//Hibernate/Hibernate Mapping DTD 3.0//EN" 
 "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
<hibernate-mapping>
    <typedef class="idv.petrie.prtm.model.GeneticMessage.Status"
        name="Status">
        <param name="enumClassName">idv.petrie.prtm.model.GeneticMessage.Status</param>
        <param name="identifierMethod">getId</param>
    </typedef>
    <class name="idv.petrie.prtm.model.GeneticMessage">
        <id name="id">
            <generator class="native" />
        </id>
        <property name="modifiedAt" />
        <property name="content" />
        <property name="status" />
        <many-to-one name="domain" class="idv.petrie.prtm.model.Domain"
            cascade="all" outer-join="true" />
        <joined-subclass name="idv.petrie.prtm.model.PreprocessedMessage">
            <key />
            <many-to-one name="message" class="idv.petrie.prtm.model.GeneticMessage"
                outer-join="true" />
            <set name="dependencies" cascade="save-update" inverse="true">
                <key property-ref="message" />
                <one-to-many class="idv.petrie.prtm.model.Dependency" />
            </set>
            <set name="tokens" cascade="save-update" inverse="true">
                <key property-ref="message" />
                <one-to-many class="idv.petrie.prtm.model.Token" />
            </set>
        </joined-subclass>
        <joined-subclass name="idv.petrie.prtm.model.Tweet">
            <key />
            <property name="tweetId" unique="true" />
            <property name="createdAt" />
            <property name="fromUserId" />
        </joined-subclass>
    </class>
</hibernate-mapping>
</code>